{"exact_match":true,"id":"retro_000b2f0d148c78a5f3a2:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target O=CCCCCCCOc1ccccc1 in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"O=CCCCCCCOc1ccccc1\", \"reactants\": [\"CCOC(=O)CCCCCCOc1ccccc1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCOC(=O)CCCCCCOc1ccccc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"CNMIJPBYQFIATB-UHFFFAOYSA-N>>PWJNOJCVYVIZSY-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"O=CCCCCCCOc1ccccc1\", \"reactants\": [\"CCOC(=O)CCCCCCOc1ccccc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CCOC(=O)CCCCCCOc1ccccc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"CCOC(=O)CCCCCCOc1ccccc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCOC(=O)CCCCCCOc1ccccc1\", \"reactants\": [\"CCOC(=O)CCCCCCBr\", \"Oc1ccccc1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCOC(=O)CCCCCCBr\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"Oc1ccccc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"ISWSIDIOOBJBQZ-UHFFFAOYSA-N.OOBFNDGMAGSNKA-UHFFFAOYSA-N>>CNMIJPBYQFIATB-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"CCOC(=O)CCCCCCOc1ccccc1\", \"reactants\": [\"CCOC(=O)CCCCCCBr\", \"Oc1ccccc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CCOC(=O)CCCCCCBr\", \"results\": [{\"inchikey\": \"OOBFNDGMAGSNKA-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CCOC(=O)CCCCCCBr\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"Oc1ccccc1\", \"results\": [{\"inchikey\": \"ISWSIDIOOBJBQZ-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Oc1ccccc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"O=CCCCCCCOc1ccccc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCOC(=O)CCCCCCOc1ccccc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCOC(=O)CCCCCCOc1ccccc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCOC(=O)CCCCCCBr\": \"precursor\", \"Oc1ccccc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCOC(=O)CCCCCCBr\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"Oc1ccccc1\", \"in_stock\": true, \"children\": []}]}]}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"O=CCCCCCCOc1ccccc1","task_id":"retro_000b2f0d148c78a5f3a2","tool_calls":6,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_0055ca13eaee62230349:reference-expert:a0","kind":"single_route","max_steps":3,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CN(C)Cc1ccc2oc(N3CCN(C4CC4)CC3)nc2c1 in at most 3 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CN(C)Cc1ccc2oc(N3CCN(C4CC4)CC3)nc2c1\", \"reactants\": [\"CNC\", \"O=Cc1ccc2oc(N3CCN(C4CC4)CC3)nc2c1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CNC\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=Cc1ccc2oc(N3CCN(C4CC4)CC3)nc2c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"LIVWDCWTXMDLCE-UHFFFAOYSA-N.ROSDSFDQCJNGOL-UHFFFAOYSA-N>>LEYHLBVTBHWGRZ-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"CN(C)Cc1ccc2oc(N3CCN(C4CC4)CC3)nc2c1\", \"reactants\": [\"CNC\", \"O=Cc1ccc2oc(N3CCN(C4CC4)CC3)nc2c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CNC\", \"results\": [{\"inchikey\": \"ROSDSFDQCJNGOL-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CNC\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"O=Cc1ccc2oc(N3CCN(C4CC4)CC3)nc2c1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"O=Cc1ccc2oc(N3CCN(C4CC4)CC3)nc2c1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"O=Cc1ccc2oc(N3CCN(C4CC4)CC3)nc2c1\", \"reactants\": [\"CO\", \"N#Cc1ccc2oc(N3CCN(C4CC4)CC3)nc2c1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CO\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"N#Cc1ccc2oc(N3CCN(C4CC4)CC3)nc2c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"OKKJLVBELUTLKV-UHFFFAOYSA-N.OPBTYQOGRDCTMA-UHFFFAOYSA-N>>LIVWDCWTXMDLCE-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"O=Cc1ccc2oc(N3CCN(C4CC4)CC3)nc2c1\", \"reactants\": [\"CO\", \"N#Cc1ccc2oc(N3CCN(C4CC4)CC3)nc2c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CO\", \"results\": [{\"inchikey\": \"OKKJLVBELUTLKV-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CO\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"N#Cc1ccc2oc(N3CCN(C4CC4)CC3)nc2c1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"N#Cc1ccc2oc(N3CCN(C4CC4)CC3)nc2c1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"N#Cc1ccc2oc(N3CCN(C4CC4)CC3)nc2c1\", \"reactants\": [\"C1CN(C2CC2)CCN1\", \"N#Cc1ccc2oc(Cl)nc2c1\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"C1CN(C2CC2)CCN1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"N#Cc1ccc2oc(Cl)nc2c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"HNZJIWIXRPBFAN-UHFFFAOYSA-N.YXXCZHJSELQADZ-UHFFFAOYSA-N>>OPBTYQOGRDCTMA-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"N#Cc1ccc2oc(N3CCN(C4CC4)CC3)nc2c1\", \"reactants\": [\"C1CN(C2CC2)CCN1\", \"N#Cc1ccc2oc(Cl)nc2c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"C1CN(C2CC2)CCN1\", \"results\": [{\"inchikey\": \"HNZJIWIXRPBFAN-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"C1CN(C2CC2)CCN1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"N#Cc1ccc2oc(Cl)nc2c1\", \"results\": [{\"inchikey\": \"YXXCZHJSELQADZ-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"N#Cc1ccc2oc(Cl)nc2c1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CN(C)Cc1ccc2oc(N3CCN(C4CC4)CC3)nc2c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CNC\": \"precursor\", \"O=Cc1ccc2oc(N3CCN(C4CC4)CC3)nc2c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CNC\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=Cc1ccc2oc(N3CCN(C4CC4)CC3)nc2c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CO\": \"precursor\", \"N#Cc1ccc2oc(N3CCN(C4CC4)CC3)nc2c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CO\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"N#Cc1ccc2oc(N3CCN(C4CC4)CC3)nc2c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"C1CN(C2CC2)CCN1\": \"precursor\", \"N#Cc1ccc2oc(Cl)nc2c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"C1CN(C2CC2)CCN1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"N#Cc1ccc2oc(Cl)nc2c1\", \"in_stock\": true, \"children\": []}]}]}]}]}]}]}]}}","name":"emit_routes"},"id":"call_4_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"CN(C)Cc1ccc2oc(N3CCN(C4CC4)CC3)nc2c1","task_id":"retro_0055ca13eaee62230349","tool_calls":10,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":4}
{"exact_match":true,"id":"retro_009579646d89416efd9b:reference-expert:a0","kind":"single_route","max_steps":3,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CCc1ccc(Nc2nc(OCc3ccccc3)ccc2N)cc1 in at most 3 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCc1ccc(Nc2nc(OCc3ccccc3)ccc2N)cc1\", \"reactants\": [\"CCc1ccc(Nc2nc(OCc3ccccc3)ccc2[N+](=O)[O-])cc1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCc1ccc(Nc2nc(OCc3ccccc3)ccc2[N+](=O)[O-])cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"GKPVQGFFIJRDIV-UHFFFAOYSA-N>>WCLDZKUKYQDLTC-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"CCc1ccc(Nc2nc(OCc3ccccc3)ccc2N)cc1\", \"reactants\": [\"CCc1ccc(Nc2nc(OCc3ccccc3)ccc2[N+](=O)[O-])cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CCc1ccc(Nc2nc(OCc3ccccc3)ccc2[N+](=O)[O-])cc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"CCc1ccc(Nc2nc(OCc3ccccc3)ccc2[N+](=O)[O-])cc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCc1ccc(Nc2nc(OCc3ccccc3)ccc2[N+](=O)[O-])cc1\", \"reactants\": [\"CCc1ccc(Nc2nc(Cl)ccc2[N+](=O)[O-])cc1\", \"OCc1ccccc1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCc1ccc(Nc2nc(Cl)ccc2[N+](=O)[O-])cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"OCc1ccccc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"OAFUWEPGTSSJRA-UHFFFAOYSA-N.WVDDGKGOMKODPV-UHFFFAOYSA-N>>GKPVQGFFIJRDIV-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"CCc1ccc(Nc2nc(OCc3ccccc3)ccc2[N+](=O)[O-])cc1\", \"reactants\": [\"CCc1ccc(Nc2nc(Cl)ccc2[N+](=O)[O-])cc1\", \"OCc1ccccc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CCc1ccc(Nc2nc(Cl)ccc2[N+](=O)[O-])cc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"OCc1ccccc1\", \"results\": [{\"inchikey\": \"WVDDGKGOMKODPV-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"OCc1ccccc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"CCc1ccc(Nc2nc(Cl)ccc2[N+](=O)[O-])cc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCc1ccc(Nc2nc(Cl)ccc2[N+](=O)[O-])cc1\", \"reactants\": [\"CCc1ccc(N)cc1\", \"O=[N+]([O-])c1ccc(Cl)nc1Cl\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCc1ccc(N)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=[N+]([O-])c1ccc(Cl)nc1Cl\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"HRXZRAXKKNUKRF-UHFFFAOYSA-N.SHCWQWRTKPNTEM-UHFFFAOYSA-N>>OAFUWEPGTSSJRA-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"CCc1ccc(Nc2nc(Cl)ccc2[N+](=O)[O-])cc1\", \"reactants\": [\"CCc1ccc(N)cc1\", \"O=[N+]([O-])c1ccc(Cl)nc1Cl\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"CCc1ccc(N)cc1\", \"results\": [{\"inchikey\": \"HRXZRAXKKNUKRF-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CCc1ccc(N)cc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"O=[N+]([O-])c1ccc(Cl)nc1Cl\", \"results\": [{\"inchikey\": \"SHCWQWRTKPNTEM-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=[N+]([O-])c1ccc(Cl)nc1Cl\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CCc1ccc(Nc2nc(OCc3ccccc3)ccc2N)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCc1ccc(Nc2nc(OCc3ccccc3)ccc2[N+](=O)[O-])cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCc1ccc(Nc2nc(OCc3ccccc3)ccc2[N+](=O)[O-])cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCc1ccc(Nc2nc(Cl)ccc2[N+](=O)[O-])cc1\": \"precursor\", \"OCc1ccccc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCc1ccc(Nc2nc(Cl)ccc2[N+](=O)[O-])cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCc1ccc(N)cc1\": \"precursor\", \"O=[N+]([O-])c1ccc(Cl)nc1Cl\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCc1ccc(N)cc1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=[N+]([O-])c1ccc(Cl)nc1Cl\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"OCc1ccccc1\", \"in_stock\": true, \"children\": []}]}]}]}]}]}}","name":"emit_routes"},"id":"call_4_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"CCc1ccc(Nc2nc(OCc3ccccc3)ccc2N)cc1","task_id":"retro_009579646d89416efd9b","tool_calls":9,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":4}
{"exact_match":false,"id":"retro_01b1c9654674ef402e78:reference-expert:a0","kind":"single_route","max_steps":3,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target Cn1cccc1C(=O)N1CCN(C(=O)Nc2ccc(N3CCC(O)CC3)cc2)CC1 in at most 3 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Cn1cccc1C(=O)N1CCN(C(=O)Nc2ccc(N3CCC(O)CC3)cc2)CC1\", \"reactants\": [\"Cn1cccc1C(=O)N1CCNCC1\", \"Nc1ccc(N2CCC(O)CC2)cc1\", \"O=C(Cl)Oc1ccc([N+](=O)[O-])cc1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"Cn1cccc1C(=O)N1CCNCC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"Nc1ccc(N2CCC(O)CC2)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"},{"function":{"arguments":"{\"query\": \"O=C(Cl)Oc1ccc([N+](=O)[O-])cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_3","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"BJXPIIDUCADEKU-UHFFFAOYSA-N.DTSCVYQDGZJOEN-UHFFFAOYSA-N.NXLNNXIXOYSCMB-UHFFFAOYSA-N>>MCIXIOJTXYAIBD-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"Cn1cccc1C(=O)N1CCN(C(=O)Nc2ccc(N3CCC(O)CC3)cc2)CC1\", \"reactants\": [\"Cn1cccc1C(=O)N1CCNCC1\", \"Nc1ccc(N2CCC(O)CC2)cc1\", \"O=C(Cl)Oc1ccc([N+](=O)[O-])cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"Cn1cccc1C(=O)N1CCNCC1\", \"results\": [{\"inchikey\": \"DTSCVYQDGZJOEN-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Cn1cccc1C(=O)N1CCNCC1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"Nc1ccc(N2CCC(O)CC2)cc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"O=C(Cl)Oc1ccc([N+](=O)[O-])cc1\", \"results\": [{\"inchikey\": \"NXLNNXIXOYSCMB-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=C(Cl)Oc1ccc([N+](=O)[O-])cc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_3"},{"content":"Nc1ccc(N2CCC(O)CC2)cc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Nc1ccc(N2CCC(O)CC2)cc1\", \"reactants\": [\"O=[N+]([O-])c1ccc(N2CCC(O)CC2)cc1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"O=[N+]([O-])c1ccc(N2CCC(O)CC2)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"RNPWPESLLCUROD-UHFFFAOYSA-N>>BJXPIIDUCADEKU-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"Nc1ccc(N2CCC(O)CC2)cc1\", \"reactants\": [\"O=[N+]([O-])c1ccc(N2CCC(O)CC2)cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"O=[N+]([O-])c1ccc(N2CCC(O)CC2)cc1\", \"results\": [{\"inchikey\": \"RNPWPESLLCUROD-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=[N+]([O-])c1ccc(N2CCC(O)CC2)cc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"Cn1cccc1C(=O)N1CCN(C(=O)Nc2ccc(N3CCC(O)CC3)cc2)CC1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"Cn1cccc1C(=O)N1CCNCC1\": \"precursor\", \"Nc1ccc(N2CCC(O)CC2)cc1\": \"precursor\", \"O=C(Cl)Oc1ccc([N+](=O)[O-])cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"Cn1cccc1C(=O)N1CCNCC1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"Nc1ccc(N2CCC(O)CC2)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"O=[N+]([O-])c1ccc(N2CCC(O)CC2)cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"O=[N+]([O-])c1ccc(N2CCC(O)CC2)cc1\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"O=C(Cl)Oc1ccc([N+](=O)[O-])cc1\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":0.866667,"source":"reference-expert","target_smiles":"Cn1cccc1C(=O)N1CCN(C(=O)Nc2ccc(N3CCC(O)CC3)cc2)CC1","task_id":"retro_01b1c9654674ef402e78","tool_calls":7,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_024d04ae0bfbcc889bd7:reference-expert:a0","kind":"single_route","max_steps":3,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target Clc1ccc(N2CCN(Cc3ccccc3-c3ccccc3)CC2)cc1 in at most 3 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Clc1ccc(N2CCN(Cc3ccccc3-c3ccccc3)CC2)cc1\", \"reactants\": [\"Clc1ccc(N2CCNCC2)cc1\", \"c1ccc(-c2ccccc2CN2CCN(c3ccccc3)CC2)cc1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"Clc1ccc(N2CCNCC2)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"c1ccc(-c2ccccc2CN2CCN(c3ccccc3)CC2)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"UCRKMUUOHCZVJX-UHFFFAOYSA-N.UNEIHNMKASENIG-UHFFFAOYSA-N>>PXKOBOQZUOWWFF-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"Clc1ccc(N2CCN(Cc3ccccc3-c3ccccc3)CC2)cc1\", \"reactants\": [\"Clc1ccc(N2CCNCC2)cc1\", \"c1ccc(-c2ccccc2CN2CCN(c3ccccc3)CC2)cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"Clc1ccc(N2CCNCC2)cc1\", \"results\": [{\"inchikey\": \"UNEIHNMKASENIG-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Clc1ccc(N2CCNCC2)cc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"c1ccc(-c2ccccc2CN2CCN(c3ccccc3)CC2)cc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"c1ccc(-c2ccccc2CN2CCN(c3ccccc3)CC2)cc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"c1ccc(-c2ccccc2CN2CCN(c3ccccc3)CC2)cc1\", \"reactants\": [\"O=Cc1ccccc1-c1ccccc1\", \"c1ccc(N2CCNCC2)cc1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"O=Cc1ccccc1-c1ccccc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"c1ccc(N2CCNCC2)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"LCRCBXLHWTVPEQ-UHFFFAOYSA-N.YZTJYBJCZXZGCT-UHFFFAOYSA-N>>UCRKMUUOHCZVJX-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"c1ccc(-c2ccccc2CN2CCN(c3ccccc3)CC2)cc1\", \"reactants\": [\"O=Cc1ccccc1-c1ccccc1\", \"c1ccc(N2CCNCC2)cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"O=Cc1ccccc1-c1ccccc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"c1ccc(N2CCNCC2)cc1\", \"results\": [{\"inchikey\": \"YZTJYBJCZXZGCT-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"c1ccc(N2CCNCC2)cc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"O=Cc1ccccc1-c1ccccc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"O=Cc1ccccc1-c1ccccc1\", \"reactants\": [\"O=Cc1ccccc1Br\", \"OB(O)c1ccccc1\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"O=Cc1ccccc1Br\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"OB(O)c1ccccc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"HXITXNWTGFUOAU-UHFFFAOYSA-N.NDOPHXWIAZIXPR-UHFFFAOYSA-N>>LCRCBXLHWTVPEQ-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"O=Cc1ccccc1-c1ccccc1\", \"reactants\": [\"O=Cc1ccccc1Br\", \"OB(O)c1ccccc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"O=Cc1ccccc1Br\", \"results\": [{\"inchikey\": \"NDOPHXWIAZIXPR-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=Cc1ccccc1Br\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"OB(O)c1ccccc1\", \"results\": [{\"inchikey\": \"HXITXNWTGFUOAU-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"OB(O)c1ccccc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"Clc1ccc(N2CCN(Cc3ccccc3-c3ccccc3)CC2)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"Clc1ccc(N2CCNCC2)cc1\": \"precursor\", \"c1ccc(-c2ccccc2CN2CCN(c3ccccc3)CC2)cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"Clc1ccc(N2CCNCC2)cc1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"c1ccc(-c2ccccc2CN2CCN(c3ccccc3)CC2)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"O=Cc1ccccc1-c1ccccc1\": \"precursor\", \"c1ccc(N2CCNCC2)cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"O=Cc1ccccc1-c1ccccc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"O=Cc1ccccc1Br\": \"precursor\", \"OB(O)c1ccccc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"O=Cc1ccccc1Br\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"OB(O)c1ccccc1\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"c1ccc(N2CCNCC2)cc1\", \"in_stock\": true, \"children\": []}]}]}]}]}]}}","name":"emit_routes"},"id":"call_4_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"Clc1ccc(N2CCN(Cc3ccccc3-c3ccccc3)CC2)cc1","task_id":"retro_024d04ae0bfbcc889bd7","tool_calls":10,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":4}
{"exact_match":true,"id":"retro_033216fe53ae26a9ed74:reference-expert:a0","kind":"single_route","max_steps":3,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CS(=O)(=O)c1ccc(NC(=O)CC2CCN(CCO)CC2)cc1 in at most 3 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CS(=O)(=O)c1ccc(NC(=O)CC2CCN(CCO)CC2)cc1\", \"reactants\": [\"CS(=O)(=O)c1ccc(NC(=O)CC2CCNCC2)cc1\", \"OCCCl\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CS(=O)(=O)c1ccc(NC(=O)CC2CCNCC2)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"OCCCl\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"OYRPZCUQLYHSBE-UHFFFAOYSA-N.SZIFAVKTNFCBPC-UHFFFAOYSA-N>>YWJMCYNOQYOTQF-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"CS(=O)(=O)c1ccc(NC(=O)CC2CCN(CCO)CC2)cc1\", \"reactants\": [\"CS(=O)(=O)c1ccc(NC(=O)CC2CCNCC2)cc1\", \"OCCCl\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CS(=O)(=O)c1ccc(NC(=O)CC2CCNCC2)cc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"OCCCl\", \"results\": [{\"inchikey\": \"SZIFAVKTNFCBPC-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"OCCCl\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"CS(=O)(=O)c1ccc(NC(=O)CC2CCNCC2)cc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CS(=O)(=O)c1ccc(NC(=O)CC2CCNCC2)cc1\", \"reactants\": [\"CC(C)(C)OC(=O)N1CCC(CC(=O)Nc2ccc(S(C)(=O)=O)cc2)CC1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)OC(=O)N1CCC(CC(=O)Nc2ccc(S(C)(=O)=O)cc2)CC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"NHSNGOOYZBDYKO-UHFFFAOYSA-N>>OYRPZCUQLYHSBE-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"CS(=O)(=O)c1ccc(NC(=O)CC2CCNCC2)cc1\", \"reactants\": [\"CC(C)(C)OC(=O)N1CCC(CC(=O)Nc2ccc(S(C)(=O)=O)cc2)CC1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CC(C)(C)OC(=O)N1CCC(CC(=O)Nc2ccc(S(C)(=O)=O)cc2)CC1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"CC(C)(C)OC(=O)N1CCC(CC(=O)Nc2ccc(S(C)(=O)=O)cc2)CC1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(C)(C)OC(=O)N1CCC(CC(=O)Nc2ccc(S(C)(=O)=O)cc2)CC1\", \"reactants\": [\"CC(C)(C)OC(=O)N1CCC(CC(=O)O)CC1\", \"CS(=O)(=O)c1ccc(N)cc1\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)OC(=O)N1CCC(CC(=O)O)CC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"CS(=O)(=O)c1ccc(N)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"XJEVFFNOMKXBLU-UHFFFAOYSA-N.ZXFLMSIMHISJFV-UHFFFAOYSA-N>>NHSNGOOYZBDYKO-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"CC(C)(C)OC(=O)N1CCC(CC(=O)Nc2ccc(S(C)(=O)=O)cc2)CC1\", \"reactants\": [\"CC(C)(C)OC(=O)N1CCC(CC(=O)O)CC1\", \"CS(=O)(=O)c1ccc(N)cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"CC(C)(C)OC(=O)N1CCC(CC(=O)O)CC1\", \"results\": [{\"inchikey\": \"ZXFLMSIMHISJFV-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CC(C)(C)OC(=O)N1CCC(CC(=O)O)CC1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"CS(=O)(=O)c1ccc(N)cc1\", \"results\": [{\"inchikey\": \"XJEVFFNOMKXBLU-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CS(=O)(=O)c1ccc(N)cc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CS(=O)(=O)c1ccc(NC(=O)CC2CCN(CCO)CC2)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CS(=O)(=O)c1ccc(NC(=O)CC2CCNCC2)cc1\": \"precursor\", \"OCCCl\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CS(=O)(=O)c1ccc(NC(=O)CC2CCNCC2)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)(C)OC(=O)N1CCC(CC(=O)Nc2ccc(S(C)(=O)=O)cc2)CC1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)OC(=O)N1CCC(CC(=O)Nc2ccc(S(C)(=O)=O)cc2)CC1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)(C)OC(=O)N1CCC(CC(=O)O)CC1\": \"precursor\", \"CS(=O)(=O)c1ccc(N)cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)OC(=O)N1CCC(CC(=O)O)CC1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"CS(=O)(=O)c1ccc(N)cc1\", \"in_stock\": true, \"children\": []}]}]}]}]}, {\"type\": \"mol\", \"smiles\": \"OCCCl\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_4_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"CS(=O)(=O)c1ccc(NC(=O)CC2CCN(CCO)CC2)cc1","task_id":"retro_033216fe53ae26a9ed74","tool_calls":9,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":4}
{"exact_match":true,"id":"retro_0439a51913912469a5be:reference-expert:a0","kind":"single_route","max_steps":4,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target COc1cc2[nH]c(N(C)Cc3cccc(OCCO)c3)nc(=O)c2c(OC)c1OC in at most 4 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COc1cc2[nH]c(N(C)Cc3cccc(OCCO)c3)nc(=O)c2c(OC)c1OC\", \"reactants\": [\"COc1cc2[nH]c(N(C)Cc3cccc(OCCO[Si](C)(C)C(C)(C)C)c3)nc(=O)c2c(OC)c1OC\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"COc1cc2[nH]c(N(C)Cc3cccc(OCCO[Si](C)(C)C(C)(C)C)c3)nc(=O)c2c(OC)c1OC\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"MHNYCRASBFTGQK-UHFFFAOYSA-N>>UOAYFSBKPHOSNM-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"COc1cc2[nH]c(N(C)Cc3cccc(OCCO)c3)nc(=O)c2c(OC)c1OC\", \"reactants\": [\"COc1cc2[nH]c(N(C)Cc3cccc(OCCO[Si](C)(C)C(C)(C)C)c3)nc(=O)c2c(OC)c1OC\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"COc1cc2[nH]c(N(C)Cc3cccc(OCCO[Si](C)(C)C(C)(C)C)c3)nc(=O)c2c(OC)c1OC\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"COc1cc2[nH]c(N(C)Cc3cccc(OCCO[Si](C)(C)C(C)(C)C)c3)nc(=O)c2c(OC)c1OC was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COc1cc2[nH]c(N(C)Cc3cccc(OCCO[Si](C)(C)C(C)(C)C)c3)nc(=O)c2c(OC)c1OC\", \"reactants\": [\"CNCc1cccc(OCCO[Si](C)(C)C(C)(C)C)c1\", \"COc1cc2[nH]c(Cl)nc(=O)c2c(OC)c1OC\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CNCc1cccc(OCCO[Si](C)(C)C(C)(C)C)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"COc1cc2[nH]c(Cl)nc(=O)c2c(OC)c1OC\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"GKPRWIVTCJUQHM-UHFFFAOYSA-N.HVYSUBVVRCLOMP-UHFFFAOYSA-N>>MHNYCRASBFTGQK-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"COc1cc2[nH]c(N(C)Cc3cccc(OCCO[Si](C)(C)C(C)(C)C)c3)nc(=O)c2c(OC)c1OC\", \"reactants\": [\"CNCc1cccc(OCCO[Si](C)(C)C(C)(C)C)c1\", \"COc1cc2[nH]c(Cl)nc(=O)c2c(OC)c1OC\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CNCc1cccc(OCCO[Si](C)(C)C(C)(C)C)c1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"COc1cc2[nH]c(Cl)nc(=O)c2c(OC)c1OC\", \"results\": [{\"inchikey\": \"GKPRWIVTCJUQHM-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"COc1cc2[nH]c(Cl)nc(=O)c2c(OC)c1OC\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"CNCc1cccc(OCCO[Si](C)(C)C(C)(C)C)c1 was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CNCc1cccc(OCCO[Si](C)(C)C(C)(C)C)c1\", \"reactants\": [\"CN=Cc1cccc(OCCO[Si](C)(C)C(C)(C)C)c1\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"CN=Cc1cccc(OCCO[Si](C)(C)C(C)(C)C)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_complete\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"WWSZLVJJSUOBEC-UHFFFAOYSA-N>>HVYSUBVVRCLOMP-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"CNCc1cccc(OCCO[Si](C)(C)C(C)(C)C)c1\", \"reactants\": [\"CN=Cc1cccc(OCCO[Si](C)(C)C(C)(C)C)c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"CN=Cc1cccc(OCCO[Si](C)(C)C(C)(C)C)c1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"CN=Cc1cccc(OCCO[Si](C)(C)C(C)(C)C)c1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CN=Cc1cccc(OCCO[Si](C)(C)C(C)(C)C)c1\", \"reactants\": [\"CC(C)(C)[Si](C)(C)OCCOc1cccc(C=O)c1\", \"CN\"]}","name":"validate_disconnection"},"id":"call_4_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)[Si](C)(C)OCCOc1cccc(C=O)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_1","type":"function"},{"function":{"arguments":"{\"query\": \"CN\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"BAVYZALUXZFZLV-UHFFFAOYSA-N.WSWLGVMHMFJCLT-UHFFFAOYSA-N>>WWSZLVJJSUOBEC-UHFFFAOYSA-N\", \"model_turns_remaining\": 12, \"product\": \"CN=Cc1cccc(OCCO[Si](C)(C)C(C)(C)C)c1\", \"reactants\": [\"CC(C)(C)[Si](C)(C)OCCOc1cccc(C=O)c1\", \"CN\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_4_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"CC(C)(C)[Si](C)(C)OCCOc1cccc(C=O)c1\", \"results\": [{\"inchikey\": \"WSWLGVMHMFJCLT-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CC(C)(C)[Si](C)(C)OCCOc1cccc(C=O)c1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"CN\", \"results\": [{\"inchikey\": \"BAVYZALUXZFZLV-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CN\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"COc1cc2[nH]c(N(C)Cc3cccc(OCCO)c3)nc(=O)c2c(OC)c1OC\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COc1cc2[nH]c(N(C)Cc3cccc(OCCO[Si](C)(C)C(C)(C)C)c3)nc(=O)c2c(OC)c1OC\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COc1cc2[nH]c(N(C)Cc3cccc(OCCO[Si](C)(C)C(C)(C)C)c3)nc(=O)c2c(OC)c1OC\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CNCc1cccc(OCCO[Si](C)(C)C(C)(C)C)c1\": \"precursor\", \"COc1cc2[nH]c(Cl)nc(=O)c2c(OC)c1OC\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CNCc1cccc(OCCO[Si](C)(C)C(C)(C)C)c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CN=Cc1cccc(OCCO[Si](C)(C)C(C)(C)C)c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CN=Cc1cccc(OCCO[Si](C)(C)C(C)(C)C)c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)(C)[Si](C)(C)OCCOc1cccc(C=O)c1\": \"precursor\", \"CN\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)[Si](C)(C)OCCOc1cccc(C=O)c1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"CN\", \"in_stock\": true, \"children\": []}]}]}]}]}, {\"type\": \"mol\", \"smiles\": \"COc1cc2[nH]c(Cl)nc(=O)c2c(OC)c1OC\", \"in_stock\": true, \"children\": []}]}]}]}]}]}}","name":"emit_routes"},"id":"call_5_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"COc1cc2[nH]c(N(C)Cc3cccc(OCCO)c3)nc(=O)c2c(OC)c1OC","task_id":"retro_0439a51913912469a5be","tool_calls":11,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":5}
{"exact_match":true,"id":"retro_04bcff2d2c47e90f1717:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target Cc1ccc2c(Br)c(O)ccc2n1 in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Cc1ccc2c(Br)c(O)ccc2n1\", \"reactants\": [\"COc1ccc2nc(C)ccc2c1Br\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"COc1ccc2nc(C)ccc2c1Br\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"UPDXSQFEBOHETE-UHFFFAOYSA-N>>CBBZBPMLSSRBGS-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"Cc1ccc2c(Br)c(O)ccc2n1\", \"reactants\": [\"COc1ccc2nc(C)ccc2c1Br\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"COc1ccc2nc(C)ccc2c1Br\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"COc1ccc2nc(C)ccc2c1Br was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COc1ccc2nc(C)ccc2c1Br\", \"reactants\": [\"COc1ccc2nc(C)ccc2c1\", \"O=C1CCC(=O)N1Br\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"COc1ccc2nc(C)ccc2c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=C1CCC(=O)N1Br\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"NAGJQQFMJKMXJQ-UHFFFAOYSA-N.PCLIMKBDDGJMGD-UHFFFAOYSA-N>>UPDXSQFEBOHETE-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"COc1ccc2nc(C)ccc2c1Br\", \"reactants\": [\"COc1ccc2nc(C)ccc2c1\", \"O=C1CCC(=O)N1Br\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"COc1ccc2nc(C)ccc2c1\", \"results\": [{\"inchikey\": \"NAGJQQFMJKMXJQ-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"COc1ccc2nc(C)ccc2c1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"O=C1CCC(=O)N1Br\", \"results\": [{\"inchikey\": \"PCLIMKBDDGJMGD-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=C1CCC(=O)N1Br\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"Cc1ccc2c(Br)c(O)ccc2n1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COc1ccc2nc(C)ccc2c1Br\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COc1ccc2nc(C)ccc2c1Br\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COc1ccc2nc(C)ccc2c1\": \"precursor\", \"O=C1CCC(=O)N1Br\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COc1ccc2nc(C)ccc2c1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=C1CCC(=O)N1Br\", \"in_stock\": true, \"children\": []}]}]}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"Cc1ccc2c(Br)c(O)ccc2n1","task_id":"retro_04bcff2d2c47e90f1717","tool_calls":6,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_0536bdd5794695313cb3:reference-expert:a0","kind":"single_route","max_steps":5,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target N#Cc1ccc(N2N=C3c4ccc(C(=O)OCC5CCCCC5)cc4CCC3C2C2CCCC2)cc1Cl in at most 5 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"N#Cc1ccc(N2N=C3c4ccc(C(=O)OCC5CCCCC5)cc4CCC3C2C2CCCC2)cc1Cl\", \"reactants\": [\"N#Cc1ccc(N2N=C3c4ccc(C(=O)O)cc4CCC3C2C2CCCC2)cc1Cl\", \"OCC1CCCCC1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"N#Cc1ccc(N2N=C3c4ccc(C(=O)O)cc4CCC3C2C2CCCC2)cc1Cl\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"OCC1CCCCC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"VSSAZBXXNIABDN-UHFFFAOYSA-N.XNULRSOGWPFPBL-UHFFFAOYSA-N>>NBZRTHQAVXBEGC-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"N#Cc1ccc(N2N=C3c4ccc(C(=O)OCC5CCCCC5)cc4CCC3C2C2CCCC2)cc1Cl\", \"reactants\": [\"N#Cc1ccc(N2N=C3c4ccc(C(=O)O)cc4CCC3C2C2CCCC2)cc1Cl\", \"OCC1CCCCC1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"N#Cc1ccc(N2N=C3c4ccc(C(=O)O)cc4CCC3C2C2CCCC2)cc1Cl\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"OCC1CCCCC1\", \"results\": [{\"inchikey\": \"VSSAZBXXNIABDN-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"OCC1CCCCC1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"N#Cc1ccc(N2N=C3c4ccc(C(=O)O)cc4CCC3C2C2CCCC2)cc1Cl was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"N#Cc1ccc(N2N=C3c4ccc(C(=O)O)cc4CCC3C2C2CCCC2)cc1Cl\", \"reactants\": [\"COC(=O)c1ccc2c(c1)CCC1C2=NN(c2ccc(C#N)c(Cl)c2)C1C1CCCC1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"COC(=O)c1ccc2c(c1)CCC1C2=NN(c2ccc(C#N)c(Cl)c2)C1C1CCCC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"MZBNNMPUCTYVEZ-UHFFFAOYSA-N>>XNULRSOGWPFPBL-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"N#Cc1ccc(N2N=C3c4ccc(C(=O)O)cc4CCC3C2C2CCCC2)cc1Cl\", \"reactants\": [\"COC(=O)c1ccc2c(c1)CCC1C2=NN(c2ccc(C#N)c(Cl)c2)C1C1CCCC1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"COC(=O)c1ccc2c(c1)CCC1C2=NN(c2ccc(C#N)c(Cl)c2)C1C1CCCC1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"COC(=O)c1ccc2c(c1)CCC1C2=NN(c2ccc(C#N)c(Cl)c2)C1C1CCCC1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COC(=O)c1ccc2c(c1)CCC1C2=NN(c2ccc(C#N)c(Cl)c2)C1C1CCCC1\", \"reactants\": [\"COC(=O)c1ccc2c(c1)CCC(=CC1CCCC1)C2=O\", \"N#Cc1ccc(NN)cc1Cl\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"COC(=O)c1ccc2c(c1)CCC(=CC1CCCC1)C2=O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"N#Cc1ccc(NN)cc1Cl\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"NRWOMMXRCHVLFK-UHFFFAOYSA-N.OWUBFRQSDPZYQG-UHFFFAOYSA-N>>MZBNNMPUCTYVEZ-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"COC(=O)c1ccc2c(c1)CCC1C2=NN(c2ccc(C#N)c(Cl)c2)C1C1CCCC1\", \"reactants\": [\"COC(=O)c1ccc2c(c1)CCC(=CC1CCCC1)C2=O\", \"N#Cc1ccc(NN)cc1Cl\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"COC(=O)c1ccc2c(c1)CCC(=CC1CCCC1)C2=O\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"N#Cc1ccc(NN)cc1Cl\", \"results\": [{\"inchikey\": \"NRWOMMXRCHVLFK-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"N#Cc1ccc(NN)cc1Cl\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"COC(=O)c1ccc2c(c1)CCC(=CC1CCCC1)C2=O was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COC(=O)c1ccc2c(c1)CCC(=CC1CCCC1)C2=O\", \"reactants\": [\"COC(=O)c1ccc2c(c1)CCCC2=O\", \"O=CC1CCCC1\"]}","name":"validate_disconnection"},"id":"call_4_0","type":"function"},{"function":{"arguments":"{\"query\": \"COC(=O)c1ccc2c(c1)CCCC2=O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=CC1CCCC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"QMICDTYERUBTNO-UHFFFAOYSA-N.VELDYOPRLMJFIK-UHFFFAOYSA-N>>OWUBFRQSDPZYQG-UHFFFAOYSA-N\", \"model_turns_remaining\": 12, \"product\": \"COC(=O)c1ccc2c(c1)CCC(=CC1CCCC1)C2=O\", \"reactants\": [\"COC(=O)c1ccc2c(c1)CCCC2=O\", \"O=CC1CCCC1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_4_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"COC(=O)c1ccc2c(c1)CCCC2=O\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"O=CC1CCCC1\", \"results\": [{\"inchikey\": \"VELDYOPRLMJFIK-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=CC1CCCC1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_2"},{"content":"COC(=O)c1ccc2c(c1)CCCC2=O was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COC(=O)c1ccc2c(c1)CCCC2=O\", \"reactants\": [\"CO\", \"O=C(O)c1ccc2c(c1)CCCC2=O\"]}","name":"validate_disconnection"},"id":"call_5_0","type":"function"},{"function":{"arguments":"{\"query\": \"CO\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_5_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=C(O)c1ccc2c(c1)CCCC2=O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_5_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"OKKJLVBELUTLKV-UHFFFAOYSA-N.QSQVJZPPZDEILK-UHFFFAOYSA-N>>QMICDTYERUBTNO-UHFFFAOYSA-N\", \"model_turns_remaining\": 11, \"product\": \"COC(=O)c1ccc2c(c1)CCCC2=O\", \"reactants\": [\"CO\", \"O=C(O)c1ccc2c(c1)CCCC2=O\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_5_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 11, \"query\": \"CO\", \"results\": [{\"inchikey\": \"OKKJLVBELUTLKV-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CO\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_5_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 11, \"query\": \"O=C(O)c1ccc2c(c1)CCCC2=O\", \"results\": [{\"inchikey\": \"QSQVJZPPZDEILK-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=C(O)c1ccc2c(c1)CCCC2=O\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_5_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"N#Cc1ccc(N2N=C3c4ccc(C(=O)OCC5CCCCC5)cc4CCC3C2C2CCCC2)cc1Cl\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"N#Cc1ccc(N2N=C3c4ccc(C(=O)O)cc4CCC3C2C2CCCC2)cc1Cl\": \"precursor\", \"OCC1CCCCC1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"N#Cc1ccc(N2N=C3c4ccc(C(=O)O)cc4CCC3C2C2CCCC2)cc1Cl\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COC(=O)c1ccc2c(c1)CCC1C2=NN(c2ccc(C#N)c(Cl)c2)C1C1CCCC1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COC(=O)c1ccc2c(c1)CCC1C2=NN(c2ccc(C#N)c(Cl)c2)C1C1CCCC1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COC(=O)c1ccc2c(c1)CCC(=CC1CCCC1)C2=O\": \"precursor\", \"N#Cc1ccc(NN)cc1Cl\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COC(=O)c1ccc2c(c1)CCC(=CC1CCCC1)C2=O\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COC(=O)c1ccc2c(c1)CCCC2=O\": \"precursor\", \"O=CC1CCCC1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COC(=O)c1ccc2c(c1)CCCC2=O\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CO\": \"precursor\", \"O=C(O)c1ccc2c(c1)CCCC2=O\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CO\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=C(O)c1ccc2c(c1)CCCC2=O\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"O=CC1CCCC1\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"N#Cc1ccc(NN)cc1Cl\", \"in_stock\": true, \"children\": []}]}]}]}]}, {\"type\": \"mol\", \"smiles\": \"OCC1CCCCC1\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_6_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"N#Cc1ccc(N2N=C3c4ccc(C(=O)OCC5CCCCC5)cc4CCC3C2C2CCCC2)cc1Cl","task_id":"retro_0536bdd5794695313cb3","tool_calls":15,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":6}
{"exact_match":true,"id":"retro_064fa6b96a631e7b91ac:reference-expert:a0","kind":"single_route","max_steps":3,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target FC(F)(F)C(F)(F)c1nc2cc(Cl)c(Oc3ccc(Cl)cc3Cl)cc2[nH]1 in at most 3 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"FC(F)(F)C(F)(F)c1nc2cc(Cl)c(Oc3ccc(Cl)cc3Cl)cc2[nH]1\", \"reactants\": [\"Nc1cc(Cl)c(Oc2ccc(Cl)cc2Cl)cc1N\", \"O=C(O)C(F)(F)C(F)(F)F\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"Nc1cc(Cl)c(Oc2ccc(Cl)cc2Cl)cc1N\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=C(O)C(F)(F)C(F)(F)F\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"CNEPOHDUVTYJBY-UHFFFAOYSA-N.LRMSQVBRUNSOJL-UHFFFAOYSA-N>>QIJLOPRKMXXRNW-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"FC(F)(F)C(F)(F)c1nc2cc(Cl)c(Oc3ccc(Cl)cc3Cl)cc2[nH]1\", \"reactants\": [\"Nc1cc(Cl)c(Oc2ccc(Cl)cc2Cl)cc1N\", \"O=C(O)C(F)(F)C(F)(F)F\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"Nc1cc(Cl)c(Oc2ccc(Cl)cc2Cl)cc1N\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"O=C(O)C(F)(F)C(F)(F)F\", \"results\": [{\"inchikey\": \"LRMSQVBRUNSOJL-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=C(O)C(F)(F)C(F)(F)F\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"Nc1cc(Cl)c(Oc2ccc(Cl)cc2Cl)cc1N was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Nc1cc(Cl)c(Oc2ccc(Cl)cc2Cl)cc1N\", \"reactants\": [\"Nc1cc(Oc2ccc(Cl)cc2Cl)c(Cl)cc1[N+](=O)[O-]\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"Nc1cc(Oc2ccc(Cl)cc2Cl)c(Cl)cc1[N+](=O)[O-]\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"OMDFBOCHJRNBTP-UHFFFAOYSA-N>>CNEPOHDUVTYJBY-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"Nc1cc(Cl)c(Oc2ccc(Cl)cc2Cl)cc1N\", \"reactants\": [\"Nc1cc(Oc2ccc(Cl)cc2Cl)c(Cl)cc1[N+](=O)[O-]\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"Nc1cc(Oc2ccc(Cl)cc2Cl)c(Cl)cc1[N+](=O)[O-]\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"Nc1cc(Oc2ccc(Cl)cc2Cl)c(Cl)cc1[N+](=O)[O-] was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Nc1cc(Oc2ccc(Cl)cc2Cl)c(Cl)cc1[N+](=O)[O-]\", \"reactants\": [\"Nc1cc(Cl)c(Cl)cc1[N+](=O)[O-]\", \"Oc1ccc(Cl)cc1Cl\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"Nc1cc(Cl)c(Cl)cc1[N+](=O)[O-]\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"Oc1ccc(Cl)cc1Cl\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"FSGTULQLEVAYRS-UHFFFAOYSA-N.HFZWRUODUSTPEG-UHFFFAOYSA-N>>OMDFBOCHJRNBTP-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"Nc1cc(Oc2ccc(Cl)cc2Cl)c(Cl)cc1[N+](=O)[O-]\", \"reactants\": [\"Nc1cc(Cl)c(Cl)cc1[N+](=O)[O-]\", \"Oc1ccc(Cl)cc1Cl\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"Nc1cc(Cl)c(Cl)cc1[N+](=O)[O-]\", \"results\": [{\"inchikey\": \"FSGTULQLEVAYRS-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Nc1cc(Cl)c(Cl)cc1[N+](=O)[O-]\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"Oc1ccc(Cl)cc1Cl\", \"results\": [{\"inchikey\": \"HFZWRUODUSTPEG-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Oc1ccc(Cl)cc1Cl\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"FC(F)(F)C(F)(F)c1nc2cc(Cl)c(Oc3ccc(Cl)cc3Cl)cc2[nH]1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"Nc1cc(Cl)c(Oc2ccc(Cl)cc2Cl)cc1N\": \"precursor\", \"O=C(O)C(F)(F)C(F)(F)F\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"Nc1cc(Cl)c(Oc2ccc(Cl)cc2Cl)cc1N\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"Nc1cc(Oc2ccc(Cl)cc2Cl)c(Cl)cc1[N+](=O)[O-]\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"Nc1cc(Oc2ccc(Cl)cc2Cl)c(Cl)cc1[N+](=O)[O-]\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"Nc1cc(Cl)c(Cl)cc1[N+](=O)[O-]\": \"precursor\", \"Oc1ccc(Cl)cc1Cl\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"Nc1cc(Cl)c(Cl)cc1[N+](=O)[O-]\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"Oc1ccc(Cl)cc1Cl\", \"in_stock\": true, \"children\": []}]}]}]}]}, {\"type\": \"mol\", \"smiles\": \"O=C(O)C(F)(F)C(F)(F)F\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_4_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"FC(F)(F)C(F)(F)c1nc2cc(Cl)c(Oc3ccc(Cl)cc3Cl)cc2[nH]1","task_id":"retro_064fa6b96a631e7b91ac","tool_calls":9,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":4}
{"exact_match":true,"id":"retro_06eb9fcea66261f56040:reference-expert:a0","kind":"single_route","max_steps":3,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target O=c1cc(NCCC2CCCCN2Cc2ccc(Cl)c(Cl)c2)[nH]c2ccccc12 in at most 3 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"O=c1cc(NCCC2CCCCN2Cc2ccc(Cl)c(Cl)c2)[nH]c2ccccc12\", \"reactants\": [\"O=c1cc(NCCC2CC=CCN2Cc2ccc(Cl)c(Cl)c2)[nH]c2ccccc12\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"O=c1cc(NCCC2CC=CCN2Cc2ccc(Cl)c(Cl)c2)[nH]c2ccccc12\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_complete\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"FUXMCEXQNHCLQI-UHFFFAOYSA-N>>JRNFRXGRTJLVBR-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"O=c1cc(NCCC2CCCCN2Cc2ccc(Cl)c(Cl)c2)[nH]c2ccccc12\", \"reactants\": [\"O=c1cc(NCCC2CC=CCN2Cc2ccc(Cl)c(Cl)c2)[nH]c2ccccc12\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"O=c1cc(NCCC2CC=CCN2Cc2ccc(Cl)c(Cl)c2)[nH]c2ccccc12\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"O=c1cc(NCCC2CC=CCN2Cc2ccc(Cl)c(Cl)c2)[nH]c2ccccc12 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"O=c1cc(NCCC2CC=CCN2Cc2ccc(Cl)c(Cl)c2)[nH]c2ccccc12\", \"reactants\": [\"NCCC1CC=CCN1Cc1ccc(Cl)c(Cl)c1\", \"O=c1cc(Cl)[nH]c2ccccc12\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"NCCC1CC=CCN1Cc1ccc(Cl)c(Cl)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=c1cc(Cl)[nH]c2ccccc12\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"FEUJCZDOWWHCKZ-UHFFFAOYSA-N.ZGFLMSYIISDCLO-UHFFFAOYSA-N>>FUXMCEXQNHCLQI-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"O=c1cc(NCCC2CC=CCN2Cc2ccc(Cl)c(Cl)c2)[nH]c2ccccc12\", \"reactants\": [\"NCCC1CC=CCN1Cc1ccc(Cl)c(Cl)c1\", \"O=c1cc(Cl)[nH]c2ccccc12\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"NCCC1CC=CCN1Cc1ccc(Cl)c(Cl)c1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"O=c1cc(Cl)[nH]c2ccccc12\", \"results\": [{\"inchikey\": \"ZGFLMSYIISDCLO-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=c1cc(Cl)[nH]c2ccccc12\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"NCCC1CC=CCN1Cc1ccc(Cl)c(Cl)c1 was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"NCCC1CC=CCN1Cc1ccc(Cl)c(Cl)c1\", \"reactants\": [\"CC(C)(C)OC(=O)NCCC1CC=CCN1Cc1ccc(Cl)c(Cl)c1\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)OC(=O)NCCC1CC=CCN1Cc1ccc(Cl)c(Cl)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"HUFASAAPVHAGKQ-UHFFFAOYSA-N>>FEUJCZDOWWHCKZ-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"NCCC1CC=CCN1Cc1ccc(Cl)c(Cl)c1\", \"reactants\": [\"CC(C)(C)OC(=O)NCCC1CC=CCN1Cc1ccc(Cl)c(Cl)c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"CC(C)(C)OC(=O)NCCC1CC=CCN1Cc1ccc(Cl)c(Cl)c1\", \"results\": [{\"inchikey\": \"HUFASAAPVHAGKQ-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CC(C)(C)OC(=O)NCCC1CC=CCN1Cc1ccc(Cl)c(Cl)c1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"O=c1cc(NCCC2CCCCN2Cc2ccc(Cl)c(Cl)c2)[nH]c2ccccc12\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"O=c1cc(NCCC2CC=CCN2Cc2ccc(Cl)c(Cl)c2)[nH]c2ccccc12\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"O=c1cc(NCCC2CC=CCN2Cc2ccc(Cl)c(Cl)c2)[nH]c2ccccc12\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"NCCC1CC=CCN1Cc1ccc(Cl)c(Cl)c1\": \"precursor\", \"O=c1cc(Cl)[nH]c2ccccc12\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"NCCC1CC=CCN1Cc1ccc(Cl)c(Cl)c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)(C)OC(=O)NCCC1CC=CCN1Cc1ccc(Cl)c(Cl)c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)OC(=O)NCCC1CC=CCN1Cc1ccc(Cl)c(Cl)c1\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"O=c1cc(Cl)[nH]c2ccccc12\", \"in_stock\": true, \"children\": []}]}]}]}]}]}}","name":"emit_routes"},"id":"call_4_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"O=c1cc(NCCC2CCCCN2Cc2ccc(Cl)c(Cl)c2)[nH]c2ccccc12","task_id":"retro_06eb9fcea66261f56040","tool_calls":8,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":4}
{"exact_match":true,"id":"retro_0742c9bb1316552343e1:reference-expert:a0","kind":"single_route","max_steps":3,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CC(C)Oc1cccc(CN2CC[C@@]3(C[C@@H]2C)CN(C)S(=O)(=O)N3c2cccc(F)c2)c1 in at most 3 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(C)Oc1cccc(CN2CC[C@@]3(C[C@@H]2C)CN(C)S(=O)(=O)N3c2cccc(F)c2)c1\", \"reactants\": [\"CC(C)Oc1cccc(CN2CC[C@]3(CNS(=O)(=O)N3c3cccc(F)c3)C[C@@H]2C)c1\", \"CI\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)Oc1cccc(CN2CC[C@]3(CNS(=O)(=O)N3c3cccc(F)c3)C[C@@H]2C)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"CI\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"CYNJHNQWUQFBEA-FDDCHVKYSA-N.INQOMBQAUSQDDS-UHFFFAOYSA-N>>CVPXZTQJPHYLAQ-YADARESESA-N\", \"model_turns_remaining\": 15, \"product\": \"CC(C)Oc1cccc(CN2CC[C@@]3(C[C@@H]2C)CN(C)S(=O)(=O)N3c2cccc(F)c2)c1\", \"reactants\": [\"CC(C)Oc1cccc(CN2CC[C@]3(CNS(=O)(=O)N3c3cccc(F)c3)C[C@@H]2C)c1\", \"CI\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CC(C)Oc1cccc(CN2CC[C@]3(CNS(=O)(=O)N3c3cccc(F)c3)C[C@@H]2C)c1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CI\", \"results\": [{\"inchikey\": \"INQOMBQAUSQDDS-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CI\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"CC(C)Oc1cccc(CN2CC[C@]3(CNS(=O)(=O)N3c3cccc(F)c3)C[C@@H]2C)c1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(C)Oc1cccc(CN2CC[C@]3(CNS(=O)(=O)N3c3cccc(F)c3)C[C@@H]2C)c1\", \"reactants\": [\"CC(C)Oc1cccc(CBr)c1\", \"C[C@H]1C[C@]2(CCN1)CNS(=O)(=O)N2c1cccc(F)c1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)Oc1cccc(CBr)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"C[C@H]1C[C@]2(CCN1)CNS(=O)(=O)N2c1cccc(F)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"CYKZAXPPHLTJOC-GXFFZTMASA-N.KDDVZGFLGMXKRC-UHFFFAOYSA-N>>CYNJHNQWUQFBEA-FDDCHVKYSA-N\", \"model_turns_remaining\": 14, \"product\": \"CC(C)Oc1cccc(CN2CC[C@]3(CNS(=O)(=O)N3c3cccc(F)c3)C[C@@H]2C)c1\", \"reactants\": [\"CC(C)Oc1cccc(CBr)c1\", \"C[C@H]1C[C@]2(CCN1)CNS(=O)(=O)N2c1cccc(F)c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CC(C)Oc1cccc(CBr)c1\", \"results\": [{\"inchikey\": \"KDDVZGFLGMXKRC-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CC(C)Oc1cccc(CBr)c1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"C[C@H]1C[C@]2(CCN1)CNS(=O)(=O)N2c1cccc(F)c1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"C[C@H]1C[C@]2(CCN1)CNS(=O)(=O)N2c1cccc(F)c1 was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"C[C@H]1C[C@]2(CCN1)CNS(=O)(=O)N2c1cccc(F)c1\", \"reactants\": [\"C[C@H]1C[C@]2(CCN1C(=O)OCc1ccccc1)CNS(=O)(=O)N2c1cccc(F)c1\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"C[C@H]1C[C@]2(CCN1C(=O)OCc1ccccc1)CNS(=O)(=O)N2c1cccc(F)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"RVDIMCUGAKSXAL-HRAATJIYSA-N>>CYKZAXPPHLTJOC-GXFFZTMASA-N\", \"model_turns_remaining\": 13, \"product\": \"C[C@H]1C[C@]2(CCN1)CNS(=O)(=O)N2c1cccc(F)c1\", \"reactants\": [\"C[C@H]1C[C@]2(CCN1C(=O)OCc1ccccc1)CNS(=O)(=O)N2c1cccc(F)c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"C[C@H]1C[C@]2(CCN1C(=O)OCc1ccccc1)CNS(=O)(=O)N2c1cccc(F)c1\", \"results\": [{\"inchikey\": \"RVDIMCUGAKSXAL-HRAATJIYSA-N\", \"similarity\": 1.0, \"smiles\": \"C[C@H]1C[C@]2(CCN1C(=O)OCc1ccccc1)CNS(=O)(=O)N2c1cccc(F)c1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CC(C)Oc1cccc(CN2CC[C@@]3(C[C@@H]2C)CN(C)S(=O)(=O)N3c2cccc(F)c2)c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)Oc1cccc(CN2CC[C@]3(CNS(=O)(=O)N3c3cccc(F)c3)C[C@@H]2C)c1\": \"precursor\", \"CI\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)Oc1cccc(CN2CC[C@]3(CNS(=O)(=O)N3c3cccc(F)c3)C[C@@H]2C)c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)Oc1cccc(CBr)c1\": \"precursor\", \"C[C@H]1C[C@]2(CCN1)CNS(=O)(=O)N2c1cccc(F)c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)Oc1cccc(CBr)c1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"C[C@H]1C[C@]2(CCN1)CNS(=O)(=O)N2c1cccc(F)c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"C[C@H]1C[C@]2(CCN1C(=O)OCc1ccccc1)CNS(=O)(=O)N2c1cccc(F)c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"C[C@H]1C[C@]2(CCN1C(=O)OCc1ccccc1)CNS(=O)(=O)N2c1cccc(F)c1\", \"in_stock\": true, \"children\": []}]}]}]}]}, {\"type\": \"mol\", \"smiles\": \"CI\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_4_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"CC(C)Oc1cccc(CN2CC[C@@]3(C[C@@H]2C)CN(C)S(=O)(=O)N3c2cccc(F)c2)c1","task_id":"retro_0742c9bb1316552343e1","tool_calls":9,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":4}
{"exact_match":true,"id":"retro_078a50a13767cadf61e7:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target COc1ccc(F)c(-c2nc(C(=O)O)ccc2F)c1 in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COc1ccc(F)c(-c2nc(C(=O)O)ccc2F)c1\", \"reactants\": [\"COc1ccc(F)c(B(O)O)c1\", \"O=C(O)c1ccc(F)c(Br)n1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"COc1ccc(F)c(B(O)O)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=C(O)c1ccc(F)c(Br)n1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"IPTZOWYBCLEBOE-UHFFFAOYSA-N.UVDJYBXHNFJTME-UHFFFAOYSA-N>>GUWOZXPWAGRWHS-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"COc1ccc(F)c(-c2nc(C(=O)O)ccc2F)c1\", \"reactants\": [\"COc1ccc(F)c(B(O)O)c1\", \"O=C(O)c1ccc(F)c(Br)n1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"COc1ccc(F)c(B(O)O)c1\", \"results\": [{\"inchikey\": \"IPTZOWYBCLEBOE-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"COc1ccc(F)c(B(O)O)c1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"O=C(O)c1ccc(F)c(Br)n1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"O=C(O)c1ccc(F)c(Br)n1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"O=C(O)c1ccc(F)c(Br)n1\", \"reactants\": [\"Cc1ccc(F)c(Br)n1\", \"O\", \"[O]=[Mn](=[O])(=[O])[OH]\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"Cc1ccc(F)c(Br)n1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"},{"function":{"arguments":"{\"query\": \"[O]=[Mn](=[O])(=[O])[OH]\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_3","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"KKVUMKHUMBXLMH-UHFFFAOYSA-N.XLYOFNOQVPJJNP-UHFFFAOYSA-N.ZJBYBXHCMWGGRR-UHFFFAOYSA-M>>UVDJYBXHNFJTME-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"O=C(O)c1ccc(F)c(Br)n1\", \"reactants\": [\"Cc1ccc(F)c(Br)n1\", \"O\", \"[O]=[Mn](=[O])(=[O])[OH]\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"Cc1ccc(F)c(Br)n1\", \"results\": [{\"inchikey\": \"KKVUMKHUMBXLMH-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Cc1ccc(F)c(Br)n1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"O\", \"results\": [{\"inchikey\": \"XLYOFNOQVPJJNP-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"[O]=[Mn](=[O])(=[O])[OH]\", \"results\": [{\"inchikey\": \"ZJBYBXHCMWGGRR-UHFFFAOYSA-M\", \"similarity\": 1.0, \"smiles\": \"[O]=[Mn](=[O])(=[O])[OH]\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_3"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"COc1ccc(F)c(-c2nc(C(=O)O)ccc2F)c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COc1ccc(F)c(B(O)O)c1\": \"precursor\", \"O=C(O)c1ccc(F)c(Br)n1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COc1ccc(F)c(B(O)O)c1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=C(O)c1ccc(F)c(Br)n1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"Cc1ccc(F)c(Br)n1\": \"precursor\", \"O\": \"precursor\", \"[O]=[Mn](=[O])(=[O])[OH]\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"Cc1ccc(F)c(Br)n1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"[O]=[Mn](=[O])(=[O])[OH]\", \"in_stock\": true, \"children\": []}]}]}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"COc1ccc(F)c(-c2nc(C(=O)O)ccc2F)c1","task_id":"retro_078a50a13767cadf61e7","tool_calls":8,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_078ea58dac044804274b:reference-expert:a0","kind":"single_route","max_steps":3,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target COc1cc(C=O)c(OC)c(OC)c1OC in at most 3 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COc1cc(C=O)c(OC)c(OC)c1OC\", \"reactants\": [\"CN(C=O)c1ccccc1\", \"COc1ccc(OC)c(OC)c1OC\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CN(C=O)c1ccccc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"COc1ccc(OC)c(OC)c1OC\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"JIKUXBYRTXDNIY-UHFFFAOYSA-N.QCNHIJXDZKTWSA-UHFFFAOYSA-N>>UVJGEUFORIIASL-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"COc1cc(C=O)c(OC)c(OC)c1OC\", \"reactants\": [\"CN(C=O)c1ccccc1\", \"COc1ccc(OC)c(OC)c1OC\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CN(C=O)c1ccccc1\", \"results\": [{\"inchikey\": \"JIKUXBYRTXDNIY-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CN(C=O)c1ccccc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"COc1ccc(OC)c(OC)c1OC\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"COc1ccc(OC)c(OC)c1OC was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COc1ccc(OC)c(OC)c1OC\", \"reactants\": [\"CI\", \"COc1ccc(O)c(OC)c1OC\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CI\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"COc1ccc(O)c(OC)c1OC\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"INQOMBQAUSQDDS-UHFFFAOYSA-N.OLUNIGWWQYXBJA-UHFFFAOYSA-N>>QCNHIJXDZKTWSA-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"COc1ccc(OC)c(OC)c1OC\", \"reactants\": [\"CI\", \"COc1ccc(O)c(OC)c1OC\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CI\", \"results\": [{\"inchikey\": \"INQOMBQAUSQDDS-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CI\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"COc1ccc(O)c(OC)c1OC\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"COc1ccc(O)c(OC)c1OC was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COc1ccc(O)c(OC)c1OC\", \"reactants\": [\"COc1ccc(C=O)c(OC)c1OC\", \"OO\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"COc1ccc(C=O)c(OC)c1OC\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"OO\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"MHAJPDPJQMAIIY-UHFFFAOYSA-N.UCTUXUGXIFRVGX-UHFFFAOYSA-N>>OLUNIGWWQYXBJA-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"COc1ccc(O)c(OC)c1OC\", \"reactants\": [\"COc1ccc(C=O)c(OC)c1OC\", \"OO\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"COc1ccc(C=O)c(OC)c1OC\", \"results\": [{\"inchikey\": \"UCTUXUGXIFRVGX-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"COc1ccc(C=O)c(OC)c1OC\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"OO\", \"results\": [{\"inchikey\": \"MHAJPDPJQMAIIY-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"OO\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"COc1cc(C=O)c(OC)c(OC)c1OC\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CN(C=O)c1ccccc1\": \"precursor\", \"COc1ccc(OC)c(OC)c1OC\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CN(C=O)c1ccccc1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"COc1ccc(OC)c(OC)c1OC\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CI\": \"precursor\", \"COc1ccc(O)c(OC)c1OC\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CI\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"COc1ccc(O)c(OC)c1OC\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COc1ccc(C=O)c(OC)c1OC\": \"precursor\", \"OO\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COc1ccc(C=O)c(OC)c1OC\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"OO\", \"in_stock\": true, \"children\": []}]}]}]}]}]}]}]}}","name":"emit_routes"},"id":"call_4_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"COc1cc(C=O)c(OC)c(OC)c1OC","task_id":"retro_078ea58dac044804274b","tool_calls":10,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":4}
{"exact_match":true,"id":"retro_0829c647bfe4f0bb9a5b:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target O=Cc1cnc(Cl)c(Cl)c1 in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"O=Cc1cnc(Cl)c(Cl)c1\", \"reactants\": [\"CON(C)C(=O)c1cnc(Cl)c(Cl)c1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CON(C)C(=O)c1cnc(Cl)c(Cl)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"YZINVISHQNRXPV-UHFFFAOYSA-N>>ROSCFXKNBQZLFC-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"O=Cc1cnc(Cl)c(Cl)c1\", \"reactants\": [\"CON(C)C(=O)c1cnc(Cl)c(Cl)c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CON(C)C(=O)c1cnc(Cl)c(Cl)c1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"CON(C)C(=O)c1cnc(Cl)c(Cl)c1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CON(C)C(=O)c1cnc(Cl)c(Cl)c1\", \"reactants\": [\"CNOC\", \"O=C(O)c1cnc(Cl)c(Cl)c1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CNOC\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=C(O)c1cnc(Cl)c(Cl)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"KRKPYFLIYNGWTE-UHFFFAOYSA-N.RNRLTTNKVLFZJS-UHFFFAOYSA-N>>YZINVISHQNRXPV-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"CON(C)C(=O)c1cnc(Cl)c(Cl)c1\", \"reactants\": [\"CNOC\", \"O=C(O)c1cnc(Cl)c(Cl)c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CNOC\", \"results\": [{\"inchikey\": \"KRKPYFLIYNGWTE-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CNOC\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"O=C(O)c1cnc(Cl)c(Cl)c1\", \"results\": [{\"inchikey\": \"RNRLTTNKVLFZJS-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=C(O)c1cnc(Cl)c(Cl)c1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"O=Cc1cnc(Cl)c(Cl)c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CON(C)C(=O)c1cnc(Cl)c(Cl)c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CON(C)C(=O)c1cnc(Cl)c(Cl)c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CNOC\": \"precursor\", \"O=C(O)c1cnc(Cl)c(Cl)c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CNOC\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=C(O)c1cnc(Cl)c(Cl)c1\", \"in_stock\": true, \"children\": []}]}]}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"O=Cc1cnc(Cl)c(Cl)c1","task_id":"retro_0829c647bfe4f0bb9a5b","tool_calls":6,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_110defbe3efbf5a90ef4:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CC(C)CN1C(=O)C(O)(CC(=O)c2ccccn2)c2ccccc21 in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(C)CN1C(=O)C(O)(CC(=O)c2ccccn2)c2ccccc21\", \"reactants\": [\"CC(=O)c1ccccn1\", \"CC(C)CN1C(=O)C(=O)c2ccccc21\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(=O)c1ccccn1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)CN1C(=O)C(=O)c2ccccc21\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_complete\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"AJKVQEKCUACUMD-UHFFFAOYSA-N.NZLZSOVOTGYGAY-UHFFFAOYSA-N>>QYAWHLNJIYLCRZ-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"CC(C)CN1C(=O)C(O)(CC(=O)c2ccccn2)c2ccccc21\", \"reactants\": [\"CC(=O)c1ccccn1\", \"CC(C)CN1C(=O)C(=O)c2ccccc21\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CC(=O)c1ccccn1\", \"results\": [{\"inchikey\": \"AJKVQEKCUACUMD-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CC(=O)c1ccccn1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CC(C)CN1C(=O)C(=O)c2ccccc21\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"CC(C)CN1C(=O)C(=O)c2ccccc21 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(C)CN1C(=O)C(=O)c2ccccc21\", \"reactants\": [\"CC(C)CBr\", \"O=C1Nc2ccccc2C1=O\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)CBr\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=C1Nc2ccccc2C1=O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"HLVFKOKELQSXIQ-UHFFFAOYSA-N.JXDYKVIHCLTXOP-UHFFFAOYSA-N>>NZLZSOVOTGYGAY-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"CC(C)CN1C(=O)C(=O)c2ccccc21\", \"reactants\": [\"CC(C)CBr\", \"O=C1Nc2ccccc2C1=O\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CC(C)CBr\", \"results\": [{\"inchikey\": \"HLVFKOKELQSXIQ-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CC(C)CBr\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"O=C1Nc2ccccc2C1=O\", \"results\": [{\"inchikey\": \"JXDYKVIHCLTXOP-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=C1Nc2ccccc2C1=O\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CC(C)CN1C(=O)C(O)(CC(=O)c2ccccn2)c2ccccc21\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(=O)c1ccccn1\": \"precursor\", \"CC(C)CN1C(=O)C(=O)c2ccccc21\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(=O)c1ccccn1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"CC(C)CN1C(=O)C(=O)c2ccccc21\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)CBr\": \"precursor\", \"O=C1Nc2ccccc2C1=O\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)CBr\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=C1Nc2ccccc2C1=O\", \"in_stock\": true, \"children\": []}]}]}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"CC(C)CN1C(=O)C(O)(CC(=O)c2ccccn2)c2ccccc21","task_id":"retro_110defbe3efbf5a90ef4","tool_calls":7,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_11819cd284cc8729c899:reference-expert:a0","kind":"single_route","max_steps":4,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target COc1cc(OC(=O)Nc2ccccc2)ccc1-c1ccc2c(c1COc1cc(F)ccc1C)C(C)=CC(C)(C)N2 in at most 4 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COc1cc(OC(=O)Nc2ccccc2)ccc1-c1ccc2c(c1COc1cc(F)ccc1C)C(C)=CC(C)(C)N2\", \"reactants\": [\"COc1cc(O)ccc1-c1ccc2c(c1COc1cc(F)ccc1C)C(C)=CC(C)(C)N2\", \"O=C=Nc1ccccc1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"COc1cc(O)ccc1-c1ccc2c(c1COc1cc(F)ccc1C)C(C)=CC(C)(C)N2\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=C=Nc1ccccc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_complete\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"DGTNSSLYPYDJGL-UHFFFAOYSA-N.PQTZJVRLEKJDFG-UHFFFAOYSA-N>>RRBNPTKRTZUOQU-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"COc1cc(OC(=O)Nc2ccccc2)ccc1-c1ccc2c(c1COc1cc(F)ccc1C)C(C)=CC(C)(C)N2\", \"reactants\": [\"COc1cc(O)ccc1-c1ccc2c(c1COc1cc(F)ccc1C)C(C)=CC(C)(C)N2\", \"O=C=Nc1ccccc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"COc1cc(O)ccc1-c1ccc2c(c1COc1cc(F)ccc1C)C(C)=CC(C)(C)N2\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"O=C=Nc1ccccc1\", \"results\": [{\"inchikey\": \"DGTNSSLYPYDJGL-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=C=Nc1ccccc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"COc1cc(O)ccc1-c1ccc2c(c1COc1cc(F)ccc1C)C(C)=CC(C)(C)N2 was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COc1cc(O)ccc1-c1ccc2c(c1COc1cc(F)ccc1C)C(C)=CC(C)(C)N2\", \"reactants\": [\"COCOc1ccc(-c2ccc3c(c2COc2cc(F)ccc2C)C(C)=CC(C)(C)N3)c(OC)c1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"COCOc1ccc(-c2ccc3c(c2COc2cc(F)ccc2C)C(C)=CC(C)(C)N3)c(OC)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"FHUHBUOAFIMMPY-UHFFFAOYSA-N>>PQTZJVRLEKJDFG-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"COc1cc(O)ccc1-c1ccc2c(c1COc1cc(F)ccc1C)C(C)=CC(C)(C)N2\", \"reactants\": [\"COCOc1ccc(-c2ccc3c(c2COc2cc(F)ccc2C)C(C)=CC(C)(C)N3)c(OC)c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"COCOc1ccc(-c2ccc3c(c2COc2cc(F)ccc2C)C(C)=CC(C)(C)N3)c(OC)c1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"COCOc1ccc(-c2ccc3c(c2COc2cc(F)ccc2C)C(C)=CC(C)(C)N3)c(OC)c1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COCOc1ccc(-c2ccc3c(c2COc2cc(F)ccc2C)C(C)=CC(C)(C)N3)c(OC)c1\", \"reactants\": [\"COCOc1ccc(-c2ccc3c(c2CO)C(C)=CC(C)(C)N3)c(OC)c1\", \"Cc1ccc(F)cc1O\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"COCOc1ccc(-c2ccc3c(c2CO)C(C)=CC(C)(C)N3)c(OC)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"Cc1ccc(F)cc1O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"CKJOSIHYVLHIER-UHFFFAOYSA-N.QSMFIXXDASGMDH-UHFFFAOYSA-N>>FHUHBUOAFIMMPY-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"COCOc1ccc(-c2ccc3c(c2COc2cc(F)ccc2C)C(C)=CC(C)(C)N3)c(OC)c1\", \"reactants\": [\"COCOc1ccc(-c2ccc3c(c2CO)C(C)=CC(C)(C)N3)c(OC)c1\", \"Cc1ccc(F)cc1O\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"COCOc1ccc(-c2ccc3c(c2CO)C(C)=CC(C)(C)N3)c(OC)c1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"Cc1ccc(F)cc1O\", \"results\": [{\"inchikey\": \"CKJOSIHYVLHIER-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Cc1ccc(F)cc1O\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"COCOc1ccc(-c2ccc3c(c2CO)C(C)=CC(C)(C)N3)c(OC)c1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COCOc1ccc(-c2ccc3c(c2CO)C(C)=CC(C)(C)N3)c(OC)c1\", \"reactants\": [\"CI\", \"COCOc1ccc(-c2ccc3c(c2CO)C(C)=CC(C)(C)N3)c(O)c1\"]}","name":"validate_disconnection"},"id":"call_4_0","type":"function"},{"function":{"arguments":"{\"query\": \"CI\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_1","type":"function"},{"function":{"arguments":"{\"query\": \"COCOc1ccc(-c2ccc3c(c2CO)C(C)=CC(C)(C)N3)c(O)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"INQOMBQAUSQDDS-UHFFFAOYSA-N.QBRYQENKISTNKJ-UHFFFAOYSA-N>>QSMFIXXDASGMDH-UHFFFAOYSA-N\", \"model_turns_remaining\": 12, \"product\": \"COCOc1ccc(-c2ccc3c(c2CO)C(C)=CC(C)(C)N3)c(OC)c1\", \"reactants\": [\"CI\", \"COCOc1ccc(-c2ccc3c(c2CO)C(C)=CC(C)(C)N3)c(O)c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_4_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"CI\", \"results\": [{\"inchikey\": \"INQOMBQAUSQDDS-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CI\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"COCOc1ccc(-c2ccc3c(c2CO)C(C)=CC(C)(C)N3)c(O)c1\", \"results\": [{\"inchikey\": \"QBRYQENKISTNKJ-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"COCOc1ccc(-c2ccc3c(c2CO)C(C)=CC(C)(C)N3)c(O)c1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"COc1cc(OC(=O)Nc2ccccc2)ccc1-c1ccc2c(c1COc1cc(F)ccc1C)C(C)=CC(C)(C)N2\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COc1cc(O)ccc1-c1ccc2c(c1COc1cc(F)ccc1C)C(C)=CC(C)(C)N2\": \"precursor\", \"O=C=Nc1ccccc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COc1cc(O)ccc1-c1ccc2c(c1COc1cc(F)ccc1C)C(C)=CC(C)(C)N2\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COCOc1ccc(-c2ccc3c(c2COc2cc(F)ccc2C)C(C)=CC(C)(C)N3)c(OC)c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COCOc1ccc(-c2ccc3c(c2COc2cc(F)ccc2C)C(C)=CC(C)(C)N3)c(OC)c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COCOc1ccc(-c2ccc3c(c2CO)C(C)=CC(C)(C)N3)c(OC)c1\": \"precursor\", \"Cc1ccc(F)cc1O\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COCOc1ccc(-c2ccc3c(c2CO)C(C)=CC(C)(C)N3)c(OC)c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CI\": \"precursor\", \"COCOc1ccc(-c2ccc3c(c2CO)C(C)=CC(C)(C)N3)c(O)c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CI\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"COCOc1ccc(-c2ccc3c(c2CO)C(C)=CC(C)(C)N3)c(O)c1\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"Cc1ccc(F)cc1O\", \"in_stock\": true, \"children\": []}]}]}]}]}, {\"type\": \"mol\", \"smiles\": \"O=C=Nc1ccccc1\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_5_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"COc1cc(OC(=O)Nc2ccccc2)ccc1-c1ccc2c(c1COc1cc(F)ccc1C)C(C)=CC(C)(C)N2","task_id":"retro_11819cd284cc8729c899","tool_calls":12,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":5}
{"exact_match":true,"id":"retro_133bfbc503a24c438b60:reference-expert:a0","kind":"single_route","max_steps":4,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target COCCNCc1cc(N2CCOCC2)nc(-c2cccc3[nH]ccc23)n1 in at most 4 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COCCNCc1cc(N2CCOCC2)nc(-c2cccc3[nH]ccc23)n1\", \"reactants\": [\"COCCNCc1cc(N2CCOCC2)nc(Cl)n1\", \"OB(O)c1cccc2[nH]ccc12\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"COCCNCc1cc(N2CCOCC2)nc(Cl)n1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"OB(O)c1cccc2[nH]ccc12\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"OXTMDHQMJWITDA-UHFFFAOYSA-N.USJUQEVUEBCLLR-UHFFFAOYSA-N>>GGAYLOLZVOHDPG-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"COCCNCc1cc(N2CCOCC2)nc(-c2cccc3[nH]ccc23)n1\", \"reactants\": [\"COCCNCc1cc(N2CCOCC2)nc(Cl)n1\", \"OB(O)c1cccc2[nH]ccc12\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"COCCNCc1cc(N2CCOCC2)nc(Cl)n1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"OB(O)c1cccc2[nH]ccc12\", \"results\": [{\"inchikey\": \"USJUQEVUEBCLLR-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"OB(O)c1cccc2[nH]ccc12\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"COCCNCc1cc(N2CCOCC2)nc(Cl)n1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COCCNCc1cc(N2CCOCC2)nc(Cl)n1\", \"reactants\": [\"COCCN\", \"O=Cc1cc(N2CCOCC2)nc(Cl)n1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"COCCN\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=Cc1cc(N2CCOCC2)nc(Cl)n1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"ASUDFOJKTJLAIK-UHFFFAOYSA-N.VVFYSDAFGDODBZ-UHFFFAOYSA-N>>OXTMDHQMJWITDA-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"COCCNCc1cc(N2CCOCC2)nc(Cl)n1\", \"reactants\": [\"COCCN\", \"O=Cc1cc(N2CCOCC2)nc(Cl)n1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"COCCN\", \"results\": [{\"inchikey\": \"ASUDFOJKTJLAIK-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"COCCN\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"O=Cc1cc(N2CCOCC2)nc(Cl)n1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"O=Cc1cc(N2CCOCC2)nc(Cl)n1 was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"O=Cc1cc(N2CCOCC2)nc(Cl)n1\", \"reactants\": [\"COC(=O)c1cc(N2CCOCC2)nc(Cl)n1\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"COC(=O)c1cc(N2CCOCC2)nc(Cl)n1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"CDCIGVQBAPSRTQ-UHFFFAOYSA-N>>VVFYSDAFGDODBZ-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"O=Cc1cc(N2CCOCC2)nc(Cl)n1\", \"reactants\": [\"COC(=O)c1cc(N2CCOCC2)nc(Cl)n1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"COC(=O)c1cc(N2CCOCC2)nc(Cl)n1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"COC(=O)c1cc(N2CCOCC2)nc(Cl)n1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COC(=O)c1cc(N2CCOCC2)nc(Cl)n1\", \"reactants\": [\"C1COCCN1\", \"COC(=O)c1cc(Cl)nc(Cl)n1\"]}","name":"validate_disconnection"},"id":"call_4_0","type":"function"},{"function":{"arguments":"{\"query\": \"C1COCCN1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_1","type":"function"},{"function":{"arguments":"{\"query\": \"COC(=O)c1cc(Cl)nc(Cl)n1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"DQNQNLWKAGZNIT-UHFFFAOYSA-N.YNAVUWVOSKDBBP-UHFFFAOYSA-N>>CDCIGVQBAPSRTQ-UHFFFAOYSA-N\", \"model_turns_remaining\": 12, \"product\": \"COC(=O)c1cc(N2CCOCC2)nc(Cl)n1\", \"reactants\": [\"C1COCCN1\", \"COC(=O)c1cc(Cl)nc(Cl)n1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_4_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"C1COCCN1\", \"results\": [{\"inchikey\": \"YNAVUWVOSKDBBP-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"C1COCCN1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"COC(=O)c1cc(Cl)nc(Cl)n1\", \"results\": [{\"inchikey\": \"DQNQNLWKAGZNIT-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"COC(=O)c1cc(Cl)nc(Cl)n1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"COCCNCc1cc(N2CCOCC2)nc(-c2cccc3[nH]ccc23)n1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COCCNCc1cc(N2CCOCC2)nc(Cl)n1\": \"precursor\", \"OB(O)c1cccc2[nH]ccc12\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COCCNCc1cc(N2CCOCC2)nc(Cl)n1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COCCN\": \"precursor\", \"O=Cc1cc(N2CCOCC2)nc(Cl)n1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COCCN\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=Cc1cc(N2CCOCC2)nc(Cl)n1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COC(=O)c1cc(N2CCOCC2)nc(Cl)n1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COC(=O)c1cc(N2CCOCC2)nc(Cl)n1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"C1COCCN1\": \"precursor\", \"COC(=O)c1cc(Cl)nc(Cl)n1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"C1COCCN1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"COC(=O)c1cc(Cl)nc(Cl)n1\", \"in_stock\": true, \"children\": []}]}]}]}]}]}]}, {\"type\": \"mol\", \"smiles\": \"OB(O)c1cccc2[nH]ccc12\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_5_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"COCCNCc1cc(N2CCOCC2)nc(-c2cccc3[nH]ccc23)n1","task_id":"retro_133bfbc503a24c438b60","tool_calls":12,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":5}
{"exact_match":true,"id":"retro_13e778bdd0f8d665e7e3:reference-expert:a0","kind":"single_route","max_steps":3,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CC(C)C1CCC(Oc2ccc3cc(CN4CCC(C(=O)O)CC4)ccc3c2)CC1 in at most 3 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(C)C1CCC(Oc2ccc3cc(CN4CCC(C(=O)O)CC4)ccc3c2)CC1\", \"reactants\": [\"CCOC(=O)C1CCN(Cc2ccc3cc(OC4CCC(C(C)C)CC4)ccc3c2)CC1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCOC(=O)C1CCN(Cc2ccc3cc(OC4CCC(C(C)C)CC4)ccc3c2)CC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"RKGTZXBLZWICJV-UHFFFAOYSA-N>>WAWOERKJBSUJQQ-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"CC(C)C1CCC(Oc2ccc3cc(CN4CCC(C(=O)O)CC4)ccc3c2)CC1\", \"reactants\": [\"CCOC(=O)C1CCN(Cc2ccc3cc(OC4CCC(C(C)C)CC4)ccc3c2)CC1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CCOC(=O)C1CCN(Cc2ccc3cc(OC4CCC(C(C)C)CC4)ccc3c2)CC1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"CCOC(=O)C1CCN(Cc2ccc3cc(OC4CCC(C(C)C)CC4)ccc3c2)CC1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCOC(=O)C1CCN(Cc2ccc3cc(OC4CCC(C(C)C)CC4)ccc3c2)CC1\", \"reactants\": [\"CC(C)C1CCC(O)CC1\", \"CCOC(=O)C1CCN(Cc2ccc3cc(O)ccc3c2)CC1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)C1CCC(O)CC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"CCOC(=O)C1CCN(Cc2ccc3cc(O)ccc3c2)CC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"DKKRDMLKVSKFMJ-UHFFFAOYSA-N.ZHYQNKOGBGHSQI-UHFFFAOYSA-N>>RKGTZXBLZWICJV-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"CCOC(=O)C1CCN(Cc2ccc3cc(OC4CCC(C(C)C)CC4)ccc3c2)CC1\", \"reactants\": [\"CC(C)C1CCC(O)CC1\", \"CCOC(=O)C1CCN(Cc2ccc3cc(O)ccc3c2)CC1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CC(C)C1CCC(O)CC1\", \"results\": [{\"inchikey\": \"DKKRDMLKVSKFMJ-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CC(C)C1CCC(O)CC1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CCOC(=O)C1CCN(Cc2ccc3cc(O)ccc3c2)CC1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"CCOC(=O)C1CCN(Cc2ccc3cc(O)ccc3c2)CC1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCOC(=O)C1CCN(Cc2ccc3cc(O)ccc3c2)CC1\", \"reactants\": [\"CCOC(=O)C1CCNCC1\", \"O=Cc1ccc2cc(O)ccc2c1\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCOC(=O)C1CCNCC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=Cc1ccc2cc(O)ccc2c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"PRYNJOJHKYNLIS-UHFFFAOYSA-N.RUJPPJYDHHAEEK-UHFFFAOYSA-N>>ZHYQNKOGBGHSQI-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"CCOC(=O)C1CCN(Cc2ccc3cc(O)ccc3c2)CC1\", \"reactants\": [\"CCOC(=O)C1CCNCC1\", \"O=Cc1ccc2cc(O)ccc2c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"CCOC(=O)C1CCNCC1\", \"results\": [{\"inchikey\": \"RUJPPJYDHHAEEK-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CCOC(=O)C1CCNCC1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"O=Cc1ccc2cc(O)ccc2c1\", \"results\": [{\"inchikey\": \"PRYNJOJHKYNLIS-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=Cc1ccc2cc(O)ccc2c1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CC(C)C1CCC(Oc2ccc3cc(CN4CCC(C(=O)O)CC4)ccc3c2)CC1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCOC(=O)C1CCN(Cc2ccc3cc(OC4CCC(C(C)C)CC4)ccc3c2)CC1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCOC(=O)C1CCN(Cc2ccc3cc(OC4CCC(C(C)C)CC4)ccc3c2)CC1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)C1CCC(O)CC1\": \"precursor\", \"CCOC(=O)C1CCN(Cc2ccc3cc(O)ccc3c2)CC1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)C1CCC(O)CC1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"CCOC(=O)C1CCN(Cc2ccc3cc(O)ccc3c2)CC1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCOC(=O)C1CCNCC1\": \"precursor\", \"O=Cc1ccc2cc(O)ccc2c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCOC(=O)C1CCNCC1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=Cc1ccc2cc(O)ccc2c1\", \"in_stock\": true, \"children\": []}]}]}]}]}]}]}]}}","name":"emit_routes"},"id":"call_4_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"CC(C)C1CCC(Oc2ccc3cc(CN4CCC(C(=O)O)CC4)ccc3c2)CC1","task_id":"retro_13e778bdd0f8d665e7e3","tool_calls":9,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":4}
{"exact_match":true,"id":"retro_14764001881fbdff3da2:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CC(=O)Nc1ccc2[nH]c(C(=O)O)cc2c1 in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(=O)Nc1ccc2[nH]c(C(=O)O)cc2c1\", \"reactants\": [\"CCOC(=O)c1cc2cc(NC(C)=O)ccc2[nH]1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCOC(=O)c1cc2cc(NC(C)=O)ccc2[nH]1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"NPIPEGMWIPYGFS-UHFFFAOYSA-N>>QAHUNXWGQVQHLT-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"CC(=O)Nc1ccc2[nH]c(C(=O)O)cc2c1\", \"reactants\": [\"CCOC(=O)c1cc2cc(NC(C)=O)ccc2[nH]1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CCOC(=O)c1cc2cc(NC(C)=O)ccc2[nH]1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"CCOC(=O)c1cc2cc(NC(C)=O)ccc2[nH]1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCOC(=O)c1cc2cc(NC(C)=O)ccc2[nH]1\", \"reactants\": [\"CC(=O)Cl\", \"CCOC(=O)c1cc2cc([N+](=O)[O-])ccc2[nH]1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(=O)Cl\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"CCOC(=O)c1cc2cc([N+](=O)[O-])ccc2[nH]1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"DVFJMQCNICEPAI-UHFFFAOYSA-N.WETWJCDKMRHUPV-UHFFFAOYSA-N>>NPIPEGMWIPYGFS-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"CCOC(=O)c1cc2cc(NC(C)=O)ccc2[nH]1\", \"reactants\": [\"CC(=O)Cl\", \"CCOC(=O)c1cc2cc([N+](=O)[O-])ccc2[nH]1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CC(=O)Cl\", \"results\": [{\"inchikey\": \"WETWJCDKMRHUPV-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CC(=O)Cl\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CCOC(=O)c1cc2cc([N+](=O)[O-])ccc2[nH]1\", \"results\": [{\"inchikey\": \"DVFJMQCNICEPAI-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CCOC(=O)c1cc2cc([N+](=O)[O-])ccc2[nH]1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CC(=O)Nc1ccc2[nH]c(C(=O)O)cc2c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCOC(=O)c1cc2cc(NC(C)=O)ccc2[nH]1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCOC(=O)c1cc2cc(NC(C)=O)ccc2[nH]1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(=O)Cl\": \"precursor\", \"CCOC(=O)c1cc2cc([N+](=O)[O-])ccc2[nH]1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(=O)Cl\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"CCOC(=O)c1cc2cc([N+](=O)[O-])ccc2[nH]1\", \"in_stock\": true, \"children\": []}]}]}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"CC(=O)Nc1ccc2[nH]c(C(=O)O)cc2c1","task_id":"retro_14764001881fbdff3da2","tool_calls":6,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_171cf73ba201e301d0b6:reference-expert:a0","kind":"single_route","max_steps":5,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CC(C)(C)OC(=O)Nc1ccc(CCOc2ccc(CC3SC(=O)NC3=O)cc2)cc1 in at most 5 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(C)(C)OC(=O)Nc1ccc(CCOc2ccc(CC3SC(=O)NC3=O)cc2)cc1\", \"reactants\": [\"CC(C)(C)OC(=O)Nc1ccc(CCOc2ccc(C=C3SC(=O)NC3=O)cc2)cc1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)OC(=O)Nc1ccc(CCOc2ccc(C=C3SC(=O)NC3=O)cc2)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_complete\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"NAFMETVAEIBQMX-UHFFFAOYSA-N>>GWFZNQBYBZGUKG-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"CC(C)(C)OC(=O)Nc1ccc(CCOc2ccc(CC3SC(=O)NC3=O)cc2)cc1\", \"reactants\": [\"CC(C)(C)OC(=O)Nc1ccc(CCOc2ccc(C=C3SC(=O)NC3=O)cc2)cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CC(C)(C)OC(=O)Nc1ccc(CCOc2ccc(C=C3SC(=O)NC3=O)cc2)cc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"CC(C)(C)OC(=O)Nc1ccc(CCOc2ccc(C=C3SC(=O)NC3=O)cc2)cc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(C)(C)OC(=O)Nc1ccc(CCOc2ccc(C=C3SC(=O)NC3=O)cc2)cc1\", \"reactants\": [\"CC(C)(C)OC(=O)Nc1ccc(CCOc2ccc(C=O)cc2)cc1\", \"O=C1CSC(=O)N1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)OC(=O)Nc1ccc(CCOc2ccc(C=O)cc2)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=C1CSC(=O)N1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"RUCNTOVFUYSUJV-UHFFFAOYSA-N.ZOBPZXTWZATXDG-UHFFFAOYSA-N>>NAFMETVAEIBQMX-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"CC(C)(C)OC(=O)Nc1ccc(CCOc2ccc(C=C3SC(=O)NC3=O)cc2)cc1\", \"reactants\": [\"CC(C)(C)OC(=O)Nc1ccc(CCOc2ccc(C=O)cc2)cc1\", \"O=C1CSC(=O)N1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CC(C)(C)OC(=O)Nc1ccc(CCOc2ccc(C=O)cc2)cc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"O=C1CSC(=O)N1\", \"results\": [{\"inchikey\": \"ZOBPZXTWZATXDG-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=C1CSC(=O)N1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"CC(C)(C)OC(=O)Nc1ccc(CCOc2ccc(C=O)cc2)cc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(C)(C)OC(=O)Nc1ccc(CCOc2ccc(C=O)cc2)cc1\", \"reactants\": [\"CC(C)(C)OC(=O)Nc1ccc(CCOS(=O)(=O)c2cccc([N+](=O)[O-])c2)cc1\", \"O=Cc1ccc(O)cc1\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)OC(=O)Nc1ccc(CCOS(=O)(=O)c2cccc([N+](=O)[O-])c2)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=Cc1ccc(O)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"RGHHSNMVTDWUBI-UHFFFAOYSA-N.YZLJRRHKDQZTFX-UHFFFAOYSA-N>>RUCNTOVFUYSUJV-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"CC(C)(C)OC(=O)Nc1ccc(CCOc2ccc(C=O)cc2)cc1\", \"reactants\": [\"CC(C)(C)OC(=O)Nc1ccc(CCOS(=O)(=O)c2cccc([N+](=O)[O-])c2)cc1\", \"O=Cc1ccc(O)cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"CC(C)(C)OC(=O)Nc1ccc(CCOS(=O)(=O)c2cccc([N+](=O)[O-])c2)cc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"O=Cc1ccc(O)cc1\", \"results\": [{\"inchikey\": \"RGHHSNMVTDWUBI-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=Cc1ccc(O)cc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"CC(C)(C)OC(=O)Nc1ccc(CCOS(=O)(=O)c2cccc([N+](=O)[O-])c2)cc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(C)(C)OC(=O)Nc1ccc(CCOS(=O)(=O)c2cccc([N+](=O)[O-])c2)cc1\", \"reactants\": [\"CC(C)(C)OC(=O)Nc1ccc(CCO)cc1\", \"O=[N+]([O-])c1cccc(S(=O)(=O)Cl)c1\"]}","name":"validate_disconnection"},"id":"call_4_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)OC(=O)Nc1ccc(CCO)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=[N+]([O-])c1cccc(S(=O)(=O)Cl)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"LVAACBVNZRPHFE-UHFFFAOYSA-N.MWWNNNAOGWPTQY-UHFFFAOYSA-N>>YZLJRRHKDQZTFX-UHFFFAOYSA-N\", \"model_turns_remaining\": 12, \"product\": \"CC(C)(C)OC(=O)Nc1ccc(CCOS(=O)(=O)c2cccc([N+](=O)[O-])c2)cc1\", \"reactants\": [\"CC(C)(C)OC(=O)Nc1ccc(CCO)cc1\", \"O=[N+]([O-])c1cccc(S(=O)(=O)Cl)c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_4_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"CC(C)(C)OC(=O)Nc1ccc(CCO)cc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"O=[N+]([O-])c1cccc(S(=O)(=O)Cl)c1\", \"results\": [{\"inchikey\": \"MWWNNNAOGWPTQY-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=[N+]([O-])c1cccc(S(=O)(=O)Cl)c1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_2"},{"content":"CC(C)(C)OC(=O)Nc1ccc(CCO)cc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(C)(C)OC(=O)Nc1ccc(CCO)cc1\", \"reactants\": [\"CC(C)(C)OC(=O)OC(=O)OC(C)(C)C\", \"Nc1ccc(CCO)cc1\"]}","name":"validate_disconnection"},"id":"call_5_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)OC(=O)OC(=O)OC(C)(C)C\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_5_1","type":"function"},{"function":{"arguments":"{\"query\": \"Nc1ccc(CCO)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_5_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"DYHSDKLCOJIUFX-UHFFFAOYSA-N.QXHDYMUPPXAMPQ-UHFFFAOYSA-N>>LVAACBVNZRPHFE-UHFFFAOYSA-N\", \"model_turns_remaining\": 11, \"product\": \"CC(C)(C)OC(=O)Nc1ccc(CCO)cc1\", \"reactants\": [\"CC(C)(C)OC(=O)OC(=O)OC(C)(C)C\", \"Nc1ccc(CCO)cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_5_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 11, \"query\": \"CC(C)(C)OC(=O)OC(=O)OC(C)(C)C\", \"results\": [{\"inchikey\": \"DYHSDKLCOJIUFX-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CC(C)(C)OC(=O)OC(=O)OC(C)(C)C\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_5_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 11, \"query\": \"Nc1ccc(CCO)cc1\", \"results\": [{\"inchikey\": \"QXHDYMUPPXAMPQ-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Nc1ccc(CCO)cc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_5_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)OC(=O)Nc1ccc(CCOc2ccc(CC3SC(=O)NC3=O)cc2)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)(C)OC(=O)Nc1ccc(CCOc2ccc(C=C3SC(=O)NC3=O)cc2)cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)OC(=O)Nc1ccc(CCOc2ccc(C=C3SC(=O)NC3=O)cc2)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)(C)OC(=O)Nc1ccc(CCOc2ccc(C=O)cc2)cc1\": \"precursor\", \"O=C1CSC(=O)N1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)OC(=O)Nc1ccc(CCOc2ccc(C=O)cc2)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)(C)OC(=O)Nc1ccc(CCOS(=O)(=O)c2cccc([N+](=O)[O-])c2)cc1\": \"precursor\", \"O=Cc1ccc(O)cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)OC(=O)Nc1ccc(CCOS(=O)(=O)c2cccc([N+](=O)[O-])c2)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)(C)OC(=O)Nc1ccc(CCO)cc1\": \"precursor\", \"O=[N+]([O-])c1cccc(S(=O)(=O)Cl)c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)OC(=O)Nc1ccc(CCO)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)(C)OC(=O)OC(=O)OC(C)(C)C\": \"precursor\", \"Nc1ccc(CCO)cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)OC(=O)OC(=O)OC(C)(C)C\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"Nc1ccc(CCO)cc1\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"O=[N+]([O-])c1cccc(S(=O)(=O)Cl)c1\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"O=Cc1ccc(O)cc1\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"O=C1CSC(=O)N1\", \"in_stock\": true, \"children\": []}]}]}]}]}]}}","name":"emit_routes"},"id":"call_6_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"CC(C)(C)OC(=O)Nc1ccc(CCOc2ccc(CC3SC(=O)NC3=O)cc2)cc1","task_id":"retro_171cf73ba201e301d0b6","tool_calls":15,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":6}
{"exact_match":true,"id":"retro_175912abdb627ff0b30f:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CCOC(=O)C1CCN(Cc2ccc3cc(O)ccc3n2)CC1 in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCOC(=O)C1CCN(Cc2ccc3cc(O)ccc3n2)CC1\", \"reactants\": [\"CCOC(=O)C1CCN(Cc2ccc3cc(O[Si](C)(C)C(C)(C)C)ccc3n2)CC1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCOC(=O)C1CCN(Cc2ccc3cc(O[Si](C)(C)C(C)(C)C)ccc3n2)CC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"SDYWTZFXSMOHTO-UHFFFAOYSA-N>>NDNNTCUUXKHTAC-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"CCOC(=O)C1CCN(Cc2ccc3cc(O)ccc3n2)CC1\", \"reactants\": [\"CCOC(=O)C1CCN(Cc2ccc3cc(O[Si](C)(C)C(C)(C)C)ccc3n2)CC1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CCOC(=O)C1CCN(Cc2ccc3cc(O[Si](C)(C)C(C)(C)C)ccc3n2)CC1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"CCOC(=O)C1CCN(Cc2ccc3cc(O[Si](C)(C)C(C)(C)C)ccc3n2)CC1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCOC(=O)C1CCN(Cc2ccc3cc(O[Si](C)(C)C(C)(C)C)ccc3n2)CC1\", \"reactants\": [\"CC(C)(C)[Si](C)(C)Oc1ccc2nc(C=O)ccc2c1\", \"CCOC(=O)C1CCNCC1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)[Si](C)(C)Oc1ccc2nc(C=O)ccc2c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"CCOC(=O)C1CCNCC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"JMHLCINNHZUZMT-UHFFFAOYSA-N.RUJPPJYDHHAEEK-UHFFFAOYSA-N>>SDYWTZFXSMOHTO-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"CCOC(=O)C1CCN(Cc2ccc3cc(O[Si](C)(C)C(C)(C)C)ccc3n2)CC1\", \"reactants\": [\"CC(C)(C)[Si](C)(C)Oc1ccc2nc(C=O)ccc2c1\", \"CCOC(=O)C1CCNCC1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CC(C)(C)[Si](C)(C)Oc1ccc2nc(C=O)ccc2c1\", \"results\": [{\"inchikey\": \"JMHLCINNHZUZMT-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CC(C)(C)[Si](C)(C)Oc1ccc2nc(C=O)ccc2c1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CCOC(=O)C1CCNCC1\", \"results\": [{\"inchikey\": \"RUJPPJYDHHAEEK-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CCOC(=O)C1CCNCC1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CCOC(=O)C1CCN(Cc2ccc3cc(O)ccc3n2)CC1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCOC(=O)C1CCN(Cc2ccc3cc(O[Si](C)(C)C(C)(C)C)ccc3n2)CC1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCOC(=O)C1CCN(Cc2ccc3cc(O[Si](C)(C)C(C)(C)C)ccc3n2)CC1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)(C)[Si](C)(C)Oc1ccc2nc(C=O)ccc2c1\": \"precursor\", \"CCOC(=O)C1CCNCC1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)[Si](C)(C)Oc1ccc2nc(C=O)ccc2c1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"CCOC(=O)C1CCNCC1\", \"in_stock\": true, \"children\": []}]}]}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"CCOC(=O)C1CCN(Cc2ccc3cc(O)ccc3n2)CC1","task_id":"retro_175912abdb627ff0b30f","tool_calls":6,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":false,"id":"retro_18840f9c960d7bb21253:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CN1CCN(C(=O)C2CCN(C(=O)OC(C)(C)C)CC2)CC1 in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CN1CCN(C(=O)C2CCN(C(=O)OC(C)(C)C)CC2)CC1\", \"reactants\": [\"CC(C)(C)OC(=O)N1CCC(C(=O)O)CC1\", \"CN1CCNCC1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)OC(=O)N1CCC(C(=O)O)CC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"CN1CCNCC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"JWOHBPPVVDQMKB-UHFFFAOYSA-N.PVOAHINGSUIXLS-UHFFFAOYSA-N>>NJCYAEJCGFMXPK-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"CN1CCN(C(=O)C2CCN(C(=O)OC(C)(C)C)CC2)CC1\", \"reactants\": [\"CC(C)(C)OC(=O)N1CCC(C(=O)O)CC1\", \"CN1CCNCC1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CC(C)(C)OC(=O)N1CCC(C(=O)O)CC1\", \"results\": [{\"inchikey\": \"JWOHBPPVVDQMKB-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CC(C)(C)OC(=O)N1CCC(C(=O)O)CC1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CN1CCNCC1\", \"results\": [{\"inchikey\": \"PVOAHINGSUIXLS-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CN1CCNCC1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CN1CCN(C(=O)C2CCN(C(=O)OC(C)(C)C)CC2)CC1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)(C)OC(=O)N1CCC(C(=O)O)CC1\": \"precursor\", \"CN1CCNCC1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)OC(=O)N1CCC(C(=O)O)CC1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"CN1CCNCC1\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_2_0","type":"function"}]}],"provider":"reference","reward":0.85,"source":"reference-expert","target_smiles":"CN1CCN(C(=O)C2CCN(C(=O)OC(C)(C)C)CC2)CC1","task_id":"retro_18840f9c960d7bb21253","tool_calls":4,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":2}
{"exact_match":true,"id":"retro_19479354a27176d97fda:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target Fc1ccc2c(-c3ccc4oc(CN5CCNCC5)nc4c3)c[nH]c2c1 in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Fc1ccc2c(-c3ccc4oc(CN5CCNCC5)nc4c3)c[nH]c2c1\", \"reactants\": [\"O=S(=O)(c1ccccc1)n1cc(-c2ccc3oc(CN4CCNCC4)nc3c2)c2ccc(F)cc21\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"O=S(=O)(c1ccccc1)n1cc(-c2ccc3oc(CN4CCNCC4)nc3c2)c2ccc(F)cc21\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"XGXGLBMCRKLPHL-UHFFFAOYSA-N>>IHYISBOONMPBBO-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"Fc1ccc2c(-c3ccc4oc(CN5CCNCC5)nc4c3)c[nH]c2c1\", \"reactants\": [\"O=S(=O)(c1ccccc1)n1cc(-c2ccc3oc(CN4CCNCC4)nc3c2)c2ccc(F)cc21\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"O=S(=O)(c1ccccc1)n1cc(-c2ccc3oc(CN4CCNCC4)nc3c2)c2ccc(F)cc21\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"O=S(=O)(c1ccccc1)n1cc(-c2ccc3oc(CN4CCNCC4)nc3c2)c2ccc(F)cc21 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"O=S(=O)(c1ccccc1)n1cc(-c2ccc3oc(CN4CCNCC4)nc3c2)c2ccc(F)cc21\", \"reactants\": [\"C1CNCCN1\", \"O=S(=O)(c1ccccc1)n1cc(-c2ccc3oc(CCl)nc3c2)c2ccc(F)cc21\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"C1CNCCN1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=S(=O)(c1ccccc1)n1cc(-c2ccc3oc(CCl)nc3c2)c2ccc(F)cc21\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"GLUUGHFHXGJENI-UHFFFAOYSA-N.PKVTZUUWLOSPHU-UHFFFAOYSA-N>>XGXGLBMCRKLPHL-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"O=S(=O)(c1ccccc1)n1cc(-c2ccc3oc(CN4CCNCC4)nc3c2)c2ccc(F)cc21\", \"reactants\": [\"C1CNCCN1\", \"O=S(=O)(c1ccccc1)n1cc(-c2ccc3oc(CCl)nc3c2)c2ccc(F)cc21\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"C1CNCCN1\", \"results\": [{\"inchikey\": \"GLUUGHFHXGJENI-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"C1CNCCN1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"O=S(=O)(c1ccccc1)n1cc(-c2ccc3oc(CCl)nc3c2)c2ccc(F)cc21\", \"results\": [{\"inchikey\": \"PKVTZUUWLOSPHU-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=S(=O)(c1ccccc1)n1cc(-c2ccc3oc(CCl)nc3c2)c2ccc(F)cc21\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"Fc1ccc2c(-c3ccc4oc(CN5CCNCC5)nc4c3)c[nH]c2c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"O=S(=O)(c1ccccc1)n1cc(-c2ccc3oc(CN4CCNCC4)nc3c2)c2ccc(F)cc21\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"O=S(=O)(c1ccccc1)n1cc(-c2ccc3oc(CN4CCNCC4)nc3c2)c2ccc(F)cc21\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"C1CNCCN1\": \"precursor\", \"O=S(=O)(c1ccccc1)n1cc(-c2ccc3oc(CCl)nc3c2)c2ccc(F)cc21\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"C1CNCCN1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=S(=O)(c1ccccc1)n1cc(-c2ccc3oc(CCl)nc3c2)c2ccc(F)cc21\", \"in_stock\": true, \"children\": []}]}]}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"Fc1ccc2c(-c3ccc4oc(CN5CCNCC5)nc4c3)c[nH]c2c1","task_id":"retro_19479354a27176d97fda","tool_calls":6,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_19527b55341b0a6bdfb4:reference-expert:a0","kind":"single_route","max_steps":3,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target Nc1cc(Cl)c(Oc2ccc(O)c(S(=O)(=O)CC3CC3)c2)c(Cl)c1 in at most 3 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Nc1cc(Cl)c(Oc2ccc(O)c(S(=O)(=O)CC3CC3)c2)c(Cl)c1\", \"reactants\": [\"O=[N+]([O-])c1cc(Cl)c(Oc2ccc(O)c(S(=O)(=O)CC3CC3)c2)c(Cl)c1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"O=[N+]([O-])c1cc(Cl)c(Oc2ccc(O)c(S(=O)(=O)CC3CC3)c2)c(Cl)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"RMCIFEXNNFFBSE-UHFFFAOYSA-N>>HAUNKTXABYETOZ-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"Nc1cc(Cl)c(Oc2ccc(O)c(S(=O)(=O)CC3CC3)c2)c(Cl)c1\", \"reactants\": [\"O=[N+]([O-])c1cc(Cl)c(Oc2ccc(O)c(S(=O)(=O)CC3CC3)c2)c(Cl)c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"O=[N+]([O-])c1cc(Cl)c(Oc2ccc(O)c(S(=O)(=O)CC3CC3)c2)c(Cl)c1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"O=[N+]([O-])c1cc(Cl)c(Oc2ccc(O)c(S(=O)(=O)CC3CC3)c2)c(Cl)c1 was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"O=[N+]([O-])c1cc(Cl)c(Oc2ccc(O)c(S(=O)(=O)CC3CC3)c2)c(Cl)c1\", \"reactants\": [\"COc1ccc(Oc2c(Cl)cc([N+](=O)[O-])cc2Cl)cc1S(=O)(=O)CC1CC1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"COc1ccc(Oc2c(Cl)cc([N+](=O)[O-])cc2Cl)cc1S(=O)(=O)CC1CC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"SCAMMKVENOELIW-UHFFFAOYSA-N>>RMCIFEXNNFFBSE-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"O=[N+]([O-])c1cc(Cl)c(Oc2ccc(O)c(S(=O)(=O)CC3CC3)c2)c(Cl)c1\", \"reactants\": [\"COc1ccc(Oc2c(Cl)cc([N+](=O)[O-])cc2Cl)cc1S(=O)(=O)CC1CC1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"COc1ccc(Oc2c(Cl)cc([N+](=O)[O-])cc2Cl)cc1S(=O)(=O)CC1CC1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"COc1ccc(Oc2c(Cl)cc([N+](=O)[O-])cc2Cl)cc1S(=O)(=O)CC1CC1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COc1ccc(Oc2c(Cl)cc([N+](=O)[O-])cc2Cl)cc1S(=O)(=O)CC1CC1\", \"reactants\": [\"BrCC1CC1\", \"COc1ccc(Oc2c(Cl)cc([N+](=O)[O-])cc2Cl)cc1S(=O)O\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"BrCC1CC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"COc1ccc(Oc2c(Cl)cc([N+](=O)[O-])cc2Cl)cc1S(=O)O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"AEILLAXRDHDKDY-UHFFFAOYSA-N.OJSIHXSNXHTTGR-UHFFFAOYSA-N>>SCAMMKVENOELIW-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"COc1ccc(Oc2c(Cl)cc([N+](=O)[O-])cc2Cl)cc1S(=O)(=O)CC1CC1\", \"reactants\": [\"BrCC1CC1\", \"COc1ccc(Oc2c(Cl)cc([N+](=O)[O-])cc2Cl)cc1S(=O)O\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"BrCC1CC1\", \"results\": [{\"inchikey\": \"AEILLAXRDHDKDY-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"BrCC1CC1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"COc1ccc(Oc2c(Cl)cc([N+](=O)[O-])cc2Cl)cc1S(=O)O\", \"results\": [{\"inchikey\": \"OJSIHXSNXHTTGR-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"COc1ccc(Oc2c(Cl)cc([N+](=O)[O-])cc2Cl)cc1S(=O)O\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"Nc1cc(Cl)c(Oc2ccc(O)c(S(=O)(=O)CC3CC3)c2)c(Cl)c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"O=[N+]([O-])c1cc(Cl)c(Oc2ccc(O)c(S(=O)(=O)CC3CC3)c2)c(Cl)c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"O=[N+]([O-])c1cc(Cl)c(Oc2ccc(O)c(S(=O)(=O)CC3CC3)c2)c(Cl)c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COc1ccc(Oc2c(Cl)cc([N+](=O)[O-])cc2Cl)cc1S(=O)(=O)CC1CC1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COc1ccc(Oc2c(Cl)cc([N+](=O)[O-])cc2Cl)cc1S(=O)(=O)CC1CC1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"BrCC1CC1\": \"precursor\", \"COc1ccc(Oc2c(Cl)cc([N+](=O)[O-])cc2Cl)cc1S(=O)O\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"BrCC1CC1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"COc1ccc(Oc2c(Cl)cc([N+](=O)[O-])cc2Cl)cc1S(=O)O\", \"in_stock\": true, \"children\": []}]}]}]}]}]}]}]}}","name":"emit_routes"},"id":"call_4_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"Nc1cc(Cl)c(Oc2ccc(O)c(S(=O)(=O)CC3CC3)c2)c(Cl)c1","task_id":"retro_19527b55341b0a6bdfb4","tool_calls":8,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":4}
{"exact_match":true,"id":"retro_1a51f47cd13754ebe873:reference-expert:a0","kind":"single_route","max_steps":3,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target NC(=O)c1nc(F)ccc1N in at most 3 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"NC(=O)c1nc(F)ccc1N\", \"reactants\": [\"NC(=O)c1nc(F)ccc1[N+](=O)[O-]\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"NC(=O)c1nc(F)ccc1[N+](=O)[O-]\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"MCZFZBZNGIJIBW-UHFFFAOYSA-N>>UKGNXGFDUODPGZ-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"NC(=O)c1nc(F)ccc1N\", \"reactants\": [\"NC(=O)c1nc(F)ccc1[N+](=O)[O-]\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"NC(=O)c1nc(F)ccc1[N+](=O)[O-]\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"NC(=O)c1nc(F)ccc1[N+](=O)[O-] was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"NC(=O)c1nc(F)ccc1[N+](=O)[O-]\", \"reactants\": [\"N#Cc1nc(F)ccc1[N+](=O)[O-]\", \"O=S(=O)(O)O\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"N#Cc1nc(F)ccc1[N+](=O)[O-]\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=S(=O)(O)O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"DOESITSDBOTCGK-UHFFFAOYSA-N.QAOWNCQODCNURD-UHFFFAOYSA-N>>MCZFZBZNGIJIBW-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"NC(=O)c1nc(F)ccc1[N+](=O)[O-]\", \"reactants\": [\"N#Cc1nc(F)ccc1[N+](=O)[O-]\", \"O=S(=O)(O)O\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"N#Cc1nc(F)ccc1[N+](=O)[O-]\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"O=S(=O)(O)O\", \"results\": [{\"inchikey\": \"QAOWNCQODCNURD-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=S(=O)(O)O\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"N#Cc1nc(F)ccc1[N+](=O)[O-] was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"N#Cc1nc(F)ccc1[N+](=O)[O-]\", \"reactants\": [\"F\", \"N#Cc1nc(Cl)ccc1[N+](=O)[O-]\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"F\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"N#Cc1nc(Cl)ccc1[N+](=O)[O-]\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"KRHYYFGTRYWZRS-UHFFFAOYSA-N.XVIHGTRTKQZJAC-UHFFFAOYSA-N>>DOESITSDBOTCGK-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"N#Cc1nc(F)ccc1[N+](=O)[O-]\", \"reactants\": [\"F\", \"N#Cc1nc(Cl)ccc1[N+](=O)[O-]\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"F\", \"results\": [{\"inchikey\": \"KRHYYFGTRYWZRS-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"F\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"N#Cc1nc(Cl)ccc1[N+](=O)[O-]\", \"results\": [{\"inchikey\": \"XVIHGTRTKQZJAC-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"N#Cc1nc(Cl)ccc1[N+](=O)[O-]\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"NC(=O)c1nc(F)ccc1N\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"NC(=O)c1nc(F)ccc1[N+](=O)[O-]\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"NC(=O)c1nc(F)ccc1[N+](=O)[O-]\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"N#Cc1nc(F)ccc1[N+](=O)[O-]\": \"precursor\", \"O=S(=O)(O)O\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"N#Cc1nc(F)ccc1[N+](=O)[O-]\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"F\": \"precursor\", \"N#Cc1nc(Cl)ccc1[N+](=O)[O-]\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"F\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"N#Cc1nc(Cl)ccc1[N+](=O)[O-]\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"O=S(=O)(O)O\", \"in_stock\": true, \"children\": []}]}]}]}]}]}}","name":"emit_routes"},"id":"call_4_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"NC(=O)c1nc(F)ccc1N","task_id":"retro_1a51f47cd13754ebe873","tool_calls":9,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":4}
{"exact_match":true,"id":"retro_1ba654acd7d0f727b09a:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target Cc1cc(Cl)ccc1OCC(=O)N1C[C@@H]2CN(C(=O)OC(C)(C)C)C[C@@H]2C1 in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Cc1cc(Cl)ccc1OCC(=O)N1C[C@@H]2CN(C(=O)OC(C)(C)C)C[C@@H]2C1\", \"reactants\": [\"CC(C)(C)OC(=O)N1C[C@H]2CN(C(=O)CBr)C[C@H]2C1\", \"Cc1cc(Cl)ccc1O\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)OC(=O)N1C[C@H]2CN(C(=O)CBr)C[C@H]2C1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"Cc1cc(Cl)ccc1O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"DUBQJHQYZUWLIH-AOOOYVTPSA-N.RHPUJHQBPORFGV-UHFFFAOYSA-N>>MUZHMCFAPGEVPJ-GASCZTMLSA-N\", \"model_turns_remaining\": 15, \"product\": \"Cc1cc(Cl)ccc1OCC(=O)N1C[C@@H]2CN(C(=O)OC(C)(C)C)C[C@@H]2C1\", \"reactants\": [\"CC(C)(C)OC(=O)N1C[C@H]2CN(C(=O)CBr)C[C@H]2C1\", \"Cc1cc(Cl)ccc1O\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CC(C)(C)OC(=O)N1C[C@H]2CN(C(=O)CBr)C[C@H]2C1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"Cc1cc(Cl)ccc1O\", \"results\": [{\"inchikey\": \"RHPUJHQBPORFGV-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Cc1cc(Cl)ccc1O\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"CC(C)(C)OC(=O)N1C[C@H]2CN(C(=O)CBr)C[C@H]2C1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(C)(C)OC(=O)N1C[C@H]2CN(C(=O)CBr)C[C@H]2C1\", \"reactants\": [\"CC(C)(C)OC(=O)N1C[C@H]2CNC[C@H]2C1\", \"O=C(Cl)CBr\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)OC(=O)N1C[C@H]2CNC[C@H]2C1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=C(Cl)CBr\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"FYUVLZRRIRGSTE-DTORHVGOSA-N.SYZRZLUNWVNNNV-UHFFFAOYSA-N>>DUBQJHQYZUWLIH-AOOOYVTPSA-N\", \"model_turns_remaining\": 14, \"product\": \"CC(C)(C)OC(=O)N1C[C@H]2CN(C(=O)CBr)C[C@H]2C1\", \"reactants\": [\"CC(C)(C)OC(=O)N1C[C@H]2CNC[C@H]2C1\", \"O=C(Cl)CBr\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CC(C)(C)OC(=O)N1C[C@H]2CNC[C@H]2C1\", \"results\": [{\"inchikey\": \"FYUVLZRRIRGSTE-DTORHVGOSA-N\", \"similarity\": 1.0, \"smiles\": \"CC(C)(C)OC(=O)N1C[C@H]2CNC[C@H]2C1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"O=C(Cl)CBr\", \"results\": [{\"inchikey\": \"SYZRZLUNWVNNNV-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=C(Cl)CBr\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"Cc1cc(Cl)ccc1OCC(=O)N1C[C@@H]2CN(C(=O)OC(C)(C)C)C[C@@H]2C1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)(C)OC(=O)N1C[C@H]2CN(C(=O)CBr)C[C@H]2C1\": \"precursor\", \"Cc1cc(Cl)ccc1O\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)OC(=O)N1C[C@H]2CN(C(=O)CBr)C[C@H]2C1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)(C)OC(=O)N1C[C@H]2CNC[C@H]2C1\": \"precursor\", \"O=C(Cl)CBr\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)OC(=O)N1C[C@H]2CNC[C@H]2C1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=C(Cl)CBr\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"Cc1cc(Cl)ccc1O\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"Cc1cc(Cl)ccc1OCC(=O)N1C[C@@H]2CN(C(=O)OC(C)(C)C)C[C@@H]2C1","task_id":"retro_1ba654acd7d0f727b09a","tool_calls":7,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_1ca089fc6a8781e514c9:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target COc1ccc(Cl)cc1C(C#N)NC(=O)CC(C)(C)O[Si](C)(C)C(C)(C)C in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COc1ccc(Cl)cc1C(C#N)NC(=O)CC(C)(C)O[Si](C)(C)C(C)(C)C\", \"reactants\": [\"CC(C)(CC(=O)O)O[Si](C)(C)C(C)(C)C\", \"COc1ccc(Cl)cc1C(N)C#N\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(CC(=O)O)O[Si](C)(C)C(C)(C)C\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"COc1ccc(Cl)cc1C(N)C#N\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"IUOPPAAEOSJNAB-UHFFFAOYSA-N.MHYGJCSLPKPBFI-UHFFFAOYSA-N>>VRSJVVDNBUXEBH-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"COc1ccc(Cl)cc1C(C#N)NC(=O)CC(C)(C)O[Si](C)(C)C(C)(C)C\", \"reactants\": [\"CC(C)(CC(=O)O)O[Si](C)(C)C(C)(C)C\", \"COc1ccc(Cl)cc1C(N)C#N\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CC(C)(CC(=O)O)O[Si](C)(C)C(C)(C)C\", \"results\": [{\"inchikey\": \"IUOPPAAEOSJNAB-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CC(C)(CC(=O)O)O[Si](C)(C)C(C)(C)C\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"COc1ccc(Cl)cc1C(N)C#N\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"COc1ccc(Cl)cc1C(N)C#N was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COc1ccc(Cl)cc1C(N)C#N\", \"reactants\": [\"C#N\", \"COc1ccc(Cl)cc1C=O\", \"N\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"C#N\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"COc1ccc(Cl)cc1C=O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"},{"function":{"arguments":"{\"query\": \"N\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_3","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"HXTWDGGMXZXOIV-UHFFFAOYSA-N.LELOWRISYMNNSU-UHFFFAOYSA-N.QGZKDVFQNNGYKY-UHFFFAOYSA-N>>MHYGJCSLPKPBFI-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"COc1ccc(Cl)cc1C(N)C#N\", \"reactants\": [\"C#N\", \"COc1ccc(Cl)cc1C=O\", \"N\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"C#N\", \"results\": [{\"inchikey\": \"LELOWRISYMNNSU-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"C#N\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"COc1ccc(Cl)cc1C=O\", \"results\": [{\"inchikey\": \"HXTWDGGMXZXOIV-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"COc1ccc(Cl)cc1C=O\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"N\", \"results\": [{\"inchikey\": \"QGZKDVFQNNGYKY-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"N\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_3"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"COc1ccc(Cl)cc1C(C#N)NC(=O)CC(C)(C)O[Si](C)(C)C(C)(C)C\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)(CC(=O)O)O[Si](C)(C)C(C)(C)C\": \"precursor\", \"COc1ccc(Cl)cc1C(N)C#N\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(CC(=O)O)O[Si](C)(C)C(C)(C)C\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"COc1ccc(Cl)cc1C(N)C#N\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"C#N\": \"precursor\", \"COc1ccc(Cl)cc1C=O\": \"precursor\", \"N\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"C#N\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"COc1ccc(Cl)cc1C=O\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"N\", \"in_stock\": true, \"children\": []}]}]}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"COc1ccc(Cl)cc1C(C#N)NC(=O)CC(C)(C)O[Si](C)(C)C(C)(C)C","task_id":"retro_1ca089fc6a8781e514c9","tool_calls":8,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_1dd779286d2baa56bb30:reference-expert:a0","kind":"single_route","max_steps":3,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target O=C(Nc1ccccc1OCCCNC1CCCC1)c1cccc2[nH]ccc12 in at most 3 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"O=C(Nc1ccccc1OCCCNC1CCCC1)c1cccc2[nH]ccc12\", \"reactants\": [\"NC1CCCC1\", \"O=C(Nc1ccccc1OCCCBr)c1cccc2[nH]ccc12\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"NC1CCCC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=C(Nc1ccccc1OCCCBr)c1cccc2[nH]ccc12\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"KINAJOVFGULSCU-UHFFFAOYSA-N.NISGSNTVMOOSJQ-UHFFFAOYSA-N>>DEXQMJHMYKWFOC-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"O=C(Nc1ccccc1OCCCNC1CCCC1)c1cccc2[nH]ccc12\", \"reactants\": [\"NC1CCCC1\", \"O=C(Nc1ccccc1OCCCBr)c1cccc2[nH]ccc12\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"NC1CCCC1\", \"results\": [{\"inchikey\": \"NISGSNTVMOOSJQ-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"NC1CCCC1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"O=C(Nc1ccccc1OCCCBr)c1cccc2[nH]ccc12\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"O=C(Nc1ccccc1OCCCBr)c1cccc2[nH]ccc12 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"O=C(Nc1ccccc1OCCCBr)c1cccc2[nH]ccc12\", \"reactants\": [\"BrCCCBr\", \"O=C(Nc1ccccc1O)c1cccc2[nH]ccc12\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"BrCCCBr\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=C(Nc1ccccc1O)c1cccc2[nH]ccc12\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"LISDAEIXWPKBCL-UHFFFAOYSA-N.VEFLKXRACNJHOV-UHFFFAOYSA-N>>KINAJOVFGULSCU-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"O=C(Nc1ccccc1OCCCBr)c1cccc2[nH]ccc12\", \"reactants\": [\"BrCCCBr\", \"O=C(Nc1ccccc1O)c1cccc2[nH]ccc12\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"BrCCCBr\", \"results\": [{\"inchikey\": \"VEFLKXRACNJHOV-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"BrCCCBr\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"O=C(Nc1ccccc1O)c1cccc2[nH]ccc12\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"O=C(Nc1ccccc1O)c1cccc2[nH]ccc12 was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"O=C(Nc1ccccc1O)c1cccc2[nH]ccc12\", \"reactants\": [\"Cc1ccc(S(=O)(=O)Oc2ccccc2NC(=O)c2cccc3[nH]ccc23)cc1\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"Cc1ccc(S(=O)(=O)Oc2ccccc2NC(=O)c2cccc3[nH]ccc23)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"CCOLTLICOCNLOH-UHFFFAOYSA-N>>LISDAEIXWPKBCL-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"O=C(Nc1ccccc1O)c1cccc2[nH]ccc12\", \"reactants\": [\"Cc1ccc(S(=O)(=O)Oc2ccccc2NC(=O)c2cccc3[nH]ccc23)cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"Cc1ccc(S(=O)(=O)Oc2ccccc2NC(=O)c2cccc3[nH]ccc23)cc1\", \"results\": [{\"inchikey\": \"CCOLTLICOCNLOH-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Cc1ccc(S(=O)(=O)Oc2ccccc2NC(=O)c2cccc3[nH]ccc23)cc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"O=C(Nc1ccccc1OCCCNC1CCCC1)c1cccc2[nH]ccc12\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"NC1CCCC1\": \"precursor\", \"O=C(Nc1ccccc1OCCCBr)c1cccc2[nH]ccc12\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"NC1CCCC1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=C(Nc1ccccc1OCCCBr)c1cccc2[nH]ccc12\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"BrCCCBr\": \"precursor\", \"O=C(Nc1ccccc1O)c1cccc2[nH]ccc12\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"BrCCCBr\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=C(Nc1ccccc1O)c1cccc2[nH]ccc12\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"Cc1ccc(S(=O)(=O)Oc2ccccc2NC(=O)c2cccc3[nH]ccc23)cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"Cc1ccc(S(=O)(=O)Oc2ccccc2NC(=O)c2cccc3[nH]ccc23)cc1\", \"in_stock\": true, \"children\": []}]}]}]}]}]}]}]}}","name":"emit_routes"},"id":"call_4_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"O=C(Nc1ccccc1OCCCNC1CCCC1)c1cccc2[nH]ccc12","task_id":"retro_1dd779286d2baa56bb30","tool_calls":9,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":4}
{"exact_match":false,"id":"retro_1e0b2ddadaa370780ac9:reference-expert:a0","kind":"single_route","max_steps":3,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CC(=O)Nc1nc(C(=O)Nc2ccc(NC(=O)OC(C)(C)C)cc2)cs1 in at most 3 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(=O)Nc1nc(C(=O)Nc2ccc(NC(=O)OC(C)(C)C)cc2)cs1\", \"reactants\": [\"CC(=O)Nc1nc(C(=O)O)cs1\", \"CC(C)(C)OC(=O)Nc1ccc(N)cc1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(=O)Nc1nc(C(=O)O)cs1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)OC(=O)Nc1ccc(N)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"WIVYTYZCVWHWSH-UHFFFAOYSA-N.ZKINQVZUSLLCJY-UHFFFAOYSA-N>>RCSFYZIHJQGXMB-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"CC(=O)Nc1nc(C(=O)Nc2ccc(NC(=O)OC(C)(C)C)cc2)cs1\", \"reactants\": [\"CC(=O)Nc1nc(C(=O)O)cs1\", \"CC(C)(C)OC(=O)Nc1ccc(N)cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CC(=O)Nc1nc(C(=O)O)cs1\", \"results\": [{\"inchikey\": \"ZKINQVZUSLLCJY-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CC(=O)Nc1nc(C(=O)O)cs1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CC(C)(C)OC(=O)Nc1ccc(N)cc1\", \"results\": [{\"inchikey\": \"WIVYTYZCVWHWSH-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CC(C)(C)OC(=O)Nc1ccc(N)cc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CC(=O)Nc1nc(C(=O)Nc2ccc(NC(=O)OC(C)(C)C)cc2)cs1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(=O)Nc1nc(C(=O)O)cs1\": \"precursor\", \"CC(C)(C)OC(=O)Nc1ccc(N)cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(=O)Nc1nc(C(=O)O)cs1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"CC(C)(C)OC(=O)Nc1ccc(N)cc1\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_2_0","type":"function"}]}],"provider":"reference","reward":0.833333,"source":"reference-expert","target_smiles":"CC(=O)Nc1nc(C(=O)Nc2ccc(NC(=O)OC(C)(C)C)cc2)cs1","task_id":"retro_1e0b2ddadaa370780ac9","tool_calls":4,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":2}
{"exact_match":true,"id":"retro_1f837774f55428b6ff11:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target COC[C@H](C)Oc1cc(Oc2ccc(C(=O)N3CCC3)nc2)cc(C(=O)O)c1 in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COC[C@H](C)Oc1cc(Oc2ccc(C(=O)N3CCC3)nc2)cc(C(=O)O)c1\", \"reactants\": [\"COC[C@H](C)Oc1cc(O)cc(C(=O)OC)c1\", \"O=C(c1ccc(Br)cn1)N1CCC1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"COC[C@H](C)Oc1cc(O)cc(C(=O)OC)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=C(c1ccc(Br)cn1)N1CCC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"IKOBNRGCSHDXFP-UHFFFAOYSA-N.JGIXKHBUAQEBSU-QMMMGPOBSA-N>>KSANYOIAOHVFBL-ZDUSSCGKSA-N\", \"model_turns_remaining\": 15, \"product\": \"COC[C@H](C)Oc1cc(Oc2ccc(C(=O)N3CCC3)nc2)cc(C(=O)O)c1\", \"reactants\": [\"COC[C@H](C)Oc1cc(O)cc(C(=O)OC)c1\", \"O=C(c1ccc(Br)cn1)N1CCC1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"COC[C@H](C)Oc1cc(O)cc(C(=O)OC)c1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"O=C(c1ccc(Br)cn1)N1CCC1\", \"results\": [{\"inchikey\": \"IKOBNRGCSHDXFP-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=C(c1ccc(Br)cn1)N1CCC1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"COC[C@H](C)Oc1cc(O)cc(C(=O)OC)c1 was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COC[C@H](C)Oc1cc(O)cc(C(=O)OC)c1\", \"reactants\": [\"COC[C@H](C)Oc1cc(OCc2ccccc2)cc(C(=O)OC)c1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"COC[C@H](C)Oc1cc(OCc2ccccc2)cc(C(=O)OC)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"JCTASGQIZHOHNP-AWEZNQCLSA-N>>JGIXKHBUAQEBSU-QMMMGPOBSA-N\", \"model_turns_remaining\": 14, \"product\": \"COC[C@H](C)Oc1cc(O)cc(C(=O)OC)c1\", \"reactants\": [\"COC[C@H](C)Oc1cc(OCc2ccccc2)cc(C(=O)OC)c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"COC[C@H](C)Oc1cc(OCc2ccccc2)cc(C(=O)OC)c1\", \"results\": [{\"inchikey\": \"JCTASGQIZHOHNP-AWEZNQCLSA-N\", \"similarity\": 1.0, \"smiles\": \"COC[C@H](C)Oc1cc(OCc2ccccc2)cc(C(=O)OC)c1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"COC[C@H](C)Oc1cc(Oc2ccc(C(=O)N3CCC3)nc2)cc(C(=O)O)c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COC[C@H](C)Oc1cc(O)cc(C(=O)OC)c1\": \"precursor\", \"O=C(c1ccc(Br)cn1)N1CCC1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COC[C@H](C)Oc1cc(O)cc(C(=O)OC)c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COC[C@H](C)Oc1cc(OCc2ccccc2)cc(C(=O)OC)c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COC[C@H](C)Oc1cc(OCc2ccccc2)cc(C(=O)OC)c1\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"O=C(c1ccc(Br)cn1)N1CCC1\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"COC[C@H](C)Oc1cc(Oc2ccc(C(=O)N3CCC3)nc2)cc(C(=O)O)c1","task_id":"retro_1f837774f55428b6ff11","tool_calls":6,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_1fe710665c70f616c670:reference-expert:a0","kind":"single_route","max_steps":3,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target N#Cc1ccc2c(C3CC(=O)NC3=O)c[nH]c2c1 in at most 3 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"N#Cc1ccc2c(C3CC(=O)NC3=O)c[nH]c2c1\", \"reactants\": [\"N#[C][Cu]\", \"O=C1CC(c2c[nH]c3cc(Br)ccc23)C(=O)N1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"N#[C][Cu]\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=C1CC(c2c[nH]c3cc(Br)ccc23)C(=O)N1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"DULSAGLWMRMKCQ-UHFFFAOYSA-N.VFSRIXMFESUYQM-UHFFFAOYSA-N>>YNIWEPZVRHRUTM-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"N#Cc1ccc2c(C3CC(=O)NC3=O)c[nH]c2c1\", \"reactants\": [\"N#[C][Cu]\", \"O=C1CC(c2c[nH]c3cc(Br)ccc23)C(=O)N1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"N#[C][Cu]\", \"results\": [{\"inchikey\": \"DULSAGLWMRMKCQ-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"N#[C][Cu]\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"O=C1CC(c2c[nH]c3cc(Br)ccc23)C(=O)N1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"O=C1CC(c2c[nH]c3cc(Br)ccc23)C(=O)N1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"O=C1CC(c2c[nH]c3cc(Br)ccc23)C(=O)N1\", \"reactants\": [\"Brc1ccc2cc[nH]c2c1\", \"O=C1CC(c2c[nH]c3ccc(F)cc23)C(=O)N1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"Brc1ccc2cc[nH]c2c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=C1CC(c2c[nH]c3ccc(F)cc23)C(=O)N1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"MAWGHOPSCKCTPA-UHFFFAOYSA-N.MXKLDYKORJEOPR-UHFFFAOYSA-N>>VFSRIXMFESUYQM-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"O=C1CC(c2c[nH]c3cc(Br)ccc23)C(=O)N1\", \"reactants\": [\"Brc1ccc2cc[nH]c2c1\", \"O=C1CC(c2c[nH]c3ccc(F)cc23)C(=O)N1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"Brc1ccc2cc[nH]c2c1\", \"results\": [{\"inchikey\": \"MAWGHOPSCKCTPA-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Brc1ccc2cc[nH]c2c1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"O=C1CC(c2c[nH]c3ccc(F)cc23)C(=O)N1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"O=C1CC(c2c[nH]c3ccc(F)cc23)C(=O)N1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"O=C1CC(c2c[nH]c3ccc(F)cc23)C(=O)N1\", \"reactants\": [\"Fc1ccc2[nH]ccc2c1\", \"O=C1C=CC(=O)N1\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"Fc1ccc2[nH]ccc2c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=C1C=CC(=O)N1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_complete\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"ODFFPRGJZRXNHZ-UHFFFAOYSA-N.PEEHTFAAVSWFBL-UHFFFAOYSA-N>>MXKLDYKORJEOPR-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"O=C1CC(c2c[nH]c3ccc(F)cc23)C(=O)N1\", \"reactants\": [\"Fc1ccc2[nH]ccc2c1\", \"O=C1C=CC(=O)N1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"Fc1ccc2[nH]ccc2c1\", \"results\": [{\"inchikey\": \"ODFFPRGJZRXNHZ-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Fc1ccc2[nH]ccc2c1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"O=C1C=CC(=O)N1\", \"results\": [{\"inchikey\": \"PEEHTFAAVSWFBL-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=C1C=CC(=O)N1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"N#Cc1ccc2c(C3CC(=O)NC3=O)c[nH]c2c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"N#[C][Cu]\": \"precursor\", \"O=C1CC(c2c[nH]c3cc(Br)ccc23)C(=O)N1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"N#[C][Cu]\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=C1CC(c2c[nH]c3cc(Br)ccc23)C(=O)N1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"Brc1ccc2cc[nH]c2c1\": \"precursor\", \"O=C1CC(c2c[nH]c3ccc(F)cc23)C(=O)N1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"Brc1ccc2cc[nH]c2c1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=C1CC(c2c[nH]c3ccc(F)cc23)C(=O)N1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"Fc1ccc2[nH]ccc2c1\": \"precursor\", \"O=C1C=CC(=O)N1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"Fc1ccc2[nH]ccc2c1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=C1C=CC(=O)N1\", \"in_stock\": true, \"children\": []}]}]}]}]}]}]}]}}","name":"emit_routes"},"id":"call_4_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"N#Cc1ccc2c(C3CC(=O)NC3=O)c[nH]c2c1","task_id":"retro_1fe710665c70f616c670","tool_calls":10,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":4}
{"exact_match":true,"id":"retro_210537567eb481a7320a:reference-expert:a0","kind":"single_route","max_steps":3,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CCN1C(=O)N(c2cccc(C(F)(F)F)c2)C2=C(C(=O)CC2)C1c1ccc(C#N)cc1S(C)(=O)=O in at most 3 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCN1C(=O)N(c2cccc(C(F)(F)F)c2)C2=C(C(=O)CC2)C1c1ccc(C#N)cc1S(C)(=O)=O\", \"reactants\": [\"CCBr\", \"CS(=O)(=O)c1cc(C#N)ccc1C1NC(=O)N(c2cccc(C(F)(F)F)c2)C2=C1C(=O)CC2\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCBr\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"CS(=O)(=O)c1cc(C#N)ccc1C1NC(=O)N(c2cccc(C(F)(F)F)c2)C2=C1C(=O)CC2\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"PIQAOEDOJPUANY-UHFFFAOYSA-N.RDHPKYGYEGBMSE-UHFFFAOYSA-N>>LPHPBGSSYQRRMZ-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"CCN1C(=O)N(c2cccc(C(F)(F)F)c2)C2=C(C(=O)CC2)C1c1ccc(C#N)cc1S(C)(=O)=O\", \"reactants\": [\"CCBr\", \"CS(=O)(=O)c1cc(C#N)ccc1C1NC(=O)N(c2cccc(C(F)(F)F)c2)C2=C1C(=O)CC2\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CCBr\", \"results\": [{\"inchikey\": \"RDHPKYGYEGBMSE-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CCBr\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CS(=O)(=O)c1cc(C#N)ccc1C1NC(=O)N(c2cccc(C(F)(F)F)c2)C2=C1C(=O)CC2\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"CS(=O)(=O)c1cc(C#N)ccc1C1NC(=O)N(c2cccc(C(F)(F)F)c2)C2=C1C(=O)CC2 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CS(=O)(=O)c1cc(C#N)ccc1C1NC(=O)N(c2cccc(C(F)(F)F)c2)C2=C1C(=O)CC2\", \"reactants\": [\"C#N\", \"CS(=O)(=O)c1cc(Br)ccc1C1NC(=O)N(c2cccc(C(F)(F)F)c2)C2=C1C(=O)CC2\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"C#N\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"CS(=O)(=O)c1cc(Br)ccc1C1NC(=O)N(c2cccc(C(F)(F)F)c2)C2=C1C(=O)CC2\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"LELOWRISYMNNSU-UHFFFAOYSA-N.OPRBHAIVJLYHSY-UHFFFAOYSA-N>>PIQAOEDOJPUANY-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"CS(=O)(=O)c1cc(C#N)ccc1C1NC(=O)N(c2cccc(C(F)(F)F)c2)C2=C1C(=O)CC2\", \"reactants\": [\"C#N\", \"CS(=O)(=O)c1cc(Br)ccc1C1NC(=O)N(c2cccc(C(F)(F)F)c2)C2=C1C(=O)CC2\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"C#N\", \"results\": [{\"inchikey\": \"LELOWRISYMNNSU-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"C#N\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CS(=O)(=O)c1cc(Br)ccc1C1NC(=O)N(c2cccc(C(F)(F)F)c2)C2=C1C(=O)CC2\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"CS(=O)(=O)c1cc(Br)ccc1C1NC(=O)N(c2cccc(C(F)(F)F)c2)C2=C1C(=O)CC2 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CS(=O)(=O)c1cc(Br)ccc1C1NC(=O)N(c2cccc(C(F)(F)F)c2)C2=C1C(=O)CC2\", \"reactants\": [\"CS(=O)(=O)c1cc(Br)ccc1C(Cl)N=C=O\", \"O=C1C=C(Nc2cccc(C(F)(F)F)c2)CC1\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"CS(=O)(=O)c1cc(Br)ccc1C(Cl)N=C=O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=C1C=C(Nc2cccc(C(F)(F)F)c2)CC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"DRZMUXUFFUWBEO-UHFFFAOYSA-N.QSJINOLVMSTCSU-UHFFFAOYSA-N>>OPRBHAIVJLYHSY-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"CS(=O)(=O)c1cc(Br)ccc1C1NC(=O)N(c2cccc(C(F)(F)F)c2)C2=C1C(=O)CC2\", \"reactants\": [\"CS(=O)(=O)c1cc(Br)ccc1C(Cl)N=C=O\", \"O=C1C=C(Nc2cccc(C(F)(F)F)c2)CC1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"CS(=O)(=O)c1cc(Br)ccc1C(Cl)N=C=O\", \"results\": [{\"inchikey\": \"QSJINOLVMSTCSU-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CS(=O)(=O)c1cc(Br)ccc1C(Cl)N=C=O\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"O=C1C=C(Nc2cccc(C(F)(F)F)c2)CC1\", \"results\": [{\"inchikey\": \"DRZMUXUFFUWBEO-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=C1C=C(Nc2cccc(C(F)(F)F)c2)CC1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CCN1C(=O)N(c2cccc(C(F)(F)F)c2)C2=C(C(=O)CC2)C1c1ccc(C#N)cc1S(C)(=O)=O\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCBr\": \"precursor\", \"CS(=O)(=O)c1cc(C#N)ccc1C1NC(=O)N(c2cccc(C(F)(F)F)c2)C2=C1C(=O)CC2\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCBr\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"CS(=O)(=O)c1cc(C#N)ccc1C1NC(=O)N(c2cccc(C(F)(F)F)c2)C2=C1C(=O)CC2\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"C#N\": \"precursor\", \"CS(=O)(=O)c1cc(Br)ccc1C1NC(=O)N(c2cccc(C(F)(F)F)c2)C2=C1C(=O)CC2\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"C#N\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"CS(=O)(=O)c1cc(Br)ccc1C1NC(=O)N(c2cccc(C(F)(F)F)c2)C2=C1C(=O)CC2\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CS(=O)(=O)c1cc(Br)ccc1C(Cl)N=C=O\": \"precursor\", \"O=C1C=C(Nc2cccc(C(F)(F)F)c2)CC1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CS(=O)(=O)c1cc(Br)ccc1C(Cl)N=C=O\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=C1C=C(Nc2cccc(C(F)(F)F)c2)CC1\", \"in_stock\": true, \"children\": []}]}]}]}]}]}]}]}}","name":"emit_routes"},"id":"call_4_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"CCN1C(=O)N(c2cccc(C(F)(F)F)c2)C2=C(C(=O)CC2)C1c1ccc(C#N)cc1S(C)(=O)=O","task_id":"retro_210537567eb481a7320a","tool_calls":10,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":4}
{"exact_match":true,"id":"retro_217f7311f70b02bce433:reference-expert:a0","kind":"single_route","max_steps":5,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target N#Cc1ccccc1S(=O)(=O)N(Cc1cccc(OC2CCCCO2)c1)c1ccc(OCCN2CCCC2)cc1 in at most 5 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"N#Cc1ccccc1S(=O)(=O)N(Cc1cccc(OC2CCCCO2)c1)c1ccc(OCCN2CCCC2)cc1\", \"reactants\": [\"N#Cc1ccccc1S(=O)(=O)Cl\", \"c1cc(CNc2ccc(OCCN3CCCC3)cc2)cc(OC2CCCCO2)c1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"N#Cc1ccccc1S(=O)(=O)Cl\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"c1cc(CNc2ccc(OCCN3CCCC3)cc2)cc(OC2CCCCO2)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"NQAYCMBZPAARNO-UHFFFAOYSA-N.NTRAISXJJWNELY-UHFFFAOYSA-N>>VGNAFQZXBSJOQF-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"N#Cc1ccccc1S(=O)(=O)N(Cc1cccc(OC2CCCCO2)c1)c1ccc(OCCN2CCCC2)cc1\", \"reactants\": [\"N#Cc1ccccc1S(=O)(=O)Cl\", \"c1cc(CNc2ccc(OCCN3CCCC3)cc2)cc(OC2CCCCO2)c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"N#Cc1ccccc1S(=O)(=O)Cl\", \"results\": [{\"inchikey\": \"NQAYCMBZPAARNO-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"N#Cc1ccccc1S(=O)(=O)Cl\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"c1cc(CNc2ccc(OCCN3CCCC3)cc2)cc(OC2CCCCO2)c1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"c1cc(CNc2ccc(OCCN3CCCC3)cc2)cc(OC2CCCCO2)c1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"c1cc(CNc2ccc(OCCN3CCCC3)cc2)cc(OC2CCCCO2)c1\", \"reactants\": [\"Nc1ccc(OCCN2CCCC2)cc1\", \"O=Cc1cccc(OC2CCCCO2)c1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"Nc1ccc(OCCN2CCCC2)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=Cc1cccc(OC2CCCCO2)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"CUOBWSLIFAJGNN-UHFFFAOYSA-N.OTYZNDKWNPQQJP-UHFFFAOYSA-N>>NTRAISXJJWNELY-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"c1cc(CNc2ccc(OCCN3CCCC3)cc2)cc(OC2CCCCO2)c1\", \"reactants\": [\"Nc1ccc(OCCN2CCCC2)cc1\", \"O=Cc1cccc(OC2CCCCO2)c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"Nc1ccc(OCCN2CCCC2)cc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"O=Cc1cccc(OC2CCCCO2)c1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Nc1ccc(OCCN2CCCC2)cc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Nc1ccc(OCCN2CCCC2)cc1\", \"reactants\": [\"O=[N+]([O-])c1ccc(OCCN2CCCC2)cc1\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"O=[N+]([O-])c1ccc(OCCN2CCCC2)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"RZIYRKYHMDDHCK-UHFFFAOYSA-N>>OTYZNDKWNPQQJP-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"Nc1ccc(OCCN2CCCC2)cc1\", \"reactants\": [\"O=[N+]([O-])c1ccc(OCCN2CCCC2)cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"O=[N+]([O-])c1ccc(OCCN2CCCC2)cc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"O=Cc1cccc(OC2CCCCO2)c1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"O=Cc1cccc(OC2CCCCO2)c1\", \"reactants\": [\"C1=COCCC1\", \"O=Cc1cccc(O)c1\"]}","name":"validate_disconnection"},"id":"call_4_0","type":"function"},{"function":{"arguments":"{\"query\": \"C1=COCCC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=Cc1cccc(O)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_complete\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"BUDQDWGNQVEFAC-UHFFFAOYSA-N.IAVREABSGIHHMO-UHFFFAOYSA-N>>CUOBWSLIFAJGNN-UHFFFAOYSA-N\", \"model_turns_remaining\": 12, \"product\": \"O=Cc1cccc(OC2CCCCO2)c1\", \"reactants\": [\"C1=COCCC1\", \"O=Cc1cccc(O)c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_4_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"C1=COCCC1\", \"results\": [{\"inchikey\": \"BUDQDWGNQVEFAC-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"C1=COCCC1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"O=Cc1cccc(O)c1\", \"results\": [{\"inchikey\": \"IAVREABSGIHHMO-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=Cc1cccc(O)c1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_2"},{"content":"O=[N+]([O-])c1ccc(OCCN2CCCC2)cc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"O=[N+]([O-])c1ccc(OCCN2CCCC2)cc1\", \"reactants\": [\"ClCCN1CCCC1\", \"O=[N+]([O-])c1ccc(O)cc1\"]}","name":"validate_disconnection"},"id":"call_5_0","type":"function"},{"function":{"arguments":"{\"query\": \"ClCCN1CCCC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_5_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=[N+]([O-])c1ccc(O)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_5_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"BTJIUGUIPKRLHP-UHFFFAOYSA-N.RMGFLMXDCGQKPS-UHFFFAOYSA-N>>RZIYRKYHMDDHCK-UHFFFAOYSA-N\", \"model_turns_remaining\": 11, \"product\": \"O=[N+]([O-])c1ccc(OCCN2CCCC2)cc1\", \"reactants\": [\"ClCCN1CCCC1\", \"O=[N+]([O-])c1ccc(O)cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_5_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 11, \"query\": \"ClCCN1CCCC1\", \"results\": [{\"inchikey\": \"RMGFLMXDCGQKPS-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"ClCCN1CCCC1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_5_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 11, \"query\": \"O=[N+]([O-])c1ccc(O)cc1\", \"results\": [{\"inchikey\": \"BTJIUGUIPKRLHP-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=[N+]([O-])c1ccc(O)cc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_5_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"N#Cc1ccccc1S(=O)(=O)N(Cc1cccc(OC2CCCCO2)c1)c1ccc(OCCN2CCCC2)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"N#Cc1ccccc1S(=O)(=O)Cl\": \"precursor\", \"c1cc(CNc2ccc(OCCN3CCCC3)cc2)cc(OC2CCCCO2)c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"N#Cc1ccccc1S(=O)(=O)Cl\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"c1cc(CNc2ccc(OCCN3CCCC3)cc2)cc(OC2CCCCO2)c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"Nc1ccc(OCCN2CCCC2)cc1\": \"precursor\", \"O=Cc1cccc(OC2CCCCO2)c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"Nc1ccc(OCCN2CCCC2)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"O=[N+]([O-])c1ccc(OCCN2CCCC2)cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"O=[N+]([O-])c1ccc(OCCN2CCCC2)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"ClCCN1CCCC1\": \"precursor\", \"O=[N+]([O-])c1ccc(O)cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"ClCCN1CCCC1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=[N+]([O-])c1ccc(O)cc1\", \"in_stock\": true, \"children\": []}]}]}]}]}, {\"type\": \"mol\", \"smiles\": \"O=Cc1cccc(OC2CCCCO2)c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"C1=COCCC1\": \"precursor\", \"O=Cc1cccc(O)c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"C1=COCCC1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=Cc1cccc(O)c1\", \"in_stock\": true, \"children\": []}]}]}]}]}]}]}]}}","name":"emit_routes"},"id":"call_6_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"N#Cc1ccccc1S(=O)(=O)N(Cc1cccc(OC2CCCCO2)c1)c1ccc(OCCN2CCCC2)cc1","task_id":"retro_217f7311f70b02bce433","tool_calls":15,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":6}
{"exact_match":true,"id":"retro_22f7a8fab24490fe94f1:reference-expert:a0","kind":"single_route","max_steps":5,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target COC(=O)c1ccc(-c2ccc(N3CCCC3=S)cc2C)cc1 in at most 5 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COC(=O)c1ccc(-c2ccc(N3CCCC3=S)cc2C)cc1\", \"reactants\": [\"COC(=O)c1ccc(-c2ccc(N3CCCC3=O)cc2C)cc1\", \"COc1ccc(P2(=S)SP(=S)(c3ccc(OC)cc3)S2)cc1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"COC(=O)c1ccc(-c2ccc(N3CCCC3=O)cc2C)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"COc1ccc(P2(=S)SP(=S)(c3ccc(OC)cc3)S2)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"CFHGBZLNZZVTAY-UHFFFAOYSA-N.OROQMVMZVDJBIK-UHFFFAOYSA-N>>OIXHMVWNDXIEOL-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"COC(=O)c1ccc(-c2ccc(N3CCCC3=S)cc2C)cc1\", \"reactants\": [\"COC(=O)c1ccc(-c2ccc(N3CCCC3=O)cc2C)cc1\", \"COc1ccc(P2(=S)SP(=S)(c3ccc(OC)cc3)S2)cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"COC(=O)c1ccc(-c2ccc(N3CCCC3=O)cc2C)cc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"COc1ccc(P2(=S)SP(=S)(c3ccc(OC)cc3)S2)cc1\", \"results\": [{\"inchikey\": \"CFHGBZLNZZVTAY-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"COc1ccc(P2(=S)SP(=S)(c3ccc(OC)cc3)S2)cc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"COC(=O)c1ccc(-c2ccc(N3CCCC3=O)cc2C)cc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COC(=O)c1ccc(-c2ccc(N3CCCC3=O)cc2C)cc1\", \"reactants\": [\"COC(=O)c1ccc(-c2ccc(NC(=O)CCCCl)cc2C)cc1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"COC(=O)c1ccc(-c2ccc(NC(=O)CCCCl)cc2C)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"DUTHKVNPKNDLKY-UHFFFAOYSA-N>>OROQMVMZVDJBIK-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"COC(=O)c1ccc(-c2ccc(N3CCCC3=O)cc2C)cc1\", \"reactants\": [\"COC(=O)c1ccc(-c2ccc(NC(=O)CCCCl)cc2C)cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"COC(=O)c1ccc(-c2ccc(NC(=O)CCCCl)cc2C)cc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"COC(=O)c1ccc(-c2ccc(NC(=O)CCCCl)cc2C)cc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COC(=O)c1ccc(-c2ccc(NC(=O)CCCCl)cc2C)cc1\", \"reactants\": [\"COC(=O)c1ccc(-c2ccc(N)cc2C)cc1\", \"O=C(Cl)CCCCl\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"COC(=O)c1ccc(-c2ccc(N)cc2C)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=C(Cl)CCCCl\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"CDIIZULDSLKBKV-UHFFFAOYSA-N.HQYVJAIESXYXDK-UHFFFAOYSA-N>>DUTHKVNPKNDLKY-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"COC(=O)c1ccc(-c2ccc(NC(=O)CCCCl)cc2C)cc1\", \"reactants\": [\"COC(=O)c1ccc(-c2ccc(N)cc2C)cc1\", \"O=C(Cl)CCCCl\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"COC(=O)c1ccc(-c2ccc(N)cc2C)cc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"O=C(Cl)CCCCl\", \"results\": [{\"inchikey\": \"CDIIZULDSLKBKV-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=C(Cl)CCCCl\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"COC(=O)c1ccc(-c2ccc(N)cc2C)cc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COC(=O)c1ccc(-c2ccc(N)cc2C)cc1\", \"reactants\": [\"CO\", \"Cc1cc(N)ccc1-c1ccc(C(=O)O)cc1\"]}","name":"validate_disconnection"},"id":"call_4_0","type":"function"},{"function":{"arguments":"{\"query\": \"CO\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_1","type":"function"},{"function":{"arguments":"{\"query\": \"Cc1cc(N)ccc1-c1ccc(C(=O)O)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"JYXTZJAVYBQZDZ-UHFFFAOYSA-N.OKKJLVBELUTLKV-UHFFFAOYSA-N>>HQYVJAIESXYXDK-UHFFFAOYSA-N\", \"model_turns_remaining\": 12, \"product\": \"COC(=O)c1ccc(-c2ccc(N)cc2C)cc1\", \"reactants\": [\"CO\", \"Cc1cc(N)ccc1-c1ccc(C(=O)O)cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_4_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"CO\", \"results\": [{\"inchikey\": \"OKKJLVBELUTLKV-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CO\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"Cc1cc(N)ccc1-c1ccc(C(=O)O)cc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_2"},{"content":"Cc1cc(N)ccc1-c1ccc(C(=O)O)cc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Cc1cc(N)ccc1-c1ccc(C(=O)O)cc1\", \"reactants\": [\"Cc1cc(N)ccc1Br\", \"O=C(O)c1ccc(B(O)O)cc1\"]}","name":"validate_disconnection"},"id":"call_5_0","type":"function"},{"function":{"arguments":"{\"query\": \"Cc1cc(N)ccc1Br\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_5_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=C(O)c1ccc(B(O)O)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_5_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"MMEGELSFOYDPQW-UHFFFAOYSA-N.SIAVMDKGVRXFAX-UHFFFAOYSA-N>>JYXTZJAVYBQZDZ-UHFFFAOYSA-N\", \"model_turns_remaining\": 11, \"product\": \"Cc1cc(N)ccc1-c1ccc(C(=O)O)cc1\", \"reactants\": [\"Cc1cc(N)ccc1Br\", \"O=C(O)c1ccc(B(O)O)cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_5_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 11, \"query\": \"Cc1cc(N)ccc1Br\", \"results\": [{\"inchikey\": \"MMEGELSFOYDPQW-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Cc1cc(N)ccc1Br\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_5_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 11, \"query\": \"O=C(O)c1ccc(B(O)O)cc1\", \"results\": [{\"inchikey\": \"SIAVMDKGVRXFAX-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=C(O)c1ccc(B(O)O)cc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_5_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"COC(=O)c1ccc(-c2ccc(N3CCCC3=S)cc2C)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COC(=O)c1ccc(-c2ccc(N3CCCC3=O)cc2C)cc1\": \"precursor\", \"COc1ccc(P2(=S)SP(=S)(c3ccc(OC)cc3)S2)cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COC(=O)c1ccc(-c2ccc(N3CCCC3=O)cc2C)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COC(=O)c1ccc(-c2ccc(NC(=O)CCCCl)cc2C)cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COC(=O)c1ccc(-c2ccc(NC(=O)CCCCl)cc2C)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COC(=O)c1ccc(-c2ccc(N)cc2C)cc1\": \"precursor\", \"O=C(Cl)CCCCl\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COC(=O)c1ccc(-c2ccc(N)cc2C)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CO\": \"precursor\", \"Cc1cc(N)ccc1-c1ccc(C(=O)O)cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CO\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"Cc1cc(N)ccc1-c1ccc(C(=O)O)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"Cc1cc(N)ccc1Br\": \"precursor\", \"O=C(O)c1ccc(B(O)O)cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"Cc1cc(N)ccc1Br\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=C(O)c1ccc(B(O)O)cc1\", \"in_stock\": true, \"children\": []}]}]}]}]}, {\"type\": \"mol\", \"smiles\": \"O=C(Cl)CCCCl\", \"in_stock\": true, \"children\": []}]}]}]}]}, {\"type\": \"mol\", \"smiles\": \"COc1ccc(P2(=S)SP(=S)(c3ccc(OC)cc3)S2)cc1\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_6_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"COC(=O)c1ccc(-c2ccc(N3CCCC3=S)cc2C)cc1","task_id":"retro_22f7a8fab24490fe94f1","tool_calls":15,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":6}
{"exact_match":true,"id":"retro_23399af77aef531bcff2:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target Cc1c[nH]c2ccc(Nc3ncnc4cc(-c5ccccc5)sc34)cc12 in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Cc1c[nH]c2ccc(Nc3ncnc4cc(-c5ccccc5)sc34)cc12\", \"reactants\": [\"O=Cc1c[nH]c2ccc(Nc3ncnc4cc(-c5ccccc5)sc34)cc12\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"O=Cc1c[nH]c2ccc(Nc3ncnc4cc(-c5ccccc5)sc34)cc12\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"BUMOVTUAOARJAN-UHFFFAOYSA-N>>RDSINGBRTMDIHM-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"Cc1c[nH]c2ccc(Nc3ncnc4cc(-c5ccccc5)sc34)cc12\", \"reactants\": [\"O=Cc1c[nH]c2ccc(Nc3ncnc4cc(-c5ccccc5)sc34)cc12\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"O=Cc1c[nH]c2ccc(Nc3ncnc4cc(-c5ccccc5)sc34)cc12\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"O=Cc1c[nH]c2ccc(Nc3ncnc4cc(-c5ccccc5)sc34)cc12 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"O=Cc1c[nH]c2ccc(Nc3ncnc4cc(-c5ccccc5)sc34)cc12\", \"reactants\": [\"COC(Cl)Cl\", \"c1ccc(-c2cc3ncnc(Nc4ccc5[nH]ccc5c4)c3s2)cc1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"COC(Cl)Cl\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"c1ccc(-c2cc3ncnc(Nc4ccc5[nH]ccc5c4)c3s2)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"CGDLXUGHZUDIDJ-UHFFFAOYSA-N.GRTGGSXWHGKRSB-UHFFFAOYSA-N>>BUMOVTUAOARJAN-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"O=Cc1c[nH]c2ccc(Nc3ncnc4cc(-c5ccccc5)sc34)cc12\", \"reactants\": [\"COC(Cl)Cl\", \"c1ccc(-c2cc3ncnc(Nc4ccc5[nH]ccc5c4)c3s2)cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"COC(Cl)Cl\", \"results\": [{\"inchikey\": \"GRTGGSXWHGKRSB-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"COC(Cl)Cl\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"c1ccc(-c2cc3ncnc(Nc4ccc5[nH]ccc5c4)c3s2)cc1\", \"results\": [{\"inchikey\": \"CGDLXUGHZUDIDJ-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"c1ccc(-c2cc3ncnc(Nc4ccc5[nH]ccc5c4)c3s2)cc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"Cc1c[nH]c2ccc(Nc3ncnc4cc(-c5ccccc5)sc34)cc12\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"O=Cc1c[nH]c2ccc(Nc3ncnc4cc(-c5ccccc5)sc34)cc12\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"O=Cc1c[nH]c2ccc(Nc3ncnc4cc(-c5ccccc5)sc34)cc12\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COC(Cl)Cl\": \"precursor\", \"c1ccc(-c2cc3ncnc(Nc4ccc5[nH]ccc5c4)c3s2)cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COC(Cl)Cl\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"c1ccc(-c2cc3ncnc(Nc4ccc5[nH]ccc5c4)c3s2)cc1\", \"in_stock\": true, \"children\": []}]}]}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"Cc1c[nH]c2ccc(Nc3ncnc4cc(-c5ccccc5)sc34)cc12","task_id":"retro_23399af77aef531bcff2","tool_calls":6,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_255632f6f5b5041450d1:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CC(=O)c1cc(C)no1 in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(=O)c1cc(C)no1\", \"reactants\": [\"Cc1cc(C(C)O)on1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"Cc1cc(C(C)O)on1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_complete\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"QLOCZOGQZFCJAZ-UHFFFAOYSA-N>>MOBMLOWIGFJSCP-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"CC(=O)c1cc(C)no1\", \"reactants\": [\"Cc1cc(C(C)O)on1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"Cc1cc(C(C)O)on1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"Cc1cc(C(C)O)on1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Cc1cc(C(C)O)on1\", \"reactants\": [\"C#CC(C)O\", \"CC=NO\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"C#CC(C)O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"CC=NO\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_complete\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"FZENGILVLUJGJX-UHFFFAOYSA-N.GKPOMITUDGXOSB-UHFFFAOYSA-N>>QLOCZOGQZFCJAZ-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"Cc1cc(C(C)O)on1\", \"reactants\": [\"C#CC(C)O\", \"CC=NO\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"C#CC(C)O\", \"results\": [{\"inchikey\": \"GKPOMITUDGXOSB-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"C#CC(C)O\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CC=NO\", \"results\": [{\"inchikey\": \"FZENGILVLUJGJX-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CC=NO\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CC(=O)c1cc(C)no1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"Cc1cc(C(C)O)on1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"Cc1cc(C(C)O)on1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"C#CC(C)O\": \"precursor\", \"CC=NO\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"C#CC(C)O\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"CC=NO\", \"in_stock\": true, \"children\": []}]}]}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"CC(=O)c1cc(C)no1","task_id":"retro_255632f6f5b5041450d1","tool_calls":6,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_26a5ab3b336335db7e67:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CC(=O)N1CCN(c2c(F)cc(OCCN3CCCCC3)cc2F)CC1 in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(=O)N1CCN(c2c(F)cc(OCCN3CCCCC3)cc2F)CC1\", \"reactants\": [\"CC(=O)N1CCN(c2c(F)cc(O)cc2F)CC1\", \"OCCN1CCCCC1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(=O)N1CCN(c2c(F)cc(O)cc2F)CC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"OCCN1CCCCC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"HHCLLQNYDZFDQK-UHFFFAOYSA-N.KZTWONRVIPPDKH-UHFFFAOYSA-N>>DORPXFKEIODVCB-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"CC(=O)N1CCN(c2c(F)cc(OCCN3CCCCC3)cc2F)CC1\", \"reactants\": [\"CC(=O)N1CCN(c2c(F)cc(O)cc2F)CC1\", \"OCCN1CCCCC1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CC(=O)N1CCN(c2c(F)cc(O)cc2F)CC1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"OCCN1CCCCC1\", \"results\": [{\"inchikey\": \"KZTWONRVIPPDKH-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"OCCN1CCCCC1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"CC(=O)N1CCN(c2c(F)cc(O)cc2F)CC1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(=O)N1CCN(c2c(F)cc(O)cc2F)CC1\", \"reactants\": [\"CC(=O)N1CCN(c2c(F)cc(N)cc2F)CC1\", \"O=NO\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(=O)N1CCN(c2c(F)cc(N)cc2F)CC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=NO\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"IOVCWXUNBOPUCH-UHFFFAOYSA-N.WANYZQAOYRXPAV-UHFFFAOYSA-N>>HHCLLQNYDZFDQK-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"CC(=O)N1CCN(c2c(F)cc(O)cc2F)CC1\", \"reactants\": [\"CC(=O)N1CCN(c2c(F)cc(N)cc2F)CC1\", \"O=NO\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CC(=O)N1CCN(c2c(F)cc(N)cc2F)CC1\", \"results\": [{\"inchikey\": \"WANYZQAOYRXPAV-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CC(=O)N1CCN(c2c(F)cc(N)cc2F)CC1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"O=NO\", \"results\": [{\"inchikey\": \"IOVCWXUNBOPUCH-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=NO\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CC(=O)N1CCN(c2c(F)cc(OCCN3CCCCC3)cc2F)CC1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(=O)N1CCN(c2c(F)cc(O)cc2F)CC1\": \"precursor\", \"OCCN1CCCCC1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(=O)N1CCN(c2c(F)cc(O)cc2F)CC1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(=O)N1CCN(c2c(F)cc(N)cc2F)CC1\": \"precursor\", \"O=NO\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(=O)N1CCN(c2c(F)cc(N)cc2F)CC1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=NO\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"OCCN1CCCCC1\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"CC(=O)N1CCN(c2c(F)cc(OCCN3CCCCC3)cc2F)CC1","task_id":"retro_26a5ab3b336335db7e67","tool_calls":7,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_2774f4279fffbd830429:reference-expert:a0","kind":"single_route","max_steps":3,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CNC(=O)c1cnc(NC(=O)C(CC2CCOCC2)c2ccc(S(C)(=O)=O)cc2)s1 in at most 3 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CNC(=O)c1cnc(NC(=O)C(CC2CCOCC2)c2ccc(S(C)(=O)=O)cc2)s1\", \"reactants\": [\"CN\", \"CS(=O)(=O)c1ccc(C(CC2CCOCC2)C(=O)Nc2ncc(C(=O)O)s2)cc1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CN\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"CS(=O)(=O)c1ccc(C(CC2CCOCC2)C(=O)Nc2ncc(C(=O)O)s2)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"BAVYZALUXZFZLV-UHFFFAOYSA-N.OXXXRRRLXQNIQC-UHFFFAOYSA-N>>RVGZUJLRHUHOBT-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"CNC(=O)c1cnc(NC(=O)C(CC2CCOCC2)c2ccc(S(C)(=O)=O)cc2)s1\", \"reactants\": [\"CN\", \"CS(=O)(=O)c1ccc(C(CC2CCOCC2)C(=O)Nc2ncc(C(=O)O)s2)cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CN\", \"results\": [{\"inchikey\": \"BAVYZALUXZFZLV-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CN\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CS(=O)(=O)c1ccc(C(CC2CCOCC2)C(=O)Nc2ncc(C(=O)O)s2)cc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"CS(=O)(=O)c1ccc(C(CC2CCOCC2)C(=O)Nc2ncc(C(=O)O)s2)cc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CS(=O)(=O)c1ccc(C(CC2CCOCC2)C(=O)Nc2ncc(C(=O)O)s2)cc1\", \"reactants\": [\"CCOC(=O)c1cnc(NC(=O)C(CC2CCOCC2)c2ccc(S(C)(=O)=O)cc2)s1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCOC(=O)c1cnc(NC(=O)C(CC2CCOCC2)c2ccc(S(C)(=O)=O)cc2)s1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"UXKULBPQQXTAQT-UHFFFAOYSA-N>>OXXXRRRLXQNIQC-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"CS(=O)(=O)c1ccc(C(CC2CCOCC2)C(=O)Nc2ncc(C(=O)O)s2)cc1\", \"reactants\": [\"CCOC(=O)c1cnc(NC(=O)C(CC2CCOCC2)c2ccc(S(C)(=O)=O)cc2)s1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CCOC(=O)c1cnc(NC(=O)C(CC2CCOCC2)c2ccc(S(C)(=O)=O)cc2)s1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"CCOC(=O)c1cnc(NC(=O)C(CC2CCOCC2)c2ccc(S(C)(=O)=O)cc2)s1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCOC(=O)c1cnc(NC(=O)C(CC2CCOCC2)c2ccc(S(C)(=O)=O)cc2)s1\", \"reactants\": [\"CCOC(=O)c1cnc(N)s1\", \"CS(=O)(=O)c1ccc(C(CC2CCOCC2)C(=O)O)cc1\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCOC(=O)c1cnc(N)s1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"CS(=O)(=O)c1ccc(C(CC2CCOCC2)C(=O)O)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"FRPKQSPLXRXUJF-UHFFFAOYSA-N.VNZXERIGKZNEKB-UHFFFAOYSA-N>>UXKULBPQQXTAQT-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"CCOC(=O)c1cnc(NC(=O)C(CC2CCOCC2)c2ccc(S(C)(=O)=O)cc2)s1\", \"reactants\": [\"CCOC(=O)c1cnc(N)s1\", \"CS(=O)(=O)c1ccc(C(CC2CCOCC2)C(=O)O)cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"CCOC(=O)c1cnc(N)s1\", \"results\": [{\"inchikey\": \"VNZXERIGKZNEKB-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CCOC(=O)c1cnc(N)s1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"CS(=O)(=O)c1ccc(C(CC2CCOCC2)C(=O)O)cc1\", \"results\": [{\"inchikey\": \"FRPKQSPLXRXUJF-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CS(=O)(=O)c1ccc(C(CC2CCOCC2)C(=O)O)cc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CNC(=O)c1cnc(NC(=O)C(CC2CCOCC2)c2ccc(S(C)(=O)=O)cc2)s1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CN\": \"precursor\", \"CS(=O)(=O)c1ccc(C(CC2CCOCC2)C(=O)Nc2ncc(C(=O)O)s2)cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CN\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"CS(=O)(=O)c1ccc(C(CC2CCOCC2)C(=O)Nc2ncc(C(=O)O)s2)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCOC(=O)c1cnc(NC(=O)C(CC2CCOCC2)c2ccc(S(C)(=O)=O)cc2)s1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCOC(=O)c1cnc(NC(=O)C(CC2CCOCC2)c2ccc(S(C)(=O)=O)cc2)s1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCOC(=O)c1cnc(N)s1\": \"precursor\", \"CS(=O)(=O)c1ccc(C(CC2CCOCC2)C(=O)O)cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCOC(=O)c1cnc(N)s1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"CS(=O)(=O)c1ccc(C(CC2CCOCC2)C(=O)O)cc1\", \"in_stock\": true, \"children\": []}]}]}]}]}]}]}]}}","name":"emit_routes"},"id":"call_4_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"CNC(=O)c1cnc(NC(=O)C(CC2CCOCC2)c2ccc(S(C)(=O)=O)cc2)s1","task_id":"retro_2774f4279fffbd830429","tool_calls":9,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":4}
{"exact_match":true,"id":"retro_289d83e5e8bad5f124e6:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CN(C)C(=O)CCC(=O)c1ccc(N2CCN(Cc3ccccc3)CC2)cc1 in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CN(C)C(=O)CCC(=O)c1ccc(N2CCN(Cc3ccccc3)CC2)cc1\", \"reactants\": [\"CN(C)C(=O)CCC(=O)c1ccc(F)cc1\", \"c1ccc(CN2CCNCC2)cc1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CN(C)C(=O)CCC(=O)c1ccc(F)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"c1ccc(CN2CCNCC2)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"IQXXEPZFOOTTBA-UHFFFAOYSA-N.KWFQYAICORJVBZ-UHFFFAOYSA-N>>AELMVWGBNONJRG-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"CN(C)C(=O)CCC(=O)c1ccc(N2CCN(Cc3ccccc3)CC2)cc1\", \"reactants\": [\"CN(C)C(=O)CCC(=O)c1ccc(F)cc1\", \"c1ccc(CN2CCNCC2)cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CN(C)C(=O)CCC(=O)c1ccc(F)cc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"c1ccc(CN2CCNCC2)cc1\", \"results\": [{\"inchikey\": \"IQXXEPZFOOTTBA-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"c1ccc(CN2CCNCC2)cc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"CN(C)C(=O)CCC(=O)c1ccc(F)cc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CN(C)C(=O)CCC(=O)c1ccc(F)cc1\", \"reactants\": [\"CNC\", \"O=C(O)CCC(=O)c1ccc(F)cc1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CNC\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=C(O)CCC(=O)c1ccc(F)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"ROSDSFDQCJNGOL-UHFFFAOYSA-N.WUYWHIAAQYQKPP-UHFFFAOYSA-N>>KWFQYAICORJVBZ-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"CN(C)C(=O)CCC(=O)c1ccc(F)cc1\", \"reactants\": [\"CNC\", \"O=C(O)CCC(=O)c1ccc(F)cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CNC\", \"results\": [{\"inchikey\": \"ROSDSFDQCJNGOL-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CNC\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"O=C(O)CCC(=O)c1ccc(F)cc1\", \"results\": [{\"inchikey\": \"WUYWHIAAQYQKPP-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=C(O)CCC(=O)c1ccc(F)cc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CN(C)C(=O)CCC(=O)c1ccc(N2CCN(Cc3ccccc3)CC2)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CN(C)C(=O)CCC(=O)c1ccc(F)cc1\": \"precursor\", \"c1ccc(CN2CCNCC2)cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CN(C)C(=O)CCC(=O)c1ccc(F)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CNC\": \"precursor\", \"O=C(O)CCC(=O)c1ccc(F)cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CNC\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=C(O)CCC(=O)c1ccc(F)cc1\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"c1ccc(CN2CCNCC2)cc1\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"CN(C)C(=O)CCC(=O)c1ccc(N2CCN(Cc3ccccc3)CC2)cc1","task_id":"retro_289d83e5e8bad5f124e6","tool_calls":7,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_2942f67a6d14e2cfc2b8:reference-expert:a0","kind":"single_route","max_steps":3,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CCOC(=O)Cc1cccc(NC(=O)c2cc(-c3ccccc3)ccc2F)c1 in at most 3 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCOC(=O)Cc1cccc(NC(=O)c2cc(-c3ccccc3)ccc2F)c1\", \"reactants\": [\"CCOC(=O)Cc1cccc(NC(=O)c2cc(Br)ccc2F)c1\", \"OB(O)c1ccccc1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCOC(=O)Cc1cccc(NC(=O)c2cc(Br)ccc2F)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"OB(O)c1ccccc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"HXITXNWTGFUOAU-UHFFFAOYSA-N.IGFBUTWRAVIUET-UHFFFAOYSA-N>>VWXIDDXSUDFGAV-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"CCOC(=O)Cc1cccc(NC(=O)c2cc(-c3ccccc3)ccc2F)c1\", \"reactants\": [\"CCOC(=O)Cc1cccc(NC(=O)c2cc(Br)ccc2F)c1\", \"OB(O)c1ccccc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CCOC(=O)Cc1cccc(NC(=O)c2cc(Br)ccc2F)c1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"OB(O)c1ccccc1\", \"results\": [{\"inchikey\": \"HXITXNWTGFUOAU-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"OB(O)c1ccccc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"CCOC(=O)Cc1cccc(NC(=O)c2cc(Br)ccc2F)c1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCOC(=O)Cc1cccc(NC(=O)c2cc(Br)ccc2F)c1\", \"reactants\": [\"CCOC(=O)Cc1cccc(N)c1\", \"O=C(O)c1cc(Br)ccc1F\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCOC(=O)Cc1cccc(N)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=C(O)c1cc(Br)ccc1F\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"JEVUURMJLRJOSG-UHFFFAOYSA-N.PEXAZYDITWXYNJ-UHFFFAOYSA-N>>IGFBUTWRAVIUET-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"CCOC(=O)Cc1cccc(NC(=O)c2cc(Br)ccc2F)c1\", \"reactants\": [\"CCOC(=O)Cc1cccc(N)c1\", \"O=C(O)c1cc(Br)ccc1F\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CCOC(=O)Cc1cccc(N)c1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"O=C(O)c1cc(Br)ccc1F\", \"results\": [{\"inchikey\": \"PEXAZYDITWXYNJ-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=C(O)c1cc(Br)ccc1F\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"CCOC(=O)Cc1cccc(N)c1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCOC(=O)Cc1cccc(N)c1\", \"reactants\": [\"CCO\", \"Nc1cccc(CC(=O)O)c1\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCO\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"Nc1cccc(CC(=O)O)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"LFQSCWFLJHTTHZ-UHFFFAOYSA-N.XUSKZLBLGHBCLD-UHFFFAOYSA-N>>JEVUURMJLRJOSG-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"CCOC(=O)Cc1cccc(N)c1\", \"reactants\": [\"CCO\", \"Nc1cccc(CC(=O)O)c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"CCO\", \"results\": [{\"inchikey\": \"LFQSCWFLJHTTHZ-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CCO\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"Nc1cccc(CC(=O)O)c1\", \"results\": [{\"inchikey\": \"XUSKZLBLGHBCLD-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Nc1cccc(CC(=O)O)c1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CCOC(=O)Cc1cccc(NC(=O)c2cc(-c3ccccc3)ccc2F)c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCOC(=O)Cc1cccc(NC(=O)c2cc(Br)ccc2F)c1\": \"precursor\", \"OB(O)c1ccccc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCOC(=O)Cc1cccc(NC(=O)c2cc(Br)ccc2F)c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCOC(=O)Cc1cccc(N)c1\": \"precursor\", \"O=C(O)c1cc(Br)ccc1F\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCOC(=O)Cc1cccc(N)c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCO\": \"precursor\", \"Nc1cccc(CC(=O)O)c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCO\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"Nc1cccc(CC(=O)O)c1\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"O=C(O)c1cc(Br)ccc1F\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"OB(O)c1ccccc1\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_4_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"CCOC(=O)Cc1cccc(NC(=O)c2cc(-c3ccccc3)ccc2F)c1","task_id":"retro_2942f67a6d14e2cfc2b8","tool_calls":10,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":4}
{"exact_match":true,"id":"retro_295d09ba7f35c8e63f84:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CCOC(=O)c1cc(F)c(N2CCC(NC(=O)OC(C)(C)C)C2)c(OC)c1F in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCOC(=O)c1cc(F)c(N2CCC(NC(=O)OC(C)(C)C)C2)c(OC)c1F\", \"reactants\": [\"CC(C)(C)OC(=O)NC1CCNC1\", \"CCOC(=O)c1cc(F)c(F)c(OC)c1F\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)OC(=O)NC1CCNC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"CCOC(=O)c1cc(F)c(F)c(OC)c1F\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"DQQJBEAXSOOCPG-UHFFFAOYSA-N.ZXFYRSUEOKXKOQ-UHFFFAOYSA-N>>AQTKJIVKYZAFNJ-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"CCOC(=O)c1cc(F)c(N2CCC(NC(=O)OC(C)(C)C)C2)c(OC)c1F\", \"reactants\": [\"CC(C)(C)OC(=O)NC1CCNC1\", \"CCOC(=O)c1cc(F)c(F)c(OC)c1F\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CC(C)(C)OC(=O)NC1CCNC1\", \"results\": [{\"inchikey\": \"DQQJBEAXSOOCPG-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CC(C)(C)OC(=O)NC1CCNC1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CCOC(=O)c1cc(F)c(F)c(OC)c1F\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"CCOC(=O)c1cc(F)c(F)c(OC)c1F was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCOC(=O)c1cc(F)c(F)c(OC)c1F\", \"reactants\": [\"CCO\", \"COc1c(F)c(F)cc(C(=O)O)c1F\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCO\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"COc1c(F)c(F)cc(C(=O)O)c1F\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"LFQSCWFLJHTTHZ-UHFFFAOYSA-N.YVJHZWWMKFQKDC-UHFFFAOYSA-N>>ZXFYRSUEOKXKOQ-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"CCOC(=O)c1cc(F)c(F)c(OC)c1F\", \"reactants\": [\"CCO\", \"COc1c(F)c(F)cc(C(=O)O)c1F\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CCO\", \"results\": [{\"inchikey\": \"LFQSCWFLJHTTHZ-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CCO\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"COc1c(F)c(F)cc(C(=O)O)c1F\", \"results\": [{\"inchikey\": \"YVJHZWWMKFQKDC-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"COc1c(F)c(F)cc(C(=O)O)c1F\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CCOC(=O)c1cc(F)c(N2CCC(NC(=O)OC(C)(C)C)C2)c(OC)c1F\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)(C)OC(=O)NC1CCNC1\": \"precursor\", \"CCOC(=O)c1cc(F)c(F)c(OC)c1F\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)OC(=O)NC1CCNC1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"CCOC(=O)c1cc(F)c(F)c(OC)c1F\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCO\": \"precursor\", \"COc1c(F)c(F)cc(C(=O)O)c1F\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCO\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"COc1c(F)c(F)cc(C(=O)O)c1F\", \"in_stock\": true, \"children\": []}]}]}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"CCOC(=O)c1cc(F)c(N2CCC(NC(=O)OC(C)(C)C)C2)c(OC)c1F","task_id":"retro_295d09ba7f35c8e63f84","tool_calls":7,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_29610a84e665d9686b25:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target COCCN(Cc1cccc(C#N)c1)C(=O)OC(C)(C)C in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COCCN(Cc1cccc(C#N)c1)C(=O)OC(C)(C)C\", \"reactants\": [\"CC(C)(C)OC(=O)OC(=O)OC(C)(C)C\", \"COCCNCc1cccc(C#N)c1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)OC(=O)OC(=O)OC(C)(C)C\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"COCCNCc1cccc(C#N)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"DYHSDKLCOJIUFX-UHFFFAOYSA-N.YMOASPSGWQPQCH-UHFFFAOYSA-N>>WFHFLSOSRULOAW-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"COCCN(Cc1cccc(C#N)c1)C(=O)OC(C)(C)C\", \"reactants\": [\"CC(C)(C)OC(=O)OC(=O)OC(C)(C)C\", \"COCCNCc1cccc(C#N)c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CC(C)(C)OC(=O)OC(=O)OC(C)(C)C\", \"results\": [{\"inchikey\": \"DYHSDKLCOJIUFX-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CC(C)(C)OC(=O)OC(=O)OC(C)(C)C\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"COCCNCc1cccc(C#N)c1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"COCCNCc1cccc(C#N)c1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COCCNCc1cccc(C#N)c1\", \"reactants\": [\"COCCN\", \"N#Cc1cccc(CBr)c1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"COCCN\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"N#Cc1cccc(CBr)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"ASUDFOJKTJLAIK-UHFFFAOYSA-N.CVKOOKPNCVYHNY-UHFFFAOYSA-N>>YMOASPSGWQPQCH-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"COCCNCc1cccc(C#N)c1\", \"reactants\": [\"COCCN\", \"N#Cc1cccc(CBr)c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"COCCN\", \"results\": [{\"inchikey\": \"ASUDFOJKTJLAIK-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"COCCN\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"N#Cc1cccc(CBr)c1\", \"results\": [{\"inchikey\": \"CVKOOKPNCVYHNY-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"N#Cc1cccc(CBr)c1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"COCCN(Cc1cccc(C#N)c1)C(=O)OC(C)(C)C\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)(C)OC(=O)OC(=O)OC(C)(C)C\": \"precursor\", \"COCCNCc1cccc(C#N)c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)OC(=O)OC(=O)OC(C)(C)C\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"COCCNCc1cccc(C#N)c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COCCN\": \"precursor\", \"N#Cc1cccc(CBr)c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COCCN\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"N#Cc1cccc(CBr)c1\", \"in_stock\": true, \"children\": []}]}]}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"COCCN(Cc1cccc(C#N)c1)C(=O)OC(C)(C)C","task_id":"retro_29610a84e665d9686b25","tool_calls":7,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_2a4a313c9fb676273dbc:reference-expert:a0","kind":"single_route","max_steps":4,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target COc1cnc2ccc(=O)n(CCN3CCC(NCc4ccc5c(n4)NC(=O)CO5)CC3)c2c1 in at most 4 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COc1cnc2ccc(=O)n(CCN3CCC(NCc4ccc5c(n4)NC(=O)CO5)CC3)c2c1\", \"reactants\": [\"COc1cnc2ccc(=O)n(CCN3CCC(N)CC3)c2c1\", \"O=Cc1ccc2c(n1)NC(=O)CO2\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"COc1cnc2ccc(=O)n(CCN3CCC(N)CC3)c2c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=Cc1ccc2c(n1)NC(=O)CO2\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"HVWABXSMSOGRGZ-UHFFFAOYSA-N.XOXXGNIBXYQQNS-UHFFFAOYSA-N>>XFRKLOKIYITRDO-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"COc1cnc2ccc(=O)n(CCN3CCC(NCc4ccc5c(n4)NC(=O)CO5)CC3)c2c1\", \"reactants\": [\"COc1cnc2ccc(=O)n(CCN3CCC(N)CC3)c2c1\", \"O=Cc1ccc2c(n1)NC(=O)CO2\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"COc1cnc2ccc(=O)n(CCN3CCC(N)CC3)c2c1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"O=Cc1ccc2c(n1)NC(=O)CO2\", \"results\": [{\"inchikey\": \"XOXXGNIBXYQQNS-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=Cc1ccc2c(n1)NC(=O)CO2\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"COc1cnc2ccc(=O)n(CCN3CCC(N)CC3)c2c1 was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COc1cnc2ccc(=O)n(CCN3CCC(N)CC3)c2c1\", \"reactants\": [\"COc1cnc2ccc(=O)n(CCN3CCC(NC(=O)OC(C)(C)C)CC3)c2c1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"COc1cnc2ccc(=O)n(CCN3CCC(NC(=O)OC(C)(C)C)CC3)c2c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"QQQIXAWRFJPILV-UHFFFAOYSA-N>>HVWABXSMSOGRGZ-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"COc1cnc2ccc(=O)n(CCN3CCC(N)CC3)c2c1\", \"reactants\": [\"COc1cnc2ccc(=O)n(CCN3CCC(NC(=O)OC(C)(C)C)CC3)c2c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"COc1cnc2ccc(=O)n(CCN3CCC(NC(=O)OC(C)(C)C)CC3)c2c1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"COc1cnc2ccc(=O)n(CCN3CCC(NC(=O)OC(C)(C)C)CC3)c2c1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COc1cnc2ccc(=O)n(CCN3CCC(NC(=O)OC(C)(C)C)CC3)c2c1\", \"reactants\": [\"CC(C)(C)OC(=O)NC1CCNCC1\", \"COc1cnc2ccc(=O)n(CC=O)c2c1\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)OC(=O)NC1CCNCC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"COc1cnc2ccc(=O)n(CC=O)c2c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"CKXZPVPIDOJLLM-UHFFFAOYSA-N.VDYYYRSDKMFHTD-UHFFFAOYSA-N>>QQQIXAWRFJPILV-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"COc1cnc2ccc(=O)n(CCN3CCC(NC(=O)OC(C)(C)C)CC3)c2c1\", \"reactants\": [\"CC(C)(C)OC(=O)NC1CCNCC1\", \"COc1cnc2ccc(=O)n(CC=O)c2c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"CC(C)(C)OC(=O)NC1CCNCC1\", \"results\": [{\"inchikey\": \"CKXZPVPIDOJLLM-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CC(C)(C)OC(=O)NC1CCNCC1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"COc1cnc2ccc(=O)n(CC=O)c2c1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"COc1cnc2ccc(=O)n(CC=O)c2c1 was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COc1cnc2ccc(=O)n(CC=O)c2c1\", \"reactants\": [\"COc1cnc2ccc(=O)n(CC3OCCO3)c2c1\"]}","name":"validate_disconnection"},"id":"call_4_0","type":"function"},{"function":{"arguments":"{\"query\": \"COc1cnc2ccc(=O)n(CC3OCCO3)c2c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"ZSFGKJXPSWKRJU-UHFFFAOYSA-N>>VDYYYRSDKMFHTD-UHFFFAOYSA-N\", \"model_turns_remaining\": 12, \"product\": \"COc1cnc2ccc(=O)n(CC=O)c2c1\", \"reactants\": [\"COc1cnc2ccc(=O)n(CC3OCCO3)c2c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_4_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"COc1cnc2ccc(=O)n(CC3OCCO3)c2c1\", \"results\": [{\"inchikey\": \"ZSFGKJXPSWKRJU-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"COc1cnc2ccc(=O)n(CC3OCCO3)c2c1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_1"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"COc1cnc2ccc(=O)n(CCN3CCC(NCc4ccc5c(n4)NC(=O)CO5)CC3)c2c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COc1cnc2ccc(=O)n(CCN3CCC(N)CC3)c2c1\": \"precursor\", \"O=Cc1ccc2c(n1)NC(=O)CO2\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COc1cnc2ccc(=O)n(CCN3CCC(N)CC3)c2c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COc1cnc2ccc(=O)n(CCN3CCC(NC(=O)OC(C)(C)C)CC3)c2c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COc1cnc2ccc(=O)n(CCN3CCC(NC(=O)OC(C)(C)C)CC3)c2c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)(C)OC(=O)NC1CCNCC1\": \"precursor\", \"COc1cnc2ccc(=O)n(CC=O)c2c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)OC(=O)NC1CCNCC1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"COc1cnc2ccc(=O)n(CC=O)c2c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COc1cnc2ccc(=O)n(CC3OCCO3)c2c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COc1cnc2ccc(=O)n(CC3OCCO3)c2c1\", \"in_stock\": true, \"children\": []}]}]}]}]}]}]}, {\"type\": \"mol\", \"smiles\": \"O=Cc1ccc2c(n1)NC(=O)CO2\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_5_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"COc1cnc2ccc(=O)n(CCN3CCC(NCc4ccc5c(n4)NC(=O)CO5)CC3)c2c1","task_id":"retro_2a4a313c9fb676273dbc","tool_calls":11,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":5}
{"exact_match":true,"id":"retro_2a9118591f5281e867f8:reference-expert:a0","kind":"single_route","max_steps":3,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CCOC(=O)c1cncc(-c2ccc(N3CCC(Oc4cc(F)ccc4Br)CC3)nc2)c1 in at most 3 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCOC(=O)c1cncc(-c2ccc(N3CCC(Oc4cc(F)ccc4Br)CC3)nc2)c1\", \"reactants\": [\"CCOC(=O)c1cncc(-c2ccc(N3CCC(O)CC3)nc2)c1\", \"Oc1cc(F)ccc1Br\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCOC(=O)c1cncc(-c2ccc(N3CCC(O)CC3)nc2)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"Oc1cc(F)ccc1Br\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"HUVAOAVBKOVPBZ-UHFFFAOYSA-N.QEWNCDFXLFGOPA-UHFFFAOYSA-N>>PMIVSEKNFFDCDX-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"CCOC(=O)c1cncc(-c2ccc(N3CCC(Oc4cc(F)ccc4Br)CC3)nc2)c1\", \"reactants\": [\"CCOC(=O)c1cncc(-c2ccc(N3CCC(O)CC3)nc2)c1\", \"Oc1cc(F)ccc1Br\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CCOC(=O)c1cncc(-c2ccc(N3CCC(O)CC3)nc2)c1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"Oc1cc(F)ccc1Br\", \"results\": [{\"inchikey\": \"HUVAOAVBKOVPBZ-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Oc1cc(F)ccc1Br\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"CCOC(=O)c1cncc(-c2ccc(N3CCC(O)CC3)nc2)c1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCOC(=O)c1cncc(-c2ccc(N3CCC(O)CC3)nc2)c1\", \"reactants\": [\"CCOC(=O)c1cncc(B2OC(C)(C)C(C)(C)O2)c1\", \"OC1CCN(c2ccc(Br)cn2)CC1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCOC(=O)c1cncc(B2OC(C)(C)C(C)(C)O2)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"OC1CCN(c2ccc(Br)cn2)CC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"LSGWHPYPLCIXCK-UHFFFAOYSA-N.ZKGQTSJZFBTEOB-UHFFFAOYSA-N>>QEWNCDFXLFGOPA-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"CCOC(=O)c1cncc(-c2ccc(N3CCC(O)CC3)nc2)c1\", \"reactants\": [\"CCOC(=O)c1cncc(B2OC(C)(C)C(C)(C)O2)c1\", \"OC1CCN(c2ccc(Br)cn2)CC1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CCOC(=O)c1cncc(B2OC(C)(C)C(C)(C)O2)c1\", \"results\": [{\"inchikey\": \"ZKGQTSJZFBTEOB-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CCOC(=O)c1cncc(B2OC(C)(C)C(C)(C)O2)c1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"OC1CCN(c2ccc(Br)cn2)CC1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"OC1CCN(c2ccc(Br)cn2)CC1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"OC1CCN(c2ccc(Br)cn2)CC1\", \"reactants\": [\"Brc1ccc(Br)nc1\", \"OC1CCNCC1\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"Brc1ccc(Br)nc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"OC1CCNCC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"HDOWRFHMPULYOA-UHFFFAOYSA-N.ZHXUWDPHUQHFOV-UHFFFAOYSA-N>>LSGWHPYPLCIXCK-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"OC1CCN(c2ccc(Br)cn2)CC1\", \"reactants\": [\"Brc1ccc(Br)nc1\", \"OC1CCNCC1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"Brc1ccc(Br)nc1\", \"results\": [{\"inchikey\": \"ZHXUWDPHUQHFOV-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Brc1ccc(Br)nc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"OC1CCNCC1\", \"results\": [{\"inchikey\": \"HDOWRFHMPULYOA-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"OC1CCNCC1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CCOC(=O)c1cncc(-c2ccc(N3CCC(Oc4cc(F)ccc4Br)CC3)nc2)c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCOC(=O)c1cncc(-c2ccc(N3CCC(O)CC3)nc2)c1\": \"precursor\", \"Oc1cc(F)ccc1Br\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCOC(=O)c1cncc(-c2ccc(N3CCC(O)CC3)nc2)c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCOC(=O)c1cncc(B2OC(C)(C)C(C)(C)O2)c1\": \"precursor\", \"OC1CCN(c2ccc(Br)cn2)CC1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCOC(=O)c1cncc(B2OC(C)(C)C(C)(C)O2)c1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"OC1CCN(c2ccc(Br)cn2)CC1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"Brc1ccc(Br)nc1\": \"precursor\", \"OC1CCNCC1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"Brc1ccc(Br)nc1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"OC1CCNCC1\", \"in_stock\": true, \"children\": []}]}]}]}]}, {\"type\": \"mol\", \"smiles\": \"Oc1cc(F)ccc1Br\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_4_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"CCOC(=O)c1cncc(-c2ccc(N3CCC(Oc4cc(F)ccc4Br)CC3)nc2)c1","task_id":"retro_2a9118591f5281e867f8","tool_calls":10,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":4}
{"exact_match":true,"id":"retro_2b34b93b957e6439c264:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CCCCNc1nc(N)c2ncn(Cc3ccc([N+](=O)[O-])cc3)c2n1 in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCCCNc1nc(N)c2ncn(Cc3ccc([N+](=O)[O-])cc3)c2n1\", \"reactants\": [\"CCCCNc1nc(N)c2nc[nH]c2n1\", \"O=[N+]([O-])c1ccc(CBr)cc1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCCCNc1nc(N)c2nc[nH]c2n1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=[N+]([O-])c1ccc(CBr)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"BYCJYBHYAVBYGC-UHFFFAOYSA-N.VOLRSQPSJGXRNJ-UHFFFAOYSA-N>>IVBCCFXAMKWBJN-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"CCCCNc1nc(N)c2ncn(Cc3ccc([N+](=O)[O-])cc3)c2n1\", \"reactants\": [\"CCCCNc1nc(N)c2nc[nH]c2n1\", \"O=[N+]([O-])c1ccc(CBr)cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CCCCNc1nc(N)c2nc[nH]c2n1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"O=[N+]([O-])c1ccc(CBr)cc1\", \"results\": [{\"inchikey\": \"VOLRSQPSJGXRNJ-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=[N+]([O-])c1ccc(CBr)cc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"CCCCNc1nc(N)c2nc[nH]c2n1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCCCNc1nc(N)c2nc[nH]c2n1\", \"reactants\": [\"CCCCN\", \"Nc1nc(Cl)nc2nc[nH]c12\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCCCN\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"Nc1nc(Cl)nc2nc[nH]c12\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"HBJGQJWNMZDFKL-UHFFFAOYSA-N.HQABUPZFAYXKJW-UHFFFAOYSA-N>>BYCJYBHYAVBYGC-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"CCCCNc1nc(N)c2nc[nH]c2n1\", \"reactants\": [\"CCCCN\", \"Nc1nc(Cl)nc2nc[nH]c12\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CCCCN\", \"results\": [{\"inchikey\": \"HQABUPZFAYXKJW-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CCCCN\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"Nc1nc(Cl)nc2nc[nH]c12\", \"results\": [{\"inchikey\": \"HBJGQJWNMZDFKL-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Nc1nc(Cl)nc2nc[nH]c12\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CCCCNc1nc(N)c2ncn(Cc3ccc([N+](=O)[O-])cc3)c2n1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCCCNc1nc(N)c2nc[nH]c2n1\": \"precursor\", \"O=[N+]([O-])c1ccc(CBr)cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCCCNc1nc(N)c2nc[nH]c2n1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCCCN\": \"precursor\", \"Nc1nc(Cl)nc2nc[nH]c12\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCCCN\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"Nc1nc(Cl)nc2nc[nH]c12\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"O=[N+]([O-])c1ccc(CBr)cc1\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"CCCCNc1nc(N)c2ncn(Cc3ccc([N+](=O)[O-])cc3)c2n1","task_id":"retro_2b34b93b957e6439c264","tool_calls":7,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_2b4eba40b64e5b2bba95:reference-expert:a0","kind":"single_route","max_steps":3,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target Cn1c(NC(C)(C)CO)nc2nn(Cc3ccc(-c4ccccc4)cc3)cc2c1=O in at most 3 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Cn1c(NC(C)(C)CO)nc2nn(Cc3ccc(-c4ccccc4)cc3)cc2c1=O\", \"reactants\": [\"CC(C)(N)CO\", \"Cn1c(Cl)nc2nn(Cc3ccc(-c4ccccc4)cc3)cc2c1=O\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(N)CO\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"Cn1c(Cl)nc2nn(Cc3ccc(-c4ccccc4)cc3)cc2c1=O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"CBTVGIZVANVGBH-UHFFFAOYSA-N.OKELOWNXOVOLDX-UHFFFAOYSA-N>>RVBOYHSNRVMXDX-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"Cn1c(NC(C)(C)CO)nc2nn(Cc3ccc(-c4ccccc4)cc3)cc2c1=O\", \"reactants\": [\"CC(C)(N)CO\", \"Cn1c(Cl)nc2nn(Cc3ccc(-c4ccccc4)cc3)cc2c1=O\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CC(C)(N)CO\", \"results\": [{\"inchikey\": \"CBTVGIZVANVGBH-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CC(C)(N)CO\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"Cn1c(Cl)nc2nn(Cc3ccc(-c4ccccc4)cc3)cc2c1=O\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"Cn1c(Cl)nc2nn(Cc3ccc(-c4ccccc4)cc3)cc2c1=O was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Cn1c(Cl)nc2nn(Cc3ccc(-c4ccccc4)cc3)cc2c1=O\", \"reactants\": [\"Cn1c(=O)[nH]c2nn(Cc3ccc(-c4ccccc4)cc3)cc2c1=O\", \"O=P(Cl)(Cl)Cl\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"Cn1c(=O)[nH]c2nn(Cc3ccc(-c4ccccc4)cc3)cc2c1=O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=P(Cl)(Cl)Cl\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"SPIZYPSHBCPKFF-UHFFFAOYSA-N.XHXFXVLFKHQFAL-UHFFFAOYSA-N>>OKELOWNXOVOLDX-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"Cn1c(Cl)nc2nn(Cc3ccc(-c4ccccc4)cc3)cc2c1=O\", \"reactants\": [\"Cn1c(=O)[nH]c2nn(Cc3ccc(-c4ccccc4)cc3)cc2c1=O\", \"O=P(Cl)(Cl)Cl\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"Cn1c(=O)[nH]c2nn(Cc3ccc(-c4ccccc4)cc3)cc2c1=O\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"O=P(Cl)(Cl)Cl\", \"results\": [{\"inchikey\": \"XHXFXVLFKHQFAL-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=P(Cl)(Cl)Cl\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Cn1c(=O)[nH]c2nn(Cc3ccc(-c4ccccc4)cc3)cc2c1=O was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Cn1c(=O)[nH]c2nn(Cc3ccc(-c4ccccc4)cc3)cc2c1=O\", \"reactants\": [\"COc1ccc(Cn2c(=O)n(C)c(=O)c3cn(Cc4ccc(-c5ccccc5)cc4)nc32)cc1\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"COc1ccc(Cn2c(=O)n(C)c(=O)c3cn(Cc4ccc(-c5ccccc5)cc4)nc32)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"WVVWJZXPWNPJJQ-UHFFFAOYSA-N>>SPIZYPSHBCPKFF-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"Cn1c(=O)[nH]c2nn(Cc3ccc(-c4ccccc4)cc3)cc2c1=O\", \"reactants\": [\"COc1ccc(Cn2c(=O)n(C)c(=O)c3cn(Cc4ccc(-c5ccccc5)cc4)nc32)cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"COc1ccc(Cn2c(=O)n(C)c(=O)c3cn(Cc4ccc(-c5ccccc5)cc4)nc32)cc1\", \"results\": [{\"inchikey\": \"WVVWJZXPWNPJJQ-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"COc1ccc(Cn2c(=O)n(C)c(=O)c3cn(Cc4ccc(-c5ccccc5)cc4)nc32)cc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"Cn1c(NC(C)(C)CO)nc2nn(Cc3ccc(-c4ccccc4)cc3)cc2c1=O\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)(N)CO\": \"precursor\", \"Cn1c(Cl)nc2nn(Cc3ccc(-c4ccccc4)cc3)cc2c1=O\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(N)CO\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"Cn1c(Cl)nc2nn(Cc3ccc(-c4ccccc4)cc3)cc2c1=O\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"Cn1c(=O)[nH]c2nn(Cc3ccc(-c4ccccc4)cc3)cc2c1=O\": \"precursor\", \"O=P(Cl)(Cl)Cl\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"Cn1c(=O)[nH]c2nn(Cc3ccc(-c4ccccc4)cc3)cc2c1=O\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COc1ccc(Cn2c(=O)n(C)c(=O)c3cn(Cc4ccc(-c5ccccc5)cc4)nc32)cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COc1ccc(Cn2c(=O)n(C)c(=O)c3cn(Cc4ccc(-c5ccccc5)cc4)nc32)cc1\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"O=P(Cl)(Cl)Cl\", \"in_stock\": true, \"children\": []}]}]}]}]}]}}","name":"emit_routes"},"id":"call_4_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"Cn1c(NC(C)(C)CO)nc2nn(Cc3ccc(-c4ccccc4)cc3)cc2c1=O","task_id":"retro_2b4eba40b64e5b2bba95","tool_calls":9,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":4}
{"exact_match":true,"id":"retro_2b98349ffff49ba1ec1d:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CCOC(=O)c1cc(=O)c2cc(F)cc(Br)c2o1 in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCOC(=O)c1cc(=O)c2cc(F)cc(Br)c2o1\", \"reactants\": [\"CC(=O)c1cc(F)cc(Br)c1O\", \"CCOC(=O)C(=O)OCC\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(=O)c1cc(F)cc(Br)c1O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"CCOC(=O)C(=O)OCC\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"OONDYRNMURZSPQ-UHFFFAOYSA-N.WYACBZDAHNBPPB-UHFFFAOYSA-N>>NIYBSDSIFPBWGM-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"CCOC(=O)c1cc(=O)c2cc(F)cc(Br)c2o1\", \"reactants\": [\"CC(=O)c1cc(F)cc(Br)c1O\", \"CCOC(=O)C(=O)OCC\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CC(=O)c1cc(F)cc(Br)c1O\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CCOC(=O)C(=O)OCC\", \"results\": [{\"inchikey\": \"WYACBZDAHNBPPB-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CCOC(=O)C(=O)OCC\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"CC(=O)c1cc(F)cc(Br)c1O was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(=O)c1cc(F)cc(Br)c1O\", \"reactants\": [\"CC(=O)Cl\", \"Oc1ccc(F)cc1Br\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(=O)Cl\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"Oc1ccc(F)cc1Br\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"MEYRABVEYCFHHB-UHFFFAOYSA-N.WETWJCDKMRHUPV-UHFFFAOYSA-N>>OONDYRNMURZSPQ-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"CC(=O)c1cc(F)cc(Br)c1O\", \"reactants\": [\"CC(=O)Cl\", \"Oc1ccc(F)cc1Br\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CC(=O)Cl\", \"results\": [{\"inchikey\": \"WETWJCDKMRHUPV-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CC(=O)Cl\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"Oc1ccc(F)cc1Br\", \"results\": [{\"inchikey\": \"MEYRABVEYCFHHB-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Oc1ccc(F)cc1Br\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CCOC(=O)c1cc(=O)c2cc(F)cc(Br)c2o1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(=O)c1cc(F)cc(Br)c1O\": \"precursor\", \"CCOC(=O)C(=O)OCC\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(=O)c1cc(F)cc(Br)c1O\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(=O)Cl\": \"precursor\", \"Oc1ccc(F)cc1Br\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(=O)Cl\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"Oc1ccc(F)cc1Br\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"CCOC(=O)C(=O)OCC\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"CCOC(=O)c1cc(=O)c2cc(F)cc(Br)c2o1","task_id":"retro_2b98349ffff49ba1ec1d","tool_calls":7,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_2c7e4cf765564a497145:reference-expert:a0","kind":"single_route","max_steps":3,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CN1CCC(Oc2cc(Cn3cnc4cc(-c5ccc(Cl)cc5)sc4c3=O)ccn2)CC1 in at most 3 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CN1CCC(Oc2cc(Cn3cnc4cc(-c5ccc(Cl)cc5)sc4c3=O)ccn2)CC1\", \"reactants\": [\"CN1CCC(Oc2cc(CN)ccn2)CC1\", \"COC(=O)c1sc(-c2ccc(Cl)cc2)cc1/N=C/N(C)C\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CN1CCC(Oc2cc(CN)ccn2)CC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"COC(=O)c1sc(-c2ccc(Cl)cc2)cc1/N=C/N(C)C\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"ALWFLYMKFZJTBB-RQZCQDPDSA-N.QRFSLPULOCIADA-UHFFFAOYSA-N>>VCJFXNCKEOOGAE-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"CN1CCC(Oc2cc(Cn3cnc4cc(-c5ccc(Cl)cc5)sc4c3=O)ccn2)CC1\", \"reactants\": [\"CN1CCC(Oc2cc(CN)ccn2)CC1\", \"COC(=O)c1sc(-c2ccc(Cl)cc2)cc1/N=C/N(C)C\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CN1CCC(Oc2cc(CN)ccn2)CC1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"COC(=O)c1sc(-c2ccc(Cl)cc2)cc1/N=C/N(C)C\", \"results\": [{\"inchikey\": \"ALWFLYMKFZJTBB-RQZCQDPDSA-N\", \"similarity\": 1.0, \"smiles\": \"COC(=O)c1sc(-c2ccc(Cl)cc2)cc1/N=C/N(C)C\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"CN1CCC(Oc2cc(CN)ccn2)CC1 was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CN1CCC(Oc2cc(CN)ccn2)CC1\", \"reactants\": [\"CN1CCC(Oc2cc(C#N)ccn2)CC1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CN1CCC(Oc2cc(C#N)ccn2)CC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_complete\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"DSBOVWOFKSMUOP-UHFFFAOYSA-N>>QRFSLPULOCIADA-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"CN1CCC(Oc2cc(CN)ccn2)CC1\", \"reactants\": [\"CN1CCC(Oc2cc(C#N)ccn2)CC1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CN1CCC(Oc2cc(C#N)ccn2)CC1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"CN1CCC(Oc2cc(C#N)ccn2)CC1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CN1CCC(Oc2cc(C#N)ccn2)CC1\", \"reactants\": [\"CN1CCC(O)CC1\", \"N#Cc1ccnc(Cl)c1\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"CN1CCC(O)CC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"N#Cc1ccnc(Cl)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"BAUWRHPMUVYFOD-UHFFFAOYSA-N.QRXBTPFMCTXCRD-UHFFFAOYSA-N>>DSBOVWOFKSMUOP-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"CN1CCC(Oc2cc(C#N)ccn2)CC1\", \"reactants\": [\"CN1CCC(O)CC1\", \"N#Cc1ccnc(Cl)c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"CN1CCC(O)CC1\", \"results\": [{\"inchikey\": \"BAUWRHPMUVYFOD-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CN1CCC(O)CC1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"N#Cc1ccnc(Cl)c1\", \"results\": [{\"inchikey\": \"QRXBTPFMCTXCRD-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"N#Cc1ccnc(Cl)c1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CN1CCC(Oc2cc(Cn3cnc4cc(-c5ccc(Cl)cc5)sc4c3=O)ccn2)CC1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CN1CCC(Oc2cc(CN)ccn2)CC1\": \"precursor\", \"COC(=O)c1sc(-c2ccc(Cl)cc2)cc1/N=C/N(C)C\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CN1CCC(Oc2cc(CN)ccn2)CC1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CN1CCC(Oc2cc(C#N)ccn2)CC1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CN1CCC(Oc2cc(C#N)ccn2)CC1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CN1CCC(O)CC1\": \"precursor\", \"N#Cc1ccnc(Cl)c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CN1CCC(O)CC1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"N#Cc1ccnc(Cl)c1\", \"in_stock\": true, \"children\": []}]}]}]}]}, {\"type\": \"mol\", \"smiles\": \"COC(=O)c1sc(-c2ccc(Cl)cc2)cc1/N=C/N(C)C\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_4_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"CN1CCC(Oc2cc(Cn3cnc4cc(-c5ccc(Cl)cc5)sc4c3=O)ccn2)CC1","task_id":"retro_2c7e4cf765564a497145","tool_calls":9,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":4}
{"exact_match":true,"id":"retro_2f5a58877bf9040ce0e1:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CCOC(=O)c1cc2cc(Oc3ccnc4cc(OC)c(OC)cc34)ccc2[nH]1 in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCOC(=O)c1cc2cc(Oc3ccnc4cc(OC)c(OC)cc34)ccc2[nH]1\", \"reactants\": [\"CCOC(=O)c1cc2cc(O)ccc2[nH]1\", \"COc1cc2nccc(Cl)c2cc1OC\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCOC(=O)c1cc2cc(O)ccc2[nH]1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"COc1cc2nccc(Cl)c2cc1OC\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"WANAXLMRGYGCPC-UHFFFAOYSA-N.WRVHQEYBCDPZEU-UHFFFAOYSA-N>>LJSHQFKWJLEHAA-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"CCOC(=O)c1cc2cc(Oc3ccnc4cc(OC)c(OC)cc34)ccc2[nH]1\", \"reactants\": [\"CCOC(=O)c1cc2cc(O)ccc2[nH]1\", \"COc1cc2nccc(Cl)c2cc1OC\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CCOC(=O)c1cc2cc(O)ccc2[nH]1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"COc1cc2nccc(Cl)c2cc1OC\", \"results\": [{\"inchikey\": \"WRVHQEYBCDPZEU-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"COc1cc2nccc(Cl)c2cc1OC\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"CCOC(=O)c1cc2cc(O)ccc2[nH]1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCOC(=O)c1cc2cc(O)ccc2[nH]1\", \"reactants\": [\"CCO\", \"O=C(O)c1cc2cc(O)ccc2[nH]1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCO\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=C(O)c1cc2cc(O)ccc2[nH]1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"BIMHWDJKNOMNLD-UHFFFAOYSA-N.LFQSCWFLJHTTHZ-UHFFFAOYSA-N>>WANAXLMRGYGCPC-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"CCOC(=O)c1cc2cc(O)ccc2[nH]1\", \"reactants\": [\"CCO\", \"O=C(O)c1cc2cc(O)ccc2[nH]1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CCO\", \"results\": [{\"inchikey\": \"LFQSCWFLJHTTHZ-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CCO\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"O=C(O)c1cc2cc(O)ccc2[nH]1\", \"results\": [{\"inchikey\": \"BIMHWDJKNOMNLD-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=C(O)c1cc2cc(O)ccc2[nH]1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CCOC(=O)c1cc2cc(Oc3ccnc4cc(OC)c(OC)cc34)ccc2[nH]1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCOC(=O)c1cc2cc(O)ccc2[nH]1\": \"precursor\", \"COc1cc2nccc(Cl)c2cc1OC\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCOC(=O)c1cc2cc(O)ccc2[nH]1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCO\": \"precursor\", \"O=C(O)c1cc2cc(O)ccc2[nH]1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCO\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=C(O)c1cc2cc(O)ccc2[nH]1\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"COc1cc2nccc(Cl)c2cc1OC\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"CCOC(=O)c1cc2cc(Oc3ccnc4cc(OC)c(OC)cc34)ccc2[nH]1","task_id":"retro_2f5a58877bf9040ce0e1","tool_calls":7,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_30200e501d95bc6af1bc:reference-expert:a0","kind":"single_route","max_steps":4,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CC(C)(C)[Si](C)(C)OCCCn1c(=O)[nH]c2ccc(Br)cc21 in at most 4 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(C)(C)[Si](C)(C)OCCCn1c(=O)[nH]c2ccc(Br)cc21\", \"reactants\": [\"CC(C)(C)[Si](C)(C)OCCCNc1cc(Br)ccc1N\", \"O=C(n1ccnc1)n1ccnc1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)[Si](C)(C)OCCCNc1cc(Br)ccc1N\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=C(n1ccnc1)n1ccnc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"MXWWRIWGWGZKFU-UHFFFAOYSA-N.PFKFTWBEEFSNDU-UHFFFAOYSA-N>>WPISYMKMLRQILB-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"CC(C)(C)[Si](C)(C)OCCCn1c(=O)[nH]c2ccc(Br)cc21\", \"reactants\": [\"CC(C)(C)[Si](C)(C)OCCCNc1cc(Br)ccc1N\", \"O=C(n1ccnc1)n1ccnc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CC(C)(C)[Si](C)(C)OCCCNc1cc(Br)ccc1N\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"O=C(n1ccnc1)n1ccnc1\", \"results\": [{\"inchikey\": \"PFKFTWBEEFSNDU-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=C(n1ccnc1)n1ccnc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"CC(C)(C)[Si](C)(C)OCCCNc1cc(Br)ccc1N was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(C)(C)[Si](C)(C)OCCCNc1cc(Br)ccc1N\", \"reactants\": [\"CC(C)(C)[Si](C)(C)OCCCNc1cc(Br)ccc1[N+](=O)[O-]\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)[Si](C)(C)OCCCNc1cc(Br)ccc1[N+](=O)[O-]\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"LJZVHDLZWDTFRC-UHFFFAOYSA-N>>MXWWRIWGWGZKFU-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"CC(C)(C)[Si](C)(C)OCCCNc1cc(Br)ccc1N\", \"reactants\": [\"CC(C)(C)[Si](C)(C)OCCCNc1cc(Br)ccc1[N+](=O)[O-]\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CC(C)(C)[Si](C)(C)OCCCNc1cc(Br)ccc1[N+](=O)[O-]\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"CC(C)(C)[Si](C)(C)OCCCNc1cc(Br)ccc1[N+](=O)[O-] was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(C)(C)[Si](C)(C)OCCCNc1cc(Br)ccc1[N+](=O)[O-]\", \"reactants\": [\"CC(C)(C)[Si](C)(C)Cl\", \"O=[N+]([O-])c1ccc(Br)cc1NCCCO\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)[Si](C)(C)Cl\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=[N+]([O-])c1ccc(Br)cc1NCCCO\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"BCNZYOJHNLTNEZ-UHFFFAOYSA-N.FQYJDQFHSGORSJ-UHFFFAOYSA-N>>LJZVHDLZWDTFRC-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"CC(C)(C)[Si](C)(C)OCCCNc1cc(Br)ccc1[N+](=O)[O-]\", \"reactants\": [\"CC(C)(C)[Si](C)(C)Cl\", \"O=[N+]([O-])c1ccc(Br)cc1NCCCO\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"CC(C)(C)[Si](C)(C)Cl\", \"results\": [{\"inchikey\": \"BCNZYOJHNLTNEZ-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CC(C)(C)[Si](C)(C)Cl\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"O=[N+]([O-])c1ccc(Br)cc1NCCCO\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"O=[N+]([O-])c1ccc(Br)cc1NCCCO was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"O=[N+]([O-])c1ccc(Br)cc1NCCCO\", \"reactants\": [\"NCCCO\", \"O=[N+]([O-])c1ccc(Br)cc1F\"]}","name":"validate_disconnection"},"id":"call_4_0","type":"function"},{"function":{"arguments":"{\"query\": \"NCCCO\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=[N+]([O-])c1ccc(Br)cc1F\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"VQCWSOYHHXXWSP-UHFFFAOYSA-N.WUGQZFFCHPXWKQ-UHFFFAOYSA-N>>FQYJDQFHSGORSJ-UHFFFAOYSA-N\", \"model_turns_remaining\": 12, \"product\": \"O=[N+]([O-])c1ccc(Br)cc1NCCCO\", \"reactants\": [\"NCCCO\", \"O=[N+]([O-])c1ccc(Br)cc1F\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_4_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"NCCCO\", \"results\": [{\"inchikey\": \"WUGQZFFCHPXWKQ-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"NCCCO\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"O=[N+]([O-])c1ccc(Br)cc1F\", \"results\": [{\"inchikey\": \"VQCWSOYHHXXWSP-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=[N+]([O-])c1ccc(Br)cc1F\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)[Si](C)(C)OCCCn1c(=O)[nH]c2ccc(Br)cc21\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)(C)[Si](C)(C)OCCCNc1cc(Br)ccc1N\": \"precursor\", \"O=C(n1ccnc1)n1ccnc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)[Si](C)(C)OCCCNc1cc(Br)ccc1N\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)(C)[Si](C)(C)OCCCNc1cc(Br)ccc1[N+](=O)[O-]\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)[Si](C)(C)OCCCNc1cc(Br)ccc1[N+](=O)[O-]\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)(C)[Si](C)(C)Cl\": \"precursor\", \"O=[N+]([O-])c1ccc(Br)cc1NCCCO\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)[Si](C)(C)Cl\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=[N+]([O-])c1ccc(Br)cc1NCCCO\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"NCCCO\": \"precursor\", \"O=[N+]([O-])c1ccc(Br)cc1F\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"NCCCO\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=[N+]([O-])c1ccc(Br)cc1F\", \"in_stock\": true, \"children\": []}]}]}]}]}]}]}, {\"type\": \"mol\", \"smiles\": \"O=C(n1ccnc1)n1ccnc1\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_5_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"CC(C)(C)[Si](C)(C)OCCCn1c(=O)[nH]c2ccc(Br)cc21","task_id":"retro_30200e501d95bc6af1bc","tool_calls":12,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":5}
{"exact_match":true,"id":"retro_305c95e96e08f1b28e0d:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CC(C)(OC1CCCCO1)c1ccccc1Br in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(C)(OC1CCCCO1)c1ccccc1Br\", \"reactants\": [\"C1=COCCC1\", \"CC(C)(O)c1ccccc1Br\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"C1=COCCC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(O)c1ccccc1Br\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_complete\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"BUDQDWGNQVEFAC-UHFFFAOYSA-N.TXQKNSQVEWHJAQ-UHFFFAOYSA-N>>OWODLTLBFDKJAK-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"CC(C)(OC1CCCCO1)c1ccccc1Br\", \"reactants\": [\"C1=COCCC1\", \"CC(C)(O)c1ccccc1Br\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"C1=COCCC1\", \"results\": [{\"inchikey\": \"BUDQDWGNQVEFAC-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"C1=COCCC1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CC(C)(O)c1ccccc1Br\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"CC(C)(O)c1ccccc1Br was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(C)(O)c1ccccc1Br\", \"reactants\": [\"CCOCC\", \"COC(=O)c1ccccc1Br\", \"[CH3][Mg][Br]\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCOCC\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"COC(=O)c1ccccc1Br\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"},{"function":{"arguments":"{\"query\": \"[CH3][Mg][Br]\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_3","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"AVFUHBJCUUTGCD-UHFFFAOYSA-M.RTZKZFJDLAIYFH-UHFFFAOYSA-N.SWGQITQOBPXVRC-UHFFFAOYSA-N>>TXQKNSQVEWHJAQ-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"CC(C)(O)c1ccccc1Br\", \"reactants\": [\"CCOCC\", \"COC(=O)c1ccccc1Br\", \"[CH3][Mg][Br]\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CCOCC\", \"results\": [{\"inchikey\": \"RTZKZFJDLAIYFH-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CCOCC\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"COC(=O)c1ccccc1Br\", \"results\": [{\"inchikey\": \"SWGQITQOBPXVRC-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"COC(=O)c1ccccc1Br\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"[CH3][Mg][Br]\", \"results\": [{\"inchikey\": \"AVFUHBJCUUTGCD-UHFFFAOYSA-M\", \"similarity\": 1.0, \"smiles\": \"[CH3][Mg][Br]\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_3"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(OC1CCCCO1)c1ccccc1Br\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"C1=COCCC1\": \"precursor\", \"CC(C)(O)c1ccccc1Br\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"C1=COCCC1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"CC(C)(O)c1ccccc1Br\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCOCC\": \"precursor\", \"COC(=O)c1ccccc1Br\": \"precursor\", \"[CH3][Mg][Br]\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCOCC\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"COC(=O)c1ccccc1Br\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"[CH3][Mg][Br]\", \"in_stock\": true, \"children\": []}]}]}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"CC(C)(OC1CCCCO1)c1ccccc1Br","task_id":"retro_305c95e96e08f1b28e0d","tool_calls":8,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":false,"id":"retro_3141b07da77a8733824d:reference-expert:a0","kind":"single_route","max_steps":4,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target O=C(CC(c1ccccc1)c1ccccc1)N1CCC(CN2CCCCC2)CC1 in at most 4 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"O=C(CC(c1ccccc1)c1ccccc1)N1CCC(CN2CCCCC2)CC1\", \"reactants\": [\"C1CCN(CC2CCNCC2)CC1\", \"O=C(O)CC(c1ccccc1)c1ccccc1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"C1CCN(CC2CCNCC2)CC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=C(O)CC(c1ccccc1)c1ccccc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"BZQGAPWJKAYCHR-UHFFFAOYSA-N.KQUQJHZJTWYGAQ-UHFFFAOYSA-N>>ZHNSWLXDONMZJJ-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"O=C(CC(c1ccccc1)c1ccccc1)N1CCC(CN2CCCCC2)CC1\", \"reactants\": [\"C1CCN(CC2CCNCC2)CC1\", \"O=C(O)CC(c1ccccc1)c1ccccc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"C1CCN(CC2CCNCC2)CC1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"O=C(O)CC(c1ccccc1)c1ccccc1\", \"results\": [{\"inchikey\": \"BZQGAPWJKAYCHR-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=C(O)CC(c1ccccc1)c1ccccc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"C1CCN(CC2CCNCC2)CC1 was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"C1CCN(CC2CCNCC2)CC1\", \"reactants\": [\"CC(C)(C)OC(=O)N1CCC(CN2CCCCC2)CC1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)OC(=O)N1CCC(CN2CCCCC2)CC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"IGENCGXZONWRMB-UHFFFAOYSA-N>>KQUQJHZJTWYGAQ-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"C1CCN(CC2CCNCC2)CC1\", \"reactants\": [\"CC(C)(C)OC(=O)N1CCC(CN2CCCCC2)CC1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CC(C)(C)OC(=O)N1CCC(CN2CCCCC2)CC1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"CC(C)(C)OC(=O)N1CCC(CN2CCCCC2)CC1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(C)(C)OC(=O)N1CCC(CN2CCCCC2)CC1\", \"reactants\": [\"C1CCNCC1\", \"CC(C)(C)OC(=O)N1CCC(C=O)CC1\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"C1CCNCC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)OC(=O)N1CCC(C=O)CC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"JYUQEWCJWDGCRX-UHFFFAOYSA-N.NQRYJNQNLNOLGT-UHFFFAOYSA-N>>IGENCGXZONWRMB-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"CC(C)(C)OC(=O)N1CCC(CN2CCCCC2)CC1\", \"reactants\": [\"C1CCNCC1\", \"CC(C)(C)OC(=O)N1CCC(C=O)CC1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"C1CCNCC1\", \"results\": [{\"inchikey\": \"NQRYJNQNLNOLGT-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"C1CCNCC1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"CC(C)(C)OC(=O)N1CCC(C=O)CC1\", \"results\": [{\"inchikey\": \"JYUQEWCJWDGCRX-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CC(C)(C)OC(=O)N1CCC(C=O)CC1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"O=C(CC(c1ccccc1)c1ccccc1)N1CCC(CN2CCCCC2)CC1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"C1CCN(CC2CCNCC2)CC1\": \"precursor\", \"O=C(O)CC(c1ccccc1)c1ccccc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"C1CCN(CC2CCNCC2)CC1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)(C)OC(=O)N1CCC(CN2CCCCC2)CC1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)OC(=O)N1CCC(CN2CCCCC2)CC1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"C1CCNCC1\": \"precursor\", \"CC(C)(C)OC(=O)N1CCC(C=O)CC1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"C1CCNCC1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"CC(C)(C)OC(=O)N1CCC(C=O)CC1\", \"in_stock\": true, \"children\": []}]}]}]}]}, {\"type\": \"mol\", \"smiles\": \"O=C(O)CC(c1ccccc1)c1ccccc1\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_4_0","type":"function"}]}],"provider":"reference","reward":0.875,"source":"reference-expert","target_smiles":"O=C(CC(c1ccccc1)c1ccccc1)N1CCC(CN2CCCCC2)CC1","task_id":"retro_3141b07da77a8733824d","tool_calls":9,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":4}
{"exact_match":true,"id":"retro_314d261c0920c451b429:reference-expert:a0","kind":"single_route","max_steps":3,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target Cc1cccc(CC2CNCCO2)c1 in at most 3 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Cc1cccc(CC2CNCCO2)c1\", \"reactants\": [\"Cc1cccc(CC2CN(Cc3ccccc3)CCO2)c1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"Cc1cccc(CC2CN(Cc3ccccc3)CCO2)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"SCVWEBZPKDIJEH-UHFFFAOYSA-N>>STZVAUCDPJMNEK-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"Cc1cccc(CC2CNCCO2)c1\", \"reactants\": [\"Cc1cccc(CC2CN(Cc3ccccc3)CCO2)c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"Cc1cccc(CC2CN(Cc3ccccc3)CCO2)c1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"Cc1cccc(CC2CN(Cc3ccccc3)CCO2)c1 was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Cc1cccc(CC2CN(Cc3ccccc3)CCO2)c1\", \"reactants\": [\"Cc1cccc(CC2OCCN(Cc3ccccc3)C2=O)c1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"Cc1cccc(CC2OCCN(Cc3ccccc3)C2=O)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"UJBCAVSLKPELFM-UHFFFAOYSA-N>>SCVWEBZPKDIJEH-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"Cc1cccc(CC2CN(Cc3ccccc3)CCO2)c1\", \"reactants\": [\"Cc1cccc(CC2OCCN(Cc3ccccc3)C2=O)c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"Cc1cccc(CC2OCCN(Cc3ccccc3)C2=O)c1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"Cc1cccc(CC2OCCN(Cc3ccccc3)C2=O)c1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Cc1cccc(CC2OCCN(Cc3ccccc3)C2=O)c1\", \"reactants\": [\"Cc1cccc(CBr)c1\", \"O=C1COCCN1Cc1ccccc1\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"Cc1cccc(CBr)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=C1COCCN1Cc1ccccc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"FWLWTILKTABGKQ-UHFFFAOYSA-N.PXAJALSKRUHGJR-UHFFFAOYSA-N>>UJBCAVSLKPELFM-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"Cc1cccc(CC2OCCN(Cc3ccccc3)C2=O)c1\", \"reactants\": [\"Cc1cccc(CBr)c1\", \"O=C1COCCN1Cc1ccccc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"Cc1cccc(CBr)c1\", \"results\": [{\"inchikey\": \"FWLWTILKTABGKQ-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Cc1cccc(CBr)c1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"O=C1COCCN1Cc1ccccc1\", \"results\": [{\"inchikey\": \"PXAJALSKRUHGJR-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=C1COCCN1Cc1ccccc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"Cc1cccc(CC2CNCCO2)c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"Cc1cccc(CC2CN(Cc3ccccc3)CCO2)c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"Cc1cccc(CC2CN(Cc3ccccc3)CCO2)c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"Cc1cccc(CC2OCCN(Cc3ccccc3)C2=O)c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"Cc1cccc(CC2OCCN(Cc3ccccc3)C2=O)c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"Cc1cccc(CBr)c1\": \"precursor\", \"O=C1COCCN1Cc1ccccc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"Cc1cccc(CBr)c1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=C1COCCN1Cc1ccccc1\", \"in_stock\": true, \"children\": []}]}]}]}]}]}]}]}}","name":"emit_routes"},"id":"call_4_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"Cc1cccc(CC2CNCCO2)c1","task_id":"retro_314d261c0920c451b429","tool_calls":8,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":4}
{"exact_match":true,"id":"retro_32945ca45923616ab086:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CC(C)(C)OC(=O)c1ccc(CCCCO)cc1 in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(C)(C)OC(=O)c1ccc(CCCCO)cc1\", \"reactants\": [\"CC(C)(C)OC(=O)c1ccc(C#CCCO)cc1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)OC(=O)c1ccc(C#CCCO)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_complete\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"BUPYFNSLTQNVOB-UHFFFAOYSA-N>>AZGAZHWQNPNDLW-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"CC(C)(C)OC(=O)c1ccc(CCCCO)cc1\", \"reactants\": [\"CC(C)(C)OC(=O)c1ccc(C#CCCO)cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CC(C)(C)OC(=O)c1ccc(C#CCCO)cc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"CC(C)(C)OC(=O)c1ccc(C#CCCO)cc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(C)(C)OC(=O)c1ccc(C#CCCO)cc1\", \"reactants\": [\"C#CCCO\", \"CC(C)(C)OC(=O)c1ccc(I)cc1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"C#CCCO\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)OC(=O)c1ccc(I)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"OTJZCIYGRUNXTP-UHFFFAOYSA-N.QHHNHUWOOFETNQ-UHFFFAOYSA-N>>BUPYFNSLTQNVOB-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"CC(C)(C)OC(=O)c1ccc(C#CCCO)cc1\", \"reactants\": [\"C#CCCO\", \"CC(C)(C)OC(=O)c1ccc(I)cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"C#CCCO\", \"results\": [{\"inchikey\": \"OTJZCIYGRUNXTP-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"C#CCCO\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CC(C)(C)OC(=O)c1ccc(I)cc1\", \"results\": [{\"inchikey\": \"QHHNHUWOOFETNQ-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CC(C)(C)OC(=O)c1ccc(I)cc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)OC(=O)c1ccc(CCCCO)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)(C)OC(=O)c1ccc(C#CCCO)cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)OC(=O)c1ccc(C#CCCO)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"C#CCCO\": \"precursor\", \"CC(C)(C)OC(=O)c1ccc(I)cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"C#CCCO\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"CC(C)(C)OC(=O)c1ccc(I)cc1\", \"in_stock\": true, \"children\": []}]}]}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"CC(C)(C)OC(=O)c1ccc(CCCCO)cc1","task_id":"retro_32945ca45923616ab086","tool_calls":6,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_32b5affddd1dc559cc57:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CC(C)(C)OC(=O)Nc1ccnc(Cl)c1C=O in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(C)(C)OC(=O)Nc1ccnc(Cl)c1C=O\", \"reactants\": [\"CC(C)(C)OC(=O)Nc1ccnc(Cl)c1\", \"CN(C)C=O\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)OC(=O)Nc1ccnc(Cl)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"CN(C)C=O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"SJCKHLJWAXGPGT-UHFFFAOYSA-N.ZMXDDKWLCZADIW-UHFFFAOYSA-N>>YNHFPXDHWTUUCL-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"CC(C)(C)OC(=O)Nc1ccnc(Cl)c1C=O\", \"reactants\": [\"CC(C)(C)OC(=O)Nc1ccnc(Cl)c1\", \"CN(C)C=O\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CC(C)(C)OC(=O)Nc1ccnc(Cl)c1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CN(C)C=O\", \"results\": [{\"inchikey\": \"ZMXDDKWLCZADIW-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CN(C)C=O\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"CC(C)(C)OC(=O)Nc1ccnc(Cl)c1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(C)(C)OC(=O)Nc1ccnc(Cl)c1\", \"reactants\": [\"CC(C)(C)OC(=O)OC(=O)OC(C)(C)C\", \"Nc1ccnc(Cl)c1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)OC(=O)OC(=O)OC(C)(C)C\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"Nc1ccnc(Cl)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"BLBDTBCGPHPIJK-UHFFFAOYSA-N.DYHSDKLCOJIUFX-UHFFFAOYSA-N>>SJCKHLJWAXGPGT-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"CC(C)(C)OC(=O)Nc1ccnc(Cl)c1\", \"reactants\": [\"CC(C)(C)OC(=O)OC(=O)OC(C)(C)C\", \"Nc1ccnc(Cl)c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CC(C)(C)OC(=O)OC(=O)OC(C)(C)C\", \"results\": [{\"inchikey\": \"DYHSDKLCOJIUFX-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CC(C)(C)OC(=O)OC(=O)OC(C)(C)C\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"Nc1ccnc(Cl)c1\", \"results\": [{\"inchikey\": \"BLBDTBCGPHPIJK-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Nc1ccnc(Cl)c1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)OC(=O)Nc1ccnc(Cl)c1C=O\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)(C)OC(=O)Nc1ccnc(Cl)c1\": \"precursor\", \"CN(C)C=O\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)OC(=O)Nc1ccnc(Cl)c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)(C)OC(=O)OC(=O)OC(C)(C)C\": \"precursor\", \"Nc1ccnc(Cl)c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)OC(=O)OC(=O)OC(C)(C)C\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"Nc1ccnc(Cl)c1\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"CN(C)C=O\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"CC(C)(C)OC(=O)Nc1ccnc(Cl)c1C=O","task_id":"retro_32b5affddd1dc559cc57","tool_calls":7,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_32e727f1e42fac2dac76:reference-expert:a0","kind":"single_route","max_steps":5,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CCOc1cccc(Nc2cc(N[C@@H]3CCCC[C@@H]3N)nnc2C(N)=O)n1 in at most 5 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCOc1cccc(Nc2cc(N[C@@H]3CCCC[C@@H]3N)nnc2C(N)=O)n1\", \"reactants\": [\"CCOc1cccc(Nc2cc(N[C@@H]3CCCC[C@@H]3NC(=O)OC(C)(C)C)nnc2C(N)=O)n1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCOc1cccc(Nc2cc(N[C@@H]3CCCC[C@@H]3NC(=O)OC(C)(C)C)nnc2C(N)=O)n1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"CFOMTRKNPRARDW-CABCVRRESA-N>>RBSCODQUYFJQIZ-NWDGAFQWSA-N\", \"model_turns_remaining\": 15, \"product\": \"CCOc1cccc(Nc2cc(N[C@@H]3CCCC[C@@H]3N)nnc2C(N)=O)n1\", \"reactants\": [\"CCOc1cccc(Nc2cc(N[C@@H]3CCCC[C@@H]3NC(=O)OC(C)(C)C)nnc2C(N)=O)n1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CCOc1cccc(Nc2cc(N[C@@H]3CCCC[C@@H]3NC(=O)OC(C)(C)C)nnc2C(N)=O)n1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"CCOc1cccc(Nc2cc(N[C@@H]3CCCC[C@@H]3NC(=O)OC(C)(C)C)nnc2C(N)=O)n1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCOc1cccc(Nc2cc(N[C@@H]3CCCC[C@@H]3NC(=O)OC(C)(C)C)nnc2C(N)=O)n1\", \"reactants\": [\"CC(C)(C)OC(=O)N[C@H]1CCCC[C@H]1N\", \"CCOc1cccc(Nc2cc(Cl)nnc2C(N)=O)n1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)OC(=O)N[C@H]1CCCC[C@H]1N\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"CCOc1cccc(Nc2cc(Cl)nnc2C(N)=O)n1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"AKVIZYGPJIWKOS-BDAKNGLRSA-N.OLAVMVUEHSFMDW-UHFFFAOYSA-N>>CFOMTRKNPRARDW-CABCVRRESA-N\", \"model_turns_remaining\": 14, \"product\": \"CCOc1cccc(Nc2cc(N[C@@H]3CCCC[C@@H]3NC(=O)OC(C)(C)C)nnc2C(N)=O)n1\", \"reactants\": [\"CC(C)(C)OC(=O)N[C@H]1CCCC[C@H]1N\", \"CCOc1cccc(Nc2cc(Cl)nnc2C(N)=O)n1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CC(C)(C)OC(=O)N[C@H]1CCCC[C@H]1N\", \"results\": [{\"inchikey\": \"AKVIZYGPJIWKOS-BDAKNGLRSA-N\", \"similarity\": 1.0, \"smiles\": \"CC(C)(C)OC(=O)N[C@H]1CCCC[C@H]1N\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CCOc1cccc(Nc2cc(Cl)nnc2C(N)=O)n1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"CCOc1cccc(Nc2cc(Cl)nnc2C(N)=O)n1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCOc1cccc(Nc2cc(Cl)nnc2C(N)=O)n1\", \"reactants\": [\"CCOC(=O)c1nnc(Cl)cc1Nc1cccc(OCC)n1\", \"N\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCOC(=O)c1nnc(Cl)cc1Nc1cccc(OCC)n1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"N\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"MBQCUUIHPKBRSI-UHFFFAOYSA-N.QGZKDVFQNNGYKY-UHFFFAOYSA-N>>OLAVMVUEHSFMDW-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"CCOc1cccc(Nc2cc(Cl)nnc2C(N)=O)n1\", \"reactants\": [\"CCOC(=O)c1nnc(Cl)cc1Nc1cccc(OCC)n1\", \"N\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"CCOC(=O)c1nnc(Cl)cc1Nc1cccc(OCC)n1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"N\", \"results\": [{\"inchikey\": \"QGZKDVFQNNGYKY-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"N\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"CCOC(=O)c1nnc(Cl)cc1Nc1cccc(OCC)n1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCOC(=O)c1nnc(Cl)cc1Nc1cccc(OCC)n1\", \"reactants\": [\"CCOC(=O)c1nnc(Cl)cc1Cl\", \"CCOc1cccc(N)n1\"]}","name":"validate_disconnection"},"id":"call_4_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCOC(=O)c1nnc(Cl)cc1Cl\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_1","type":"function"},{"function":{"arguments":"{\"query\": \"CCOc1cccc(N)n1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"MOWPWJUYSRHMHS-UHFFFAOYSA-N.VRZIITVWIJSXOA-UHFFFAOYSA-N>>MBQCUUIHPKBRSI-UHFFFAOYSA-N\", \"model_turns_remaining\": 12, \"product\": \"CCOC(=O)c1nnc(Cl)cc1Nc1cccc(OCC)n1\", \"reactants\": [\"CCOC(=O)c1nnc(Cl)cc1Cl\", \"CCOc1cccc(N)n1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_4_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"CCOC(=O)c1nnc(Cl)cc1Cl\", \"results\": [{\"inchikey\": \"MOWPWJUYSRHMHS-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CCOC(=O)c1nnc(Cl)cc1Cl\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"CCOc1cccc(N)n1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_2"},{"content":"CCOc1cccc(N)n1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCOc1cccc(N)n1\", \"reactants\": [\"CCO\", \"Nc1cccc(Cl)n1\"]}","name":"validate_disconnection"},"id":"call_5_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCO\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_5_1","type":"function"},{"function":{"arguments":"{\"query\": \"Nc1cccc(Cl)n1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_5_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"LFQSCWFLJHTTHZ-UHFFFAOYSA-N.OBYJTLDIQBWBHM-UHFFFAOYSA-N>>VRZIITVWIJSXOA-UHFFFAOYSA-N\", \"model_turns_remaining\": 11, \"product\": \"CCOc1cccc(N)n1\", \"reactants\": [\"CCO\", \"Nc1cccc(Cl)n1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_5_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 11, \"query\": \"CCO\", \"results\": [{\"inchikey\": \"LFQSCWFLJHTTHZ-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CCO\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_5_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 11, \"query\": \"Nc1cccc(Cl)n1\", \"results\": [{\"inchikey\": \"OBYJTLDIQBWBHM-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Nc1cccc(Cl)n1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_5_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CCOc1cccc(Nc2cc(N[C@@H]3CCCC[C@@H]3N)nnc2C(N)=O)n1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCOc1cccc(Nc2cc(N[C@@H]3CCCC[C@@H]3NC(=O)OC(C)(C)C)nnc2C(N)=O)n1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCOc1cccc(Nc2cc(N[C@@H]3CCCC[C@@H]3NC(=O)OC(C)(C)C)nnc2C(N)=O)n1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)(C)OC(=O)N[C@H]1CCCC[C@H]1N\": \"precursor\", \"CCOc1cccc(Nc2cc(Cl)nnc2C(N)=O)n1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)OC(=O)N[C@H]1CCCC[C@H]1N\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"CCOc1cccc(Nc2cc(Cl)nnc2C(N)=O)n1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCOC(=O)c1nnc(Cl)cc1Nc1cccc(OCC)n1\": \"precursor\", \"N\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCOC(=O)c1nnc(Cl)cc1Nc1cccc(OCC)n1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCOC(=O)c1nnc(Cl)cc1Cl\": \"precursor\", \"CCOc1cccc(N)n1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCOC(=O)c1nnc(Cl)cc1Cl\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"CCOc1cccc(N)n1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCO\": \"precursor\", \"Nc1cccc(Cl)n1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCO\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"Nc1cccc(Cl)n1\", \"in_stock\": true, \"children\": []}]}]}]}]}, {\"type\": \"mol\", \"smiles\": \"N\", \"in_stock\": true, \"children\": []}]}]}]}]}]}]}]}}","name":"emit_routes"},"id":"call_6_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"CCOc1cccc(Nc2cc(N[C@@H]3CCCC[C@@H]3N)nnc2C(N)=O)n1","task_id":"retro_32e727f1e42fac2dac76","tool_calls":15,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":6}
{"exact_match":true,"id":"retro_344492892fc3d4cb20a9:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CC[C@@H]1C[C@H](NC(C)=O)C[C@@H]1C(=O)NNc1cnc2c(ccn2S(=O)(=O)c2ccc(C)cc2)n1 in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC[C@@H]1C[C@H](NC(C)=O)C[C@@H]1C(=O)NNc1cnc2c(ccn2S(=O)(=O)c2ccc(C)cc2)n1\", \"reactants\": [\"CC[C@@H]1C[C@H](NC(C)=O)C[C@@H]1C(=O)O\", \"Cc1ccc(S(=O)(=O)n2ccc3nc(NN)cnc32)cc1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC[C@@H]1C[C@H](NC(C)=O)C[C@@H]1C(=O)O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"Cc1ccc(S(=O)(=O)n2ccc3nc(NN)cnc32)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"CLQQMOFYVSCEJZ-UHFFFAOYSA-N.LHOZEVPCFZRGAU-VGMNWLOBSA-N>>GQVQRCRXRSVYEC-AOIWGVFYSA-N\", \"model_turns_remaining\": 15, \"product\": \"CC[C@@H]1C[C@H](NC(C)=O)C[C@@H]1C(=O)NNc1cnc2c(ccn2S(=O)(=O)c2ccc(C)cc2)n1\", \"reactants\": [\"CC[C@@H]1C[C@H](NC(C)=O)C[C@@H]1C(=O)O\", \"Cc1ccc(S(=O)(=O)n2ccc3nc(NN)cnc32)cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CC[C@@H]1C[C@H](NC(C)=O)C[C@@H]1C(=O)O\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"Cc1ccc(S(=O)(=O)n2ccc3nc(NN)cnc32)cc1\", \"results\": [{\"inchikey\": \"CLQQMOFYVSCEJZ-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Cc1ccc(S(=O)(=O)n2ccc3nc(NN)cnc32)cc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"CC[C@@H]1C[C@H](NC(C)=O)C[C@@H]1C(=O)O was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC[C@@H]1C[C@H](NC(C)=O)C[C@@H]1C(=O)O\", \"reactants\": [\"CCOC(=O)[C@H]1C[C@@H](NC(C)=O)C[C@H]1CC\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCOC(=O)[C@H]1C[C@@H](NC(C)=O)C[C@H]1CC\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"JOMMQSXKIQIBQH-VWYCJHECSA-N>>LHOZEVPCFZRGAU-VGMNWLOBSA-N\", \"model_turns_remaining\": 14, \"product\": \"CC[C@@H]1C[C@H](NC(C)=O)C[C@@H]1C(=O)O\", \"reactants\": [\"CCOC(=O)[C@H]1C[C@@H](NC(C)=O)C[C@H]1CC\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CCOC(=O)[C@H]1C[C@@H](NC(C)=O)C[C@H]1CC\", \"results\": [{\"inchikey\": \"JOMMQSXKIQIBQH-VWYCJHECSA-N\", \"similarity\": 1.0, \"smiles\": \"CCOC(=O)[C@H]1C[C@@H](NC(C)=O)C[C@H]1CC\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CC[C@@H]1C[C@H](NC(C)=O)C[C@@H]1C(=O)NNc1cnc2c(ccn2S(=O)(=O)c2ccc(C)cc2)n1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC[C@@H]1C[C@H](NC(C)=O)C[C@@H]1C(=O)O\": \"precursor\", \"Cc1ccc(S(=O)(=O)n2ccc3nc(NN)cnc32)cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC[C@@H]1C[C@H](NC(C)=O)C[C@@H]1C(=O)O\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCOC(=O)[C@H]1C[C@@H](NC(C)=O)C[C@H]1CC\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCOC(=O)[C@H]1C[C@@H](NC(C)=O)C[C@H]1CC\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"Cc1ccc(S(=O)(=O)n2ccc3nc(NN)cnc32)cc1\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"CC[C@@H]1C[C@H](NC(C)=O)C[C@@H]1C(=O)NNc1cnc2c(ccn2S(=O)(=O)c2ccc(C)cc2)n1","task_id":"retro_344492892fc3d4cb20a9","tool_calls":6,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_3576a41d867518fc5512:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target O=CC1CCCN(CCOc2ccccc2)C1 in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"O=CC1CCCN(CCOc2ccccc2)C1\", \"reactants\": [\"CCOC(=O)C1CCCN(CCOc2ccccc2)C1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCOC(=O)C1CCCN(CCOc2ccccc2)C1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"GMBZVLWEYIAFSY-UHFFFAOYSA-N>>NVYJBJSYMURZBV-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"O=CC1CCCN(CCOc2ccccc2)C1\", \"reactants\": [\"CCOC(=O)C1CCCN(CCOc2ccccc2)C1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CCOC(=O)C1CCCN(CCOc2ccccc2)C1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"CCOC(=O)C1CCCN(CCOc2ccccc2)C1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCOC(=O)C1CCCN(CCOc2ccccc2)C1\", \"reactants\": [\"BrCCOc1ccccc1\", \"CCOC(=O)C1CCCNC1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"BrCCOc1ccccc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"CCOC(=O)C1CCCNC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"JJFOBACUIRKUPN-UHFFFAOYSA-N.XIWBSOUNZWSFKU-UHFFFAOYSA-N>>GMBZVLWEYIAFSY-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"CCOC(=O)C1CCCN(CCOc2ccccc2)C1\", \"reactants\": [\"BrCCOc1ccccc1\", \"CCOC(=O)C1CCCNC1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"BrCCOc1ccccc1\", \"results\": [{\"inchikey\": \"JJFOBACUIRKUPN-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"BrCCOc1ccccc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CCOC(=O)C1CCCNC1\", \"results\": [{\"inchikey\": \"XIWBSOUNZWSFKU-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CCOC(=O)C1CCCNC1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"O=CC1CCCN(CCOc2ccccc2)C1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCOC(=O)C1CCCN(CCOc2ccccc2)C1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCOC(=O)C1CCCN(CCOc2ccccc2)C1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"BrCCOc1ccccc1\": \"precursor\", \"CCOC(=O)C1CCCNC1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"BrCCOc1ccccc1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"CCOC(=O)C1CCCNC1\", \"in_stock\": true, \"children\": []}]}]}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"O=CC1CCCN(CCOc2ccccc2)C1","task_id":"retro_3576a41d867518fc5512","tool_calls":6,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_35b67c61b30cda639318:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target C=CCC(CO)c1ccccc1 in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"C=CCC(CO)c1ccccc1\", \"reactants\": [\"C=CCC(C(=O)OCC)c1ccccc1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"C=CCC(C(=O)OCC)c1ccccc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"UVIIDCMCSMXQGO-UHFFFAOYSA-N>>YZQOZSHPDOZAGU-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"C=CCC(CO)c1ccccc1\", \"reactants\": [\"C=CCC(C(=O)OCC)c1ccccc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"C=CCC(C(=O)OCC)c1ccccc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"C=CCC(C(=O)OCC)c1ccccc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"C=CCC(C(=O)OCC)c1ccccc1\", \"reactants\": [\"C=CCC(C#N)c1ccccc1\", \"CCO\", \"O=S(=O)(O)O\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"C=CCC(C#N)c1ccccc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"CCO\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"},{"function":{"arguments":"{\"query\": \"O=S(=O)(O)O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_3","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"LFQSCWFLJHTTHZ-UHFFFAOYSA-N.QAOWNCQODCNURD-UHFFFAOYSA-N.UPGWWAVLPCHBAC-UHFFFAOYSA-N>>UVIIDCMCSMXQGO-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"C=CCC(C(=O)OCC)c1ccccc1\", \"reactants\": [\"C=CCC(C#N)c1ccccc1\", \"CCO\", \"O=S(=O)(O)O\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"C=CCC(C#N)c1ccccc1\", \"results\": [{\"inchikey\": \"UPGWWAVLPCHBAC-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"C=CCC(C#N)c1ccccc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CCO\", \"results\": [{\"inchikey\": \"LFQSCWFLJHTTHZ-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CCO\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"O=S(=O)(O)O\", \"results\": [{\"inchikey\": \"QAOWNCQODCNURD-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=S(=O)(O)O\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_3"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"C=CCC(CO)c1ccccc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"C=CCC(C(=O)OCC)c1ccccc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"C=CCC(C(=O)OCC)c1ccccc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"C=CCC(C#N)c1ccccc1\": \"precursor\", \"CCO\": \"precursor\", \"O=S(=O)(O)O\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"C=CCC(C#N)c1ccccc1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"CCO\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=S(=O)(O)O\", \"in_stock\": true, \"children\": []}]}]}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"C=CCC(CO)c1ccccc1","task_id":"retro_35b67c61b30cda639318","tool_calls":7,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_379b3e3e1bdd2974c4fd:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target Fc1ccc(OC[C@@H]2CC[C@H]3CN(c4ccc(Cl)nn4)CCN3C2)cc1 in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Fc1ccc(OC[C@@H]2CC[C@H]3CN(c4ccc(Cl)nn4)CCN3C2)cc1\", \"reactants\": [\"Clc1ccc(Cl)nn1\", \"Fc1ccc(OC[C@@H]2CC[C@H]3CNCCN3C2)cc1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"Clc1ccc(Cl)nn1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"Fc1ccc(OC[C@@H]2CC[C@H]3CNCCN3C2)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"GOZHDJSDJOBSNX-OCCSQVGLSA-N.GUSWJGOYDXFJSI-UHFFFAOYSA-N>>QMPHXAJBGDGFLK-ZBFHGGJFSA-N\", \"model_turns_remaining\": 15, \"product\": \"Fc1ccc(OC[C@@H]2CC[C@H]3CN(c4ccc(Cl)nn4)CCN3C2)cc1\", \"reactants\": [\"Clc1ccc(Cl)nn1\", \"Fc1ccc(OC[C@@H]2CC[C@H]3CNCCN3C2)cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"Clc1ccc(Cl)nn1\", \"results\": [{\"inchikey\": \"GUSWJGOYDXFJSI-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Clc1ccc(Cl)nn1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"Fc1ccc(OC[C@@H]2CC[C@H]3CNCCN3C2)cc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"Fc1ccc(OC[C@@H]2CC[C@H]3CNCCN3C2)cc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Fc1ccc(OC[C@@H]2CC[C@H]3CNCCN3C2)cc1\", \"reactants\": [\"CC(C)(C)OC(=O)N1CCN2C[C@H](COc3ccc(F)cc3)CC[C@H]2C1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)OC(=O)N1CCN2C[C@H](COc3ccc(F)cc3)CC[C@H]2C1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"MLWBXVYVVUSYKA-WBVHZDCISA-N>>GOZHDJSDJOBSNX-OCCSQVGLSA-N\", \"model_turns_remaining\": 14, \"product\": \"Fc1ccc(OC[C@@H]2CC[C@H]3CNCCN3C2)cc1\", \"reactants\": [\"CC(C)(C)OC(=O)N1CCN2C[C@H](COc3ccc(F)cc3)CC[C@H]2C1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CC(C)(C)OC(=O)N1CCN2C[C@H](COc3ccc(F)cc3)CC[C@H]2C1\", \"results\": [{\"inchikey\": \"MLWBXVYVVUSYKA-WBVHZDCISA-N\", \"similarity\": 1.0, \"smiles\": \"CC(C)(C)OC(=O)N1CCN2C[C@H](COc3ccc(F)cc3)CC[C@H]2C1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"Fc1ccc(OC[C@@H]2CC[C@H]3CN(c4ccc(Cl)nn4)CCN3C2)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"Clc1ccc(Cl)nn1\": \"precursor\", \"Fc1ccc(OC[C@@H]2CC[C@H]3CNCCN3C2)cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"Clc1ccc(Cl)nn1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"Fc1ccc(OC[C@@H]2CC[C@H]3CNCCN3C2)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)(C)OC(=O)N1CCN2C[C@H](COc3ccc(F)cc3)CC[C@H]2C1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)OC(=O)N1CCN2C[C@H](COc3ccc(F)cc3)CC[C@H]2C1\", \"in_stock\": true, \"children\": []}]}]}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"Fc1ccc(OC[C@@H]2CC[C@H]3CN(c4ccc(Cl)nn4)CCN3C2)cc1","task_id":"retro_379b3e3e1bdd2974c4fd","tool_calls":6,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_39776d62a7ea4cc07f8c:reference-expert:a0","kind":"single_route","max_steps":3,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target O=C(Nc1cc(F)ccc1N1CCCCC1)c1ccncc1 in at most 3 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"O=C(Nc1cc(F)ccc1N1CCCCC1)c1ccncc1\", \"reactants\": [\"Nc1cc(F)ccc1N1CCCCC1\", \"O=C(Cl)c1ccncc1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"Nc1cc(F)ccc1N1CCCCC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=C(Cl)c1ccncc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"CCSBEAVDBGCSOQ-UHFFFAOYSA-N.RVQZKNOMKUSGCI-UHFFFAOYSA-N>>LRLTZGIZRIKVOC-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"O=C(Nc1cc(F)ccc1N1CCCCC1)c1ccncc1\", \"reactants\": [\"Nc1cc(F)ccc1N1CCCCC1\", \"O=C(Cl)c1ccncc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"Nc1cc(F)ccc1N1CCCCC1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"O=C(Cl)c1ccncc1\", \"results\": [{\"inchikey\": \"RVQZKNOMKUSGCI-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=C(Cl)c1ccncc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"Nc1cc(F)ccc1N1CCCCC1 was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Nc1cc(F)ccc1N1CCCCC1\", \"reactants\": [\"O=[N+]([O-])c1cc(F)ccc1N1CCCCC1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"O=[N+]([O-])c1cc(F)ccc1N1CCCCC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"YSBDMNNCMGUEAL-UHFFFAOYSA-N>>CCSBEAVDBGCSOQ-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"Nc1cc(F)ccc1N1CCCCC1\", \"reactants\": [\"O=[N+]([O-])c1cc(F)ccc1N1CCCCC1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"O=[N+]([O-])c1cc(F)ccc1N1CCCCC1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"O=[N+]([O-])c1cc(F)ccc1N1CCCCC1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"O=[N+]([O-])c1cc(F)ccc1N1CCCCC1\", \"reactants\": [\"C1CCNCC1\", \"O=[N+]([O-])c1cc(F)ccc1F\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"C1CCNCC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=[N+]([O-])c1cc(F)ccc1F\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"NQRYJNQNLNOLGT-UHFFFAOYSA-N.XNJAYQHWXYJBBD-UHFFFAOYSA-N>>YSBDMNNCMGUEAL-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"O=[N+]([O-])c1cc(F)ccc1N1CCCCC1\", \"reactants\": [\"C1CCNCC1\", \"O=[N+]([O-])c1cc(F)ccc1F\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"C1CCNCC1\", \"results\": [{\"inchikey\": \"NQRYJNQNLNOLGT-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"C1CCNCC1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"O=[N+]([O-])c1cc(F)ccc1F\", \"results\": [{\"inchikey\": \"XNJAYQHWXYJBBD-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=[N+]([O-])c1cc(F)ccc1F\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"O=C(Nc1cc(F)ccc1N1CCCCC1)c1ccncc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"Nc1cc(F)ccc1N1CCCCC1\": \"precursor\", \"O=C(Cl)c1ccncc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"Nc1cc(F)ccc1N1CCCCC1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"O=[N+]([O-])c1cc(F)ccc1N1CCCCC1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"O=[N+]([O-])c1cc(F)ccc1N1CCCCC1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"C1CCNCC1\": \"precursor\", \"O=[N+]([O-])c1cc(F)ccc1F\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"C1CCNCC1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=[N+]([O-])c1cc(F)ccc1F\", \"in_stock\": true, \"children\": []}]}]}]}]}, {\"type\": \"mol\", \"smiles\": \"O=C(Cl)c1ccncc1\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_4_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"O=C(Nc1cc(F)ccc1N1CCCCC1)c1ccncc1","task_id":"retro_39776d62a7ea4cc07f8c","tool_calls":9,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":4}
{"exact_match":true,"id":"retro_3ba4d0fef506e88f0f32:reference-expert:a0","kind":"single_route","max_steps":3,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CC(C)(C)[Si](C)(C)O[C@H]1CC[C@H](Nc2c(N)cnc3c2ccn3S(=O)(=O)c2ccccc2)CC1 in at most 3 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(C)(C)[Si](C)(C)O[C@H]1CC[C@H](Nc2c(N)cnc3c2ccn3S(=O)(=O)c2ccccc2)CC1\", \"reactants\": [\"CC(C)(C)[Si](C)(C)OS(=O)(=O)C(F)(F)F\", \"Nc1cnc2c(ccn2S(=O)(=O)c2ccccc2)c1N[C@H]1CC[C@H](O)CC1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)[Si](C)(C)OS(=O)(=O)C(F)(F)F\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"Nc1cnc2c(ccn2S(=O)(=O)c2ccccc2)c1N[C@H]1CC[C@H](O)CC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"CUZSLXWWYCSXAP-HDJSIYSDSA-N.WLLIXJBWWFGEHT-UHFFFAOYSA-N>>BXJMMTWMCXZUFJ-WGSAOQKQSA-N\", \"model_turns_remaining\": 15, \"product\": \"CC(C)(C)[Si](C)(C)O[C@H]1CC[C@H](Nc2c(N)cnc3c2ccn3S(=O)(=O)c2ccccc2)CC1\", \"reactants\": [\"CC(C)(C)[Si](C)(C)OS(=O)(=O)C(F)(F)F\", \"Nc1cnc2c(ccn2S(=O)(=O)c2ccccc2)c1N[C@H]1CC[C@H](O)CC1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CC(C)(C)[Si](C)(C)OS(=O)(=O)C(F)(F)F\", \"results\": [{\"inchikey\": \"WLLIXJBWWFGEHT-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CC(C)(C)[Si](C)(C)OS(=O)(=O)C(F)(F)F\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"Nc1cnc2c(ccn2S(=O)(=O)c2ccccc2)c1N[C@H]1CC[C@H](O)CC1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"Nc1cnc2c(ccn2S(=O)(=O)c2ccccc2)c1N[C@H]1CC[C@H](O)CC1 was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Nc1cnc2c(ccn2S(=O)(=O)c2ccccc2)c1N[C@H]1CC[C@H](O)CC1\", \"reactants\": [\"O=[N+]([O-])c1cnc2c(ccn2S(=O)(=O)c2ccccc2)c1N[C@H]1CC[C@H](O)CC1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"O=[N+]([O-])c1cnc2c(ccn2S(=O)(=O)c2ccccc2)c1N[C@H]1CC[C@H](O)CC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"DXRVKMYVWXEJSQ-HDJSIYSDSA-N>>CUZSLXWWYCSXAP-HDJSIYSDSA-N\", \"model_turns_remaining\": 14, \"product\": \"Nc1cnc2c(ccn2S(=O)(=O)c2ccccc2)c1N[C@H]1CC[C@H](O)CC1\", \"reactants\": [\"O=[N+]([O-])c1cnc2c(ccn2S(=O)(=O)c2ccccc2)c1N[C@H]1CC[C@H](O)CC1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"O=[N+]([O-])c1cnc2c(ccn2S(=O)(=O)c2ccccc2)c1N[C@H]1CC[C@H](O)CC1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"O=[N+]([O-])c1cnc2c(ccn2S(=O)(=O)c2ccccc2)c1N[C@H]1CC[C@H](O)CC1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"O=[N+]([O-])c1cnc2c(ccn2S(=O)(=O)c2ccccc2)c1N[C@H]1CC[C@H](O)CC1\", \"reactants\": [\"N[C@H]1CC[C@H](O)CC1\", \"O=[N+]([O-])c1cnc2c(ccn2S(=O)(=O)c2ccccc2)c1Cl\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"N[C@H]1CC[C@H](O)CC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=[N+]([O-])c1cnc2c(ccn2S(=O)(=O)c2ccccc2)c1Cl\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"IMLXLGZJLAOKJN-IZLXSQMJSA-N.VDNRYINHXTYMIT-UHFFFAOYSA-N>>DXRVKMYVWXEJSQ-HDJSIYSDSA-N\", \"model_turns_remaining\": 13, \"product\": \"O=[N+]([O-])c1cnc2c(ccn2S(=O)(=O)c2ccccc2)c1N[C@H]1CC[C@H](O)CC1\", \"reactants\": [\"N[C@H]1CC[C@H](O)CC1\", \"O=[N+]([O-])c1cnc2c(ccn2S(=O)(=O)c2ccccc2)c1Cl\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"N[C@H]1CC[C@H](O)CC1\", \"results\": [{\"inchikey\": \"IMLXLGZJLAOKJN-IZLXSQMJSA-N\", \"similarity\": 1.0, \"smiles\": \"N[C@H]1CC[C@H](O)CC1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"O=[N+]([O-])c1cnc2c(ccn2S(=O)(=O)c2ccccc2)c1Cl\", \"results\": [{\"inchikey\": \"VDNRYINHXTYMIT-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=[N+]([O-])c1cnc2c(ccn2S(=O)(=O)c2ccccc2)c1Cl\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)[Si](C)(C)O[C@H]1CC[C@H](Nc2c(N)cnc3c2ccn3S(=O)(=O)c2ccccc2)CC1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)(C)[Si](C)(C)OS(=O)(=O)C(F)(F)F\": \"precursor\", \"Nc1cnc2c(ccn2S(=O)(=O)c2ccccc2)c1N[C@H]1CC[C@H](O)CC1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)[Si](C)(C)OS(=O)(=O)C(F)(F)F\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"Nc1cnc2c(ccn2S(=O)(=O)c2ccccc2)c1N[C@H]1CC[C@H](O)CC1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"O=[N+]([O-])c1cnc2c(ccn2S(=O)(=O)c2ccccc2)c1N[C@H]1CC[C@H](O)CC1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"O=[N+]([O-])c1cnc2c(ccn2S(=O)(=O)c2ccccc2)c1N[C@H]1CC[C@H](O)CC1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"N[C@H]1CC[C@H](O)CC1\": \"precursor\", \"O=[N+]([O-])c1cnc2c(ccn2S(=O)(=O)c2ccccc2)c1Cl\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"N[C@H]1CC[C@H](O)CC1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=[N+]([O-])c1cnc2c(ccn2S(=O)(=O)c2ccccc2)c1Cl\", \"in_stock\": true, \"children\": []}]}]}]}]}]}]}]}}","name":"emit_routes"},"id":"call_4_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"CC(C)(C)[Si](C)(C)O[C@H]1CC[C@H](Nc2c(N)cnc3c2ccn3S(=O)(=O)c2ccccc2)CC1","task_id":"retro_3ba4d0fef506e88f0f32","tool_calls":9,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":4}
{"exact_match":true,"id":"retro_3c5d789efd85bd632dc0:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target O=C1CNc2nc(Cl)ccc2N1 in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"O=C1CNc2nc(Cl)ccc2N1\", \"reactants\": [\"COC(=O)CNc1nc(Cl)ccc1[N+](=O)[O-]\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"COC(=O)CNc1nc(Cl)ccc1[N+](=O)[O-]\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"BDTYRYFAISJXMY-UHFFFAOYSA-N>>PVPSHOHSPGMOLI-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"O=C1CNc2nc(Cl)ccc2N1\", \"reactants\": [\"COC(=O)CNc1nc(Cl)ccc1[N+](=O)[O-]\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"COC(=O)CNc1nc(Cl)ccc1[N+](=O)[O-]\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"COC(=O)CNc1nc(Cl)ccc1[N+](=O)[O-] was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COC(=O)CNc1nc(Cl)ccc1[N+](=O)[O-]\", \"reactants\": [\"COC(=O)CN\", \"O=[N+]([O-])c1ccc(Cl)nc1Cl\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"COC(=O)CN\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=[N+]([O-])c1ccc(Cl)nc1Cl\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"KQSSATDQUYCRGS-UHFFFAOYSA-N.SHCWQWRTKPNTEM-UHFFFAOYSA-N>>BDTYRYFAISJXMY-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"COC(=O)CNc1nc(Cl)ccc1[N+](=O)[O-]\", \"reactants\": [\"COC(=O)CN\", \"O=[N+]([O-])c1ccc(Cl)nc1Cl\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"COC(=O)CN\", \"results\": [{\"inchikey\": \"KQSSATDQUYCRGS-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"COC(=O)CN\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"O=[N+]([O-])c1ccc(Cl)nc1Cl\", \"results\": [{\"inchikey\": \"SHCWQWRTKPNTEM-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=[N+]([O-])c1ccc(Cl)nc1Cl\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"O=C1CNc2nc(Cl)ccc2N1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COC(=O)CNc1nc(Cl)ccc1[N+](=O)[O-]\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COC(=O)CNc1nc(Cl)ccc1[N+](=O)[O-]\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COC(=O)CN\": \"precursor\", \"O=[N+]([O-])c1ccc(Cl)nc1Cl\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COC(=O)CN\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=[N+]([O-])c1ccc(Cl)nc1Cl\", \"in_stock\": true, \"children\": []}]}]}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"O=C1CNc2nc(Cl)ccc2N1","task_id":"retro_3c5d789efd85bd632dc0","tool_calls":6,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_3df5347155e45f2b50ca:reference-expert:a0","kind":"single_route","max_steps":3,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CN(C)CCOc1nc(-c2ccccc2C(F)(F)F)cc2nc(-c3c(Cl)c(C(C)(C)C)nn3C)[nH]c12 in at most 3 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CN(C)CCOc1nc(-c2ccccc2C(F)(F)F)cc2nc(-c3c(Cl)c(C(C)(C)C)nn3C)[nH]c12\", \"reactants\": [\"CNC\", \"Cn1nc(C(C)(C)C)c(Cl)c1-c1nc2cc(-c3ccccc3C(F)(F)F)nc(OCC=O)c2[nH]1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CNC\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"Cn1nc(C(C)(C)C)c(Cl)c1-c1nc2cc(-c3ccccc3C(F)(F)F)nc(OCC=O)c2[nH]1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"CQVBZVGYCWUILZ-UHFFFAOYSA-N.ROSDSFDQCJNGOL-UHFFFAOYSA-N>>KONOROVOTNCQLF-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"CN(C)CCOc1nc(-c2ccccc2C(F)(F)F)cc2nc(-c3c(Cl)c(C(C)(C)C)nn3C)[nH]c12\", \"reactants\": [\"CNC\", \"Cn1nc(C(C)(C)C)c(Cl)c1-c1nc2cc(-c3ccccc3C(F)(F)F)nc(OCC=O)c2[nH]1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CNC\", \"results\": [{\"inchikey\": \"ROSDSFDQCJNGOL-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CNC\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"Cn1nc(C(C)(C)C)c(Cl)c1-c1nc2cc(-c3ccccc3C(F)(F)F)nc(OCC=O)c2[nH]1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"Cn1nc(C(C)(C)C)c(Cl)c1-c1nc2cc(-c3ccccc3C(F)(F)F)nc(OCC=O)c2[nH]1 was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Cn1nc(C(C)(C)C)c(Cl)c1-c1nc2cc(-c3ccccc3C(F)(F)F)nc(OCC=O)c2[nH]1\", \"reactants\": [\"Cn1nc(C(C)(C)C)c(Cl)c1-c1nc2cc(-c3ccccc3C(F)(F)F)nc(OCCO)c2[nH]1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"Cn1nc(C(C)(C)C)c(Cl)c1-c1nc2cc(-c3ccccc3C(F)(F)F)nc(OCCO)c2[nH]1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_complete\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"BGTPZTXCQSEPJR-UHFFFAOYSA-N>>CQVBZVGYCWUILZ-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"Cn1nc(C(C)(C)C)c(Cl)c1-c1nc2cc(-c3ccccc3C(F)(F)F)nc(OCC=O)c2[nH]1\", \"reactants\": [\"Cn1nc(C(C)(C)C)c(Cl)c1-c1nc2cc(-c3ccccc3C(F)(F)F)nc(OCCO)c2[nH]1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"Cn1nc(C(C)(C)C)c(Cl)c1-c1nc2cc(-c3ccccc3C(F)(F)F)nc(OCCO)c2[nH]1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"Cn1nc(C(C)(C)C)c(Cl)c1-c1nc2cc(-c3ccccc3C(F)(F)F)nc(OCCO)c2[nH]1 was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Cn1nc(C(C)(C)C)c(Cl)c1-c1nc2cc(-c3ccccc3C(F)(F)F)nc(OCCO)c2[nH]1\", \"reactants\": [\"Cn1nc(C(C)(C)C)c(Cl)c1-c1nc2cc(-c3ccccc3C(F)(F)F)nc(OCCO[Si](C)(C)C(C)(C)C)c2[nH]1\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"Cn1nc(C(C)(C)C)c(Cl)c1-c1nc2cc(-c3ccccc3C(F)(F)F)nc(OCCO[Si](C)(C)C(C)(C)C)c2[nH]1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"GWBBZFRMWSXZBB-UHFFFAOYSA-N>>BGTPZTXCQSEPJR-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"Cn1nc(C(C)(C)C)c(Cl)c1-c1nc2cc(-c3ccccc3C(F)(F)F)nc(OCCO)c2[nH]1\", \"reactants\": [\"Cn1nc(C(C)(C)C)c(Cl)c1-c1nc2cc(-c3ccccc3C(F)(F)F)nc(OCCO[Si](C)(C)C(C)(C)C)c2[nH]1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"Cn1nc(C(C)(C)C)c(Cl)c1-c1nc2cc(-c3ccccc3C(F)(F)F)nc(OCCO[Si](C)(C)C(C)(C)C)c2[nH]1\", \"results\": [{\"inchikey\": \"GWBBZFRMWSXZBB-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Cn1nc(C(C)(C)C)c(Cl)c1-c1nc2cc(-c3ccccc3C(F)(F)F)nc(OCCO[Si](C)(C)C(C)(C)C)c2[nH]1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CN(C)CCOc1nc(-c2ccccc2C(F)(F)F)cc2nc(-c3c(Cl)c(C(C)(C)C)nn3C)[nH]c12\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CNC\": \"precursor\", \"Cn1nc(C(C)(C)C)c(Cl)c1-c1nc2cc(-c3ccccc3C(F)(F)F)nc(OCC=O)c2[nH]1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CNC\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"Cn1nc(C(C)(C)C)c(Cl)c1-c1nc2cc(-c3ccccc3C(F)(F)F)nc(OCC=O)c2[nH]1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"Cn1nc(C(C)(C)C)c(Cl)c1-c1nc2cc(-c3ccccc3C(F)(F)F)nc(OCCO)c2[nH]1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"Cn1nc(C(C)(C)C)c(Cl)c1-c1nc2cc(-c3ccccc3C(F)(F)F)nc(OCCO)c2[nH]1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"Cn1nc(C(C)(C)C)c(Cl)c1-c1nc2cc(-c3ccccc3C(F)(F)F)nc(OCCO[Si](C)(C)C(C)(C)C)c2[nH]1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"Cn1nc(C(C)(C)C)c(Cl)c1-c1nc2cc(-c3ccccc3C(F)(F)F)nc(OCCO[Si](C)(C)C(C)(C)C)c2[nH]1\", \"in_stock\": true, \"children\": []}]}]}]}]}]}]}]}}","name":"emit_routes"},"id":"call_4_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"CN(C)CCOc1nc(-c2ccccc2C(F)(F)F)cc2nc(-c3c(Cl)c(C(C)(C)C)nn3C)[nH]c12","task_id":"retro_3df5347155e45f2b50ca","tool_calls":8,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":4}
{"exact_match":true,"id":"retro_3f34d4eae34a6498325c:reference-expert:a0","kind":"single_route","max_steps":3,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target COc1ccc(Cn2cnc3c(-c4ccco4)nc(I)nc32)cc1 in at most 3 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COc1ccc(Cn2cnc3c(-c4ccco4)nc(I)nc32)cc1\", \"reactants\": [\"COc1ccc(Cn2cnc3c(-c4ccco4)nc(N)nc32)cc1\", \"ICI\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"COc1ccc(Cn2cnc3c(-c4ccco4)nc(N)nc32)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"ICI\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"LCUMBBXSKKIJQK-UHFFFAOYSA-N.NZZFYRREKKOMAT-UHFFFAOYSA-N>>GUDKXSDAJRCSRC-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"COc1ccc(Cn2cnc3c(-c4ccco4)nc(I)nc32)cc1\", \"reactants\": [\"COc1ccc(Cn2cnc3c(-c4ccco4)nc(N)nc32)cc1\", \"ICI\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"COc1ccc(Cn2cnc3c(-c4ccco4)nc(N)nc32)cc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"ICI\", \"results\": [{\"inchikey\": \"NZZFYRREKKOMAT-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"ICI\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"COc1ccc(Cn2cnc3c(-c4ccco4)nc(N)nc32)cc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COc1ccc(Cn2cnc3c(-c4ccco4)nc(N)nc32)cc1\", \"reactants\": [\"CCC[CH2][Sn]([CH2]CCC)([CH2]CCC)[c]1ccco1\", \"COc1ccc(Cn2cnc3c(Cl)nc(N)nc32)cc1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCC[CH2][Sn]([CH2]CCC)([CH2]CCC)[c]1ccco1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"COc1ccc(Cn2cnc3c(Cl)nc(N)nc32)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"LEXCEQVTQKBTBX-UHFFFAOYSA-N.SANWDQJIWZEKOD-UHFFFAOYSA-N>>LCUMBBXSKKIJQK-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"COc1ccc(Cn2cnc3c(-c4ccco4)nc(N)nc32)cc1\", \"reactants\": [\"CCC[CH2][Sn]([CH2]CCC)([CH2]CCC)[c]1ccco1\", \"COc1ccc(Cn2cnc3c(Cl)nc(N)nc32)cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CCC[CH2][Sn]([CH2]CCC)([CH2]CCC)[c]1ccco1\", \"results\": [{\"inchikey\": \"SANWDQJIWZEKOD-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CCC[CH2][Sn]([CH2]CCC)([CH2]CCC)[c]1ccco1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"COc1ccc(Cn2cnc3c(Cl)nc(N)nc32)cc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"COc1ccc(Cn2cnc3c(Cl)nc(N)nc32)cc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COc1ccc(Cn2cnc3c(Cl)nc(N)nc32)cc1\", \"reactants\": [\"COc1ccc(CCl)cc1\", \"Nc1nc(Cl)c2nc[nH]c2n1\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"COc1ccc(CCl)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"Nc1nc(Cl)c2nc[nH]c2n1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"MOHYOXXOKFQHDC-UHFFFAOYSA-N.RYYIULNRIVUMTQ-UHFFFAOYSA-N>>LEXCEQVTQKBTBX-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"COc1ccc(Cn2cnc3c(Cl)nc(N)nc32)cc1\", \"reactants\": [\"COc1ccc(CCl)cc1\", \"Nc1nc(Cl)c2nc[nH]c2n1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"COc1ccc(CCl)cc1\", \"results\": [{\"inchikey\": \"MOHYOXXOKFQHDC-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"COc1ccc(CCl)cc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"Nc1nc(Cl)c2nc[nH]c2n1\", \"results\": [{\"inchikey\": \"RYYIULNRIVUMTQ-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Nc1nc(Cl)c2nc[nH]c2n1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"COc1ccc(Cn2cnc3c(-c4ccco4)nc(I)nc32)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COc1ccc(Cn2cnc3c(-c4ccco4)nc(N)nc32)cc1\": \"precursor\", \"ICI\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COc1ccc(Cn2cnc3c(-c4ccco4)nc(N)nc32)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCC[CH2][Sn]([CH2]CCC)([CH2]CCC)[c]1ccco1\": \"precursor\", \"COc1ccc(Cn2cnc3c(Cl)nc(N)nc32)cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCC[CH2][Sn]([CH2]CCC)([CH2]CCC)[c]1ccco1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"COc1ccc(Cn2cnc3c(Cl)nc(N)nc32)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COc1ccc(CCl)cc1\": \"precursor\", \"Nc1nc(Cl)c2nc[nH]c2n1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COc1ccc(CCl)cc1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"Nc1nc(Cl)c2nc[nH]c2n1\", \"in_stock\": true, \"children\": []}]}]}]}]}, {\"type\": \"mol\", \"smiles\": \"ICI\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_4_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"COc1ccc(Cn2cnc3c(-c4ccco4)nc(I)nc32)cc1","task_id":"retro_3f34d4eae34a6498325c","tool_calls":10,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":4}
{"exact_match":true,"id":"retro_4131a4b6c416dba3925a:reference-expert:a0","kind":"single_route","max_steps":4,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CCCC(C(=O)O)c1c(C)nc(-c2ccccc2)nc1N1CCc2ccccc2C1 in at most 4 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCCC(C(=O)O)c1c(C)nc(-c2ccccc2)nc1N1CCc2ccccc2C1\", \"reactants\": [\"CCCC(C(=O)OC)c1c(C)nc(-c2ccccc2)nc1N1CCc2ccccc2C1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCCC(C(=O)OC)c1c(C)nc(-c2ccccc2)nc1N1CCc2ccccc2C1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"JXKCUNGIRXGDNZ-UHFFFAOYSA-N>>MZLDXZQOZRPRSU-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"CCCC(C(=O)O)c1c(C)nc(-c2ccccc2)nc1N1CCc2ccccc2C1\", \"reactants\": [\"CCCC(C(=O)OC)c1c(C)nc(-c2ccccc2)nc1N1CCc2ccccc2C1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CCCC(C(=O)OC)c1c(C)nc(-c2ccccc2)nc1N1CCc2ccccc2C1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"CCCC(C(=O)OC)c1c(C)nc(-c2ccccc2)nc1N1CCc2ccccc2C1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCCC(C(=O)OC)c1c(C)nc(-c2ccccc2)nc1N1CCc2ccccc2C1\", \"reactants\": [\"CCCC(C(=O)OC)c1c(C)nc(-c2ccccc2)nc1Cl\", \"c1ccc2c(c1)CCNC2\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCCC(C(=O)OC)c1c(C)nc(-c2ccccc2)nc1Cl\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"c1ccc2c(c1)CCNC2\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"RDAQAQVTZGSONV-UHFFFAOYSA-N.UWYZHKAOTLEWKK-UHFFFAOYSA-N>>JXKCUNGIRXGDNZ-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"CCCC(C(=O)OC)c1c(C)nc(-c2ccccc2)nc1N1CCc2ccccc2C1\", \"reactants\": [\"CCCC(C(=O)OC)c1c(C)nc(-c2ccccc2)nc1Cl\", \"c1ccc2c(c1)CCNC2\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CCCC(C(=O)OC)c1c(C)nc(-c2ccccc2)nc1Cl\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"c1ccc2c(c1)CCNC2\", \"results\": [{\"inchikey\": \"UWYZHKAOTLEWKK-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"c1ccc2c(c1)CCNC2\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"CCCC(C(=O)OC)c1c(C)nc(-c2ccccc2)nc1Cl was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCCC(C(=O)OC)c1c(C)nc(-c2ccccc2)nc1Cl\", \"reactants\": [\"CCCC(C(=O)OC)c1c(C)nc(-c2ccccc2)[nH]c1=O\", \"O=P(Cl)(Cl)Cl\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCCC(C(=O)OC)c1c(C)nc(-c2ccccc2)[nH]c1=O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=P(Cl)(Cl)Cl\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"FOLXQYYSUWTMNB-UHFFFAOYSA-N.XHXFXVLFKHQFAL-UHFFFAOYSA-N>>RDAQAQVTZGSONV-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"CCCC(C(=O)OC)c1c(C)nc(-c2ccccc2)nc1Cl\", \"reactants\": [\"CCCC(C(=O)OC)c1c(C)nc(-c2ccccc2)[nH]c1=O\", \"O=P(Cl)(Cl)Cl\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"CCCC(C(=O)OC)c1c(C)nc(-c2ccccc2)[nH]c1=O\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"O=P(Cl)(Cl)Cl\", \"results\": [{\"inchikey\": \"XHXFXVLFKHQFAL-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=P(Cl)(Cl)Cl\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"CCCC(C(=O)OC)c1c(C)nc(-c2ccccc2)[nH]c1=O was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCCC(C(=O)OC)c1c(C)nc(-c2ccccc2)[nH]c1=O\", \"reactants\": [\"CCCC(C(=O)O)c1c(C)nc(-c2ccccc2)[nH]c1=O\", \"CO\"]}","name":"validate_disconnection"},"id":"call_4_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCCC(C(=O)O)c1c(C)nc(-c2ccccc2)[nH]c1=O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_1","type":"function"},{"function":{"arguments":"{\"query\": \"CO\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"JRHJKDRTSFFKCK-UHFFFAOYSA-N.OKKJLVBELUTLKV-UHFFFAOYSA-N>>FOLXQYYSUWTMNB-UHFFFAOYSA-N\", \"model_turns_remaining\": 12, \"product\": \"CCCC(C(=O)OC)c1c(C)nc(-c2ccccc2)[nH]c1=O\", \"reactants\": [\"CCCC(C(=O)O)c1c(C)nc(-c2ccccc2)[nH]c1=O\", \"CO\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_4_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"CCCC(C(=O)O)c1c(C)nc(-c2ccccc2)[nH]c1=O\", \"results\": [{\"inchikey\": \"JRHJKDRTSFFKCK-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CCCC(C(=O)O)c1c(C)nc(-c2ccccc2)[nH]c1=O\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"CO\", \"results\": [{\"inchikey\": \"OKKJLVBELUTLKV-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CO\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CCCC(C(=O)O)c1c(C)nc(-c2ccccc2)nc1N1CCc2ccccc2C1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCCC(C(=O)OC)c1c(C)nc(-c2ccccc2)nc1N1CCc2ccccc2C1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCCC(C(=O)OC)c1c(C)nc(-c2ccccc2)nc1N1CCc2ccccc2C1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCCC(C(=O)OC)c1c(C)nc(-c2ccccc2)nc1Cl\": \"precursor\", \"c1ccc2c(c1)CCNC2\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCCC(C(=O)OC)c1c(C)nc(-c2ccccc2)nc1Cl\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCCC(C(=O)OC)c1c(C)nc(-c2ccccc2)[nH]c1=O\": \"precursor\", \"O=P(Cl)(Cl)Cl\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCCC(C(=O)OC)c1c(C)nc(-c2ccccc2)[nH]c1=O\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCCC(C(=O)O)c1c(C)nc(-c2ccccc2)[nH]c1=O\": \"precursor\", \"CO\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCCC(C(=O)O)c1c(C)nc(-c2ccccc2)[nH]c1=O\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"CO\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"O=P(Cl)(Cl)Cl\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"c1ccc2c(c1)CCNC2\", \"in_stock\": true, \"children\": []}]}]}]}]}]}}","name":"emit_routes"},"id":"call_5_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"CCCC(C(=O)O)c1c(C)nc(-c2ccccc2)nc1N1CCc2ccccc2C1","task_id":"retro_4131a4b6c416dba3925a","tool_calls":12,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":5}
{"exact_match":true,"id":"retro_422bb3f3fcbbfb100193:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CS(=O)(=O)c1ccc(-n2ccc(O)cc2=O)cc1 in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CS(=O)(=O)c1ccc(-n2ccc(O)cc2=O)cc1\", \"reactants\": [\"CS(=O)(=O)c1ccc(-n2ccc(OCc3ccccc3)cc2=O)cc1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CS(=O)(=O)c1ccc(-n2ccc(OCc3ccccc3)cc2=O)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"JZYNYXBCONGKPX-UHFFFAOYSA-N>>HRJFEFHOQBDDMT-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"CS(=O)(=O)c1ccc(-n2ccc(O)cc2=O)cc1\", \"reactants\": [\"CS(=O)(=O)c1ccc(-n2ccc(OCc3ccccc3)cc2=O)cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CS(=O)(=O)c1ccc(-n2ccc(OCc3ccccc3)cc2=O)cc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"CS(=O)(=O)c1ccc(-n2ccc(OCc3ccccc3)cc2=O)cc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CS(=O)(=O)c1ccc(-n2ccc(OCc3ccccc3)cc2=O)cc1\", \"reactants\": [\"CS(=O)(=O)c1ccc(Br)cc1\", \"O=c1cc(OCc2ccccc2)cc[nH]1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CS(=O)(=O)c1ccc(Br)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=c1cc(OCc2ccccc2)cc[nH]1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"DOVNUEPFPBWTSV-UHFFFAOYSA-N.FJLFSYRGFJDJMQ-UHFFFAOYSA-N>>JZYNYXBCONGKPX-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"CS(=O)(=O)c1ccc(-n2ccc(OCc3ccccc3)cc2=O)cc1\", \"reactants\": [\"CS(=O)(=O)c1ccc(Br)cc1\", \"O=c1cc(OCc2ccccc2)cc[nH]1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CS(=O)(=O)c1ccc(Br)cc1\", \"results\": [{\"inchikey\": \"FJLFSYRGFJDJMQ-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CS(=O)(=O)c1ccc(Br)cc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"O=c1cc(OCc2ccccc2)cc[nH]1\", \"results\": [{\"inchikey\": \"DOVNUEPFPBWTSV-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=c1cc(OCc2ccccc2)cc[nH]1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CS(=O)(=O)c1ccc(-n2ccc(O)cc2=O)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CS(=O)(=O)c1ccc(-n2ccc(OCc3ccccc3)cc2=O)cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CS(=O)(=O)c1ccc(-n2ccc(OCc3ccccc3)cc2=O)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CS(=O)(=O)c1ccc(Br)cc1\": \"precursor\", \"O=c1cc(OCc2ccccc2)cc[nH]1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CS(=O)(=O)c1ccc(Br)cc1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=c1cc(OCc2ccccc2)cc[nH]1\", \"in_stock\": true, \"children\": []}]}]}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"CS(=O)(=O)c1ccc(-n2ccc(O)cc2=O)cc1","task_id":"retro_422bb3f3fcbbfb100193","tool_calls":6,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_4254dffcf93ab4faab4a:reference-expert:a0","kind":"single_route","max_steps":4,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target NC(=O)C1CCN(CC2(c3ccc(OCCCN4CCCC4)cc3)CCOCC2)CC1 in at most 4 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"NC(=O)C1CCN(CC2(c3ccc(OCCCN4CCCC4)cc3)CCOCC2)CC1\", \"reactants\": [\"NC(=O)C1CCNCC1\", \"O=CC1(c2ccc(OCCCN3CCCC3)cc2)CCOCC1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"NC(=O)C1CCNCC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=CC1(c2ccc(OCCCN3CCCC3)cc2)CCOCC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"DPBWFNDFMCCGGJ-UHFFFAOYSA-N.OFLQDYJSAAJMIQ-UHFFFAOYSA-N>>FIQWXWSGBVMDNA-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"NC(=O)C1CCN(CC2(c3ccc(OCCCN4CCCC4)cc3)CCOCC2)CC1\", \"reactants\": [\"NC(=O)C1CCNCC1\", \"O=CC1(c2ccc(OCCCN3CCCC3)cc2)CCOCC1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"NC(=O)C1CCNCC1\", \"results\": [{\"inchikey\": \"DPBWFNDFMCCGGJ-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"NC(=O)C1CCNCC1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"O=CC1(c2ccc(OCCCN3CCCC3)cc2)CCOCC1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"O=CC1(c2ccc(OCCCN3CCCC3)cc2)CCOCC1 was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"O=CC1(c2ccc(OCCCN3CCCC3)cc2)CCOCC1\", \"reactants\": [\"OCC1(c2ccc(OCCCN3CCCC3)cc2)CCOCC1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"OCC1(c2ccc(OCCCN3CCCC3)cc2)CCOCC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_complete\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"UEXNBAKMACUHKK-UHFFFAOYSA-N>>OFLQDYJSAAJMIQ-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"O=CC1(c2ccc(OCCCN3CCCC3)cc2)CCOCC1\", \"reactants\": [\"OCC1(c2ccc(OCCCN3CCCC3)cc2)CCOCC1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"OCC1(c2ccc(OCCCN3CCCC3)cc2)CCOCC1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"OCC1(c2ccc(OCCCN3CCCC3)cc2)CCOCC1 was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"OCC1(c2ccc(OCCCN3CCCC3)cc2)CCOCC1\", \"reactants\": [\"COC(=O)C1(c2ccc(OCCCN3CCCC3)cc2)CCOCC1\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"COC(=O)C1(c2ccc(OCCCN3CCCC3)cc2)CCOCC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"PHFWPZLMPBRBFM-UHFFFAOYSA-N>>UEXNBAKMACUHKK-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"OCC1(c2ccc(OCCCN3CCCC3)cc2)CCOCC1\", \"reactants\": [\"COC(=O)C1(c2ccc(OCCCN3CCCC3)cc2)CCOCC1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"COC(=O)C1(c2ccc(OCCCN3CCCC3)cc2)CCOCC1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"COC(=O)C1(c2ccc(OCCCN3CCCC3)cc2)CCOCC1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COC(=O)C1(c2ccc(OCCCN3CCCC3)cc2)CCOCC1\", \"reactants\": [\"CO\", \"O=C(O)C1(c2ccc(OCCCN3CCCC3)cc2)CCOCC1\"]}","name":"validate_disconnection"},"id":"call_4_0","type":"function"},{"function":{"arguments":"{\"query\": \"CO\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=C(O)C1(c2ccc(OCCCN3CCCC3)cc2)CCOCC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"MSNKLEMTHNAVNT-UHFFFAOYSA-N.OKKJLVBELUTLKV-UHFFFAOYSA-N>>PHFWPZLMPBRBFM-UHFFFAOYSA-N\", \"model_turns_remaining\": 12, \"product\": \"COC(=O)C1(c2ccc(OCCCN3CCCC3)cc2)CCOCC1\", \"reactants\": [\"CO\", \"O=C(O)C1(c2ccc(OCCCN3CCCC3)cc2)CCOCC1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_4_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"CO\", \"results\": [{\"inchikey\": \"OKKJLVBELUTLKV-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CO\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"O=C(O)C1(c2ccc(OCCCN3CCCC3)cc2)CCOCC1\", \"results\": [{\"inchikey\": \"MSNKLEMTHNAVNT-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=C(O)C1(c2ccc(OCCCN3CCCC3)cc2)CCOCC1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"NC(=O)C1CCN(CC2(c3ccc(OCCCN4CCCC4)cc3)CCOCC2)CC1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"NC(=O)C1CCNCC1\": \"precursor\", \"O=CC1(c2ccc(OCCCN3CCCC3)cc2)CCOCC1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"NC(=O)C1CCNCC1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=CC1(c2ccc(OCCCN3CCCC3)cc2)CCOCC1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"OCC1(c2ccc(OCCCN3CCCC3)cc2)CCOCC1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"OCC1(c2ccc(OCCCN3CCCC3)cc2)CCOCC1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COC(=O)C1(c2ccc(OCCCN3CCCC3)cc2)CCOCC1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COC(=O)C1(c2ccc(OCCCN3CCCC3)cc2)CCOCC1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CO\": \"precursor\", \"O=C(O)C1(c2ccc(OCCCN3CCCC3)cc2)CCOCC1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CO\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=C(O)C1(c2ccc(OCCCN3CCCC3)cc2)CCOCC1\", \"in_stock\": true, \"children\": []}]}]}]}]}]}]}]}]}]}}","name":"emit_routes"},"id":"call_5_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"NC(=O)C1CCN(CC2(c3ccc(OCCCN4CCCC4)cc3)CCOCC2)CC1","task_id":"retro_4254dffcf93ab4faab4a","tool_calls":11,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":5}
{"exact_match":true,"id":"retro_42b777111b3612ae6ee3:reference-expert:a0","kind":"single_route","max_steps":4,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target O=C(O)c1c(-c2ccc(F)cc2)oc2cc(N3CCCC3=O)c(Br)cc12 in at most 4 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"O=C(O)c1c(-c2ccc(F)cc2)oc2cc(N3CCCC3=O)c(Br)cc12\", \"reactants\": [\"CCOC(=O)c1c(-c2ccc(F)cc2)oc2cc(N3CCCC3=O)c(Br)cc12\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCOC(=O)c1c(-c2ccc(F)cc2)oc2cc(N3CCCC3=O)c(Br)cc12\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"XLBHQUFRRWAEAJ-UHFFFAOYSA-N>>LUNRSFSUALZQTH-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"O=C(O)c1c(-c2ccc(F)cc2)oc2cc(N3CCCC3=O)c(Br)cc12\", \"reactants\": [\"CCOC(=O)c1c(-c2ccc(F)cc2)oc2cc(N3CCCC3=O)c(Br)cc12\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CCOC(=O)c1c(-c2ccc(F)cc2)oc2cc(N3CCCC3=O)c(Br)cc12\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"CCOC(=O)c1c(-c2ccc(F)cc2)oc2cc(N3CCCC3=O)c(Br)cc12 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCOC(=O)c1c(-c2ccc(F)cc2)oc2cc(N3CCCC3=O)c(Br)cc12\", \"reactants\": [\"CCOC(=O)c1c(-c2ccc(F)cc2)oc2cc(N)c(Br)cc12\", \"O=C(Cl)CCCCl\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCOC(=O)c1c(-c2ccc(F)cc2)oc2cc(N)c(Br)cc12\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=C(Cl)CCCCl\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"CDIIZULDSLKBKV-UHFFFAOYSA-N.LWEDBLLJQZRMGD-UHFFFAOYSA-N>>XLBHQUFRRWAEAJ-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"CCOC(=O)c1c(-c2ccc(F)cc2)oc2cc(N3CCCC3=O)c(Br)cc12\", \"reactants\": [\"CCOC(=O)c1c(-c2ccc(F)cc2)oc2cc(N)c(Br)cc12\", \"O=C(Cl)CCCCl\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CCOC(=O)c1c(-c2ccc(F)cc2)oc2cc(N)c(Br)cc12\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"O=C(Cl)CCCCl\", \"results\": [{\"inchikey\": \"CDIIZULDSLKBKV-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=C(Cl)CCCCl\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"CCOC(=O)c1c(-c2ccc(F)cc2)oc2cc(N)c(Br)cc12 was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCOC(=O)c1c(-c2ccc(F)cc2)oc2cc(N)c(Br)cc12\", \"reactants\": [\"CCOC(=O)c1c(-c2ccc(F)cc2)oc2cc([N+](=O)[O-])c(Br)cc12\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCOC(=O)c1c(-c2ccc(F)cc2)oc2cc([N+](=O)[O-])c(Br)cc12\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"PNADZXBALPWPEG-UHFFFAOYSA-N>>LWEDBLLJQZRMGD-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"CCOC(=O)c1c(-c2ccc(F)cc2)oc2cc(N)c(Br)cc12\", \"reactants\": [\"CCOC(=O)c1c(-c2ccc(F)cc2)oc2cc([N+](=O)[O-])c(Br)cc12\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"CCOC(=O)c1c(-c2ccc(F)cc2)oc2cc([N+](=O)[O-])c(Br)cc12\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"CCOC(=O)c1c(-c2ccc(F)cc2)oc2cc([N+](=O)[O-])c(Br)cc12 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCOC(=O)c1c(-c2ccc(F)cc2)oc2cc([N+](=O)[O-])c(Br)cc12\", \"reactants\": [\"CCOC(=O)c1c(-c2ccc(F)cc2)oc2ccc(Br)cc12\", \"O=[N+]([O-])O\"]}","name":"validate_disconnection"},"id":"call_4_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCOC(=O)c1c(-c2ccc(F)cc2)oc2ccc(Br)cc12\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=[N+]([O-])O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"GRYLNZFGIOXLOG-UHFFFAOYSA-N.ICCOIKSJMYKUFO-UHFFFAOYSA-N>>PNADZXBALPWPEG-UHFFFAOYSA-N\", \"model_turns_remaining\": 12, \"product\": \"CCOC(=O)c1c(-c2ccc(F)cc2)oc2cc([N+](=O)[O-])c(Br)cc12\", \"reactants\": [\"CCOC(=O)c1c(-c2ccc(F)cc2)oc2ccc(Br)cc12\", \"O=[N+]([O-])O\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_4_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"CCOC(=O)c1c(-c2ccc(F)cc2)oc2ccc(Br)cc12\", \"results\": [{\"inchikey\": \"ICCOIKSJMYKUFO-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CCOC(=O)c1c(-c2ccc(F)cc2)oc2ccc(Br)cc12\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"O=[N+]([O-])O\", \"results\": [{\"inchikey\": \"GRYLNZFGIOXLOG-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=[N+]([O-])O\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"O=C(O)c1c(-c2ccc(F)cc2)oc2cc(N3CCCC3=O)c(Br)cc12\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCOC(=O)c1c(-c2ccc(F)cc2)oc2cc(N3CCCC3=O)c(Br)cc12\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCOC(=O)c1c(-c2ccc(F)cc2)oc2cc(N3CCCC3=O)c(Br)cc12\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCOC(=O)c1c(-c2ccc(F)cc2)oc2cc(N)c(Br)cc12\": \"precursor\", \"O=C(Cl)CCCCl\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCOC(=O)c1c(-c2ccc(F)cc2)oc2cc(N)c(Br)cc12\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCOC(=O)c1c(-c2ccc(F)cc2)oc2cc([N+](=O)[O-])c(Br)cc12\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCOC(=O)c1c(-c2ccc(F)cc2)oc2cc([N+](=O)[O-])c(Br)cc12\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCOC(=O)c1c(-c2ccc(F)cc2)oc2ccc(Br)cc12\": \"precursor\", \"O=[N+]([O-])O\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCOC(=O)c1c(-c2ccc(F)cc2)oc2ccc(Br)cc12\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=[N+]([O-])O\", \"in_stock\": true, \"children\": []}]}]}]}]}, {\"type\": \"mol\", \"smiles\": \"O=C(Cl)CCCCl\", \"in_stock\": true, \"children\": []}]}]}]}]}]}}","name":"emit_routes"},"id":"call_5_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"O=C(O)c1c(-c2ccc(F)cc2)oc2cc(N3CCCC3=O)c(Br)cc12","task_id":"retro_42b777111b3612ae6ee3","tool_calls":11,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":5}
{"exact_match":true,"id":"retro_435f951c743e0ffcacae:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target NNC(=O)C(c1ccccc1)c1ccccc1 in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"NNC(=O)C(c1ccccc1)c1ccccc1\", \"reactants\": [\"COC(=O)C(c1ccccc1)c1ccccc1\", \"NN\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"COC(=O)C(c1ccccc1)c1ccccc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"NN\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"AORIUCNKPVHMTN-UHFFFAOYSA-N.OAKJQQAXSVQMHS-UHFFFAOYSA-N>>YBBSKAGTEPBSNK-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"NNC(=O)C(c1ccccc1)c1ccccc1\", \"reactants\": [\"COC(=O)C(c1ccccc1)c1ccccc1\", \"NN\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"COC(=O)C(c1ccccc1)c1ccccc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"NN\", \"results\": [{\"inchikey\": \"OAKJQQAXSVQMHS-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"NN\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"COC(=O)C(c1ccccc1)c1ccccc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COC(=O)C(c1ccccc1)c1ccccc1\", \"reactants\": [\"CO\", \"O=C(O)C(c1ccccc1)c1ccccc1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CO\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=C(O)C(c1ccccc1)c1ccccc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"OKKJLVBELUTLKV-UHFFFAOYSA-N.PYHXGXCGESYPCW-UHFFFAOYSA-N>>AORIUCNKPVHMTN-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"COC(=O)C(c1ccccc1)c1ccccc1\", \"reactants\": [\"CO\", \"O=C(O)C(c1ccccc1)c1ccccc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CO\", \"results\": [{\"inchikey\": \"OKKJLVBELUTLKV-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CO\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"O=C(O)C(c1ccccc1)c1ccccc1\", \"results\": [{\"inchikey\": \"PYHXGXCGESYPCW-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=C(O)C(c1ccccc1)c1ccccc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"NNC(=O)C(c1ccccc1)c1ccccc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COC(=O)C(c1ccccc1)c1ccccc1\": \"precursor\", \"NN\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COC(=O)C(c1ccccc1)c1ccccc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CO\": \"precursor\", \"O=C(O)C(c1ccccc1)c1ccccc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CO\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=C(O)C(c1ccccc1)c1ccccc1\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"NN\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"NNC(=O)C(c1ccccc1)c1ccccc1","task_id":"retro_435f951c743e0ffcacae","tool_calls":7,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_439772e1ef292049bdd7:reference-expert:a0","kind":"single_route","max_steps":5,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target COC(=O)Cc1ccc(C#Cc2cc(O)c3c(c2)C(C)(C)CCC3=O)cc1 in at most 5 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COC(=O)Cc1ccc(C#Cc2cc(O)c3c(c2)C(C)(C)CCC3=O)cc1\", \"reactants\": [\"C#Cc1cc(O)c2c(c1)C(C)(C)CCC2=O\", \"COC(=O)Cc1ccc(I)cc1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"C#Cc1cc(O)c2c(c1)C(C)(C)CCC2=O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"COC(=O)Cc1ccc(I)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"IYIVBGQBEMSRLO-UHFFFAOYSA-N.RKCWVAWAWDWBRN-UHFFFAOYSA-N>>IVAOHUGBTZPYIY-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"COC(=O)Cc1ccc(C#Cc2cc(O)c3c(c2)C(C)(C)CCC3=O)cc1\", \"reactants\": [\"C#Cc1cc(O)c2c(c1)C(C)(C)CCC2=O\", \"COC(=O)Cc1ccc(I)cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"C#Cc1cc(O)c2c(c1)C(C)(C)CCC2=O\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"COC(=O)Cc1ccc(I)cc1\", \"results\": [{\"inchikey\": \"IYIVBGQBEMSRLO-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"COC(=O)Cc1ccc(I)cc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"C#Cc1cc(O)c2c(c1)C(C)(C)CCC2=O was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"C#Cc1cc(O)c2c(c1)C(C)(C)CCC2=O\", \"reactants\": [\"CC1(C)CCC(=O)c2c(O)cc(C#C[Si](C)(C)C)cc21\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC1(C)CCC(=O)c2c(O)cc(C#C[Si](C)(C)C)cc21\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"RNTVAPJYIHGXEA-UHFFFAOYSA-N>>RKCWVAWAWDWBRN-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"C#Cc1cc(O)c2c(c1)C(C)(C)CCC2=O\", \"reactants\": [\"CC1(C)CCC(=O)c2c(O)cc(C#C[Si](C)(C)C)cc21\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CC1(C)CCC(=O)c2c(O)cc(C#C[Si](C)(C)C)cc21\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"CC1(C)CCC(=O)c2c(O)cc(C#C[Si](C)(C)C)cc21 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC1(C)CCC(=O)c2c(O)cc(C#C[Si](C)(C)C)cc21\", \"reactants\": [\"C#C[Si](C)(C)C\", \"CC1(C)CCC(=O)c2c(O)cc(Br)cc21\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"C#C[Si](C)(C)C\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"CC1(C)CCC(=O)c2c(O)cc(Br)cc21\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"CWMFRHBXRUITQE-UHFFFAOYSA-N.LCTKBYBCVVBKLG-UHFFFAOYSA-N>>RNTVAPJYIHGXEA-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"CC1(C)CCC(=O)c2c(O)cc(C#C[Si](C)(C)C)cc21\", \"reactants\": [\"C#C[Si](C)(C)C\", \"CC1(C)CCC(=O)c2c(O)cc(Br)cc21\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"C#C[Si](C)(C)C\", \"results\": [{\"inchikey\": \"CWMFRHBXRUITQE-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"C#C[Si](C)(C)C\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"CC1(C)CCC(=O)c2c(O)cc(Br)cc21\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"CC1(C)CCC(=O)c2c(O)cc(Br)cc21 was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC1(C)CCC(=O)c2c(O)cc(Br)cc21\", \"reactants\": [\"COc1cc(Br)cc2c1C(=O)CCC2(C)C\"]}","name":"validate_disconnection"},"id":"call_4_0","type":"function"},{"function":{"arguments":"{\"query\": \"COc1cc(Br)cc2c1C(=O)CCC2(C)C\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"YWTITWZHVYDTNO-UHFFFAOYSA-N>>LCTKBYBCVVBKLG-UHFFFAOYSA-N\", \"model_turns_remaining\": 12, \"product\": \"CC1(C)CCC(=O)c2c(O)cc(Br)cc21\", \"reactants\": [\"COc1cc(Br)cc2c1C(=O)CCC2(C)C\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_4_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"COc1cc(Br)cc2c1C(=O)CCC2(C)C\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_1"},{"content":"COc1cc(Br)cc2c1C(=O)CCC2(C)C was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COc1cc(Br)cc2c1C(=O)CCC2(C)C\", \"reactants\": [\"COc1cc(Br)cc2c1CCCC2(C)C\", \"O\"]}","name":"validate_disconnection"},"id":"call_5_0","type":"function"},{"function":{"arguments":"{\"query\": \"COc1cc(Br)cc2c1CCCC2(C)C\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_5_1","type":"function"},{"function":{"arguments":"{\"query\": \"O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_5_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_complete\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"HECMVQJEBMLRKB-UHFFFAOYSA-N.XLYOFNOQVPJJNP-UHFFFAOYSA-N>>YWTITWZHVYDTNO-UHFFFAOYSA-N\", \"model_turns_remaining\": 11, \"product\": \"COc1cc(Br)cc2c1C(=O)CCC2(C)C\", \"reactants\": [\"COc1cc(Br)cc2c1CCCC2(C)C\", \"O\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_5_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 11, \"query\": \"COc1cc(Br)cc2c1CCCC2(C)C\", \"results\": [{\"inchikey\": \"HECMVQJEBMLRKB-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"COc1cc(Br)cc2c1CCCC2(C)C\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_5_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 11, \"query\": \"O\", \"results\": [{\"inchikey\": \"XLYOFNOQVPJJNP-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_5_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"COC(=O)Cc1ccc(C#Cc2cc(O)c3c(c2)C(C)(C)CCC3=O)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"C#Cc1cc(O)c2c(c1)C(C)(C)CCC2=O\": \"precursor\", \"COC(=O)Cc1ccc(I)cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"C#Cc1cc(O)c2c(c1)C(C)(C)CCC2=O\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC1(C)CCC(=O)c2c(O)cc(C#C[Si](C)(C)C)cc21\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC1(C)CCC(=O)c2c(O)cc(C#C[Si](C)(C)C)cc21\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"C#C[Si](C)(C)C\": \"precursor\", \"CC1(C)CCC(=O)c2c(O)cc(Br)cc21\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"C#C[Si](C)(C)C\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"CC1(C)CCC(=O)c2c(O)cc(Br)cc21\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COc1cc(Br)cc2c1C(=O)CCC2(C)C\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COc1cc(Br)cc2c1C(=O)CCC2(C)C\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COc1cc(Br)cc2c1CCCC2(C)C\": \"precursor\", \"O\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COc1cc(Br)cc2c1CCCC2(C)C\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O\", \"in_stock\": true, \"children\": []}]}]}]}]}]}]}]}]}, {\"type\": \"mol\", \"smiles\": \"COC(=O)Cc1ccc(I)cc1\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_6_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"COC(=O)Cc1ccc(C#Cc2cc(O)c3c(c2)C(C)(C)CCC3=O)cc1","task_id":"retro_439772e1ef292049bdd7","tool_calls":14,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":6}
{"exact_match":true,"id":"retro_44da8c77483d22f3d758:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target N#Cc1ccc(-c2cc([N+](=O)[O-])ccc2F)cc1 in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"N#Cc1ccc(-c2cc([N+](=O)[O-])ccc2F)cc1\", \"reactants\": [\"CC1(C)OB(c2cc([N+](=O)[O-])ccc2F)OC1(C)C\", \"N#Cc1ccc(Br)cc1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC1(C)OB(c2cc([N+](=O)[O-])ccc2F)OC1(C)C\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"N#Cc1ccc(Br)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"FXEVKZIXXGDLFW-UHFFFAOYSA-N.HQSCPPCMBMFJJN-UHFFFAOYSA-N>>QTWONSAXNKQSKP-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"N#Cc1ccc(-c2cc([N+](=O)[O-])ccc2F)cc1\", \"reactants\": [\"CC1(C)OB(c2cc([N+](=O)[O-])ccc2F)OC1(C)C\", \"N#Cc1ccc(Br)cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CC1(C)OB(c2cc([N+](=O)[O-])ccc2F)OC1(C)C\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"N#Cc1ccc(Br)cc1\", \"results\": [{\"inchikey\": \"HQSCPPCMBMFJJN-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"N#Cc1ccc(Br)cc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"CC1(C)OB(c2cc([N+](=O)[O-])ccc2F)OC1(C)C was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC1(C)OB(c2cc([N+](=O)[O-])ccc2F)OC1(C)C\", \"reactants\": [\"CC1(C)OB(B2OC(C)(C)C(C)(C)O2)OC1(C)C\", \"O=[N+]([O-])c1ccc(F)c(Br)c1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC1(C)OB(B2OC(C)(C)C(C)(C)O2)OC1(C)C\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=[N+]([O-])c1ccc(F)c(Br)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"FAWMTDSAMOCUAR-UHFFFAOYSA-N.IPWKHHSGDUIRAH-UHFFFAOYSA-N>>FXEVKZIXXGDLFW-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"CC1(C)OB(c2cc([N+](=O)[O-])ccc2F)OC1(C)C\", \"reactants\": [\"CC1(C)OB(B2OC(C)(C)C(C)(C)O2)OC1(C)C\", \"O=[N+]([O-])c1ccc(F)c(Br)c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CC1(C)OB(B2OC(C)(C)C(C)(C)O2)OC1(C)C\", \"results\": [{\"inchikey\": \"IPWKHHSGDUIRAH-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CC1(C)OB(B2OC(C)(C)C(C)(C)O2)OC1(C)C\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"O=[N+]([O-])c1ccc(F)c(Br)c1\", \"results\": [{\"inchikey\": \"FAWMTDSAMOCUAR-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=[N+]([O-])c1ccc(F)c(Br)c1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"N#Cc1ccc(-c2cc([N+](=O)[O-])ccc2F)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC1(C)OB(c2cc([N+](=O)[O-])ccc2F)OC1(C)C\": \"precursor\", \"N#Cc1ccc(Br)cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC1(C)OB(c2cc([N+](=O)[O-])ccc2F)OC1(C)C\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC1(C)OB(B2OC(C)(C)C(C)(C)O2)OC1(C)C\": \"precursor\", \"O=[N+]([O-])c1ccc(F)c(Br)c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC1(C)OB(B2OC(C)(C)C(C)(C)O2)OC1(C)C\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=[N+]([O-])c1ccc(F)c(Br)c1\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"N#Cc1ccc(Br)cc1\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"N#Cc1ccc(-c2cc([N+](=O)[O-])ccc2F)cc1","task_id":"retro_44da8c77483d22f3d758","tool_calls":7,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_45e99d13467f7864b771:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target Fc1cc(F)cc(NC(=S)c2ccccn2)c1 in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Fc1cc(F)cc(NC(=S)c2ccccn2)c1\", \"reactants\": [\"COc1ccc(P2(=S)SP(=S)(c3ccc(OC)cc3)S2)cc1\", \"O=C(Nc1cc(F)cc(F)c1)c1ccccn1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"COc1ccc(P2(=S)SP(=S)(c3ccc(OC)cc3)S2)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=C(Nc1cc(F)cc(F)c1)c1ccccn1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"CFHGBZLNZZVTAY-UHFFFAOYSA-N.MFWLXNBJXHTAPH-UHFFFAOYSA-N>>AANZPLWMKOLXIU-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"Fc1cc(F)cc(NC(=S)c2ccccn2)c1\", \"reactants\": [\"COc1ccc(P2(=S)SP(=S)(c3ccc(OC)cc3)S2)cc1\", \"O=C(Nc1cc(F)cc(F)c1)c1ccccn1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"COc1ccc(P2(=S)SP(=S)(c3ccc(OC)cc3)S2)cc1\", \"results\": [{\"inchikey\": \"CFHGBZLNZZVTAY-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"COc1ccc(P2(=S)SP(=S)(c3ccc(OC)cc3)S2)cc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"O=C(Nc1cc(F)cc(F)c1)c1ccccn1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"O=C(Nc1cc(F)cc(F)c1)c1ccccn1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"O=C(Nc1cc(F)cc(F)c1)c1ccccn1\", \"reactants\": [\"Nc1cc(F)cc(F)c1\", \"O=C(O)c1ccccn1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"Nc1cc(F)cc(F)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=C(O)c1ccccn1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"KQOIBXZRCYFZSO-UHFFFAOYSA-N.SIOXPEMLGUPBBT-UHFFFAOYSA-N>>MFWLXNBJXHTAPH-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"O=C(Nc1cc(F)cc(F)c1)c1ccccn1\", \"reactants\": [\"Nc1cc(F)cc(F)c1\", \"O=C(O)c1ccccn1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"Nc1cc(F)cc(F)c1\", \"results\": [{\"inchikey\": \"KQOIBXZRCYFZSO-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Nc1cc(F)cc(F)c1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"O=C(O)c1ccccn1\", \"results\": [{\"inchikey\": \"SIOXPEMLGUPBBT-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=C(O)c1ccccn1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"Fc1cc(F)cc(NC(=S)c2ccccn2)c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COc1ccc(P2(=S)SP(=S)(c3ccc(OC)cc3)S2)cc1\": \"precursor\", \"O=C(Nc1cc(F)cc(F)c1)c1ccccn1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COc1ccc(P2(=S)SP(=S)(c3ccc(OC)cc3)S2)cc1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=C(Nc1cc(F)cc(F)c1)c1ccccn1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"Nc1cc(F)cc(F)c1\": \"precursor\", \"O=C(O)c1ccccn1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"Nc1cc(F)cc(F)c1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=C(O)c1ccccn1\", \"in_stock\": true, \"children\": []}]}]}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"Fc1cc(F)cc(NC(=S)c2ccccn2)c1","task_id":"retro_45e99d13467f7864b771","tool_calls":7,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_4617f007c3a12bd00f7e:reference-expert:a0","kind":"single_route","max_steps":4,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target Cc1ccc(S(=O)(=O)OCCOCCOCCOc2ccc(/C=C/c3ccc(N(C)C)cc3)cn2)cc1 in at most 4 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Cc1ccc(S(=O)(=O)OCCOCCOCCOc2ccc(/C=C/c3ccc(N(C)C)cc3)cn2)cc1\", \"reactants\": [\"CN(C)c1ccc(/C=C/c2ccc(OCCOCCOCCO)nc2)cc1\", \"Cc1ccc(S(=O)(=O)Cl)cc1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CN(C)c1ccc(/C=C/c2ccc(OCCOCCOCCO)nc2)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"Cc1ccc(S(=O)(=O)Cl)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"RMVDTGLZMNQRAH-ONEGZZNKSA-N.YYROPELSRYBVMQ-UHFFFAOYSA-N>>RDZUORKQODTGFP-VOTSOKGWSA-N\", \"model_turns_remaining\": 15, \"product\": \"Cc1ccc(S(=O)(=O)OCCOCCOCCOc2ccc(/C=C/c3ccc(N(C)C)cc3)cn2)cc1\", \"reactants\": [\"CN(C)c1ccc(/C=C/c2ccc(OCCOCCOCCO)nc2)cc1\", \"Cc1ccc(S(=O)(=O)Cl)cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CN(C)c1ccc(/C=C/c2ccc(OCCOCCOCCO)nc2)cc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"Cc1ccc(S(=O)(=O)Cl)cc1\", \"results\": [{\"inchikey\": \"YYROPELSRYBVMQ-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Cc1ccc(S(=O)(=O)Cl)cc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"CN(C)c1ccc(/C=C/c2ccc(OCCOCCOCCO)nc2)cc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CN(C)c1ccc(/C=C/c2ccc(OCCOCCOCCO)nc2)cc1\", \"reactants\": [\"BC#N\", \"C=O\", \"Nc1ccc(/C=C/c2ccc(OCCOCCOCCO)nc2)cc1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"BC#N\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"C=O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"},{"function":{"arguments":"{\"query\": \"Nc1ccc(/C=C/c2ccc(OCCOCCOCCO)nc2)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_3","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"SRSPILBBEHNEHD-UHFFFAOYSA-N.WSFSSNUMVMOOMR-UHFFFAOYSA-N.YTRHFRDQQSDDRB-OWOJBTEDSA-N>>RMVDTGLZMNQRAH-ONEGZZNKSA-N\", \"model_turns_remaining\": 14, \"product\": \"CN(C)c1ccc(/C=C/c2ccc(OCCOCCOCCO)nc2)cc1\", \"reactants\": [\"BC#N\", \"C=O\", \"Nc1ccc(/C=C/c2ccc(OCCOCCOCCO)nc2)cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"BC#N\", \"results\": [{\"inchikey\": \"SRSPILBBEHNEHD-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"BC#N\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"C=O\", \"results\": [{\"inchikey\": \"WSFSSNUMVMOOMR-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"C=O\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"Nc1ccc(/C=C/c2ccc(OCCOCCOCCO)nc2)cc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_3"},{"content":"Nc1ccc(/C=C/c2ccc(OCCOCCOCCO)nc2)cc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Nc1ccc(/C=C/c2ccc(OCCOCCOCCO)nc2)cc1\", \"reactants\": [\"O=[N+]([O-])c1ccc(/C=C/c2ccc(OCCOCCOCCO)nc2)cc1\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"O=[N+]([O-])c1ccc(/C=C/c2ccc(OCCOCCOCCO)nc2)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"BRHSFMBLRMVBBH-OWOJBTEDSA-N>>YTRHFRDQQSDDRB-OWOJBTEDSA-N\", \"model_turns_remaining\": 13, \"product\": \"Nc1ccc(/C=C/c2ccc(OCCOCCOCCO)nc2)cc1\", \"reactants\": [\"O=[N+]([O-])c1ccc(/C=C/c2ccc(OCCOCCOCCO)nc2)cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"O=[N+]([O-])c1ccc(/C=C/c2ccc(OCCOCCOCCO)nc2)cc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"O=[N+]([O-])c1ccc(/C=C/c2ccc(OCCOCCOCCO)nc2)cc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"O=[N+]([O-])c1ccc(/C=C/c2ccc(OCCOCCOCCO)nc2)cc1\", \"reactants\": [\"O=[N+]([O-])c1ccc(/C=C/c2ccc(Cl)nc2)cc1\", \"OCCOCCOCCO\"]}","name":"validate_disconnection"},"id":"call_4_0","type":"function"},{"function":{"arguments":"{\"query\": \"O=[N+]([O-])c1ccc(/C=C/c2ccc(Cl)nc2)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_1","type":"function"},{"function":{"arguments":"{\"query\": \"OCCOCCOCCO\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"DNHVFKKPWZTKCO-OWOJBTEDSA-N.ZIBGPFATKBEMQZ-UHFFFAOYSA-N>>BRHSFMBLRMVBBH-OWOJBTEDSA-N\", \"model_turns_remaining\": 12, \"product\": \"O=[N+]([O-])c1ccc(/C=C/c2ccc(OCCOCCOCCO)nc2)cc1\", \"reactants\": [\"O=[N+]([O-])c1ccc(/C=C/c2ccc(Cl)nc2)cc1\", \"OCCOCCOCCO\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_4_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"O=[N+]([O-])c1ccc(/C=C/c2ccc(Cl)nc2)cc1\", \"results\": [{\"inchikey\": \"DNHVFKKPWZTKCO-OWOJBTEDSA-N\", \"similarity\": 1.0, \"smiles\": \"O=[N+]([O-])c1ccc(/C=C/c2ccc(Cl)nc2)cc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"OCCOCCOCCO\", \"results\": [{\"inchikey\": \"ZIBGPFATKBEMQZ-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"OCCOCCOCCO\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"Cc1ccc(S(=O)(=O)OCCOCCOCCOc2ccc(/C=C/c3ccc(N(C)C)cc3)cn2)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CN(C)c1ccc(/C=C/c2ccc(OCCOCCOCCO)nc2)cc1\": \"precursor\", \"Cc1ccc(S(=O)(=O)Cl)cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CN(C)c1ccc(/C=C/c2ccc(OCCOCCOCCO)nc2)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"BC#N\": \"precursor\", \"C=O\": \"precursor\", \"Nc1ccc(/C=C/c2ccc(OCCOCCOCCO)nc2)cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"BC#N\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"C=O\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"Nc1ccc(/C=C/c2ccc(OCCOCCOCCO)nc2)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"O=[N+]([O-])c1ccc(/C=C/c2ccc(OCCOCCOCCO)nc2)cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"O=[N+]([O-])c1ccc(/C=C/c2ccc(OCCOCCOCCO)nc2)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"O=[N+]([O-])c1ccc(/C=C/c2ccc(Cl)nc2)cc1\": \"precursor\", \"OCCOCCOCCO\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"O=[N+]([O-])c1ccc(/C=C/c2ccc(Cl)nc2)cc1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"OCCOCCOCCO\", \"in_stock\": true, \"children\": []}]}]}]}]}]}]}, {\"type\": \"mol\", \"smiles\": \"Cc1ccc(S(=O)(=O)Cl)cc1\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_5_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"Cc1ccc(S(=O)(=O)OCCOCCOCCOc2ccc(/C=C/c3ccc(N(C)C)cc3)cn2)cc1","task_id":"retro_4617f007c3a12bd00f7e","tool_calls":13,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":5}
{"exact_match":true,"id":"retro_47223b6e8d5da4f8648c:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CC(=O)Oc1ccc(N)cc1F in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(=O)Oc1ccc(N)cc1F\", \"reactants\": [\"CC(=O)Oc1ccc([N+](=O)[O-])cc1F\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(=O)Oc1ccc([N+](=O)[O-])cc1F\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"IYIKOSPRDLRAQK-UHFFFAOYSA-N>>UBBCCOPIOZOABQ-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"CC(=O)Oc1ccc(N)cc1F\", \"reactants\": [\"CC(=O)Oc1ccc([N+](=O)[O-])cc1F\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CC(=O)Oc1ccc([N+](=O)[O-])cc1F\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"CC(=O)Oc1ccc([N+](=O)[O-])cc1F was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(=O)Oc1ccc([N+](=O)[O-])cc1F\", \"reactants\": [\"CC(=O)OC(C)=O\", \"O=[N+]([O-])c1ccc(O)c(F)c1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(=O)OC(C)=O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=[N+]([O-])c1ccc(O)c(F)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"ORPHLVJBJOCHBR-UHFFFAOYSA-N.WFDIJRYMOXRFFG-UHFFFAOYSA-N>>IYIKOSPRDLRAQK-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"CC(=O)Oc1ccc([N+](=O)[O-])cc1F\", \"reactants\": [\"CC(=O)OC(C)=O\", \"O=[N+]([O-])c1ccc(O)c(F)c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CC(=O)OC(C)=O\", \"results\": [{\"inchikey\": \"WFDIJRYMOXRFFG-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CC(=O)OC(C)=O\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"O=[N+]([O-])c1ccc(O)c(F)c1\", \"results\": [{\"inchikey\": \"ORPHLVJBJOCHBR-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=[N+]([O-])c1ccc(O)c(F)c1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CC(=O)Oc1ccc(N)cc1F\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(=O)Oc1ccc([N+](=O)[O-])cc1F\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(=O)Oc1ccc([N+](=O)[O-])cc1F\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(=O)OC(C)=O\": \"precursor\", \"O=[N+]([O-])c1ccc(O)c(F)c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(=O)OC(C)=O\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=[N+]([O-])c1ccc(O)c(F)c1\", \"in_stock\": true, \"children\": []}]}]}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"CC(=O)Oc1ccc(N)cc1F","task_id":"retro_47223b6e8d5da4f8648c","tool_calls":6,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_482137c669aafbac5fd1:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target OCc1cncc(-c2ccc(OC(F)(F)F)cc2)c1 in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"OCc1cncc(-c2ccc(OC(F)(F)F)cc2)c1\", \"reactants\": [\"COC(=O)c1cncc(-c2ccc(OC(F)(F)F)cc2)c1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"COC(=O)c1cncc(-c2ccc(OC(F)(F)F)cc2)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"NBKIDIHNPZMOMY-UHFFFAOYSA-N>>QEGPRUSHNJXPID-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"OCc1cncc(-c2ccc(OC(F)(F)F)cc2)c1\", \"reactants\": [\"COC(=O)c1cncc(-c2ccc(OC(F)(F)F)cc2)c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"COC(=O)c1cncc(-c2ccc(OC(F)(F)F)cc2)c1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"COC(=O)c1cncc(-c2ccc(OC(F)(F)F)cc2)c1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COC(=O)c1cncc(-c2ccc(OC(F)(F)F)cc2)c1\", \"reactants\": [\"COC(=O)c1cncc(Br)c1\", \"OB(O)c1ccc(OC(F)(F)F)cc1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"COC(=O)c1cncc(Br)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"OB(O)c1ccc(OC(F)(F)F)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"AAJZXPWBILCHAW-UHFFFAOYSA-N.HUOFUOCSQCYFPW-UHFFFAOYSA-N>>NBKIDIHNPZMOMY-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"COC(=O)c1cncc(-c2ccc(OC(F)(F)F)cc2)c1\", \"reactants\": [\"COC(=O)c1cncc(Br)c1\", \"OB(O)c1ccc(OC(F)(F)F)cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"COC(=O)c1cncc(Br)c1\", \"results\": [{\"inchikey\": \"AAJZXPWBILCHAW-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"COC(=O)c1cncc(Br)c1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"OB(O)c1ccc(OC(F)(F)F)cc1\", \"results\": [{\"inchikey\": \"HUOFUOCSQCYFPW-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"OB(O)c1ccc(OC(F)(F)F)cc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"OCc1cncc(-c2ccc(OC(F)(F)F)cc2)c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COC(=O)c1cncc(-c2ccc(OC(F)(F)F)cc2)c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COC(=O)c1cncc(-c2ccc(OC(F)(F)F)cc2)c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COC(=O)c1cncc(Br)c1\": \"precursor\", \"OB(O)c1ccc(OC(F)(F)F)cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COC(=O)c1cncc(Br)c1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"OB(O)c1ccc(OC(F)(F)F)cc1\", \"in_stock\": true, \"children\": []}]}]}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"OCc1cncc(-c2ccc(OC(F)(F)F)cc2)c1","task_id":"retro_482137c669aafbac5fd1","tool_calls":6,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_49afe18284651078fd5f:reference-expert:a0","kind":"single_route","max_steps":5,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target Cc1ccc(-c2cc(Cl)ccc2OCc2ccccc2)n1-c1ccc(C(=O)NCc2ccncc2)cc1 in at most 5 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Cc1ccc(-c2cc(Cl)ccc2OCc2ccccc2)n1-c1ccc(C(=O)NCc2ccncc2)cc1\", \"reactants\": [\"Cc1ccc(-c2cc(Cl)ccc2OCc2ccccc2)n1-c1ccc(C(=O)O)cc1\", \"NCc1ccncc1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"Cc1ccc(-c2cc(Cl)ccc2OCc2ccccc2)n1-c1ccc(C(=O)O)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"NCc1ccncc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"TXQWFIVRZNOPCK-UHFFFAOYSA-N.XWRMCNIOHUDTQU-UHFFFAOYSA-N>>DAZWJNWYRZYONG-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"Cc1ccc(-c2cc(Cl)ccc2OCc2ccccc2)n1-c1ccc(C(=O)NCc2ccncc2)cc1\", \"reactants\": [\"Cc1ccc(-c2cc(Cl)ccc2OCc2ccccc2)n1-c1ccc(C(=O)O)cc1\", \"NCc1ccncc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"Cc1ccc(-c2cc(Cl)ccc2OCc2ccccc2)n1-c1ccc(C(=O)O)cc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"NCc1ccncc1\", \"results\": [{\"inchikey\": \"TXQWFIVRZNOPCK-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"NCc1ccncc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"Cc1ccc(-c2cc(Cl)ccc2OCc2ccccc2)n1-c1ccc(C(=O)O)cc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Cc1ccc(-c2cc(Cl)ccc2OCc2ccccc2)n1-c1ccc(C(=O)O)cc1\", \"reactants\": [\"COC(=O)c1ccc(-n2c(C)ccc2-c2cc(Cl)ccc2OCc2ccccc2)cc1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"COC(=O)c1ccc(-n2c(C)ccc2-c2cc(Cl)ccc2OCc2ccccc2)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"VPBHHCPPEIDFLG-UHFFFAOYSA-N>>XWRMCNIOHUDTQU-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"Cc1ccc(-c2cc(Cl)ccc2OCc2ccccc2)n1-c1ccc(C(=O)O)cc1\", \"reactants\": [\"COC(=O)c1ccc(-n2c(C)ccc2-c2cc(Cl)ccc2OCc2ccccc2)cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"COC(=O)c1ccc(-n2c(C)ccc2-c2cc(Cl)ccc2OCc2ccccc2)cc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"COC(=O)c1ccc(-n2c(C)ccc2-c2cc(Cl)ccc2OCc2ccccc2)cc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COC(=O)c1ccc(-n2c(C)ccc2-c2cc(Cl)ccc2OCc2ccccc2)cc1\", \"reactants\": [\"CC(=O)CCC(=O)c1cc(Cl)ccc1OCc1ccccc1\", \"COC(=O)c1ccc(N)cc1\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(=O)CCC(=O)c1cc(Cl)ccc1OCc1ccccc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"COC(=O)c1ccc(N)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"LZXXNPOYQCLXRS-UHFFFAOYSA-N.RHIXXNCHQLWUGY-UHFFFAOYSA-N>>VPBHHCPPEIDFLG-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"COC(=O)c1ccc(-n2c(C)ccc2-c2cc(Cl)ccc2OCc2ccccc2)cc1\", \"reactants\": [\"CC(=O)CCC(=O)c1cc(Cl)ccc1OCc1ccccc1\", \"COC(=O)c1ccc(N)cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"CC(=O)CCC(=O)c1cc(Cl)ccc1OCc1ccccc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"COC(=O)c1ccc(N)cc1\", \"results\": [{\"inchikey\": \"LZXXNPOYQCLXRS-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"COC(=O)c1ccc(N)cc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"CC(=O)CCC(=O)c1cc(Cl)ccc1OCc1ccccc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(=O)CCC(=O)c1cc(Cl)ccc1OCc1ccccc1\", \"reactants\": [\"C=CC(C)=O\", \"O=Cc1cc(Cl)ccc1OCc1ccccc1\"]}","name":"validate_disconnection"},"id":"call_4_0","type":"function"},{"function":{"arguments":"{\"query\": \"C=CC(C)=O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=Cc1cc(Cl)ccc1OCc1ccccc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_complete\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"FUSUHKVFWTUUBE-UHFFFAOYSA-N.UKVVPQTUCJPTNI-UHFFFAOYSA-N>>RHIXXNCHQLWUGY-UHFFFAOYSA-N\", \"model_turns_remaining\": 12, \"product\": \"CC(=O)CCC(=O)c1cc(Cl)ccc1OCc1ccccc1\", \"reactants\": [\"C=CC(C)=O\", \"O=Cc1cc(Cl)ccc1OCc1ccccc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_4_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"C=CC(C)=O\", \"results\": [{\"inchikey\": \"FUSUHKVFWTUUBE-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"C=CC(C)=O\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"O=Cc1cc(Cl)ccc1OCc1ccccc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_2"},{"content":"O=Cc1cc(Cl)ccc1OCc1ccccc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"O=Cc1cc(Cl)ccc1OCc1ccccc1\", \"reactants\": [\"BrCc1ccccc1\", \"O=Cc1cc(Cl)ccc1O\"]}","name":"validate_disconnection"},"id":"call_5_0","type":"function"},{"function":{"arguments":"{\"query\": \"BrCc1ccccc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_5_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=Cc1cc(Cl)ccc1O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_5_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"AGEZXYOZHKGVCM-UHFFFAOYSA-N.FUGKCSRLAQKUHG-UHFFFAOYSA-N>>UKVVPQTUCJPTNI-UHFFFAOYSA-N\", \"model_turns_remaining\": 11, \"product\": \"O=Cc1cc(Cl)ccc1OCc1ccccc1\", \"reactants\": [\"BrCc1ccccc1\", \"O=Cc1cc(Cl)ccc1O\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_5_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 11, \"query\": \"BrCc1ccccc1\", \"results\": [{\"inchikey\": \"AGEZXYOZHKGVCM-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"BrCc1ccccc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_5_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 11, \"query\": \"O=Cc1cc(Cl)ccc1O\", \"results\": [{\"inchikey\": \"FUGKCSRLAQKUHG-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=Cc1cc(Cl)ccc1O\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_5_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"Cc1ccc(-c2cc(Cl)ccc2OCc2ccccc2)n1-c1ccc(C(=O)NCc2ccncc2)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"Cc1ccc(-c2cc(Cl)ccc2OCc2ccccc2)n1-c1ccc(C(=O)O)cc1\": \"precursor\", \"NCc1ccncc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"Cc1ccc(-c2cc(Cl)ccc2OCc2ccccc2)n1-c1ccc(C(=O)O)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COC(=O)c1ccc(-n2c(C)ccc2-c2cc(Cl)ccc2OCc2ccccc2)cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COC(=O)c1ccc(-n2c(C)ccc2-c2cc(Cl)ccc2OCc2ccccc2)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(=O)CCC(=O)c1cc(Cl)ccc1OCc1ccccc1\": \"precursor\", \"COC(=O)c1ccc(N)cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(=O)CCC(=O)c1cc(Cl)ccc1OCc1ccccc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"C=CC(C)=O\": \"precursor\", \"O=Cc1cc(Cl)ccc1OCc1ccccc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"C=CC(C)=O\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=Cc1cc(Cl)ccc1OCc1ccccc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"BrCc1ccccc1\": \"precursor\", \"O=Cc1cc(Cl)ccc1O\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"BrCc1ccccc1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=Cc1cc(Cl)ccc1O\", \"in_stock\": true, \"children\": []}]}]}]}]}, {\"type\": \"mol\", \"smiles\": \"COC(=O)c1ccc(N)cc1\", \"in_stock\": true, \"children\": []}]}]}]}]}, {\"type\": \"mol\", \"smiles\": \"NCc1ccncc1\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_6_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"Cc1ccc(-c2cc(Cl)ccc2OCc2ccccc2)n1-c1ccc(C(=O)NCc2ccncc2)cc1","task_id":"retro_49afe18284651078fd5f","tool_calls":15,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":6}
{"exact_match":true,"id":"retro_4c2c41dd532013f031af:reference-expert:a0","kind":"single_route","max_steps":4,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CCCCc1nc(N)c2[nH]cc(CCCCCCN3CCCC3)c2n1 in at most 4 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCCCc1nc(N)c2[nH]cc(CCCCCCN3CCCC3)c2n1\", \"reactants\": [\"CCCCc1nc(N)c2c(n1)c(C#CCCCCN1CCCC1)cn2COCc1ccccc1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCCCc1nc(N)c2c(n1)c(C#CCCCCN1CCCC1)cn2COCc1ccccc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"CPSGQCCGFDOFGR-UHFFFAOYSA-N>>HGKIESKSVLFTCX-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"CCCCc1nc(N)c2[nH]cc(CCCCCCN3CCCC3)c2n1\", \"reactants\": [\"CCCCc1nc(N)c2c(n1)c(C#CCCCCN1CCCC1)cn2COCc1ccccc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CCCCc1nc(N)c2c(n1)c(C#CCCCCN1CCCC1)cn2COCc1ccccc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"CCCCc1nc(N)c2c(n1)c(C#CCCCCN1CCCC1)cn2COCc1ccccc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCCCc1nc(N)c2c(n1)c(C#CCCCCN1CCCC1)cn2COCc1ccccc1\", \"reactants\": [\"C1CCNC1\", \"CCCCc1nc(N)c2c(n1)c(C#CCCCC=O)cn2COCc1ccccc1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"C1CCNC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"CCCCc1nc(N)c2c(n1)c(C#CCCCC=O)cn2COCc1ccccc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"AGVGJDLQGWKZLI-UHFFFAOYSA-N.RWRDLPDLKQPQOW-UHFFFAOYSA-N>>CPSGQCCGFDOFGR-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"CCCCc1nc(N)c2c(n1)c(C#CCCCCN1CCCC1)cn2COCc1ccccc1\", \"reactants\": [\"C1CCNC1\", \"CCCCc1nc(N)c2c(n1)c(C#CCCCC=O)cn2COCc1ccccc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"C1CCNC1\", \"results\": [{\"inchikey\": \"RWRDLPDLKQPQOW-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"C1CCNC1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CCCCc1nc(N)c2c(n1)c(C#CCCCC=O)cn2COCc1ccccc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"CCCCc1nc(N)c2c(n1)c(C#CCCCC=O)cn2COCc1ccccc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCCCc1nc(N)c2c(n1)c(C#CCCCC=O)cn2COCc1ccccc1\", \"reactants\": [\"CCCCc1nc(N)c2c(n1)c(C#CCCCCO)cn2COCc1ccccc1\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCCCc1nc(N)c2c(n1)c(C#CCCCCO)cn2COCc1ccccc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_complete\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"YXNWTJTYMZGUEJ-UHFFFAOYSA-N>>AGVGJDLQGWKZLI-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"CCCCc1nc(N)c2c(n1)c(C#CCCCC=O)cn2COCc1ccccc1\", \"reactants\": [\"CCCCc1nc(N)c2c(n1)c(C#CCCCCO)cn2COCc1ccccc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"CCCCc1nc(N)c2c(n1)c(C#CCCCCO)cn2COCc1ccccc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"CCCCc1nc(N)c2c(n1)c(C#CCCCCO)cn2COCc1ccccc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCCCc1nc(N)c2c(n1)c(C#CCCCCO)cn2COCc1ccccc1\", \"reactants\": [\"C#CCCCCO\", \"CCCCc1nc(N)c2c(n1)c(I)cn2COCc1ccccc1\"]}","name":"validate_disconnection"},"id":"call_4_0","type":"function"},{"function":{"arguments":"{\"query\": \"C#CCCCCO\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_1","type":"function"},{"function":{"arguments":"{\"query\": \"CCCCc1nc(N)c2c(n1)c(I)cn2COCc1ccccc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"GOQJMMHTSOQIEI-UHFFFAOYSA-N.PZEWYNBJBPXQPT-UHFFFAOYSA-N>>YXNWTJTYMZGUEJ-UHFFFAOYSA-N\", \"model_turns_remaining\": 12, \"product\": \"CCCCc1nc(N)c2c(n1)c(C#CCCCCO)cn2COCc1ccccc1\", \"reactants\": [\"C#CCCCCO\", \"CCCCc1nc(N)c2c(n1)c(I)cn2COCc1ccccc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_4_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"C#CCCCCO\", \"results\": [{\"inchikey\": \"GOQJMMHTSOQIEI-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"C#CCCCCO\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"CCCCc1nc(N)c2c(n1)c(I)cn2COCc1ccccc1\", \"results\": [{\"inchikey\": \"PZEWYNBJBPXQPT-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CCCCc1nc(N)c2c(n1)c(I)cn2COCc1ccccc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CCCCc1nc(N)c2[nH]cc(CCCCCCN3CCCC3)c2n1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCCCc1nc(N)c2c(n1)c(C#CCCCCN1CCCC1)cn2COCc1ccccc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCCCc1nc(N)c2c(n1)c(C#CCCCCN1CCCC1)cn2COCc1ccccc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"C1CCNC1\": \"precursor\", \"CCCCc1nc(N)c2c(n1)c(C#CCCCC=O)cn2COCc1ccccc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"C1CCNC1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"CCCCc1nc(N)c2c(n1)c(C#CCCCC=O)cn2COCc1ccccc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCCCc1nc(N)c2c(n1)c(C#CCCCCO)cn2COCc1ccccc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCCCc1nc(N)c2c(n1)c(C#CCCCCO)cn2COCc1ccccc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"C#CCCCCO\": \"precursor\", \"CCCCc1nc(N)c2c(n1)c(I)cn2COCc1ccccc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"C#CCCCCO\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"CCCCc1nc(N)c2c(n1)c(I)cn2COCc1ccccc1\", \"in_stock\": true, \"children\": []}]}]}]}]}]}]}]}]}]}}","name":"emit_routes"},"id":"call_5_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"CCCCc1nc(N)c2[nH]cc(CCCCCCN3CCCC3)c2n1","task_id":"retro_4c2c41dd532013f031af","tool_calls":11,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":5}
{"exact_match":true,"id":"retro_4d229c0fe7ee1421e4f2:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CC(C)(C)OC(=O)Nc1cccc2ccc(O[Si](C)(C)C(C)(C)C)cc12 in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(C)(C)OC(=O)Nc1cccc2ccc(O[Si](C)(C)C(C)(C)C)cc12\", \"reactants\": [\"CC(C)(C)OC(=O)Nc1cccc2ccc(O)cc12\", \"CC(C)(C)[Si](C)(C)Cl\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)OC(=O)Nc1cccc2ccc(O)cc12\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)[Si](C)(C)Cl\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"BCNZYOJHNLTNEZ-UHFFFAOYSA-N.ZZJUPBDUWFQJJQ-UHFFFAOYSA-N>>IZGJGOWIKKJLPT-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"CC(C)(C)OC(=O)Nc1cccc2ccc(O[Si](C)(C)C(C)(C)C)cc12\", \"reactants\": [\"CC(C)(C)OC(=O)Nc1cccc2ccc(O)cc12\", \"CC(C)(C)[Si](C)(C)Cl\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CC(C)(C)OC(=O)Nc1cccc2ccc(O)cc12\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CC(C)(C)[Si](C)(C)Cl\", \"results\": [{\"inchikey\": \"BCNZYOJHNLTNEZ-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CC(C)(C)[Si](C)(C)Cl\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"CC(C)(C)OC(=O)Nc1cccc2ccc(O)cc12 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(C)(C)OC(=O)Nc1cccc2ccc(O)cc12\", \"reactants\": [\"CC(C)(C)OC(=O)OC(=O)OC(C)(C)C\", \"Nc1cccc2ccc(O)cc12\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)OC(=O)OC(=O)OC(C)(C)C\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"Nc1cccc2ccc(O)cc12\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"DYHSDKLCOJIUFX-UHFFFAOYSA-N.KVHHMYZBFBSVDI-UHFFFAOYSA-N>>ZZJUPBDUWFQJJQ-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"CC(C)(C)OC(=O)Nc1cccc2ccc(O)cc12\", \"reactants\": [\"CC(C)(C)OC(=O)OC(=O)OC(C)(C)C\", \"Nc1cccc2ccc(O)cc12\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CC(C)(C)OC(=O)OC(=O)OC(C)(C)C\", \"results\": [{\"inchikey\": \"DYHSDKLCOJIUFX-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CC(C)(C)OC(=O)OC(=O)OC(C)(C)C\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"Nc1cccc2ccc(O)cc12\", \"results\": [{\"inchikey\": \"KVHHMYZBFBSVDI-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Nc1cccc2ccc(O)cc12\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)OC(=O)Nc1cccc2ccc(O[Si](C)(C)C(C)(C)C)cc12\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)(C)OC(=O)Nc1cccc2ccc(O)cc12\": \"precursor\", \"CC(C)(C)[Si](C)(C)Cl\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)OC(=O)Nc1cccc2ccc(O)cc12\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)(C)OC(=O)OC(=O)OC(C)(C)C\": \"precursor\", \"Nc1cccc2ccc(O)cc12\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)OC(=O)OC(=O)OC(C)(C)C\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"Nc1cccc2ccc(O)cc12\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"CC(C)(C)[Si](C)(C)Cl\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"CC(C)(C)OC(=O)Nc1cccc2ccc(O[Si](C)(C)C(C)(C)C)cc12","task_id":"retro_4d229c0fe7ee1421e4f2","tool_calls":7,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_4d9dd4c0c68bad37c0f9:reference-expert:a0","kind":"single_route","max_steps":4,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target Fc1cc(-c2nc(F)ccc2F)c(Cl)cn1 in at most 4 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Fc1cc(-c2nc(F)ccc2F)c(Cl)cn1\", \"reactants\": [\"O=S(=O)(Oc1nc(F)ccc1F)C(F)(F)F\", \"OB(O)c1cc(F)ncc1Cl\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"O=S(=O)(Oc1nc(F)ccc1F)C(F)(F)F\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"OB(O)c1cc(F)ncc1Cl\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"KUSCQHRJDQQDBY-UHFFFAOYSA-N.UTCNOKCGQCXVAK-UHFFFAOYSA-N>>JBSBUPQBZMCNDV-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"Fc1cc(-c2nc(F)ccc2F)c(Cl)cn1\", \"reactants\": [\"O=S(=O)(Oc1nc(F)ccc1F)C(F)(F)F\", \"OB(O)c1cc(F)ncc1Cl\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"O=S(=O)(Oc1nc(F)ccc1F)C(F)(F)F\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"OB(O)c1cc(F)ncc1Cl\", \"results\": [{\"inchikey\": \"UTCNOKCGQCXVAK-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"OB(O)c1cc(F)ncc1Cl\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"O=S(=O)(Oc1nc(F)ccc1F)C(F)(F)F was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"O=S(=O)(Oc1nc(F)ccc1F)C(F)(F)F\", \"reactants\": [\"O=S(=O)(OS(=O)(=O)C(F)(F)F)C(F)(F)F\", \"Oc1nc(F)ccc1F\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"O=S(=O)(OS(=O)(=O)C(F)(F)F)C(F)(F)F\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"Oc1nc(F)ccc1F\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"QQLOTHOYYBLZGU-UHFFFAOYSA-N.WJKHJLXJJJATHN-UHFFFAOYSA-N>>KUSCQHRJDQQDBY-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"O=S(=O)(Oc1nc(F)ccc1F)C(F)(F)F\", \"reactants\": [\"O=S(=O)(OS(=O)(=O)C(F)(F)F)C(F)(F)F\", \"Oc1nc(F)ccc1F\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"O=S(=O)(OS(=O)(=O)C(F)(F)F)C(F)(F)F\", \"results\": [{\"inchikey\": \"WJKHJLXJJJATHN-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=S(=O)(OS(=O)(=O)C(F)(F)F)C(F)(F)F\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"Oc1nc(F)ccc1F\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Oc1nc(F)ccc1F was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Oc1nc(F)ccc1F\", \"reactants\": [\"COc1nc(F)ccc1F\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"COc1nc(F)ccc1F\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"PDETXUKXCGKHKX-UHFFFAOYSA-N>>QQLOTHOYYBLZGU-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"Oc1nc(F)ccc1F\", \"reactants\": [\"COc1nc(F)ccc1F\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"COc1nc(F)ccc1F\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"COc1nc(F)ccc1F was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COc1nc(F)ccc1F\", \"reactants\": [\"CO\", \"Fc1ccc(F)c(F)n1\"]}","name":"validate_disconnection"},"id":"call_4_0","type":"function"},{"function":{"arguments":"{\"query\": \"CO\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_1","type":"function"},{"function":{"arguments":"{\"query\": \"Fc1ccc(F)c(F)n1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"HRLIANGJWPJFKW-UHFFFAOYSA-N.OKKJLVBELUTLKV-UHFFFAOYSA-N>>PDETXUKXCGKHKX-UHFFFAOYSA-N\", \"model_turns_remaining\": 12, \"product\": \"COc1nc(F)ccc1F\", \"reactants\": [\"CO\", \"Fc1ccc(F)c(F)n1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_4_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"CO\", \"results\": [{\"inchikey\": \"OKKJLVBELUTLKV-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CO\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"Fc1ccc(F)c(F)n1\", \"results\": [{\"inchikey\": \"HRLIANGJWPJFKW-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Fc1ccc(F)c(F)n1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"Fc1cc(-c2nc(F)ccc2F)c(Cl)cn1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"O=S(=O)(Oc1nc(F)ccc1F)C(F)(F)F\": \"precursor\", \"OB(O)c1cc(F)ncc1Cl\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"O=S(=O)(Oc1nc(F)ccc1F)C(F)(F)F\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"O=S(=O)(OS(=O)(=O)C(F)(F)F)C(F)(F)F\": \"precursor\", \"Oc1nc(F)ccc1F\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"O=S(=O)(OS(=O)(=O)C(F)(F)F)C(F)(F)F\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"Oc1nc(F)ccc1F\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COc1nc(F)ccc1F\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COc1nc(F)ccc1F\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CO\": \"precursor\", \"Fc1ccc(F)c(F)n1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CO\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"Fc1ccc(F)c(F)n1\", \"in_stock\": true, \"children\": []}]}]}]}]}]}]}, {\"type\": \"mol\", \"smiles\": \"OB(O)c1cc(F)ncc1Cl\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_5_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"Fc1cc(-c2nc(F)ccc2F)c(Cl)cn1","task_id":"retro_4d9dd4c0c68bad37c0f9","tool_calls":12,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":5}
{"exact_match":true,"id":"retro_4dfd0734e70f47d5f6dc:reference-expert:a0","kind":"single_route","max_steps":3,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CC(C)(C)c1ccc(OCc2ccccc2)c(CCl)c1 in at most 3 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(C)(C)c1ccc(OCc2ccccc2)c(CCl)c1\", \"reactants\": [\"CC(C)(C)c1ccc(OCc2ccccc2)c(CO)c1\", \"ClCCl\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)c1ccc(OCc2ccccc2)c(CO)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"ClCCl\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"UFLPOMDYTCFGTE-UHFFFAOYSA-N.YMWUJEATGCHHMB-UHFFFAOYSA-N>>MSCSBDFDWKDWLQ-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"CC(C)(C)c1ccc(OCc2ccccc2)c(CCl)c1\", \"reactants\": [\"CC(C)(C)c1ccc(OCc2ccccc2)c(CO)c1\", \"ClCCl\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CC(C)(C)c1ccc(OCc2ccccc2)c(CO)c1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"ClCCl\", \"results\": [{\"inchikey\": \"YMWUJEATGCHHMB-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"ClCCl\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"CC(C)(C)c1ccc(OCc2ccccc2)c(CO)c1 was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(C)(C)c1ccc(OCc2ccccc2)c(CO)c1\", \"reactants\": [\"CC(C)(C)c1ccc(OCc2ccccc2)c(C=O)c1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)c1ccc(OCc2ccccc2)c(C=O)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_complete\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"UJTIMZSCOMGULE-UHFFFAOYSA-N>>UFLPOMDYTCFGTE-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"CC(C)(C)c1ccc(OCc2ccccc2)c(CO)c1\", \"reactants\": [\"CC(C)(C)c1ccc(OCc2ccccc2)c(C=O)c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CC(C)(C)c1ccc(OCc2ccccc2)c(C=O)c1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"CC(C)(C)c1ccc(OCc2ccccc2)c(C=O)c1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(C)(C)c1ccc(OCc2ccccc2)c(C=O)c1\", \"reactants\": [\"CC(C)(C)c1ccc(O)c(C=O)c1\", \"ClCc1ccccc1\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)c1ccc(O)c(C=O)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"ClCc1ccccc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"KCXMKQUNVWSEMD-UHFFFAOYSA-N.ZVCQQLGWGRTXGC-UHFFFAOYSA-N>>UJTIMZSCOMGULE-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"CC(C)(C)c1ccc(OCc2ccccc2)c(C=O)c1\", \"reactants\": [\"CC(C)(C)c1ccc(O)c(C=O)c1\", \"ClCc1ccccc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"CC(C)(C)c1ccc(O)c(C=O)c1\", \"results\": [{\"inchikey\": \"ZVCQQLGWGRTXGC-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CC(C)(C)c1ccc(O)c(C=O)c1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"ClCc1ccccc1\", \"results\": [{\"inchikey\": \"KCXMKQUNVWSEMD-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"ClCc1ccccc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)c1ccc(OCc2ccccc2)c(CCl)c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)(C)c1ccc(OCc2ccccc2)c(CO)c1\": \"precursor\", \"ClCCl\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)c1ccc(OCc2ccccc2)c(CO)c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)(C)c1ccc(OCc2ccccc2)c(C=O)c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)c1ccc(OCc2ccccc2)c(C=O)c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)(C)c1ccc(O)c(C=O)c1\": \"precursor\", \"ClCc1ccccc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)c1ccc(O)c(C=O)c1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"ClCc1ccccc1\", \"in_stock\": true, \"children\": []}]}]}]}]}, {\"type\": \"mol\", \"smiles\": \"ClCCl\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_4_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"CC(C)(C)c1ccc(OCc2ccccc2)c(CCl)c1","task_id":"retro_4dfd0734e70f47d5f6dc","tool_calls":9,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":4}
{"exact_match":true,"id":"retro_4f4a3eea413e7e9e816d:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CC1(C)CCc2cc(O)c(Br)cc21 in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC1(C)CCc2cc(O)c(Br)cc21\", \"reactants\": [\"COc1cc2c(cc1Br)C(C)(C)CC2\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"COc1cc2c(cc1Br)C(C)(C)CC2\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"BRGINFVWQZKELS-UHFFFAOYSA-N>>FGGDDHBBDLHADV-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"CC1(C)CCc2cc(O)c(Br)cc21\", \"reactants\": [\"COc1cc2c(cc1Br)C(C)(C)CC2\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"COc1cc2c(cc1Br)C(C)(C)CC2\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"COc1cc2c(cc1Br)C(C)(C)CC2 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COc1cc2c(cc1Br)C(C)(C)CC2\", \"reactants\": [\"COc1ccc2c(c1)CCC2(C)C\", \"O=C1CCC(=O)N1Br\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"COc1ccc2c(c1)CCC2(C)C\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=C1CCC(=O)N1Br\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"DVIQJHKQDUMLBP-UHFFFAOYSA-N.PCLIMKBDDGJMGD-UHFFFAOYSA-N>>BRGINFVWQZKELS-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"COc1cc2c(cc1Br)C(C)(C)CC2\", \"reactants\": [\"COc1ccc2c(c1)CCC2(C)C\", \"O=C1CCC(=O)N1Br\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"COc1ccc2c(c1)CCC2(C)C\", \"results\": [{\"inchikey\": \"DVIQJHKQDUMLBP-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"COc1ccc2c(c1)CCC2(C)C\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"O=C1CCC(=O)N1Br\", \"results\": [{\"inchikey\": \"PCLIMKBDDGJMGD-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=C1CCC(=O)N1Br\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CC1(C)CCc2cc(O)c(Br)cc21\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COc1cc2c(cc1Br)C(C)(C)CC2\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COc1cc2c(cc1Br)C(C)(C)CC2\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COc1ccc2c(c1)CCC2(C)C\": \"precursor\", \"O=C1CCC(=O)N1Br\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COc1ccc2c(c1)CCC2(C)C\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=C1CCC(=O)N1Br\", \"in_stock\": true, \"children\": []}]}]}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"CC1(C)CCc2cc(O)c(Br)cc21","task_id":"retro_4f4a3eea413e7e9e816d","tool_calls":6,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_5035eedf2d5e92ea5f0b:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target O=C(O)c1cnc(Nc2cccc(Cl)c2)nc1C(F)(F)F in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"O=C(O)c1cnc(Nc2cccc(Cl)c2)nc1C(F)(F)F\", \"reactants\": [\"COC(=O)c1cnc(Nc2cccc(Cl)c2)nc1C(F)(F)F\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"COC(=O)c1cnc(Nc2cccc(Cl)c2)nc1C(F)(F)F\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"IMRYYHVTBCTRRU-UHFFFAOYSA-N>>FADYEGZICLBRGO-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"O=C(O)c1cnc(Nc2cccc(Cl)c2)nc1C(F)(F)F\", \"reactants\": [\"COC(=O)c1cnc(Nc2cccc(Cl)c2)nc1C(F)(F)F\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"COC(=O)c1cnc(Nc2cccc(Cl)c2)nc1C(F)(F)F\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"COC(=O)c1cnc(Nc2cccc(Cl)c2)nc1C(F)(F)F was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COC(=O)c1cnc(Nc2cccc(Cl)c2)nc1C(F)(F)F\", \"reactants\": [\"COC(=O)c1cnc(Cl)nc1C(F)(F)F\", \"Nc1cccc(Cl)c1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"COC(=O)c1cnc(Cl)nc1C(F)(F)F\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"Nc1cccc(Cl)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"PNPCRKVUWYDDST-UHFFFAOYSA-N.VLUBJYUOPNGBOQ-UHFFFAOYSA-N>>IMRYYHVTBCTRRU-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"COC(=O)c1cnc(Nc2cccc(Cl)c2)nc1C(F)(F)F\", \"reactants\": [\"COC(=O)c1cnc(Cl)nc1C(F)(F)F\", \"Nc1cccc(Cl)c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"COC(=O)c1cnc(Cl)nc1C(F)(F)F\", \"results\": [{\"inchikey\": \"VLUBJYUOPNGBOQ-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"COC(=O)c1cnc(Cl)nc1C(F)(F)F\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"Nc1cccc(Cl)c1\", \"results\": [{\"inchikey\": \"PNPCRKVUWYDDST-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Nc1cccc(Cl)c1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"O=C(O)c1cnc(Nc2cccc(Cl)c2)nc1C(F)(F)F\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COC(=O)c1cnc(Nc2cccc(Cl)c2)nc1C(F)(F)F\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COC(=O)c1cnc(Nc2cccc(Cl)c2)nc1C(F)(F)F\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COC(=O)c1cnc(Cl)nc1C(F)(F)F\": \"precursor\", \"Nc1cccc(Cl)c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COC(=O)c1cnc(Cl)nc1C(F)(F)F\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"Nc1cccc(Cl)c1\", \"in_stock\": true, \"children\": []}]}]}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"O=C(O)c1cnc(Nc2cccc(Cl)c2)nc1C(F)(F)F","task_id":"retro_5035eedf2d5e92ea5f0b","tool_calls":6,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_51841506c9fb8440bad9:reference-expert:a0","kind":"single_route","max_steps":5,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CC(C)(C)OC(=O)NCc1cc(F)c(Cl)c(N=C=S)c1Cl in at most 5 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(C)(C)OC(=O)NCc1cc(F)c(Cl)c(N=C=S)c1Cl\", \"reactants\": [\"CC(C)(C)OC(=O)NCc1cc(F)c(Cl)c(N)c1Cl\", \"O=c1ccccn1C(=S)n1ccccc1=O\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)OC(=O)NCc1cc(F)c(Cl)c(N)c1Cl\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=c1ccccn1C(=S)n1ccccc1=O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"KXMMNJQMGILZDB-UHFFFAOYSA-N.SQCGLRFZEIZWHD-UHFFFAOYSA-N>>QOCKPOAKGAFZEP-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"CC(C)(C)OC(=O)NCc1cc(F)c(Cl)c(N=C=S)c1Cl\", \"reactants\": [\"CC(C)(C)OC(=O)NCc1cc(F)c(Cl)c(N)c1Cl\", \"O=c1ccccn1C(=S)n1ccccc1=O\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CC(C)(C)OC(=O)NCc1cc(F)c(Cl)c(N)c1Cl\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"O=c1ccccn1C(=S)n1ccccc1=O\", \"results\": [{\"inchikey\": \"KXMMNJQMGILZDB-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=c1ccccn1C(=S)n1ccccc1=O\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"CC(C)(C)OC(=O)NCc1cc(F)c(Cl)c(N)c1Cl was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(C)(C)OC(=O)NCc1cc(F)c(Cl)c(N)c1Cl\", \"reactants\": [\"CC(C)(C)OC(=O)OC(=O)OC(C)(C)C\", \"NCc1cc(F)c(Cl)c(N)c1Cl\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)OC(=O)OC(=O)OC(C)(C)C\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"NCc1cc(F)c(Cl)c(N)c1Cl\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"DYHSDKLCOJIUFX-UHFFFAOYSA-N.HZMXEHWAYMUJDL-UHFFFAOYSA-N>>SQCGLRFZEIZWHD-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"CC(C)(C)OC(=O)NCc1cc(F)c(Cl)c(N)c1Cl\", \"reactants\": [\"CC(C)(C)OC(=O)OC(=O)OC(C)(C)C\", \"NCc1cc(F)c(Cl)c(N)c1Cl\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CC(C)(C)OC(=O)OC(=O)OC(C)(C)C\", \"results\": [{\"inchikey\": \"DYHSDKLCOJIUFX-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CC(C)(C)OC(=O)OC(=O)OC(C)(C)C\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"NCc1cc(F)c(Cl)c(N)c1Cl\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"NCc1cc(F)c(Cl)c(N)c1Cl was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"NCc1cc(F)c(Cl)c(N)c1Cl\", \"reactants\": [\"NC(=O)c1cc(F)c(Cl)c(N)c1Cl\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"NC(=O)c1cc(F)c(Cl)c(N)c1Cl\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"HZHFBJKDYSBTPC-UHFFFAOYSA-N>>HZMXEHWAYMUJDL-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"NCc1cc(F)c(Cl)c(N)c1Cl\", \"reactants\": [\"NC(=O)c1cc(F)c(Cl)c(N)c1Cl\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"NC(=O)c1cc(F)c(Cl)c(N)c1Cl\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"NC(=O)c1cc(F)c(Cl)c(N)c1Cl was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"NC(=O)c1cc(F)c(Cl)c(N)c1Cl\", \"reactants\": [\"NC(=O)c1cc(F)c(Cl)c([N+](=O)[O-])c1Cl\"]}","name":"validate_disconnection"},"id":"call_4_0","type":"function"},{"function":{"arguments":"{\"query\": \"NC(=O)c1cc(F)c(Cl)c([N+](=O)[O-])c1Cl\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"VHRRJKPFDGZQPN-UHFFFAOYSA-N>>HZHFBJKDYSBTPC-UHFFFAOYSA-N\", \"model_turns_remaining\": 12, \"product\": \"NC(=O)c1cc(F)c(Cl)c(N)c1Cl\", \"reactants\": [\"NC(=O)c1cc(F)c(Cl)c([N+](=O)[O-])c1Cl\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_4_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"NC(=O)c1cc(F)c(Cl)c([N+](=O)[O-])c1Cl\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_1"},{"content":"NC(=O)c1cc(F)c(Cl)c([N+](=O)[O-])c1Cl was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"NC(=O)c1cc(F)c(Cl)c([N+](=O)[O-])c1Cl\", \"reactants\": [\"N\", \"O=C(Cl)c1cc(F)c(Cl)c([N+](=O)[O-])c1Cl\"]}","name":"validate_disconnection"},"id":"call_5_0","type":"function"},{"function":{"arguments":"{\"query\": \"N\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_5_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=C(Cl)c1cc(F)c(Cl)c([N+](=O)[O-])c1Cl\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_5_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"BWQMAOINYNKMSK-UHFFFAOYSA-N.QGZKDVFQNNGYKY-UHFFFAOYSA-N>>VHRRJKPFDGZQPN-UHFFFAOYSA-N\", \"model_turns_remaining\": 11, \"product\": \"NC(=O)c1cc(F)c(Cl)c([N+](=O)[O-])c1Cl\", \"reactants\": [\"N\", \"O=C(Cl)c1cc(F)c(Cl)c([N+](=O)[O-])c1Cl\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_5_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 11, \"query\": \"N\", \"results\": [{\"inchikey\": \"QGZKDVFQNNGYKY-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"N\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_5_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 11, \"query\": \"O=C(Cl)c1cc(F)c(Cl)c([N+](=O)[O-])c1Cl\", \"results\": [{\"inchikey\": \"BWQMAOINYNKMSK-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=C(Cl)c1cc(F)c(Cl)c([N+](=O)[O-])c1Cl\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_5_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)OC(=O)NCc1cc(F)c(Cl)c(N=C=S)c1Cl\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)(C)OC(=O)NCc1cc(F)c(Cl)c(N)c1Cl\": \"precursor\", \"O=c1ccccn1C(=S)n1ccccc1=O\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)OC(=O)NCc1cc(F)c(Cl)c(N)c1Cl\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)(C)OC(=O)OC(=O)OC(C)(C)C\": \"precursor\", \"NCc1cc(F)c(Cl)c(N)c1Cl\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)OC(=O)OC(=O)OC(C)(C)C\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"NCc1cc(F)c(Cl)c(N)c1Cl\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"NC(=O)c1cc(F)c(Cl)c(N)c1Cl\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"NC(=O)c1cc(F)c(Cl)c(N)c1Cl\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"NC(=O)c1cc(F)c(Cl)c([N+](=O)[O-])c1Cl\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"NC(=O)c1cc(F)c(Cl)c([N+](=O)[O-])c1Cl\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"N\": \"precursor\", \"O=C(Cl)c1cc(F)c(Cl)c([N+](=O)[O-])c1Cl\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"N\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=C(Cl)c1cc(F)c(Cl)c([N+](=O)[O-])c1Cl\", \"in_stock\": true, \"children\": []}]}]}]}]}]}]}]}]}, {\"type\": \"mol\", \"smiles\": \"O=c1ccccn1C(=S)n1ccccc1=O\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_6_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"CC(C)(C)OC(=O)NCc1cc(F)c(Cl)c(N=C=S)c1Cl","task_id":"retro_51841506c9fb8440bad9","tool_calls":14,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":6}
{"exact_match":false,"id":"retro_52a05c6695622d6290b2:reference-expert:a0","kind":"single_route","max_steps":5,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target COc1c(Br)ccc(C(=O)O)c1F in at most 5 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COc1c(Br)ccc(C(=O)O)c1F\", \"reactants\": [\"COc1c(F)cccc1Br\", \"O=C=O\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"COc1c(F)cccc1Br\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=C=O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_complete\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"CURLTUGMZLYLDI-UHFFFAOYSA-N.RLSQPLJXDTXSCL-UHFFFAOYSA-N>>FJOKKTOXWITJGO-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"COc1c(Br)ccc(C(=O)O)c1F\", \"reactants\": [\"COc1c(F)cccc1Br\", \"O=C=O\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"COc1c(F)cccc1Br\", \"results\": [{\"inchikey\": \"RLSQPLJXDTXSCL-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"COc1c(F)cccc1Br\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"O=C=O\", \"results\": [{\"inchikey\": \"CURLTUGMZLYLDI-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=C=O\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"COc1c(Br)ccc(C(=O)O)c1F\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COc1c(F)cccc1Br\": \"precursor\", \"O=C=O\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COc1c(F)cccc1Br\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=C=O\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_2_0","type":"function"}]}],"provider":"reference","reward":0.82,"source":"reference-expert","target_smiles":"COc1c(Br)ccc(C(=O)O)c1F","task_id":"retro_52a05c6695622d6290b2","tool_calls":4,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":2}
{"exact_match":true,"id":"retro_5300106d7bbc742d688e:reference-expert:a0","kind":"single_route","max_steps":3,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target Cn1c(=O)n(C)c2cc(Oc3cccc(OCCCCNC(=O)OC(C)(C)C)c3)c(N)cc21 in at most 3 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Cn1c(=O)n(C)c2cc(Oc3cccc(OCCCCNC(=O)OC(C)(C)C)c3)c(N)cc21\", \"reactants\": [\"CC(C)(C)OC(=O)NCCCCBr\", \"Cn1c(=O)n(C)c2cc(Oc3cccc(O)c3)c(N)cc21\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)OC(=O)NCCCCBr\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"Cn1c(=O)n(C)c2cc(Oc3cccc(O)c3)c(N)cc21\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"GKGFAEREWWZBKY-UHFFFAOYSA-N.ILTFHEUCZSGPQB-UHFFFAOYSA-N>>GVYAPPXSPBEJCP-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"Cn1c(=O)n(C)c2cc(Oc3cccc(OCCCCNC(=O)OC(C)(C)C)c3)c(N)cc21\", \"reactants\": [\"CC(C)(C)OC(=O)NCCCCBr\", \"Cn1c(=O)n(C)c2cc(Oc3cccc(O)c3)c(N)cc21\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CC(C)(C)OC(=O)NCCCCBr\", \"results\": [{\"inchikey\": \"GKGFAEREWWZBKY-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CC(C)(C)OC(=O)NCCCCBr\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"Cn1c(=O)n(C)c2cc(Oc3cccc(O)c3)c(N)cc21\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"Cn1c(=O)n(C)c2cc(Oc3cccc(O)c3)c(N)cc21 was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Cn1c(=O)n(C)c2cc(Oc3cccc(O)c3)c(N)cc21\", \"reactants\": [\"Cn1c(=O)n(C)c2cc(Oc3cccc(OCc4ccccc4)c3)c(N)cc21\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"Cn1c(=O)n(C)c2cc(Oc3cccc(OCc4ccccc4)c3)c(N)cc21\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"RQUXTWCPAXSCSP-UHFFFAOYSA-N>>ILTFHEUCZSGPQB-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"Cn1c(=O)n(C)c2cc(Oc3cccc(O)c3)c(N)cc21\", \"reactants\": [\"Cn1c(=O)n(C)c2cc(Oc3cccc(OCc4ccccc4)c3)c(N)cc21\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"Cn1c(=O)n(C)c2cc(Oc3cccc(OCc4ccccc4)c3)c(N)cc21\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"Cn1c(=O)n(C)c2cc(Oc3cccc(OCc4ccccc4)c3)c(N)cc21 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Cn1c(=O)n(C)c2cc(Oc3cccc(OCc4ccccc4)c3)c(N)cc21\", \"reactants\": [\"Cn1c(=O)n(C)c2cc(Br)c(N)cc21\", \"Oc1cccc(OCc2ccccc2)c1\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"Cn1c(=O)n(C)c2cc(Br)c(N)cc21\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"Oc1cccc(OCc2ccccc2)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"FOTVZLOJAIEAOY-UHFFFAOYSA-N.SXPRALARBJCCIH-UHFFFAOYSA-N>>RQUXTWCPAXSCSP-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"Cn1c(=O)n(C)c2cc(Oc3cccc(OCc4ccccc4)c3)c(N)cc21\", \"reactants\": [\"Cn1c(=O)n(C)c2cc(Br)c(N)cc21\", \"Oc1cccc(OCc2ccccc2)c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"Cn1c(=O)n(C)c2cc(Br)c(N)cc21\", \"results\": [{\"inchikey\": \"SXPRALARBJCCIH-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Cn1c(=O)n(C)c2cc(Br)c(N)cc21\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"Oc1cccc(OCc2ccccc2)c1\", \"results\": [{\"inchikey\": \"FOTVZLOJAIEAOY-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Oc1cccc(OCc2ccccc2)c1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"Cn1c(=O)n(C)c2cc(Oc3cccc(OCCCCNC(=O)OC(C)(C)C)c3)c(N)cc21\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)(C)OC(=O)NCCCCBr\": \"precursor\", \"Cn1c(=O)n(C)c2cc(Oc3cccc(O)c3)c(N)cc21\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)OC(=O)NCCCCBr\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"Cn1c(=O)n(C)c2cc(Oc3cccc(O)c3)c(N)cc21\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"Cn1c(=O)n(C)c2cc(Oc3cccc(OCc4ccccc4)c3)c(N)cc21\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"Cn1c(=O)n(C)c2cc(Oc3cccc(OCc4ccccc4)c3)c(N)cc21\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"Cn1c(=O)n(C)c2cc(Br)c(N)cc21\": \"precursor\", \"Oc1cccc(OCc2ccccc2)c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"Cn1c(=O)n(C)c2cc(Br)c(N)cc21\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"Oc1cccc(OCc2ccccc2)c1\", \"in_stock\": true, \"children\": []}]}]}]}]}]}]}]}}","name":"emit_routes"},"id":"call_4_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"Cn1c(=O)n(C)c2cc(Oc3cccc(OCCCCNC(=O)OC(C)(C)C)c3)c(N)cc21","task_id":"retro_5300106d7bbc742d688e","tool_calls":9,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":4}
{"exact_match":true,"id":"retro_55e2c57faf514ae04a85:reference-expert:a0","kind":"single_route","max_steps":3,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CCOC(=O)c1cc(Oc2ccc(C#N)cc2)cc(Oc2c(F)cc(CNC(=O)OC(C)(C)C)cc2F)c1 in at most 3 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCOC(=O)c1cc(Oc2ccc(C#N)cc2)cc(Oc2c(F)cc(CNC(=O)OC(C)(C)C)cc2F)c1\", \"reactants\": [\"CCOC(=O)c1cc(O)cc(Oc2c(F)cc(CNC(=O)OC(C)(C)C)cc2F)c1\", \"N#Cc1ccc(F)cc1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCOC(=O)c1cc(O)cc(Oc2c(F)cc(CNC(=O)OC(C)(C)C)cc2F)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"N#Cc1ccc(F)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"AEKVBBNGWBBYLL-UHFFFAOYSA-N.CPWYQILPUTXFGH-UHFFFAOYSA-N>>PEZMTPRKWBJUIS-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"CCOC(=O)c1cc(Oc2ccc(C#N)cc2)cc(Oc2c(F)cc(CNC(=O)OC(C)(C)C)cc2F)c1\", \"reactants\": [\"CCOC(=O)c1cc(O)cc(Oc2c(F)cc(CNC(=O)OC(C)(C)C)cc2F)c1\", \"N#Cc1ccc(F)cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CCOC(=O)c1cc(O)cc(Oc2c(F)cc(CNC(=O)OC(C)(C)C)cc2F)c1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"N#Cc1ccc(F)cc1\", \"results\": [{\"inchikey\": \"AEKVBBNGWBBYLL-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"N#Cc1ccc(F)cc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"CCOC(=O)c1cc(O)cc(Oc2c(F)cc(CNC(=O)OC(C)(C)C)cc2F)c1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCOC(=O)c1cc(O)cc(Oc2c(F)cc(CNC(=O)OC(C)(C)C)cc2F)c1\", \"reactants\": [\"CC(C)(C)OC(=O)OC(=O)OC(C)(C)C\", \"CCOC(=O)c1cc(O)cc(Oc2c(F)cc(C#N)cc2F)c1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)OC(=O)OC(=O)OC(C)(C)C\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"CCOC(=O)c1cc(O)cc(Oc2c(F)cc(C#N)cc2F)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"DYHSDKLCOJIUFX-UHFFFAOYSA-N.JNFHKGCJPPCHCU-UHFFFAOYSA-N>>CPWYQILPUTXFGH-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"CCOC(=O)c1cc(O)cc(Oc2c(F)cc(CNC(=O)OC(C)(C)C)cc2F)c1\", \"reactants\": [\"CC(C)(C)OC(=O)OC(=O)OC(C)(C)C\", \"CCOC(=O)c1cc(O)cc(Oc2c(F)cc(C#N)cc2F)c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CC(C)(C)OC(=O)OC(=O)OC(C)(C)C\", \"results\": [{\"inchikey\": \"DYHSDKLCOJIUFX-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CC(C)(C)OC(=O)OC(=O)OC(C)(C)C\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CCOC(=O)c1cc(O)cc(Oc2c(F)cc(C#N)cc2F)c1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"CCOC(=O)c1cc(O)cc(Oc2c(F)cc(C#N)cc2F)c1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCOC(=O)c1cc(O)cc(Oc2c(F)cc(C#N)cc2F)c1\", \"reactants\": [\"CCOC(=O)c1cc(O)cc(O)c1\", \"N#Cc1cc(F)c(F)c(F)c1\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCOC(=O)c1cc(O)cc(O)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"N#Cc1cc(F)c(F)c(F)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"APHYVLPIZUVDTK-UHFFFAOYSA-N.XFKYJMGXZXJYBS-UHFFFAOYSA-N>>JNFHKGCJPPCHCU-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"CCOC(=O)c1cc(O)cc(Oc2c(F)cc(C#N)cc2F)c1\", \"reactants\": [\"CCOC(=O)c1cc(O)cc(O)c1\", \"N#Cc1cc(F)c(F)c(F)c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"CCOC(=O)c1cc(O)cc(O)c1\", \"results\": [{\"inchikey\": \"APHYVLPIZUVDTK-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CCOC(=O)c1cc(O)cc(O)c1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"N#Cc1cc(F)c(F)c(F)c1\", \"results\": [{\"inchikey\": \"XFKYJMGXZXJYBS-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"N#Cc1cc(F)c(F)c(F)c1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CCOC(=O)c1cc(Oc2ccc(C#N)cc2)cc(Oc2c(F)cc(CNC(=O)OC(C)(C)C)cc2F)c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCOC(=O)c1cc(O)cc(Oc2c(F)cc(CNC(=O)OC(C)(C)C)cc2F)c1\": \"precursor\", \"N#Cc1ccc(F)cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCOC(=O)c1cc(O)cc(Oc2c(F)cc(CNC(=O)OC(C)(C)C)cc2F)c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)(C)OC(=O)OC(=O)OC(C)(C)C\": \"precursor\", \"CCOC(=O)c1cc(O)cc(Oc2c(F)cc(C#N)cc2F)c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)OC(=O)OC(=O)OC(C)(C)C\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"CCOC(=O)c1cc(O)cc(Oc2c(F)cc(C#N)cc2F)c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCOC(=O)c1cc(O)cc(O)c1\": \"precursor\", \"N#Cc1cc(F)c(F)c(F)c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCOC(=O)c1cc(O)cc(O)c1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"N#Cc1cc(F)c(F)c(F)c1\", \"in_stock\": true, \"children\": []}]}]}]}]}, {\"type\": \"mol\", \"smiles\": \"N#Cc1ccc(F)cc1\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_4_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"CCOC(=O)c1cc(Oc2ccc(C#N)cc2)cc(Oc2c(F)cc(CNC(=O)OC(C)(C)C)cc2F)c1","task_id":"retro_55e2c57faf514ae04a85","tool_calls":10,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":4}
{"exact_match":true,"id":"retro_574fdd069d417053cd0f:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target C=C(C)c1ccc(O[Si](C)(C)C(C)(C)C)cc1 in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"C=C(C)c1ccc(O[Si](C)(C)C(C)(C)C)cc1\", \"reactants\": [\"CC(=O)c1ccc(O[Si](C)(C)C(C)(C)C)cc1\", \"C[P+](c1ccccc1)(c1ccccc1)c1ccccc1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(=O)c1ccc(O[Si](C)(C)C(C)(C)C)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"C[P+](c1ccccc1)(c1ccccc1)c1ccccc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"AZFQCTBZOPUVOW-UHFFFAOYSA-N.GPJCOEQTQFSCML-UHFFFAOYSA-N>>GANAAUIATAGRLR-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"C=C(C)c1ccc(O[Si](C)(C)C(C)(C)C)cc1\", \"reactants\": [\"CC(=O)c1ccc(O[Si](C)(C)C(C)(C)C)cc1\", \"C[P+](c1ccccc1)(c1ccccc1)c1ccccc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CC(=O)c1ccc(O[Si](C)(C)C(C)(C)C)cc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"C[P+](c1ccccc1)(c1ccccc1)c1ccccc1\", \"results\": [{\"inchikey\": \"AZFQCTBZOPUVOW-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"C[P+](c1ccccc1)(c1ccccc1)c1ccccc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"CC(=O)c1ccc(O[Si](C)(C)C(C)(C)C)cc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(=O)c1ccc(O[Si](C)(C)C(C)(C)C)cc1\", \"reactants\": [\"CC(=O)c1ccc(O)cc1\", \"CC(C)(C)[Si](C)(C)Cl\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(=O)c1ccc(O)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)[Si](C)(C)Cl\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"BCNZYOJHNLTNEZ-UHFFFAOYSA-N.TXFPEBPIARQUIG-UHFFFAOYSA-N>>GPJCOEQTQFSCML-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"CC(=O)c1ccc(O[Si](C)(C)C(C)(C)C)cc1\", \"reactants\": [\"CC(=O)c1ccc(O)cc1\", \"CC(C)(C)[Si](C)(C)Cl\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CC(=O)c1ccc(O)cc1\", \"results\": [{\"inchikey\": \"TXFPEBPIARQUIG-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CC(=O)c1ccc(O)cc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CC(C)(C)[Si](C)(C)Cl\", \"results\": [{\"inchikey\": \"BCNZYOJHNLTNEZ-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CC(C)(C)[Si](C)(C)Cl\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"C=C(C)c1ccc(O[Si](C)(C)C(C)(C)C)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(=O)c1ccc(O[Si](C)(C)C(C)(C)C)cc1\": \"precursor\", \"C[P+](c1ccccc1)(c1ccccc1)c1ccccc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(=O)c1ccc(O[Si](C)(C)C(C)(C)C)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(=O)c1ccc(O)cc1\": \"precursor\", \"CC(C)(C)[Si](C)(C)Cl\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(=O)c1ccc(O)cc1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"CC(C)(C)[Si](C)(C)Cl\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"C[P+](c1ccccc1)(c1ccccc1)c1ccccc1\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"C=C(C)c1ccc(O[Si](C)(C)C(C)(C)C)cc1","task_id":"retro_574fdd069d417053cd0f","tool_calls":7,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_586d6b1ff191fd3ad426:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target COC(=O)Cc1ccc(C)c(C)c1 in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COC(=O)Cc1ccc(C)c(C)c1\", \"reactants\": [\"CO\", \"Cc1ccc(CC#N)cc1C\", \"O=S(=O)(O)O\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CO\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"Cc1ccc(CC#N)cc1C\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"},{"function":{"arguments":"{\"query\": \"O=S(=O)(O)O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_3","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"OKKJLVBELUTLKV-UHFFFAOYSA-N.QAOWNCQODCNURD-UHFFFAOYSA-N.XNSHCUIBMZSUGL-UHFFFAOYSA-N>>YOOQHVXUOFXSEN-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"COC(=O)Cc1ccc(C)c(C)c1\", \"reactants\": [\"CO\", \"Cc1ccc(CC#N)cc1C\", \"O=S(=O)(O)O\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CO\", \"results\": [{\"inchikey\": \"OKKJLVBELUTLKV-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CO\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"Cc1ccc(CC#N)cc1C\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"O=S(=O)(O)O\", \"results\": [{\"inchikey\": \"QAOWNCQODCNURD-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=S(=O)(O)O\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_3"},{"content":"Cc1ccc(CC#N)cc1C was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Cc1ccc(CC#N)cc1C\", \"reactants\": [\"C#N\", \"Cc1ccc(CCl)cc1C\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"C#N\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"Cc1ccc(CCl)cc1C\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"LELOWRISYMNNSU-UHFFFAOYSA-N.UBQRAAXAHIKWRI-UHFFFAOYSA-N>>XNSHCUIBMZSUGL-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"Cc1ccc(CC#N)cc1C\", \"reactants\": [\"C#N\", \"Cc1ccc(CCl)cc1C\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"C#N\", \"results\": [{\"inchikey\": \"LELOWRISYMNNSU-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"C#N\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"Cc1ccc(CCl)cc1C\", \"results\": [{\"inchikey\": \"UBQRAAXAHIKWRI-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Cc1ccc(CCl)cc1C\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"COC(=O)Cc1ccc(C)c(C)c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CO\": \"precursor\", \"Cc1ccc(CC#N)cc1C\": \"precursor\", \"O=S(=O)(O)O\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CO\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"Cc1ccc(CC#N)cc1C\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"C#N\": \"precursor\", \"Cc1ccc(CCl)cc1C\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"C#N\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"Cc1ccc(CCl)cc1C\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"O=S(=O)(O)O\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"COC(=O)Cc1ccc(C)c(C)c1","task_id":"retro_586d6b1ff191fd3ad426","tool_calls":8,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_58870c17a563c01a22db:reference-expert:a0","kind":"single_route","max_steps":3,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target COCCOCOc1ccc(Cl)cc1CCl in at most 3 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COCCOCOc1ccc(Cl)cc1CCl\", \"reactants\": [\"COCCOCOc1ccc(Cl)cc1CO\", \"CS(=O)(=O)Cl\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"COCCOCOc1ccc(Cl)cc1CO\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"CS(=O)(=O)Cl\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"QARBMVPHQWIHKH-UHFFFAOYSA-N.RBUCQAANHGFTNA-UHFFFAOYSA-N>>LYCWFBMFDZWPOB-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"COCCOCOc1ccc(Cl)cc1CCl\", \"reactants\": [\"COCCOCOc1ccc(Cl)cc1CO\", \"CS(=O)(=O)Cl\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"COCCOCOc1ccc(Cl)cc1CO\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CS(=O)(=O)Cl\", \"results\": [{\"inchikey\": \"QARBMVPHQWIHKH-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CS(=O)(=O)Cl\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"COCCOCOc1ccc(Cl)cc1CO was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COCCOCOc1ccc(Cl)cc1CO\", \"reactants\": [\"COCCOCOc1ccc(Cl)cc1C=O\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"COCCOCOc1ccc(Cl)cc1C=O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_complete\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"OXTSFAOWBHJGKK-UHFFFAOYSA-N>>RBUCQAANHGFTNA-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"COCCOCOc1ccc(Cl)cc1CO\", \"reactants\": [\"COCCOCOc1ccc(Cl)cc1C=O\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"COCCOCOc1ccc(Cl)cc1C=O\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"COCCOCOc1ccc(Cl)cc1C=O was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COCCOCOc1ccc(Cl)cc1C=O\", \"reactants\": [\"COCCOCCl\", \"O=Cc1cc(Cl)ccc1O\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"COCCOCCl\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=Cc1cc(Cl)ccc1O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"BIAAQBNMRITRDV-UHFFFAOYSA-N.FUGKCSRLAQKUHG-UHFFFAOYSA-N>>OXTSFAOWBHJGKK-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"COCCOCOc1ccc(Cl)cc1C=O\", \"reactants\": [\"COCCOCCl\", \"O=Cc1cc(Cl)ccc1O\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"COCCOCCl\", \"results\": [{\"inchikey\": \"BIAAQBNMRITRDV-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"COCCOCCl\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"O=Cc1cc(Cl)ccc1O\", \"results\": [{\"inchikey\": \"FUGKCSRLAQKUHG-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=Cc1cc(Cl)ccc1O\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"COCCOCOc1ccc(Cl)cc1CCl\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COCCOCOc1ccc(Cl)cc1CO\": \"precursor\", \"CS(=O)(=O)Cl\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COCCOCOc1ccc(Cl)cc1CO\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COCCOCOc1ccc(Cl)cc1C=O\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COCCOCOc1ccc(Cl)cc1C=O\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COCCOCCl\": \"precursor\", \"O=Cc1cc(Cl)ccc1O\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COCCOCCl\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=Cc1cc(Cl)ccc1O\", \"in_stock\": true, \"children\": []}]}]}]}]}, {\"type\": \"mol\", \"smiles\": \"CS(=O)(=O)Cl\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_4_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"COCCOCOc1ccc(Cl)cc1CCl","task_id":"retro_58870c17a563c01a22db","tool_calls":9,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":4}
{"exact_match":true,"id":"retro_5986288847b92f81385b:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CP(C)(=O)c1ccc(Nc2nc(Cl)nc(NCC34CC5CC(CC(C5)C3)C4)n2)cc1 in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CP(C)(=O)c1ccc(Nc2nc(Cl)nc(NCC34CC5CC(CC(C5)C3)C4)n2)cc1\", \"reactants\": [\"CP(C)(=O)c1ccc(Nc2nc(Cl)nc(Cl)n2)cc1\", \"NCC12CC3CC(CC(C3)C1)C2\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CP(C)(=O)c1ccc(Nc2nc(Cl)nc(Cl)n2)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"NCC12CC3CC(CC(C3)C1)C2\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"LBVBPVBSMCLHKO-UHFFFAOYSA-N.XSOHXMFFSKTSIT-UHFFFAOYSA-N>>ZWVRFJOFZOYAIS-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"CP(C)(=O)c1ccc(Nc2nc(Cl)nc(NCC34CC5CC(CC(C5)C3)C4)n2)cc1\", \"reactants\": [\"CP(C)(=O)c1ccc(Nc2nc(Cl)nc(Cl)n2)cc1\", \"NCC12CC3CC(CC(C3)C1)C2\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CP(C)(=O)c1ccc(Nc2nc(Cl)nc(Cl)n2)cc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"NCC12CC3CC(CC(C3)C1)C2\", \"results\": [{\"inchikey\": \"XSOHXMFFSKTSIT-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"NCC12CC3CC(CC(C3)C1)C2\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"CP(C)(=O)c1ccc(Nc2nc(Cl)nc(Cl)n2)cc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CP(C)(=O)c1ccc(Nc2nc(Cl)nc(Cl)n2)cc1\", \"reactants\": [\"CP(C)(=O)c1ccc(N)cc1\", \"Clc1nc(Cl)nc(Cl)n1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CP(C)(=O)c1ccc(N)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"Clc1nc(Cl)nc(Cl)n1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"MGNCLNQXLYJVJD-UHFFFAOYSA-N.OHARHHSJWGEMMN-UHFFFAOYSA-N>>LBVBPVBSMCLHKO-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"CP(C)(=O)c1ccc(Nc2nc(Cl)nc(Cl)n2)cc1\", \"reactants\": [\"CP(C)(=O)c1ccc(N)cc1\", \"Clc1nc(Cl)nc(Cl)n1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CP(C)(=O)c1ccc(N)cc1\", \"results\": [{\"inchikey\": \"OHARHHSJWGEMMN-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CP(C)(=O)c1ccc(N)cc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"Clc1nc(Cl)nc(Cl)n1\", \"results\": [{\"inchikey\": \"MGNCLNQXLYJVJD-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Clc1nc(Cl)nc(Cl)n1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CP(C)(=O)c1ccc(Nc2nc(Cl)nc(NCC34CC5CC(CC(C5)C3)C4)n2)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CP(C)(=O)c1ccc(Nc2nc(Cl)nc(Cl)n2)cc1\": \"precursor\", \"NCC12CC3CC(CC(C3)C1)C2\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CP(C)(=O)c1ccc(Nc2nc(Cl)nc(Cl)n2)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CP(C)(=O)c1ccc(N)cc1\": \"precursor\", \"Clc1nc(Cl)nc(Cl)n1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CP(C)(=O)c1ccc(N)cc1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"Clc1nc(Cl)nc(Cl)n1\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"NCC12CC3CC(CC(C3)C1)C2\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"CP(C)(=O)c1ccc(Nc2nc(Cl)nc(NCC34CC5CC(CC(C5)C3)C4)n2)cc1","task_id":"retro_5986288847b92f81385b","tool_calls":7,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_5a5de73b717049e213cc:reference-expert:a0","kind":"single_route","max_steps":3,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target O=C(O)c1cc2cc(NS(=O)(=O)CCCN3CCCCC3)ccc2[nH]1 in at most 3 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"O=C(O)c1cc2cc(NS(=O)(=O)CCCN3CCCCC3)ccc2[nH]1\", \"reactants\": [\"CCOC(=O)c1cc2cc(NS(=O)(=O)CCCN3CCCCC3)ccc2[nH]1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCOC(=O)c1cc2cc(NS(=O)(=O)CCCN3CCCCC3)ccc2[nH]1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"WAMZBCVUUJCUJJ-UHFFFAOYSA-N>>XNYDJOKLAWTRII-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"O=C(O)c1cc2cc(NS(=O)(=O)CCCN3CCCCC3)ccc2[nH]1\", \"reactants\": [\"CCOC(=O)c1cc2cc(NS(=O)(=O)CCCN3CCCCC3)ccc2[nH]1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CCOC(=O)c1cc2cc(NS(=O)(=O)CCCN3CCCCC3)ccc2[nH]1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"CCOC(=O)c1cc2cc(NS(=O)(=O)CCCN3CCCCC3)ccc2[nH]1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCOC(=O)c1cc2cc(NS(=O)(=O)CCCN3CCCCC3)ccc2[nH]1\", \"reactants\": [\"C1CCNCC1\", \"CCOC(=O)c1cc2cc(NS(=O)(=O)CCCCl)ccc2[nH]1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"C1CCNCC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"CCOC(=O)c1cc2cc(NS(=O)(=O)CCCCl)ccc2[nH]1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"NQRYJNQNLNOLGT-UHFFFAOYSA-N.WYRFWKUMLSSJHN-UHFFFAOYSA-N>>WAMZBCVUUJCUJJ-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"CCOC(=O)c1cc2cc(NS(=O)(=O)CCCN3CCCCC3)ccc2[nH]1\", \"reactants\": [\"C1CCNCC1\", \"CCOC(=O)c1cc2cc(NS(=O)(=O)CCCCl)ccc2[nH]1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"C1CCNCC1\", \"results\": [{\"inchikey\": \"NQRYJNQNLNOLGT-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"C1CCNCC1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CCOC(=O)c1cc2cc(NS(=O)(=O)CCCCl)ccc2[nH]1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"CCOC(=O)c1cc2cc(NS(=O)(=O)CCCCl)ccc2[nH]1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCOC(=O)c1cc2cc(NS(=O)(=O)CCCCl)ccc2[nH]1\", \"reactants\": [\"CCOC(=O)c1cc2cc(N)ccc2[nH]1\", \"O=S(=O)(Cl)CCCCl\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCOC(=O)c1cc2cc(N)ccc2[nH]1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=S(=O)(Cl)CCCCl\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"GPKDGVXBXQTHRY-UHFFFAOYSA-N.WCGCOZXVVVIAEF-UHFFFAOYSA-N>>WYRFWKUMLSSJHN-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"CCOC(=O)c1cc2cc(NS(=O)(=O)CCCCl)ccc2[nH]1\", \"reactants\": [\"CCOC(=O)c1cc2cc(N)ccc2[nH]1\", \"O=S(=O)(Cl)CCCCl\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"CCOC(=O)c1cc2cc(N)ccc2[nH]1\", \"results\": [{\"inchikey\": \"WCGCOZXVVVIAEF-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CCOC(=O)c1cc2cc(N)ccc2[nH]1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"O=S(=O)(Cl)CCCCl\", \"results\": [{\"inchikey\": \"GPKDGVXBXQTHRY-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=S(=O)(Cl)CCCCl\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"O=C(O)c1cc2cc(NS(=O)(=O)CCCN3CCCCC3)ccc2[nH]1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCOC(=O)c1cc2cc(NS(=O)(=O)CCCN3CCCCC3)ccc2[nH]1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCOC(=O)c1cc2cc(NS(=O)(=O)CCCN3CCCCC3)ccc2[nH]1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"C1CCNCC1\": \"precursor\", \"CCOC(=O)c1cc2cc(NS(=O)(=O)CCCCl)ccc2[nH]1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"C1CCNCC1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"CCOC(=O)c1cc2cc(NS(=O)(=O)CCCCl)ccc2[nH]1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCOC(=O)c1cc2cc(N)ccc2[nH]1\": \"precursor\", \"O=S(=O)(Cl)CCCCl\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCOC(=O)c1cc2cc(N)ccc2[nH]1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=S(=O)(Cl)CCCCl\", \"in_stock\": true, \"children\": []}]}]}]}]}]}]}]}}","name":"emit_routes"},"id":"call_4_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"O=C(O)c1cc2cc(NS(=O)(=O)CCCN3CCCCC3)ccc2[nH]1","task_id":"retro_5a5de73b717049e213cc","tool_calls":9,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":4}
{"exact_match":true,"id":"retro_5bd41dad029a192068c9:reference-expert:a0","kind":"single_route","max_steps":4,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CCCC(C(=O)O)c1c(C)nc(-c2ccccc2)nc1-c1ccc2c(c1)CCCO2 in at most 4 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCCC(C(=O)O)c1c(C)nc(-c2ccccc2)nc1-c1ccc2c(c1)CCCO2\", \"reactants\": [\"CCCC(C(=O)OC)c1c(C)nc(-c2ccccc2)nc1-c1ccc2c(c1)CCCO2\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCCC(C(=O)OC)c1c(C)nc(-c2ccccc2)nc1-c1ccc2c(c1)CCCO2\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"ZJOXTAOBHKMNPY-UHFFFAOYSA-N>>BMFFWAJJDHCACQ-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"CCCC(C(=O)O)c1c(C)nc(-c2ccccc2)nc1-c1ccc2c(c1)CCCO2\", \"reactants\": [\"CCCC(C(=O)OC)c1c(C)nc(-c2ccccc2)nc1-c1ccc2c(c1)CCCO2\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CCCC(C(=O)OC)c1c(C)nc(-c2ccccc2)nc1-c1ccc2c(c1)CCCO2\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"CCCC(C(=O)OC)c1c(C)nc(-c2ccccc2)nc1-c1ccc2c(c1)CCCO2 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCCC(C(=O)OC)c1c(C)nc(-c2ccccc2)nc1-c1ccc2c(c1)CCCO2\", \"reactants\": [\"CC1(C)OB(c2ccc3c(c2)CCCO3)OC1(C)C\", \"CCCC(C(=O)OC)c1c(C)nc(-c2ccccc2)nc1Cl\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC1(C)OB(c2ccc3c(c2)CCCO3)OC1(C)C\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"CCCC(C(=O)OC)c1c(C)nc(-c2ccccc2)nc1Cl\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"NDSHAELUPJMEBM-UHFFFAOYSA-N.RDAQAQVTZGSONV-UHFFFAOYSA-N>>ZJOXTAOBHKMNPY-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"CCCC(C(=O)OC)c1c(C)nc(-c2ccccc2)nc1-c1ccc2c(c1)CCCO2\", \"reactants\": [\"CC1(C)OB(c2ccc3c(c2)CCCO3)OC1(C)C\", \"CCCC(C(=O)OC)c1c(C)nc(-c2ccccc2)nc1Cl\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CC1(C)OB(c2ccc3c(c2)CCCO3)OC1(C)C\", \"results\": [{\"inchikey\": \"NDSHAELUPJMEBM-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CC1(C)OB(c2ccc3c(c2)CCCO3)OC1(C)C\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CCCC(C(=O)OC)c1c(C)nc(-c2ccccc2)nc1Cl\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"CCCC(C(=O)OC)c1c(C)nc(-c2ccccc2)nc1Cl was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCCC(C(=O)OC)c1c(C)nc(-c2ccccc2)nc1Cl\", \"reactants\": [\"CCCC(C(=O)OC)c1c(C)nc(-c2ccccc2)[nH]c1=O\", \"O=P(Cl)(Cl)Cl\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCCC(C(=O)OC)c1c(C)nc(-c2ccccc2)[nH]c1=O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=P(Cl)(Cl)Cl\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"FOLXQYYSUWTMNB-UHFFFAOYSA-N.XHXFXVLFKHQFAL-UHFFFAOYSA-N>>RDAQAQVTZGSONV-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"CCCC(C(=O)OC)c1c(C)nc(-c2ccccc2)nc1Cl\", \"reactants\": [\"CCCC(C(=O)OC)c1c(C)nc(-c2ccccc2)[nH]c1=O\", \"O=P(Cl)(Cl)Cl\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"CCCC(C(=O)OC)c1c(C)nc(-c2ccccc2)[nH]c1=O\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"O=P(Cl)(Cl)Cl\", \"results\": [{\"inchikey\": \"XHXFXVLFKHQFAL-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=P(Cl)(Cl)Cl\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"CCCC(C(=O)OC)c1c(C)nc(-c2ccccc2)[nH]c1=O was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCCC(C(=O)OC)c1c(C)nc(-c2ccccc2)[nH]c1=O\", \"reactants\": [\"CCCC(C(=O)O)c1c(C)nc(-c2ccccc2)[nH]c1=O\", \"CO\"]}","name":"validate_disconnection"},"id":"call_4_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCCC(C(=O)O)c1c(C)nc(-c2ccccc2)[nH]c1=O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_1","type":"function"},{"function":{"arguments":"{\"query\": \"CO\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"JRHJKDRTSFFKCK-UHFFFAOYSA-N.OKKJLVBELUTLKV-UHFFFAOYSA-N>>FOLXQYYSUWTMNB-UHFFFAOYSA-N\", \"model_turns_remaining\": 12, \"product\": \"CCCC(C(=O)OC)c1c(C)nc(-c2ccccc2)[nH]c1=O\", \"reactants\": [\"CCCC(C(=O)O)c1c(C)nc(-c2ccccc2)[nH]c1=O\", \"CO\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_4_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"CCCC(C(=O)O)c1c(C)nc(-c2ccccc2)[nH]c1=O\", \"results\": [{\"inchikey\": \"JRHJKDRTSFFKCK-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CCCC(C(=O)O)c1c(C)nc(-c2ccccc2)[nH]c1=O\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"CO\", \"results\": [{\"inchikey\": \"OKKJLVBELUTLKV-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CO\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CCCC(C(=O)O)c1c(C)nc(-c2ccccc2)nc1-c1ccc2c(c1)CCCO2\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCCC(C(=O)OC)c1c(C)nc(-c2ccccc2)nc1-c1ccc2c(c1)CCCO2\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCCC(C(=O)OC)c1c(C)nc(-c2ccccc2)nc1-c1ccc2c(c1)CCCO2\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC1(C)OB(c2ccc3c(c2)CCCO3)OC1(C)C\": \"precursor\", \"CCCC(C(=O)OC)c1c(C)nc(-c2ccccc2)nc1Cl\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC1(C)OB(c2ccc3c(c2)CCCO3)OC1(C)C\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"CCCC(C(=O)OC)c1c(C)nc(-c2ccccc2)nc1Cl\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCCC(C(=O)OC)c1c(C)nc(-c2ccccc2)[nH]c1=O\": \"precursor\", \"O=P(Cl)(Cl)Cl\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCCC(C(=O)OC)c1c(C)nc(-c2ccccc2)[nH]c1=O\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCCC(C(=O)O)c1c(C)nc(-c2ccccc2)[nH]c1=O\": \"precursor\", \"CO\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCCC(C(=O)O)c1c(C)nc(-c2ccccc2)[nH]c1=O\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"CO\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"O=P(Cl)(Cl)Cl\", \"in_stock\": true, \"children\": []}]}]}]}]}]}]}]}}","name":"emit_routes"},"id":"call_5_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"CCCC(C(=O)O)c1c(C)nc(-c2ccccc2)nc1-c1ccc2c(c1)CCCO2","task_id":"retro_5bd41dad029a192068c9","tool_calls":12,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":5}
{"exact_match":true,"id":"retro_5c2107754a738abc5939:reference-expert:a0","kind":"single_route","max_steps":3,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target O=C1CC(=O)N(c2ccc(Cl)cc2)c2ccccc2N1 in at most 3 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"O=C1CC(=O)N(c2ccc(Cl)cc2)c2ccccc2N1\", \"reactants\": [\"Nc1ccccc1Nc1ccc(Cl)cc1\", \"O=C(Cl)CC(=O)Cl\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"Nc1ccccc1Nc1ccc(Cl)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=C(Cl)CC(=O)Cl\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"SXYFKXOFMCIXQW-UHFFFAOYSA-N.WEUBIWJPIRTWDF-UHFFFAOYSA-N>>CLQNPFKAUZRQHE-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"O=C1CC(=O)N(c2ccc(Cl)cc2)c2ccccc2N1\", \"reactants\": [\"Nc1ccccc1Nc1ccc(Cl)cc1\", \"O=C(Cl)CC(=O)Cl\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"Nc1ccccc1Nc1ccc(Cl)cc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"O=C(Cl)CC(=O)Cl\", \"results\": [{\"inchikey\": \"SXYFKXOFMCIXQW-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=C(Cl)CC(=O)Cl\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"Nc1ccccc1Nc1ccc(Cl)cc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Nc1ccccc1Nc1ccc(Cl)cc1\", \"reactants\": [\"O=[N+]([O-])c1ccccc1Nc1ccc(Cl)cc1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"O=[N+]([O-])c1ccccc1Nc1ccc(Cl)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"RCLKXSIRDRWUGX-UHFFFAOYSA-N>>WEUBIWJPIRTWDF-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"Nc1ccccc1Nc1ccc(Cl)cc1\", \"reactants\": [\"O=[N+]([O-])c1ccccc1Nc1ccc(Cl)cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"O=[N+]([O-])c1ccccc1Nc1ccc(Cl)cc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"O=[N+]([O-])c1ccccc1Nc1ccc(Cl)cc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"O=[N+]([O-])c1ccccc1Nc1ccc(Cl)cc1\", \"reactants\": [\"Nc1ccc(Cl)cc1\", \"O=[N+]([O-])c1ccccc1F\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"Nc1ccc(Cl)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=[N+]([O-])c1ccccc1F\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"PWKNBLFSJAVFAB-UHFFFAOYSA-N.QSNSCYSYFYORTR-UHFFFAOYSA-N>>RCLKXSIRDRWUGX-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"O=[N+]([O-])c1ccccc1Nc1ccc(Cl)cc1\", \"reactants\": [\"Nc1ccc(Cl)cc1\", \"O=[N+]([O-])c1ccccc1F\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"Nc1ccc(Cl)cc1\", \"results\": [{\"inchikey\": \"QSNSCYSYFYORTR-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Nc1ccc(Cl)cc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"O=[N+]([O-])c1ccccc1F\", \"results\": [{\"inchikey\": \"PWKNBLFSJAVFAB-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=[N+]([O-])c1ccccc1F\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"O=C1CC(=O)N(c2ccc(Cl)cc2)c2ccccc2N1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"Nc1ccccc1Nc1ccc(Cl)cc1\": \"precursor\", \"O=C(Cl)CC(=O)Cl\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"Nc1ccccc1Nc1ccc(Cl)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"O=[N+]([O-])c1ccccc1Nc1ccc(Cl)cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"O=[N+]([O-])c1ccccc1Nc1ccc(Cl)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"Nc1ccc(Cl)cc1\": \"precursor\", \"O=[N+]([O-])c1ccccc1F\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"Nc1ccc(Cl)cc1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=[N+]([O-])c1ccccc1F\", \"in_stock\": true, \"children\": []}]}]}]}]}, {\"type\": \"mol\", \"smiles\": \"O=C(Cl)CC(=O)Cl\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_4_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"O=C1CC(=O)N(c2ccc(Cl)cc2)c2ccccc2N1","task_id":"retro_5c2107754a738abc5939","tool_calls":9,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":4}
{"exact_match":true,"id":"retro_5c616158b4d42e91045f:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target O=C(O)c1ccc(-c2ccc(F)cc2)cc1 in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"O=C(O)c1ccc(-c2ccc(F)cc2)cc1\", \"reactants\": [\"COC(=O)c1ccc(-c2ccc(F)cc2)cc1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"COC(=O)c1ccc(-c2ccc(F)cc2)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"ACJGXBVKOGLYEL-UHFFFAOYSA-N>>LXWNTLBMNCXRQN-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"O=C(O)c1ccc(-c2ccc(F)cc2)cc1\", \"reactants\": [\"COC(=O)c1ccc(-c2ccc(F)cc2)cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"COC(=O)c1ccc(-c2ccc(F)cc2)cc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"COC(=O)c1ccc(-c2ccc(F)cc2)cc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COC(=O)c1ccc(-c2ccc(F)cc2)cc1\", \"reactants\": [\"COC(=O)c1ccc(Br)cc1\", \"OB(O)c1ccc(F)cc1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"COC(=O)c1ccc(Br)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"OB(O)c1ccc(F)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"CZNGTXVOZOWWKM-UHFFFAOYSA-N.LBUNNMJLXWQQBY-UHFFFAOYSA-N>>ACJGXBVKOGLYEL-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"COC(=O)c1ccc(-c2ccc(F)cc2)cc1\", \"reactants\": [\"COC(=O)c1ccc(Br)cc1\", \"OB(O)c1ccc(F)cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"COC(=O)c1ccc(Br)cc1\", \"results\": [{\"inchikey\": \"CZNGTXVOZOWWKM-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"COC(=O)c1ccc(Br)cc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"OB(O)c1ccc(F)cc1\", \"results\": [{\"inchikey\": \"LBUNNMJLXWQQBY-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"OB(O)c1ccc(F)cc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"O=C(O)c1ccc(-c2ccc(F)cc2)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COC(=O)c1ccc(-c2ccc(F)cc2)cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COC(=O)c1ccc(-c2ccc(F)cc2)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COC(=O)c1ccc(Br)cc1\": \"precursor\", \"OB(O)c1ccc(F)cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COC(=O)c1ccc(Br)cc1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"OB(O)c1ccc(F)cc1\", \"in_stock\": true, \"children\": []}]}]}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"O=C(O)c1ccc(-c2ccc(F)cc2)cc1","task_id":"retro_5c616158b4d42e91045f","tool_calls":6,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_5d680a80a375b85aa6cd:reference-expert:a0","kind":"single_route","max_steps":3,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target O=Cc1cccc2nnc(-c3ccccc3)cc12 in at most 3 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"O=Cc1cccc2nnc(-c3ccccc3)cc12\", \"reactants\": [\"Cc1cccc2nnc(-c3ccccc3)cc12\", \"O=[Se]=O\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"Cc1cccc2nnc(-c3ccccc3)cc12\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=[Se]=O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"JPJALAQPGMAKDF-UHFFFAOYSA-N.OQCVYWLQUGSWOO-UHFFFAOYSA-N>>QZTZMEATCCBKNZ-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"O=Cc1cccc2nnc(-c3ccccc3)cc12\", \"reactants\": [\"Cc1cccc2nnc(-c3ccccc3)cc12\", \"O=[Se]=O\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"Cc1cccc2nnc(-c3ccccc3)cc12\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"O=[Se]=O\", \"results\": [{\"inchikey\": \"JPJALAQPGMAKDF-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=[Se]=O\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"Cc1cccc2nnc(-c3ccccc3)cc12 was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Cc1cccc2nnc(-c3ccccc3)cc12\", \"reactants\": [\"Cc1cccc2nnc(-c3ccccc3)c(Cl)c12\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"Cc1cccc2nnc(-c3ccccc3)c(Cl)c12\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"UDCSZEIMDVHMAX-UHFFFAOYSA-N>>OQCVYWLQUGSWOO-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"Cc1cccc2nnc(-c3ccccc3)cc12\", \"reactants\": [\"Cc1cccc2nnc(-c3ccccc3)c(Cl)c12\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"Cc1cccc2nnc(-c3ccccc3)c(Cl)c12\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"Cc1cccc2nnc(-c3ccccc3)c(Cl)c12 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Cc1cccc2nnc(-c3ccccc3)c(Cl)c12\", \"reactants\": [\"Cc1cccc2nnc(-c3ccccc3)c(O)c12\", \"O=P(Cl)(Cl)Cl\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"Cc1cccc2nnc(-c3ccccc3)c(O)c12\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=P(Cl)(Cl)Cl\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"JMLWIBYBBQDTTH-UHFFFAOYSA-N.XHXFXVLFKHQFAL-UHFFFAOYSA-N>>UDCSZEIMDVHMAX-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"Cc1cccc2nnc(-c3ccccc3)c(Cl)c12\", \"reactants\": [\"Cc1cccc2nnc(-c3ccccc3)c(O)c12\", \"O=P(Cl)(Cl)Cl\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"Cc1cccc2nnc(-c3ccccc3)c(O)c12\", \"results\": [{\"inchikey\": \"JMLWIBYBBQDTTH-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Cc1cccc2nnc(-c3ccccc3)c(O)c12\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"O=P(Cl)(Cl)Cl\", \"results\": [{\"inchikey\": \"XHXFXVLFKHQFAL-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=P(Cl)(Cl)Cl\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"O=Cc1cccc2nnc(-c3ccccc3)cc12\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"Cc1cccc2nnc(-c3ccccc3)cc12\": \"precursor\", \"O=[Se]=O\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"Cc1cccc2nnc(-c3ccccc3)cc12\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"Cc1cccc2nnc(-c3ccccc3)c(Cl)c12\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"Cc1cccc2nnc(-c3ccccc3)c(Cl)c12\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"Cc1cccc2nnc(-c3ccccc3)c(O)c12\": \"precursor\", \"O=P(Cl)(Cl)Cl\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"Cc1cccc2nnc(-c3ccccc3)c(O)c12\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=P(Cl)(Cl)Cl\", \"in_stock\": true, \"children\": []}]}]}]}]}, {\"type\": \"mol\", \"smiles\": \"O=[Se]=O\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_4_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"O=Cc1cccc2nnc(-c3ccccc3)cc12","task_id":"retro_5d680a80a375b85aa6cd","tool_calls":9,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":4}
{"exact_match":true,"id":"retro_5da74dd512073a4bd429:reference-expert:a0","kind":"single_route","max_steps":4,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target Cc1n[nH]c2ccc(-c3cncc(N[C@@H](CNC(=O)C4CCCCC4)c4ccccc4)c3)cc12 in at most 4 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Cc1n[nH]c2ccc(-c3cncc(N[C@@H](CNC(=O)C4CCCCC4)c4ccccc4)c3)cc12\", \"reactants\": [\"Cc1n[nH]c2ccc(Br)cc12\", \"O=C(NC[C@H](Nc1cncc(Br)c1)c1ccccc1)C1CCCCC1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"Cc1n[nH]c2ccc(Br)cc12\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=C(NC[C@H](Nc1cncc(Br)c1)c1ccccc1)C1CCCCC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"BLYHEOJGLPFXEB-IBGZPJMESA-N.XDJNHYAQZWCIAH-UHFFFAOYSA-N>>UZELDQYICONQCB-MHZLTWQESA-N\", \"model_turns_remaining\": 15, \"product\": \"Cc1n[nH]c2ccc(-c3cncc(N[C@@H](CNC(=O)C4CCCCC4)c4ccccc4)c3)cc12\", \"reactants\": [\"Cc1n[nH]c2ccc(Br)cc12\", \"O=C(NC[C@H](Nc1cncc(Br)c1)c1ccccc1)C1CCCCC1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"Cc1n[nH]c2ccc(Br)cc12\", \"results\": [{\"inchikey\": \"XDJNHYAQZWCIAH-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Cc1n[nH]c2ccc(Br)cc12\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"O=C(NC[C@H](Nc1cncc(Br)c1)c1ccccc1)C1CCCCC1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"O=C(NC[C@H](Nc1cncc(Br)c1)c1ccccc1)C1CCCCC1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"O=C(NC[C@H](Nc1cncc(Br)c1)c1ccccc1)C1CCCCC1\", \"reactants\": [\"NC[C@H](Nc1cncc(Br)c1)c1ccccc1\", \"O=C(Cl)C1CCCCC1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"NC[C@H](Nc1cncc(Br)c1)c1ccccc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=C(Cl)C1CCCCC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"FUQRWWNSHSOGQF-ZDUSSCGKSA-N.RVOJTCZRIKWHDX-UHFFFAOYSA-N>>BLYHEOJGLPFXEB-IBGZPJMESA-N\", \"model_turns_remaining\": 14, \"product\": \"O=C(NC[C@H](Nc1cncc(Br)c1)c1ccccc1)C1CCCCC1\", \"reactants\": [\"NC[C@H](Nc1cncc(Br)c1)c1ccccc1\", \"O=C(Cl)C1CCCCC1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"NC[C@H](Nc1cncc(Br)c1)c1ccccc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"O=C(Cl)C1CCCCC1\", \"results\": [{\"inchikey\": \"RVOJTCZRIKWHDX-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=C(Cl)C1CCCCC1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"NC[C@H](Nc1cncc(Br)c1)c1ccccc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"NC[C@H](Nc1cncc(Br)c1)c1ccccc1\", \"reactants\": [\"O=C1c2ccccc2C(=O)N1C[C@H](Nc1cncc(Br)c1)c1ccccc1\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"O=C1c2ccccc2C(=O)N1C[C@H](Nc1cncc(Br)c1)c1ccccc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"BBGIWSXOONHDIR-IBGZPJMESA-N>>FUQRWWNSHSOGQF-ZDUSSCGKSA-N\", \"model_turns_remaining\": 13, \"product\": \"NC[C@H](Nc1cncc(Br)c1)c1ccccc1\", \"reactants\": [\"O=C1c2ccccc2C(=O)N1C[C@H](Nc1cncc(Br)c1)c1ccccc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"O=C1c2ccccc2C(=O)N1C[C@H](Nc1cncc(Br)c1)c1ccccc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"O=C1c2ccccc2C(=O)N1C[C@H](Nc1cncc(Br)c1)c1ccccc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"O=C1c2ccccc2C(=O)N1C[C@H](Nc1cncc(Br)c1)c1ccccc1\", \"reactants\": [\"O=C1NC(=O)c2ccccc21\", \"OC[C@H](Nc1cncc(Br)c1)c1ccccc1\"]}","name":"validate_disconnection"},"id":"call_4_0","type":"function"},{"function":{"arguments":"{\"query\": \"O=C1NC(=O)c2ccccc21\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_1","type":"function"},{"function":{"arguments":"{\"query\": \"OC[C@H](Nc1cncc(Br)c1)c1ccccc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"XKJCHHZQLQNZHY-UHFFFAOYSA-N.XSDKZHAOTWDLQC-ZDUSSCGKSA-N>>BBGIWSXOONHDIR-IBGZPJMESA-N\", \"model_turns_remaining\": 12, \"product\": \"O=C1c2ccccc2C(=O)N1C[C@H](Nc1cncc(Br)c1)c1ccccc1\", \"reactants\": [\"O=C1NC(=O)c2ccccc21\", \"OC[C@H](Nc1cncc(Br)c1)c1ccccc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_4_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"O=C1NC(=O)c2ccccc21\", \"results\": [{\"inchikey\": \"XKJCHHZQLQNZHY-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=C1NC(=O)c2ccccc21\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"OC[C@H](Nc1cncc(Br)c1)c1ccccc1\", \"results\": [{\"inchikey\": \"XSDKZHAOTWDLQC-ZDUSSCGKSA-N\", \"similarity\": 1.0, \"smiles\": \"OC[C@H](Nc1cncc(Br)c1)c1ccccc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"Cc1n[nH]c2ccc(-c3cncc(N[C@@H](CNC(=O)C4CCCCC4)c4ccccc4)c3)cc12\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"Cc1n[nH]c2ccc(Br)cc12\": \"precursor\", \"O=C(NC[C@H](Nc1cncc(Br)c1)c1ccccc1)C1CCCCC1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"Cc1n[nH]c2ccc(Br)cc12\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=C(NC[C@H](Nc1cncc(Br)c1)c1ccccc1)C1CCCCC1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"NC[C@H](Nc1cncc(Br)c1)c1ccccc1\": \"precursor\", \"O=C(Cl)C1CCCCC1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"NC[C@H](Nc1cncc(Br)c1)c1ccccc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"O=C1c2ccccc2C(=O)N1C[C@H](Nc1cncc(Br)c1)c1ccccc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"O=C1c2ccccc2C(=O)N1C[C@H](Nc1cncc(Br)c1)c1ccccc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"O=C1NC(=O)c2ccccc21\": \"precursor\", \"OC[C@H](Nc1cncc(Br)c1)c1ccccc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"O=C1NC(=O)c2ccccc21\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"OC[C@H](Nc1cncc(Br)c1)c1ccccc1\", \"in_stock\": true, \"children\": []}]}]}]}]}, {\"type\": \"mol\", \"smiles\": \"O=C(Cl)C1CCCCC1\", \"in_stock\": true, \"children\": []}]}]}]}]}]}}","name":"emit_routes"},"id":"call_5_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"Cc1n[nH]c2ccc(-c3cncc(N[C@@H](CNC(=O)C4CCCCC4)c4ccccc4)c3)cc12","task_id":"retro_5da74dd512073a4bd429","tool_calls":12,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":5}
{"exact_match":true,"id":"retro_5e809559093d48f2d0cd:reference-expert:a0","kind":"single_route","max_steps":4,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target COC(=O)c1ccc(Oc2ccc(COCC(=O)O)cc2)cc1 in at most 4 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COC(=O)c1ccc(Oc2ccc(COCC(=O)O)cc2)cc1\", \"reactants\": [\"COC(=O)c1ccc(Oc2ccc(COCC(=O)OC(C)(C)C)cc2)cc1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"COC(=O)c1ccc(Oc2ccc(COCC(=O)OC(C)(C)C)cc2)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"AXRVFZKPCGZIDW-UHFFFAOYSA-N>>QLIKFBITPBEHOC-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"COC(=O)c1ccc(Oc2ccc(COCC(=O)O)cc2)cc1\", \"reactants\": [\"COC(=O)c1ccc(Oc2ccc(COCC(=O)OC(C)(C)C)cc2)cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"COC(=O)c1ccc(Oc2ccc(COCC(=O)OC(C)(C)C)cc2)cc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"COC(=O)c1ccc(Oc2ccc(COCC(=O)OC(C)(C)C)cc2)cc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COC(=O)c1ccc(Oc2ccc(COCC(=O)OC(C)(C)C)cc2)cc1\", \"reactants\": [\"CC(C)(C)OC(=O)CBr\", \"COC(=O)c1ccc(Oc2ccc(CO)cc2)cc1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)OC(=O)CBr\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"COC(=O)c1ccc(Oc2ccc(CO)cc2)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"BNWCETAHAJSBFG-UHFFFAOYSA-N.JWXMZGZHOKHQFO-UHFFFAOYSA-N>>AXRVFZKPCGZIDW-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"COC(=O)c1ccc(Oc2ccc(COCC(=O)OC(C)(C)C)cc2)cc1\", \"reactants\": [\"CC(C)(C)OC(=O)CBr\", \"COC(=O)c1ccc(Oc2ccc(CO)cc2)cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CC(C)(C)OC(=O)CBr\", \"results\": [{\"inchikey\": \"BNWCETAHAJSBFG-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CC(C)(C)OC(=O)CBr\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"COC(=O)c1ccc(Oc2ccc(CO)cc2)cc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"COC(=O)c1ccc(Oc2ccc(CO)cc2)cc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COC(=O)c1ccc(Oc2ccc(CO)cc2)cc1\", \"reactants\": [\"COC(=O)c1ccc(Oc2ccc(C=O)cc2)cc1\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"COC(=O)c1ccc(Oc2ccc(C=O)cc2)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_complete\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"SVESMWAUWYDHSK-UHFFFAOYSA-N>>JWXMZGZHOKHQFO-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"COC(=O)c1ccc(Oc2ccc(CO)cc2)cc1\", \"reactants\": [\"COC(=O)c1ccc(Oc2ccc(C=O)cc2)cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"COC(=O)c1ccc(Oc2ccc(C=O)cc2)cc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"COC(=O)c1ccc(Oc2ccc(C=O)cc2)cc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COC(=O)c1ccc(Oc2ccc(C=O)cc2)cc1\", \"reactants\": [\"COC(=O)c1ccc(O)cc1\", \"O=Cc1ccc(F)cc1\"]}","name":"validate_disconnection"},"id":"call_4_0","type":"function"},{"function":{"arguments":"{\"query\": \"COC(=O)c1ccc(O)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=Cc1ccc(F)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"LXCFILQKKLGQFO-UHFFFAOYSA-N.UOQXIWFBQSVDPP-UHFFFAOYSA-N>>SVESMWAUWYDHSK-UHFFFAOYSA-N\", \"model_turns_remaining\": 12, \"product\": \"COC(=O)c1ccc(Oc2ccc(C=O)cc2)cc1\", \"reactants\": [\"COC(=O)c1ccc(O)cc1\", \"O=Cc1ccc(F)cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_4_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"COC(=O)c1ccc(O)cc1\", \"results\": [{\"inchikey\": \"LXCFILQKKLGQFO-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"COC(=O)c1ccc(O)cc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"O=Cc1ccc(F)cc1\", \"results\": [{\"inchikey\": \"UOQXIWFBQSVDPP-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=Cc1ccc(F)cc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"COC(=O)c1ccc(Oc2ccc(COCC(=O)O)cc2)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COC(=O)c1ccc(Oc2ccc(COCC(=O)OC(C)(C)C)cc2)cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COC(=O)c1ccc(Oc2ccc(COCC(=O)OC(C)(C)C)cc2)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)(C)OC(=O)CBr\": \"precursor\", \"COC(=O)c1ccc(Oc2ccc(CO)cc2)cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)OC(=O)CBr\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"COC(=O)c1ccc(Oc2ccc(CO)cc2)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COC(=O)c1ccc(Oc2ccc(C=O)cc2)cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COC(=O)c1ccc(Oc2ccc(C=O)cc2)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COC(=O)c1ccc(O)cc1\": \"precursor\", \"O=Cc1ccc(F)cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COC(=O)c1ccc(O)cc1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=Cc1ccc(F)cc1\", \"in_stock\": true, \"children\": []}]}]}]}]}]}]}]}]}]}}","name":"emit_routes"},"id":"call_5_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"COC(=O)c1ccc(Oc2ccc(COCC(=O)O)cc2)cc1","task_id":"retro_5e809559093d48f2d0cd","tool_calls":11,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":5}
{"exact_match":false,"id":"retro_5e875a65ef116911c820:reference-expert:a0","kind":"single_route","max_steps":3,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CC(C)(C)[Si](C)(C)OCc1cccc(CN)c1 in at most 3 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(C)(C)[Si](C)(C)OCc1cccc(CN)c1\", \"reactants\": [\"CC(C)(C)[Si](C)(C)OCc1cccc(C#N)c1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)[Si](C)(C)OCc1cccc(C#N)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_complete\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"AWMMPWPVCLDCDU-UHFFFAOYSA-N>>XVYYLKBIICHPSO-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"CC(C)(C)[Si](C)(C)OCc1cccc(CN)c1\", \"reactants\": [\"CC(C)(C)[Si](C)(C)OCc1cccc(C#N)c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CC(C)(C)[Si](C)(C)OCc1cccc(C#N)c1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"CC(C)(C)[Si](C)(C)OCc1cccc(C#N)c1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(C)(C)[Si](C)(C)OCc1cccc(C#N)c1\", \"reactants\": [\"CC(C)(C)[Si](C)(C)Cl\", \"N#Cc1cccc(CO)c1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)[Si](C)(C)Cl\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"N#Cc1cccc(CO)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"BCNZYOJHNLTNEZ-UHFFFAOYSA-N.PCOFIIVWHXIDGT-UHFFFAOYSA-N>>AWMMPWPVCLDCDU-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"CC(C)(C)[Si](C)(C)OCc1cccc(C#N)c1\", \"reactants\": [\"CC(C)(C)[Si](C)(C)Cl\", \"N#Cc1cccc(CO)c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CC(C)(C)[Si](C)(C)Cl\", \"results\": [{\"inchikey\": \"BCNZYOJHNLTNEZ-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CC(C)(C)[Si](C)(C)Cl\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"N#Cc1cccc(CO)c1\", \"results\": [{\"inchikey\": \"PCOFIIVWHXIDGT-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"N#Cc1cccc(CO)c1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)[Si](C)(C)OCc1cccc(CN)c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)(C)[Si](C)(C)OCc1cccc(C#N)c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)[Si](C)(C)OCc1cccc(C#N)c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)(C)[Si](C)(C)Cl\": \"precursor\", \"N#Cc1cccc(CO)c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)[Si](C)(C)Cl\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"N#Cc1cccc(CO)c1\", \"in_stock\": true, \"children\": []}]}]}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":0.866667,"source":"reference-expert","target_smiles":"CC(C)(C)[Si](C)(C)OCc1cccc(CN)c1","task_id":"retro_5e875a65ef116911c820","tool_calls":6,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_628868c96e6c17e67195:reference-expert:a0","kind":"single_route","max_steps":3,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target O=C1NC2(CCCCCC2)Nc2cc(-c3ccncc3)sc21 in at most 3 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"O=C1NC2(CCCCCC2)Nc2cc(-c3ccncc3)sc21\", \"reactants\": [\"NC(=O)c1sc(-c2ccncc2)cc1N\", \"O=C1CCCCCC1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"NC(=O)c1sc(-c2ccncc2)cc1N\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=C1CCCCCC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"CGZZMOTZOONQIA-UHFFFAOYSA-N.ZVSCZFDPBANIAB-UHFFFAOYSA-N>>FCNATYJSJSHBTN-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"O=C1NC2(CCCCCC2)Nc2cc(-c3ccncc3)sc21\", \"reactants\": [\"NC(=O)c1sc(-c2ccncc2)cc1N\", \"O=C1CCCCCC1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"NC(=O)c1sc(-c2ccncc2)cc1N\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"O=C1CCCCCC1\", \"results\": [{\"inchikey\": \"CGZZMOTZOONQIA-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=C1CCCCCC1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"NC(=O)c1sc(-c2ccncc2)cc1N was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"NC(=O)c1sc(-c2ccncc2)cc1N\", \"reactants\": [\"N\", \"Nc1cc(-c2ccncc2)sc1C(=O)O\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"N\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"Nc1cc(-c2ccncc2)sc1C(=O)O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"KLKGICPGTDUYLZ-UHFFFAOYSA-N.QGZKDVFQNNGYKY-UHFFFAOYSA-N>>ZVSCZFDPBANIAB-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"NC(=O)c1sc(-c2ccncc2)cc1N\", \"reactants\": [\"N\", \"Nc1cc(-c2ccncc2)sc1C(=O)O\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"N\", \"results\": [{\"inchikey\": \"QGZKDVFQNNGYKY-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"N\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"Nc1cc(-c2ccncc2)sc1C(=O)O\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Nc1cc(-c2ccncc2)sc1C(=O)O was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Nc1cc(-c2ccncc2)sc1C(=O)O\", \"reactants\": [\"COC(=O)c1sc(-c2ccncc2)cc1N\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"COC(=O)c1sc(-c2ccncc2)cc1N\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"MTWPBJBUARILTH-UHFFFAOYSA-N>>KLKGICPGTDUYLZ-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"Nc1cc(-c2ccncc2)sc1C(=O)O\", \"reactants\": [\"COC(=O)c1sc(-c2ccncc2)cc1N\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"COC(=O)c1sc(-c2ccncc2)cc1N\", \"results\": [{\"inchikey\": \"MTWPBJBUARILTH-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"COC(=O)c1sc(-c2ccncc2)cc1N\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"O=C1NC2(CCCCCC2)Nc2cc(-c3ccncc3)sc21\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"NC(=O)c1sc(-c2ccncc2)cc1N\": \"precursor\", \"O=C1CCCCCC1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"NC(=O)c1sc(-c2ccncc2)cc1N\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"N\": \"precursor\", \"Nc1cc(-c2ccncc2)sc1C(=O)O\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"N\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"Nc1cc(-c2ccncc2)sc1C(=O)O\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COC(=O)c1sc(-c2ccncc2)cc1N\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COC(=O)c1sc(-c2ccncc2)cc1N\", \"in_stock\": true, \"children\": []}]}]}]}]}, {\"type\": \"mol\", \"smiles\": \"O=C1CCCCCC1\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_4_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"O=C1NC2(CCCCCC2)Nc2cc(-c3ccncc3)sc21","task_id":"retro_628868c96e6c17e67195","tool_calls":9,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":4}
{"exact_match":true,"id":"retro_62a46617a0707665e278:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target Brc1ccc2ocnc2c1 in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Brc1ccc2ocnc2c1\", \"reactants\": [\"CCOC(OCC)OCC\", \"Nc1cc(Br)ccc1O\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCOC(OCC)OCC\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"Nc1cc(Br)ccc1O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"GKASDNZWUGIAMG-UHFFFAOYSA-N.JHRIPENGTGSNPJ-UHFFFAOYSA-N>>PGOGTWDYLFKOHI-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"Brc1ccc2ocnc2c1\", \"reactants\": [\"CCOC(OCC)OCC\", \"Nc1cc(Br)ccc1O\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CCOC(OCC)OCC\", \"results\": [{\"inchikey\": \"GKASDNZWUGIAMG-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CCOC(OCC)OCC\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"Nc1cc(Br)ccc1O\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"Nc1cc(Br)ccc1O was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Nc1cc(Br)ccc1O\", \"reactants\": [\"O=[N+]([O-])c1cc(Br)ccc1O\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"O=[N+]([O-])c1cc(Br)ccc1O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"CUTFAPGINUFNQM-UHFFFAOYSA-N>>JHRIPENGTGSNPJ-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"Nc1cc(Br)ccc1O\", \"reactants\": [\"O=[N+]([O-])c1cc(Br)ccc1O\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"O=[N+]([O-])c1cc(Br)ccc1O\", \"results\": [{\"inchikey\": \"CUTFAPGINUFNQM-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=[N+]([O-])c1cc(Br)ccc1O\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"Brc1ccc2ocnc2c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCOC(OCC)OCC\": \"precursor\", \"Nc1cc(Br)ccc1O\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCOC(OCC)OCC\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"Nc1cc(Br)ccc1O\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"O=[N+]([O-])c1cc(Br)ccc1O\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"O=[N+]([O-])c1cc(Br)ccc1O\", \"in_stock\": true, \"children\": []}]}]}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"Brc1ccc2ocnc2c1","task_id":"retro_62a46617a0707665e278","tool_calls":6,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_638adc2d70640e709ac2:reference-expert:a0","kind":"single_route","max_steps":3,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CS(=O)(=O)OCc1c(Cl)cccc1C(F)(F)F in at most 3 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CS(=O)(=O)OCc1c(Cl)cccc1C(F)(F)F\", \"reactants\": [\"CS(=O)(=O)Cl\", \"OCc1c(Cl)cccc1C(F)(F)F\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CS(=O)(=O)Cl\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"OCc1c(Cl)cccc1C(F)(F)F\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"AIXZCUCSYPVDQR-UHFFFAOYSA-N.QARBMVPHQWIHKH-UHFFFAOYSA-N>>SKSKPZRDBKZMEB-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"CS(=O)(=O)OCc1c(Cl)cccc1C(F)(F)F\", \"reactants\": [\"CS(=O)(=O)Cl\", \"OCc1c(Cl)cccc1C(F)(F)F\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CS(=O)(=O)Cl\", \"results\": [{\"inchikey\": \"QARBMVPHQWIHKH-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CS(=O)(=O)Cl\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"OCc1c(Cl)cccc1C(F)(F)F\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"OCc1c(Cl)cccc1C(F)(F)F was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"OCc1c(Cl)cccc1C(F)(F)F\", \"reactants\": [\"COC(=O)c1c(Cl)cccc1C(F)(F)F\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"COC(=O)c1c(Cl)cccc1C(F)(F)F\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"AFRJOFHMWLLAGS-UHFFFAOYSA-N>>AIXZCUCSYPVDQR-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"OCc1c(Cl)cccc1C(F)(F)F\", \"reactants\": [\"COC(=O)c1c(Cl)cccc1C(F)(F)F\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"COC(=O)c1c(Cl)cccc1C(F)(F)F\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"COC(=O)c1c(Cl)cccc1C(F)(F)F was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COC(=O)c1c(Cl)cccc1C(F)(F)F\", \"reactants\": [\"CO\", \"O=C(O)c1c(Cl)cccc1C(F)(F)F\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"CO\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=C(O)c1c(Cl)cccc1C(F)(F)F\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"OHWGZCNPFKBCDJ-UHFFFAOYSA-N.OKKJLVBELUTLKV-UHFFFAOYSA-N>>AFRJOFHMWLLAGS-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"COC(=O)c1c(Cl)cccc1C(F)(F)F\", \"reactants\": [\"CO\", \"O=C(O)c1c(Cl)cccc1C(F)(F)F\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"CO\", \"results\": [{\"inchikey\": \"OKKJLVBELUTLKV-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CO\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"O=C(O)c1c(Cl)cccc1C(F)(F)F\", \"results\": [{\"inchikey\": \"OHWGZCNPFKBCDJ-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=C(O)c1c(Cl)cccc1C(F)(F)F\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CS(=O)(=O)OCc1c(Cl)cccc1C(F)(F)F\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CS(=O)(=O)Cl\": \"precursor\", \"OCc1c(Cl)cccc1C(F)(F)F\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CS(=O)(=O)Cl\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"OCc1c(Cl)cccc1C(F)(F)F\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COC(=O)c1c(Cl)cccc1C(F)(F)F\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COC(=O)c1c(Cl)cccc1C(F)(F)F\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CO\": \"precursor\", \"O=C(O)c1c(Cl)cccc1C(F)(F)F\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CO\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=C(O)c1c(Cl)cccc1C(F)(F)F\", \"in_stock\": true, \"children\": []}]}]}]}]}]}]}]}}","name":"emit_routes"},"id":"call_4_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"CS(=O)(=O)OCc1c(Cl)cccc1C(F)(F)F","task_id":"retro_638adc2d70640e709ac2","tool_calls":9,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":4}
{"exact_match":true,"id":"retro_6657cd73253379597ae4:reference-expert:a0","kind":"single_route","max_steps":3,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target Clc1cccc(N2CCCC2)c1CN1CCNCC1 in at most 3 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Clc1cccc(N2CCCC2)c1CN1CCNCC1\", \"reactants\": [\"CC(C)(C)OC(=O)N1CCN(Cc2c(Cl)cccc2N2CCCC2)CC1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)OC(=O)N1CCN(Cc2c(Cl)cccc2N2CCCC2)CC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"BXVPKMQIDJSPJO-UHFFFAOYSA-N>>MAVCOHWJHCZWCH-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"Clc1cccc(N2CCCC2)c1CN1CCNCC1\", \"reactants\": [\"CC(C)(C)OC(=O)N1CCN(Cc2c(Cl)cccc2N2CCCC2)CC1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CC(C)(C)OC(=O)N1CCN(Cc2c(Cl)cccc2N2CCCC2)CC1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"CC(C)(C)OC(=O)N1CCN(Cc2c(Cl)cccc2N2CCCC2)CC1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(C)(C)OC(=O)N1CCN(Cc2c(Cl)cccc2N2CCCC2)CC1\", \"reactants\": [\"CC(C)(C)OC(=O)N1CCNCC1\", \"O=Cc1c(Cl)cccc1N1CCCC1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)OC(=O)N1CCNCC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=Cc1c(Cl)cccc1N1CCCC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"AFHHLLAGAHZCKB-UHFFFAOYSA-N.CWXPZXBSDSIRCS-UHFFFAOYSA-N>>BXVPKMQIDJSPJO-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"CC(C)(C)OC(=O)N1CCN(Cc2c(Cl)cccc2N2CCCC2)CC1\", \"reactants\": [\"CC(C)(C)OC(=O)N1CCNCC1\", \"O=Cc1c(Cl)cccc1N1CCCC1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CC(C)(C)OC(=O)N1CCNCC1\", \"results\": [{\"inchikey\": \"CWXPZXBSDSIRCS-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CC(C)(C)OC(=O)N1CCNCC1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"O=Cc1c(Cl)cccc1N1CCCC1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"O=Cc1c(Cl)cccc1N1CCCC1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"O=Cc1c(Cl)cccc1N1CCCC1\", \"reactants\": [\"C1CCNC1\", \"O=Cc1c(F)cccc1Cl\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"C1CCNC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=Cc1c(F)cccc1Cl\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"OACPOWYLLGHGCR-UHFFFAOYSA-N.RWRDLPDLKQPQOW-UHFFFAOYSA-N>>AFHHLLAGAHZCKB-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"O=Cc1c(Cl)cccc1N1CCCC1\", \"reactants\": [\"C1CCNC1\", \"O=Cc1c(F)cccc1Cl\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"C1CCNC1\", \"results\": [{\"inchikey\": \"RWRDLPDLKQPQOW-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"C1CCNC1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"O=Cc1c(F)cccc1Cl\", \"results\": [{\"inchikey\": \"OACPOWYLLGHGCR-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=Cc1c(F)cccc1Cl\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"Clc1cccc(N2CCCC2)c1CN1CCNCC1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)(C)OC(=O)N1CCN(Cc2c(Cl)cccc2N2CCCC2)CC1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)OC(=O)N1CCN(Cc2c(Cl)cccc2N2CCCC2)CC1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)(C)OC(=O)N1CCNCC1\": \"precursor\", \"O=Cc1c(Cl)cccc1N1CCCC1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)OC(=O)N1CCNCC1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=Cc1c(Cl)cccc1N1CCCC1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"C1CCNC1\": \"precursor\", \"O=Cc1c(F)cccc1Cl\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"C1CCNC1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=Cc1c(F)cccc1Cl\", \"in_stock\": true, \"children\": []}]}]}]}]}]}]}]}}","name":"emit_routes"},"id":"call_4_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"Clc1cccc(N2CCCC2)c1CN1CCNCC1","task_id":"retro_6657cd73253379597ae4","tool_calls":9,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":4}
{"exact_match":true,"id":"retro_66dc64a416a93c42bca2:reference-expert:a0","kind":"single_route","max_steps":3,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target COc1ccc(C(OCc2cccc(CN=C=S)c2)(c2ccccc2)c2ccc(OC)cc2)cc1 in at most 3 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COc1ccc(C(OCc2cccc(CN=C=S)c2)(c2ccccc2)c2ccc(OC)cc2)cc1\", \"reactants\": [\"COc1ccc(C(OCc2cccc(CN)c2)(c2ccccc2)c2ccc(OC)cc2)cc1\", \"S=C=S\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"COc1ccc(C(OCc2cccc(CN)c2)(c2ccccc2)c2ccc(OC)cc2)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"S=C=S\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"GVNSTHUWGACHEX-UHFFFAOYSA-N.QGJOPFRUJISHPQ-UHFFFAOYSA-N>>OLRLZGQEVGQVNB-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"COc1ccc(C(OCc2cccc(CN=C=S)c2)(c2ccccc2)c2ccc(OC)cc2)cc1\", \"reactants\": [\"COc1ccc(C(OCc2cccc(CN)c2)(c2ccccc2)c2ccc(OC)cc2)cc1\", \"S=C=S\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"COc1ccc(C(OCc2cccc(CN)c2)(c2ccccc2)c2ccc(OC)cc2)cc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"S=C=S\", \"results\": [{\"inchikey\": \"QGJOPFRUJISHPQ-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"S=C=S\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"COc1ccc(C(OCc2cccc(CN)c2)(c2ccccc2)c2ccc(OC)cc2)cc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COc1ccc(C(OCc2cccc(CN)c2)(c2ccccc2)c2ccc(OC)cc2)cc1\", \"reactants\": [\"COc1ccc(C(OCc2cccc(C#N)c2)(c2ccccc2)c2ccc(OC)cc2)cc1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"COc1ccc(C(OCc2cccc(C#N)c2)(c2ccccc2)c2ccc(OC)cc2)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_complete\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"SKBRETRSERXGJE-UHFFFAOYSA-N>>GVNSTHUWGACHEX-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"COc1ccc(C(OCc2cccc(CN)c2)(c2ccccc2)c2ccc(OC)cc2)cc1\", \"reactants\": [\"COc1ccc(C(OCc2cccc(C#N)c2)(c2ccccc2)c2ccc(OC)cc2)cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"COc1ccc(C(OCc2cccc(C#N)c2)(c2ccccc2)c2ccc(OC)cc2)cc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"COc1ccc(C(OCc2cccc(C#N)c2)(c2ccccc2)c2ccc(OC)cc2)cc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COc1ccc(C(OCc2cccc(C#N)c2)(c2ccccc2)c2ccc(OC)cc2)cc1\", \"reactants\": [\"COc1ccc(C(Cl)(c2ccccc2)c2ccc(OC)cc2)cc1\", \"N#Cc1cccc(CO)c1\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"COc1ccc(C(Cl)(c2ccccc2)c2ccc(OC)cc2)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"N#Cc1cccc(CO)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"JBWYRBLDOOOJEU-UHFFFAOYSA-N.PCOFIIVWHXIDGT-UHFFFAOYSA-N>>SKBRETRSERXGJE-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"COc1ccc(C(OCc2cccc(C#N)c2)(c2ccccc2)c2ccc(OC)cc2)cc1\", \"reactants\": [\"COc1ccc(C(Cl)(c2ccccc2)c2ccc(OC)cc2)cc1\", \"N#Cc1cccc(CO)c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"COc1ccc(C(Cl)(c2ccccc2)c2ccc(OC)cc2)cc1\", \"results\": [{\"inchikey\": \"JBWYRBLDOOOJEU-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"COc1ccc(C(Cl)(c2ccccc2)c2ccc(OC)cc2)cc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"N#Cc1cccc(CO)c1\", \"results\": [{\"inchikey\": \"PCOFIIVWHXIDGT-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"N#Cc1cccc(CO)c1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"COc1ccc(C(OCc2cccc(CN=C=S)c2)(c2ccccc2)c2ccc(OC)cc2)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COc1ccc(C(OCc2cccc(CN)c2)(c2ccccc2)c2ccc(OC)cc2)cc1\": \"precursor\", \"S=C=S\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COc1ccc(C(OCc2cccc(CN)c2)(c2ccccc2)c2ccc(OC)cc2)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COc1ccc(C(OCc2cccc(C#N)c2)(c2ccccc2)c2ccc(OC)cc2)cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COc1ccc(C(OCc2cccc(C#N)c2)(c2ccccc2)c2ccc(OC)cc2)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COc1ccc(C(Cl)(c2ccccc2)c2ccc(OC)cc2)cc1\": \"precursor\", \"N#Cc1cccc(CO)c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COc1ccc(C(Cl)(c2ccccc2)c2ccc(OC)cc2)cc1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"N#Cc1cccc(CO)c1\", \"in_stock\": true, \"children\": []}]}]}]}]}, {\"type\": \"mol\", \"smiles\": \"S=C=S\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_4_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"COc1ccc(C(OCc2cccc(CN=C=S)c2)(c2ccccc2)c2ccc(OC)cc2)cc1","task_id":"retro_66dc64a416a93c42bca2","tool_calls":9,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":4}
{"exact_match":true,"id":"retro_67bf0f1c3c625e96358a:reference-expert:a0","kind":"single_route","max_steps":3,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target O=CNCc1ccc(CN2CCN(c3ccccc3)CC2)cc1 in at most 3 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"O=CNCc1ccc(CN2CCN(c3ccccc3)CC2)cc1\", \"reactants\": [\"NCc1ccc(CN2CCN(c3ccccc3)CC2)cc1\", \"O=CO\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"NCc1ccc(CN2CCN(c3ccccc3)CC2)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=CO\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"BDAGIHXWWSANSR-UHFFFAOYSA-N.ZYNZANRHADJREE-UHFFFAOYSA-N>>CJORNJBPVPKTIJ-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"O=CNCc1ccc(CN2CCN(c3ccccc3)CC2)cc1\", \"reactants\": [\"NCc1ccc(CN2CCN(c3ccccc3)CC2)cc1\", \"O=CO\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"NCc1ccc(CN2CCN(c3ccccc3)CC2)cc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"O=CO\", \"results\": [{\"inchikey\": \"BDAGIHXWWSANSR-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=CO\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"NCc1ccc(CN2CCN(c3ccccc3)CC2)cc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"NCc1ccc(CN2CCN(c3ccccc3)CC2)cc1\", \"reactants\": [\"CC(=O)NCc1ccc(CN2CCN(c3ccccc3)CC2)cc1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(=O)NCc1ccc(CN2CCN(c3ccccc3)CC2)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"ZCHBUYAQIKDSED-UHFFFAOYSA-N>>ZYNZANRHADJREE-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"NCc1ccc(CN2CCN(c3ccccc3)CC2)cc1\", \"reactants\": [\"CC(=O)NCc1ccc(CN2CCN(c3ccccc3)CC2)cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CC(=O)NCc1ccc(CN2CCN(c3ccccc3)CC2)cc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"CC(=O)NCc1ccc(CN2CCN(c3ccccc3)CC2)cc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(=O)NCc1ccc(CN2CCN(c3ccccc3)CC2)cc1\", \"reactants\": [\"CC(=O)NCc1ccc(CCl)cc1\", \"c1ccc(N2CCNCC2)cc1\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(=O)NCc1ccc(CCl)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"c1ccc(N2CCNCC2)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"UADHOMUWKSPYAI-UHFFFAOYSA-N.YZTJYBJCZXZGCT-UHFFFAOYSA-N>>ZCHBUYAQIKDSED-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"CC(=O)NCc1ccc(CN2CCN(c3ccccc3)CC2)cc1\", \"reactants\": [\"CC(=O)NCc1ccc(CCl)cc1\", \"c1ccc(N2CCNCC2)cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"CC(=O)NCc1ccc(CCl)cc1\", \"results\": [{\"inchikey\": \"UADHOMUWKSPYAI-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CC(=O)NCc1ccc(CCl)cc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"c1ccc(N2CCNCC2)cc1\", \"results\": [{\"inchikey\": \"YZTJYBJCZXZGCT-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"c1ccc(N2CCNCC2)cc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"O=CNCc1ccc(CN2CCN(c3ccccc3)CC2)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"NCc1ccc(CN2CCN(c3ccccc3)CC2)cc1\": \"precursor\", \"O=CO\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"NCc1ccc(CN2CCN(c3ccccc3)CC2)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(=O)NCc1ccc(CN2CCN(c3ccccc3)CC2)cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(=O)NCc1ccc(CN2CCN(c3ccccc3)CC2)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(=O)NCc1ccc(CCl)cc1\": \"precursor\", \"c1ccc(N2CCNCC2)cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(=O)NCc1ccc(CCl)cc1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"c1ccc(N2CCNCC2)cc1\", \"in_stock\": true, \"children\": []}]}]}]}]}, {\"type\": \"mol\", \"smiles\": \"O=CO\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_4_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"O=CNCc1ccc(CN2CCN(c3ccccc3)CC2)cc1","task_id":"retro_67bf0f1c3c625e96358a","tool_calls":9,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":4}
{"exact_match":true,"id":"retro_67e6c05e5c41801d50e5:reference-expert:a0","kind":"single_route","max_steps":3,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target c1ccc2ncc(Nc3ncnc4c3CN(CC3CCCCC3)C4)cc2c1 in at most 3 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"c1ccc2ncc(Nc3ncnc4c3CN(CC3CCCCC3)C4)cc2c1\", \"reactants\": [\"O=CC1CCCCC1\", \"c1ccc2ncc(Nc3ncnc4c3CNC4)cc2c1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"O=CC1CCCCC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"c1ccc2ncc(Nc3ncnc4c3CNC4)cc2c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"APYZBCVYDZOEQP-UHFFFAOYSA-N.KVFDZFBHBWTVID-UHFFFAOYSA-N>>NMPMKPIPOOEJHL-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"c1ccc2ncc(Nc3ncnc4c3CN(CC3CCCCC3)C4)cc2c1\", \"reactants\": [\"O=CC1CCCCC1\", \"c1ccc2ncc(Nc3ncnc4c3CNC4)cc2c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"O=CC1CCCCC1\", \"results\": [{\"inchikey\": \"KVFDZFBHBWTVID-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=CC1CCCCC1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"c1ccc2ncc(Nc3ncnc4c3CNC4)cc2c1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"c1ccc2ncc(Nc3ncnc4c3CNC4)cc2c1 was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"c1ccc2ncc(Nc3ncnc4c3CNC4)cc2c1\", \"reactants\": [\"CC(C)(C)OC(=O)N1Cc2ncnc(Nc3cnc4ccccc4c3)c2C1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)OC(=O)N1Cc2ncnc(Nc3cnc4ccccc4c3)c2C1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"AXIUFDZXPKAKMV-UHFFFAOYSA-N>>APYZBCVYDZOEQP-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"c1ccc2ncc(Nc3ncnc4c3CNC4)cc2c1\", \"reactants\": [\"CC(C)(C)OC(=O)N1Cc2ncnc(Nc3cnc4ccccc4c3)c2C1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CC(C)(C)OC(=O)N1Cc2ncnc(Nc3cnc4ccccc4c3)c2C1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"CC(C)(C)OC(=O)N1Cc2ncnc(Nc3cnc4ccccc4c3)c2C1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(C)(C)OC(=O)N1Cc2ncnc(Nc3cnc4ccccc4c3)c2C1\", \"reactants\": [\"Brc1cnc2ccccc2c1\", \"CC(C)(C)OC(=O)N1Cc2ncnc(N)c2C1\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"Brc1cnc2ccccc2c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)OC(=O)N1Cc2ncnc(N)c2C1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"ZGFSOAJSURGSAF-UHFFFAOYSA-N.ZGIKWINFUGEQEO-UHFFFAOYSA-N>>AXIUFDZXPKAKMV-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"CC(C)(C)OC(=O)N1Cc2ncnc(Nc3cnc4ccccc4c3)c2C1\", \"reactants\": [\"Brc1cnc2ccccc2c1\", \"CC(C)(C)OC(=O)N1Cc2ncnc(N)c2C1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"Brc1cnc2ccccc2c1\", \"results\": [{\"inchikey\": \"ZGIKWINFUGEQEO-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Brc1cnc2ccccc2c1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"CC(C)(C)OC(=O)N1Cc2ncnc(N)c2C1\", \"results\": [{\"inchikey\": \"ZGFSOAJSURGSAF-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CC(C)(C)OC(=O)N1Cc2ncnc(N)c2C1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"c1ccc2ncc(Nc3ncnc4c3CN(CC3CCCCC3)C4)cc2c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"O=CC1CCCCC1\": \"precursor\", \"c1ccc2ncc(Nc3ncnc4c3CNC4)cc2c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"O=CC1CCCCC1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"c1ccc2ncc(Nc3ncnc4c3CNC4)cc2c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)(C)OC(=O)N1Cc2ncnc(Nc3cnc4ccccc4c3)c2C1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)OC(=O)N1Cc2ncnc(Nc3cnc4ccccc4c3)c2C1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"Brc1cnc2ccccc2c1\": \"precursor\", \"CC(C)(C)OC(=O)N1Cc2ncnc(N)c2C1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"Brc1cnc2ccccc2c1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"CC(C)(C)OC(=O)N1Cc2ncnc(N)c2C1\", \"in_stock\": true, \"children\": []}]}]}]}]}]}]}]}}","name":"emit_routes"},"id":"call_4_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"c1ccc2ncc(Nc3ncnc4c3CN(CC3CCCCC3)C4)cc2c1","task_id":"retro_67e6c05e5c41801d50e5","tool_calls":9,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":4}
{"exact_match":true,"id":"retro_69005cad836e4ae82bd3:reference-expert:a0","kind":"single_route","max_steps":3,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CCOC(=O)c1cc2cc(CO)ccn2c1-c1cccnc1 in at most 3 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCOC(=O)c1cc2cc(CO)ccn2c1-c1cccnc1\", \"reactants\": [\"Brc1cccnc1\", \"CCOC(=O)c1cc2cc(CO)ccn2c1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"Brc1cccnc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"CCOC(=O)c1cc2cc(CO)ccn2c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"GHNRCTUDBZRJKL-UHFFFAOYSA-N.NYPYPOZNGOXYSU-UHFFFAOYSA-N>>JCDWUFRCDPDQEN-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"CCOC(=O)c1cc2cc(CO)ccn2c1-c1cccnc1\", \"reactants\": [\"Brc1cccnc1\", \"CCOC(=O)c1cc2cc(CO)ccn2c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"Brc1cccnc1\", \"results\": [{\"inchikey\": \"NYPYPOZNGOXYSU-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Brc1cccnc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CCOC(=O)c1cc2cc(CO)ccn2c1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"CCOC(=O)c1cc2cc(CO)ccn2c1 was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCOC(=O)c1cc2cc(CO)ccn2c1\", \"reactants\": [\"CCOC(=O)c1cc2cc(C(C)(C)O[SiH2]C(C)(C)C)ccn2c1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCOC(=O)c1cc2cc(C(C)(C)O[SiH2]C(C)(C)C)ccn2c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"CMJKQJVEZXGOKO-UHFFFAOYSA-N>>GHNRCTUDBZRJKL-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"CCOC(=O)c1cc2cc(CO)ccn2c1\", \"reactants\": [\"CCOC(=O)c1cc2cc(C(C)(C)O[SiH2]C(C)(C)C)ccn2c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CCOC(=O)c1cc2cc(C(C)(C)O[SiH2]C(C)(C)C)ccn2c1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"CCOC(=O)c1cc2cc(C(C)(C)O[SiH2]C(C)(C)C)ccn2c1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCOC(=O)c1cc2cc(C(C)(C)O[SiH2]C(C)(C)C)ccn2c1\", \"reactants\": [\"CCOC(=O)C(=O)CBr\", \"Cc1cc(C(C)(C)O[SiH2]C(C)(C)C)ccn1\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCOC(=O)C(=O)CBr\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"Cc1cc(C(C)(C)O[SiH2]C(C)(C)C)ccn1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"DOCQMVQMOGMLLY-UHFFFAOYSA-N.VICYTAYPKBLQFB-UHFFFAOYSA-N>>CMJKQJVEZXGOKO-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"CCOC(=O)c1cc2cc(C(C)(C)O[SiH2]C(C)(C)C)ccn2c1\", \"reactants\": [\"CCOC(=O)C(=O)CBr\", \"Cc1cc(C(C)(C)O[SiH2]C(C)(C)C)ccn1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"CCOC(=O)C(=O)CBr\", \"results\": [{\"inchikey\": \"VICYTAYPKBLQFB-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CCOC(=O)C(=O)CBr\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"Cc1cc(C(C)(C)O[SiH2]C(C)(C)C)ccn1\", \"results\": [{\"inchikey\": \"DOCQMVQMOGMLLY-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Cc1cc(C(C)(C)O[SiH2]C(C)(C)C)ccn1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CCOC(=O)c1cc2cc(CO)ccn2c1-c1cccnc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"Brc1cccnc1\": \"precursor\", \"CCOC(=O)c1cc2cc(CO)ccn2c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"Brc1cccnc1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"CCOC(=O)c1cc2cc(CO)ccn2c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCOC(=O)c1cc2cc(C(C)(C)O[SiH2]C(C)(C)C)ccn2c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCOC(=O)c1cc2cc(C(C)(C)O[SiH2]C(C)(C)C)ccn2c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCOC(=O)C(=O)CBr\": \"precursor\", \"Cc1cc(C(C)(C)O[SiH2]C(C)(C)C)ccn1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCOC(=O)C(=O)CBr\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"Cc1cc(C(C)(C)O[SiH2]C(C)(C)C)ccn1\", \"in_stock\": true, \"children\": []}]}]}]}]}]}]}]}}","name":"emit_routes"},"id":"call_4_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"CCOC(=O)c1cc2cc(CO)ccn2c1-c1cccnc1","task_id":"retro_69005cad836e4ae82bd3","tool_calls":9,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":4}
{"exact_match":true,"id":"retro_690a76e1d554af634a2e:reference-expert:a0","kind":"single_route","max_steps":3,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target COc1ccc(-c2c(-c3ccccc3F)oc3ncnc(NCCCCCC(=O)O)c23)cc1 in at most 3 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COc1ccc(-c2c(-c3ccccc3F)oc3ncnc(NCCCCCC(=O)O)c23)cc1\", \"reactants\": [\"COC(=O)CCCCCNc1ncnc2oc(-c3ccccc3F)c(-c3ccc(OC)cc3)c12\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"COC(=O)CCCCCNc1ncnc2oc(-c3ccccc3F)c(-c3ccc(OC)cc3)c12\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"FJPVLJLYMIJFKD-UHFFFAOYSA-N>>NFDJMMHBZGQHSE-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"COc1ccc(-c2c(-c3ccccc3F)oc3ncnc(NCCCCCC(=O)O)c23)cc1\", \"reactants\": [\"COC(=O)CCCCCNc1ncnc2oc(-c3ccccc3F)c(-c3ccc(OC)cc3)c12\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"COC(=O)CCCCCNc1ncnc2oc(-c3ccccc3F)c(-c3ccc(OC)cc3)c12\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"COC(=O)CCCCCNc1ncnc2oc(-c3ccccc3F)c(-c3ccc(OC)cc3)c12 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COC(=O)CCCCCNc1ncnc2oc(-c3ccccc3F)c(-c3ccc(OC)cc3)c12\", \"reactants\": [\"COC(=O)CCCCCNc1ncnc2oc(Br)c(-c3ccc(OC)cc3)c12\", \"OB(O)c1ccccc1F\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"COC(=O)CCCCCNc1ncnc2oc(Br)c(-c3ccc(OC)cc3)c12\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"OB(O)c1ccccc1F\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"DXYMXBLVOFCNQB-UHFFFAOYSA-N.QCSLIRFWJPOENV-UHFFFAOYSA-N>>FJPVLJLYMIJFKD-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"COC(=O)CCCCCNc1ncnc2oc(-c3ccccc3F)c(-c3ccc(OC)cc3)c12\", \"reactants\": [\"COC(=O)CCCCCNc1ncnc2oc(Br)c(-c3ccc(OC)cc3)c12\", \"OB(O)c1ccccc1F\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"COC(=O)CCCCCNc1ncnc2oc(Br)c(-c3ccc(OC)cc3)c12\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"OB(O)c1ccccc1F\", \"results\": [{\"inchikey\": \"QCSLIRFWJPOENV-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"OB(O)c1ccccc1F\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"COC(=O)CCCCCNc1ncnc2oc(Br)c(-c3ccc(OC)cc3)c12 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COC(=O)CCCCCNc1ncnc2oc(Br)c(-c3ccc(OC)cc3)c12\", \"reactants\": [\"COC(=O)CCCCCNc1ncnc2occ(-c3ccc(OC)cc3)c12\", \"O=C1CCC(=O)N1Br\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"COC(=O)CCCCCNc1ncnc2occ(-c3ccc(OC)cc3)c12\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=C1CCC(=O)N1Br\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"PCLIMKBDDGJMGD-UHFFFAOYSA-N.XAALIEIEMNWCCF-UHFFFAOYSA-N>>DXYMXBLVOFCNQB-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"COC(=O)CCCCCNc1ncnc2oc(Br)c(-c3ccc(OC)cc3)c12\", \"reactants\": [\"COC(=O)CCCCCNc1ncnc2occ(-c3ccc(OC)cc3)c12\", \"O=C1CCC(=O)N1Br\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"COC(=O)CCCCCNc1ncnc2occ(-c3ccc(OC)cc3)c12\", \"results\": [{\"inchikey\": \"XAALIEIEMNWCCF-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"COC(=O)CCCCCNc1ncnc2occ(-c3ccc(OC)cc3)c12\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"O=C1CCC(=O)N1Br\", \"results\": [{\"inchikey\": \"PCLIMKBDDGJMGD-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=C1CCC(=O)N1Br\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"COc1ccc(-c2c(-c3ccccc3F)oc3ncnc(NCCCCCC(=O)O)c23)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COC(=O)CCCCCNc1ncnc2oc(-c3ccccc3F)c(-c3ccc(OC)cc3)c12\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COC(=O)CCCCCNc1ncnc2oc(-c3ccccc3F)c(-c3ccc(OC)cc3)c12\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COC(=O)CCCCCNc1ncnc2oc(Br)c(-c3ccc(OC)cc3)c12\": \"precursor\", \"OB(O)c1ccccc1F\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COC(=O)CCCCCNc1ncnc2oc(Br)c(-c3ccc(OC)cc3)c12\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COC(=O)CCCCCNc1ncnc2occ(-c3ccc(OC)cc3)c12\": \"precursor\", \"O=C1CCC(=O)N1Br\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COC(=O)CCCCCNc1ncnc2occ(-c3ccc(OC)cc3)c12\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=C1CCC(=O)N1Br\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"OB(O)c1ccccc1F\", \"in_stock\": true, \"children\": []}]}]}]}]}]}}","name":"emit_routes"},"id":"call_4_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"COc1ccc(-c2c(-c3ccccc3F)oc3ncnc(NCCCCCC(=O)O)c23)cc1","task_id":"retro_690a76e1d554af634a2e","tool_calls":9,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":4}
{"exact_match":true,"id":"retro_693b20c0c9255292cc53:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target N[C@@H](Cc1cccnc1)C(=O)NC(CCCc1ccccc1)CCCc1ccccc1 in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"N[C@@H](Cc1cccnc1)C(=O)NC(CCCc1ccccc1)CCCc1ccccc1\", \"reactants\": [\"CC(C)(C)OC(=O)N[C@@H](Cc1cccnc1)C(=O)NC(CCCc1ccccc1)CCCc1ccccc1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)OC(=O)N[C@@H](Cc1cccnc1)C(=O)NC(CCCc1ccccc1)CCCc1ccccc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"KWUQVVLYXGTGNL-LJAQVGFWSA-N>>OHRUUWGDCUOSCB-SANMLTNESA-N\", \"model_turns_remaining\": 15, \"product\": \"N[C@@H](Cc1cccnc1)C(=O)NC(CCCc1ccccc1)CCCc1ccccc1\", \"reactants\": [\"CC(C)(C)OC(=O)N[C@@H](Cc1cccnc1)C(=O)NC(CCCc1ccccc1)CCCc1ccccc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CC(C)(C)OC(=O)N[C@@H](Cc1cccnc1)C(=O)NC(CCCc1ccccc1)CCCc1ccccc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"CC(C)(C)OC(=O)N[C@@H](Cc1cccnc1)C(=O)NC(CCCc1ccccc1)CCCc1ccccc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(C)(C)OC(=O)N[C@@H](Cc1cccnc1)C(=O)NC(CCCc1ccccc1)CCCc1ccccc1\", \"reactants\": [\"CC(C)(C)OC(=O)N[C@@H](Cc1cccnc1)C(=O)O\", \"NC(CCCc1ccccc1)CCCc1ccccc1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)OC(=O)N[C@@H](Cc1cccnc1)C(=O)O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"NC(CCCc1ccccc1)CCCc1ccccc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"JLBCSWWZSSVXRQ-JTQLQIEISA-N.VVMIDIFEFVJUCD-UHFFFAOYSA-N>>KWUQVVLYXGTGNL-LJAQVGFWSA-N\", \"model_turns_remaining\": 14, \"product\": \"CC(C)(C)OC(=O)N[C@@H](Cc1cccnc1)C(=O)NC(CCCc1ccccc1)CCCc1ccccc1\", \"reactants\": [\"CC(C)(C)OC(=O)N[C@@H](Cc1cccnc1)C(=O)O\", \"NC(CCCc1ccccc1)CCCc1ccccc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CC(C)(C)OC(=O)N[C@@H](Cc1cccnc1)C(=O)O\", \"results\": [{\"inchikey\": \"JLBCSWWZSSVXRQ-JTQLQIEISA-N\", \"similarity\": 1.0, \"smiles\": \"CC(C)(C)OC(=O)N[C@@H](Cc1cccnc1)C(=O)O\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"NC(CCCc1ccccc1)CCCc1ccccc1\", \"results\": [{\"inchikey\": \"VVMIDIFEFVJUCD-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"NC(CCCc1ccccc1)CCCc1ccccc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"N[C@@H](Cc1cccnc1)C(=O)NC(CCCc1ccccc1)CCCc1ccccc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)(C)OC(=O)N[C@@H](Cc1cccnc1)C(=O)NC(CCCc1ccccc1)CCCc1ccccc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)OC(=O)N[C@@H](Cc1cccnc1)C(=O)NC(CCCc1ccccc1)CCCc1ccccc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)(C)OC(=O)N[C@@H](Cc1cccnc1)C(=O)O\": \"precursor\", \"NC(CCCc1ccccc1)CCCc1ccccc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)OC(=O)N[C@@H](Cc1cccnc1)C(=O)O\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"NC(CCCc1ccccc1)CCCc1ccccc1\", \"in_stock\": true, \"children\": []}]}]}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"N[C@@H](Cc1cccnc1)C(=O)NC(CCCc1ccccc1)CCCc1ccccc1","task_id":"retro_693b20c0c9255292cc53","tool_calls":6,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_69b1d14d9d5466eb7558:reference-expert:a0","kind":"single_route","max_steps":4,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CNC(=O)CCCC1CCN(C(=O)Nc2cc(Oc3ccc4c(ccn4C(=O)NC)c3)ccn2)CC1 in at most 4 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CNC(=O)CCCC1CCN(C(=O)Nc2cc(Oc3ccc4c(ccn4C(=O)NC)c3)ccn2)CC1\", \"reactants\": [\"CN\", \"CNC(=O)n1ccc2cc(Oc3ccnc(NC(=O)N4CCC(CCCC(=O)O)CC4)c3)ccc21\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CN\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"CNC(=O)n1ccc2cc(Oc3ccnc(NC(=O)N4CCC(CCCC(=O)O)CC4)c3)ccc21\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"BAVYZALUXZFZLV-UHFFFAOYSA-N.WMWYGLBTZIBXFH-UHFFFAOYSA-N>>OAHDZWNFYBZOEH-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"CNC(=O)CCCC1CCN(C(=O)Nc2cc(Oc3ccc4c(ccn4C(=O)NC)c3)ccn2)CC1\", \"reactants\": [\"CN\", \"CNC(=O)n1ccc2cc(Oc3ccnc(NC(=O)N4CCC(CCCC(=O)O)CC4)c3)ccc21\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CN\", \"results\": [{\"inchikey\": \"BAVYZALUXZFZLV-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CN\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CNC(=O)n1ccc2cc(Oc3ccnc(NC(=O)N4CCC(CCCC(=O)O)CC4)c3)ccc21\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"CNC(=O)n1ccc2cc(Oc3ccnc(NC(=O)N4CCC(CCCC(=O)O)CC4)c3)ccc21 was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CNC(=O)n1ccc2cc(Oc3ccnc(NC(=O)N4CCC(CCCC(=O)O)CC4)c3)ccc21\", \"reactants\": [\"CCOC(=O)CCCC1CCN(C(=O)Nc2cc(Oc3ccc4c(ccn4C(=O)NC)c3)ccn2)CC1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCOC(=O)CCCC1CCN(C(=O)Nc2cc(Oc3ccc4c(ccn4C(=O)NC)c3)ccn2)CC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"WYJKQOIPJSAIIF-UHFFFAOYSA-N>>WMWYGLBTZIBXFH-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"CNC(=O)n1ccc2cc(Oc3ccnc(NC(=O)N4CCC(CCCC(=O)O)CC4)c3)ccc21\", \"reactants\": [\"CCOC(=O)CCCC1CCN(C(=O)Nc2cc(Oc3ccc4c(ccn4C(=O)NC)c3)ccn2)CC1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CCOC(=O)CCCC1CCN(C(=O)Nc2cc(Oc3ccc4c(ccn4C(=O)NC)c3)ccn2)CC1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"CCOC(=O)CCCC1CCN(C(=O)Nc2cc(Oc3ccc4c(ccn4C(=O)NC)c3)ccn2)CC1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCOC(=O)CCCC1CCN(C(=O)Nc2cc(Oc3ccc4c(ccn4C(=O)NC)c3)ccn2)CC1\", \"reactants\": [\"CCOC(=O)CCCC1CCNCC1\", \"CNC(=O)n1ccc2cc(Oc3ccnc(N(C(=O)Oc4ccccc4)C(=O)Oc4ccccc4)c3)ccc21\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCOC(=O)CCCC1CCNCC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"CNC(=O)n1ccc2cc(Oc3ccnc(N(C(=O)Oc4ccccc4)C(=O)Oc4ccccc4)c3)ccc21\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"BIIPKMCNNFYSRL-UHFFFAOYSA-N.XGABTHFOTUYVMO-UHFFFAOYSA-N>>WYJKQOIPJSAIIF-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"CCOC(=O)CCCC1CCN(C(=O)Nc2cc(Oc3ccc4c(ccn4C(=O)NC)c3)ccn2)CC1\", \"reactants\": [\"CCOC(=O)CCCC1CCNCC1\", \"CNC(=O)n1ccc2cc(Oc3ccnc(N(C(=O)Oc4ccccc4)C(=O)Oc4ccccc4)c3)ccc21\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"CCOC(=O)CCCC1CCNCC1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"CNC(=O)n1ccc2cc(Oc3ccnc(N(C(=O)Oc4ccccc4)C(=O)Oc4ccccc4)c3)ccc21\", \"results\": [{\"inchikey\": \"BIIPKMCNNFYSRL-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CNC(=O)n1ccc2cc(Oc3ccnc(N(C(=O)Oc4ccccc4)C(=O)Oc4ccccc4)c3)ccc21\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"CCOC(=O)CCCC1CCNCC1 was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCOC(=O)CCCC1CCNCC1\", \"reactants\": [\"CCOC(=O)CCCC1CCN(C(=O)OC(C)(C)C)CC1\"]}","name":"validate_disconnection"},"id":"call_4_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCOC(=O)CCCC1CCN(C(=O)OC(C)(C)C)CC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"BJEDOFBBFSVQCP-UHFFFAOYSA-N>>XGABTHFOTUYVMO-UHFFFAOYSA-N\", \"model_turns_remaining\": 12, \"product\": \"CCOC(=O)CCCC1CCNCC1\", \"reactants\": [\"CCOC(=O)CCCC1CCN(C(=O)OC(C)(C)C)CC1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_4_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"CCOC(=O)CCCC1CCN(C(=O)OC(C)(C)C)CC1\", \"results\": [{\"inchikey\": \"BJEDOFBBFSVQCP-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CCOC(=O)CCCC1CCN(C(=O)OC(C)(C)C)CC1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_1"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CNC(=O)CCCC1CCN(C(=O)Nc2cc(Oc3ccc4c(ccn4C(=O)NC)c3)ccn2)CC1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CN\": \"precursor\", \"CNC(=O)n1ccc2cc(Oc3ccnc(NC(=O)N4CCC(CCCC(=O)O)CC4)c3)ccc21\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CN\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"CNC(=O)n1ccc2cc(Oc3ccnc(NC(=O)N4CCC(CCCC(=O)O)CC4)c3)ccc21\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCOC(=O)CCCC1CCN(C(=O)Nc2cc(Oc3ccc4c(ccn4C(=O)NC)c3)ccn2)CC1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCOC(=O)CCCC1CCN(C(=O)Nc2cc(Oc3ccc4c(ccn4C(=O)NC)c3)ccn2)CC1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCOC(=O)CCCC1CCNCC1\": \"precursor\", \"CNC(=O)n1ccc2cc(Oc3ccnc(N(C(=O)Oc4ccccc4)C(=O)Oc4ccccc4)c3)ccc21\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCOC(=O)CCCC1CCNCC1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCOC(=O)CCCC1CCN(C(=O)OC(C)(C)C)CC1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCOC(=O)CCCC1CCN(C(=O)OC(C)(C)C)CC1\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"CNC(=O)n1ccc2cc(Oc3ccnc(N(C(=O)Oc4ccccc4)C(=O)Oc4ccccc4)c3)ccc21\", \"in_stock\": true, \"children\": []}]}]}]}]}]}]}]}}","name":"emit_routes"},"id":"call_5_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"CNC(=O)CCCC1CCN(C(=O)Nc2cc(Oc3ccc4c(ccn4C(=O)NC)c3)ccn2)CC1","task_id":"retro_69b1d14d9d5466eb7558","tool_calls":11,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":5}
{"exact_match":true,"id":"retro_69c141311d51e74df092:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target O=[N+]([O-])c1ccccc1CCN1CCN(c2nsc3ccccc23)CC1 in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"O=[N+]([O-])c1ccccc1CCN1CCN(c2nsc3ccccc23)CC1\", \"reactants\": [\"Cc1ccc(S(=O)(=O)OCCc2ccccc2[N+](=O)[O-])cc1\", \"c1ccc2c(N3CCNCC3)nsc2c1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"Cc1ccc(S(=O)(=O)OCCc2ccccc2[N+](=O)[O-])cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"c1ccc2c(N3CCNCC3)nsc2c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"FBLDLJMRGSZGCD-UHFFFAOYSA-N.KRDOFMHJLWKXIU-UHFFFAOYSA-N>>HGKATBPTEASSCS-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"O=[N+]([O-])c1ccccc1CCN1CCN(c2nsc3ccccc23)CC1\", \"reactants\": [\"Cc1ccc(S(=O)(=O)OCCc2ccccc2[N+](=O)[O-])cc1\", \"c1ccc2c(N3CCNCC3)nsc2c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"Cc1ccc(S(=O)(=O)OCCc2ccccc2[N+](=O)[O-])cc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"c1ccc2c(N3CCNCC3)nsc2c1\", \"results\": [{\"inchikey\": \"KRDOFMHJLWKXIU-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"c1ccc2c(N3CCNCC3)nsc2c1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"Cc1ccc(S(=O)(=O)OCCc2ccccc2[N+](=O)[O-])cc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Cc1ccc(S(=O)(=O)OCCc2ccccc2[N+](=O)[O-])cc1\", \"reactants\": [\"Cc1ccc(S(=O)(=O)Cl)cc1\", \"O=[N+]([O-])c1ccccc1CCO\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"Cc1ccc(S(=O)(=O)Cl)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=[N+]([O-])c1ccccc1CCO\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"SLRIOXRBAPBGEI-UHFFFAOYSA-N.YYROPELSRYBVMQ-UHFFFAOYSA-N>>FBLDLJMRGSZGCD-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"Cc1ccc(S(=O)(=O)OCCc2ccccc2[N+](=O)[O-])cc1\", \"reactants\": [\"Cc1ccc(S(=O)(=O)Cl)cc1\", \"O=[N+]([O-])c1ccccc1CCO\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"Cc1ccc(S(=O)(=O)Cl)cc1\", \"results\": [{\"inchikey\": \"YYROPELSRYBVMQ-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Cc1ccc(S(=O)(=O)Cl)cc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"O=[N+]([O-])c1ccccc1CCO\", \"results\": [{\"inchikey\": \"SLRIOXRBAPBGEI-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=[N+]([O-])c1ccccc1CCO\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"O=[N+]([O-])c1ccccc1CCN1CCN(c2nsc3ccccc23)CC1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"Cc1ccc(S(=O)(=O)OCCc2ccccc2[N+](=O)[O-])cc1\": \"precursor\", \"c1ccc2c(N3CCNCC3)nsc2c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"Cc1ccc(S(=O)(=O)OCCc2ccccc2[N+](=O)[O-])cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"Cc1ccc(S(=O)(=O)Cl)cc1\": \"precursor\", \"O=[N+]([O-])c1ccccc1CCO\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"Cc1ccc(S(=O)(=O)Cl)cc1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=[N+]([O-])c1ccccc1CCO\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"c1ccc2c(N3CCNCC3)nsc2c1\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"O=[N+]([O-])c1ccccc1CCN1CCN(c2nsc3ccccc23)CC1","task_id":"retro_69c141311d51e74df092","tool_calls":7,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_6aa50c0ed8a1a916177b:reference-expert:a0","kind":"single_route","max_steps":3,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target O=C(CC1CCCC1)Nc1c(F)cc(N2CCOCC2)cc1F in at most 3 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"O=C(CC1CCCC1)Nc1c(F)cc(N2CCOCC2)cc1F\", \"reactants\": [\"Nc1c(F)cc(N2CCOCC2)cc1F\", \"O=C(Cl)CC1CCCC1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"Nc1c(F)cc(N2CCOCC2)cc1F\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=C(Cl)CC1CCCC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"NILLIUYSJFTTRH-UHFFFAOYSA-N.PNHFLURQDGGAII-UHFFFAOYSA-N>>XBHFMQFTDNMLBJ-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"O=C(CC1CCCC1)Nc1c(F)cc(N2CCOCC2)cc1F\", \"reactants\": [\"Nc1c(F)cc(N2CCOCC2)cc1F\", \"O=C(Cl)CC1CCCC1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"Nc1c(F)cc(N2CCOCC2)cc1F\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"O=C(Cl)CC1CCCC1\", \"results\": [{\"inchikey\": \"NILLIUYSJFTTRH-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=C(Cl)CC1CCCC1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"Nc1c(F)cc(N2CCOCC2)cc1F was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Nc1c(F)cc(N2CCOCC2)cc1F\", \"reactants\": [\"O=[N+]([O-])c1c(F)cc(N2CCOCC2)cc1F\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"O=[N+]([O-])c1c(F)cc(N2CCOCC2)cc1F\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"QCFJPJLUWBSMRZ-UHFFFAOYSA-N>>PNHFLURQDGGAII-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"Nc1c(F)cc(N2CCOCC2)cc1F\", \"reactants\": [\"O=[N+]([O-])c1c(F)cc(N2CCOCC2)cc1F\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"O=[N+]([O-])c1c(F)cc(N2CCOCC2)cc1F\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"O=[N+]([O-])c1c(F)cc(N2CCOCC2)cc1F was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"O=[N+]([O-])c1c(F)cc(N2CCOCC2)cc1F\", \"reactants\": [\"C1COCCN1\", \"O=[N+]([O-])c1c(F)cc(F)cc1F\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"C1COCCN1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=[N+]([O-])c1c(F)cc(F)cc1F\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"PWRFDGYYJWQIAB-UHFFFAOYSA-N.YNAVUWVOSKDBBP-UHFFFAOYSA-N>>QCFJPJLUWBSMRZ-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"O=[N+]([O-])c1c(F)cc(N2CCOCC2)cc1F\", \"reactants\": [\"C1COCCN1\", \"O=[N+]([O-])c1c(F)cc(F)cc1F\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"C1COCCN1\", \"results\": [{\"inchikey\": \"YNAVUWVOSKDBBP-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"C1COCCN1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"O=[N+]([O-])c1c(F)cc(F)cc1F\", \"results\": [{\"inchikey\": \"PWRFDGYYJWQIAB-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=[N+]([O-])c1c(F)cc(F)cc1F\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"O=C(CC1CCCC1)Nc1c(F)cc(N2CCOCC2)cc1F\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"Nc1c(F)cc(N2CCOCC2)cc1F\": \"precursor\", \"O=C(Cl)CC1CCCC1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"Nc1c(F)cc(N2CCOCC2)cc1F\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"O=[N+]([O-])c1c(F)cc(N2CCOCC2)cc1F\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"O=[N+]([O-])c1c(F)cc(N2CCOCC2)cc1F\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"C1COCCN1\": \"precursor\", \"O=[N+]([O-])c1c(F)cc(F)cc1F\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"C1COCCN1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=[N+]([O-])c1c(F)cc(F)cc1F\", \"in_stock\": true, \"children\": []}]}]}]}]}, {\"type\": \"mol\", \"smiles\": \"O=C(Cl)CC1CCCC1\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_4_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"O=C(CC1CCCC1)Nc1c(F)cc(N2CCOCC2)cc1F","task_id":"retro_6aa50c0ed8a1a916177b","tool_calls":9,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":4}
{"exact_match":true,"id":"retro_6c587b56d92f3f5d57d6:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target O=C(c1ccc2cncc(-c3ccc(Cl)cc3)c2n1)N1CCCCC1 in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"O=C(c1ccc2cncc(-c3ccc(Cl)cc3)c2n1)N1CCCCC1\", \"reactants\": [\"C1CCNCC1\", \"O=C(O)c1ccc2cncc(-c3ccc(Cl)cc3)c2n1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"C1CCNCC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=C(O)c1ccc2cncc(-c3ccc(Cl)cc3)c2n1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"DXWJNLPWXHZDKE-UHFFFAOYSA-N.NQRYJNQNLNOLGT-UHFFFAOYSA-N>>XRPJGVWRICTFDX-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"O=C(c1ccc2cncc(-c3ccc(Cl)cc3)c2n1)N1CCCCC1\", \"reactants\": [\"C1CCNCC1\", \"O=C(O)c1ccc2cncc(-c3ccc(Cl)cc3)c2n1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"C1CCNCC1\", \"results\": [{\"inchikey\": \"NQRYJNQNLNOLGT-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"C1CCNCC1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"O=C(O)c1ccc2cncc(-c3ccc(Cl)cc3)c2n1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"O=C(O)c1ccc2cncc(-c3ccc(Cl)cc3)c2n1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"O=C(O)c1ccc2cncc(-c3ccc(Cl)cc3)c2n1\", \"reactants\": [\"O=C(O)c1ccc2cncc(Br)c2n1\", \"OB(O)c1ccc(Cl)cc1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"O=C(O)c1ccc2cncc(Br)c2n1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"OB(O)c1ccc(Cl)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"CAYQIZIAYYNFCS-UHFFFAOYSA-N.ISJKXVUODLFGIU-UHFFFAOYSA-N>>DXWJNLPWXHZDKE-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"O=C(O)c1ccc2cncc(-c3ccc(Cl)cc3)c2n1\", \"reactants\": [\"O=C(O)c1ccc2cncc(Br)c2n1\", \"OB(O)c1ccc(Cl)cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"O=C(O)c1ccc2cncc(Br)c2n1\", \"results\": [{\"inchikey\": \"ISJKXVUODLFGIU-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=C(O)c1ccc2cncc(Br)c2n1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"OB(O)c1ccc(Cl)cc1\", \"results\": [{\"inchikey\": \"CAYQIZIAYYNFCS-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"OB(O)c1ccc(Cl)cc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"O=C(c1ccc2cncc(-c3ccc(Cl)cc3)c2n1)N1CCCCC1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"C1CCNCC1\": \"precursor\", \"O=C(O)c1ccc2cncc(-c3ccc(Cl)cc3)c2n1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"C1CCNCC1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=C(O)c1ccc2cncc(-c3ccc(Cl)cc3)c2n1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"O=C(O)c1ccc2cncc(Br)c2n1\": \"precursor\", \"OB(O)c1ccc(Cl)cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"O=C(O)c1ccc2cncc(Br)c2n1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"OB(O)c1ccc(Cl)cc1\", \"in_stock\": true, \"children\": []}]}]}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"O=C(c1ccc2cncc(-c3ccc(Cl)cc3)c2n1)N1CCCCC1","task_id":"retro_6c587b56d92f3f5d57d6","tool_calls":7,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_6ddc02059e83c190a19d:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target OCc1ccc(Oc2ccc(F)cc2F)c(Br)c1 in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"OCc1ccc(Oc2ccc(F)cc2F)c(Br)c1\", \"reactants\": [\"O=Cc1ccc(Oc2ccc(F)cc2F)c(Br)c1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"O=Cc1ccc(Oc2ccc(F)cc2F)c(Br)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_complete\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"DIOUKWHIEHYMEE-UHFFFAOYSA-N>>IIGQACCPUYFJOV-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"OCc1ccc(Oc2ccc(F)cc2F)c(Br)c1\", \"reactants\": [\"O=Cc1ccc(Oc2ccc(F)cc2F)c(Br)c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"O=Cc1ccc(Oc2ccc(F)cc2F)c(Br)c1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"O=Cc1ccc(Oc2ccc(F)cc2F)c(Br)c1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"O=Cc1ccc(Oc2ccc(F)cc2F)c(Br)c1\", \"reactants\": [\"O=Cc1ccc(F)c(Br)c1\", \"Oc1ccc(F)cc1F\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"O=Cc1ccc(F)c(Br)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"Oc1ccc(F)cc1F\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"FAHZIKXYYRGSHF-UHFFFAOYSA-N.NVWVWEWVLBKPSM-UHFFFAOYSA-N>>DIOUKWHIEHYMEE-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"O=Cc1ccc(Oc2ccc(F)cc2F)c(Br)c1\", \"reactants\": [\"O=Cc1ccc(F)c(Br)c1\", \"Oc1ccc(F)cc1F\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"O=Cc1ccc(F)c(Br)c1\", \"results\": [{\"inchikey\": \"FAHZIKXYYRGSHF-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=Cc1ccc(F)c(Br)c1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"Oc1ccc(F)cc1F\", \"results\": [{\"inchikey\": \"NVWVWEWVLBKPSM-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Oc1ccc(F)cc1F\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"OCc1ccc(Oc2ccc(F)cc2F)c(Br)c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"O=Cc1ccc(Oc2ccc(F)cc2F)c(Br)c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"O=Cc1ccc(Oc2ccc(F)cc2F)c(Br)c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"O=Cc1ccc(F)c(Br)c1\": \"precursor\", \"Oc1ccc(F)cc1F\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"O=Cc1ccc(F)c(Br)c1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"Oc1ccc(F)cc1F\", \"in_stock\": true, \"children\": []}]}]}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"OCc1ccc(Oc2ccc(F)cc2F)c(Br)c1","task_id":"retro_6ddc02059e83c190a19d","tool_calls":6,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_706cef2fe33831d05f77:reference-expert:a0","kind":"single_route","max_steps":3,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target O=C(c1cc2cc(Cl)ccc2[nH]1)N1CCN(CCO)CC1 in at most 3 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"O=C(c1cc2cc(Cl)ccc2[nH]1)N1CCN(CCO)CC1\", \"reactants\": [\"O=C(c1cc2cc(Cl)ccc2[nH]1)N1CCNCC1\", \"OCCBr\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"O=C(c1cc2cc(Cl)ccc2[nH]1)N1CCNCC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"OCCBr\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"LDLCZOVUSADOIV-UHFFFAOYSA-N.RNGVSSIIHLHHSN-UHFFFAOYSA-N>>WCYVEJCFMBLHSF-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"O=C(c1cc2cc(Cl)ccc2[nH]1)N1CCN(CCO)CC1\", \"reactants\": [\"O=C(c1cc2cc(Cl)ccc2[nH]1)N1CCNCC1\", \"OCCBr\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"O=C(c1cc2cc(Cl)ccc2[nH]1)N1CCNCC1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"OCCBr\", \"results\": [{\"inchikey\": \"LDLCZOVUSADOIV-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"OCCBr\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"O=C(c1cc2cc(Cl)ccc2[nH]1)N1CCNCC1 was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"O=C(c1cc2cc(Cl)ccc2[nH]1)N1CCNCC1\", \"reactants\": [\"CC(C)(C)OC(=O)N1CCN(C(=O)c2cc3cc(Cl)ccc3[nH]2)CC1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)OC(=O)N1CCN(C(=O)c2cc3cc(Cl)ccc3[nH]2)CC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"IGAYAPIUWITGHC-UHFFFAOYSA-N>>RNGVSSIIHLHHSN-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"O=C(c1cc2cc(Cl)ccc2[nH]1)N1CCNCC1\", \"reactants\": [\"CC(C)(C)OC(=O)N1CCN(C(=O)c2cc3cc(Cl)ccc3[nH]2)CC1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CC(C)(C)OC(=O)N1CCN(C(=O)c2cc3cc(Cl)ccc3[nH]2)CC1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"CC(C)(C)OC(=O)N1CCN(C(=O)c2cc3cc(Cl)ccc3[nH]2)CC1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(C)(C)OC(=O)N1CCN(C(=O)c2cc3cc(Cl)ccc3[nH]2)CC1\", \"reactants\": [\"CC(C)(C)OC(=O)N1CCNCC1\", \"O=C(O)c1cc2cc(Cl)ccc2[nH]1\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)OC(=O)N1CCNCC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=C(O)c1cc2cc(Cl)ccc2[nH]1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"CWXPZXBSDSIRCS-UHFFFAOYSA-N.FUQOTYRCMBZFOL-UHFFFAOYSA-N>>IGAYAPIUWITGHC-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"CC(C)(C)OC(=O)N1CCN(C(=O)c2cc3cc(Cl)ccc3[nH]2)CC1\", \"reactants\": [\"CC(C)(C)OC(=O)N1CCNCC1\", \"O=C(O)c1cc2cc(Cl)ccc2[nH]1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"CC(C)(C)OC(=O)N1CCNCC1\", \"results\": [{\"inchikey\": \"CWXPZXBSDSIRCS-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CC(C)(C)OC(=O)N1CCNCC1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"O=C(O)c1cc2cc(Cl)ccc2[nH]1\", \"results\": [{\"inchikey\": \"FUQOTYRCMBZFOL-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=C(O)c1cc2cc(Cl)ccc2[nH]1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"O=C(c1cc2cc(Cl)ccc2[nH]1)N1CCN(CCO)CC1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"O=C(c1cc2cc(Cl)ccc2[nH]1)N1CCNCC1\": \"precursor\", \"OCCBr\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"O=C(c1cc2cc(Cl)ccc2[nH]1)N1CCNCC1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)(C)OC(=O)N1CCN(C(=O)c2cc3cc(Cl)ccc3[nH]2)CC1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)OC(=O)N1CCN(C(=O)c2cc3cc(Cl)ccc3[nH]2)CC1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)(C)OC(=O)N1CCNCC1\": \"precursor\", \"O=C(O)c1cc2cc(Cl)ccc2[nH]1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)OC(=O)N1CCNCC1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=C(O)c1cc2cc(Cl)ccc2[nH]1\", \"in_stock\": true, \"children\": []}]}]}]}]}, {\"type\": \"mol\", \"smiles\": \"OCCBr\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_4_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"O=C(c1cc2cc(Cl)ccc2[nH]1)N1CCN(CCO)CC1","task_id":"retro_706cef2fe33831d05f77","tool_calls":9,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":4}
{"exact_match":true,"id":"retro_70f8e8e6d2bb3e3d5c76:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target Cc1cc(I)c(NC(=O)OC(C)C)cc1C(F)(F)F in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Cc1cc(I)c(NC(=O)OC(C)C)cc1C(F)(F)F\", \"reactants\": [\"CC(C)OC(=O)Cl\", \"Cc1cc(I)c(N)cc1C(F)(F)F\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)OC(=O)Cl\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"Cc1cc(I)c(N)cc1C(F)(F)F\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"IVRIRQXJSNCSPQ-UHFFFAOYSA-N.OEHDGSONCOREHH-UHFFFAOYSA-N>>UXNZFDBAZQQRQU-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"Cc1cc(I)c(NC(=O)OC(C)C)cc1C(F)(F)F\", \"reactants\": [\"CC(C)OC(=O)Cl\", \"Cc1cc(I)c(N)cc1C(F)(F)F\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CC(C)OC(=O)Cl\", \"results\": [{\"inchikey\": \"IVRIRQXJSNCSPQ-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CC(C)OC(=O)Cl\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"Cc1cc(I)c(N)cc1C(F)(F)F\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"Cc1cc(I)c(N)cc1C(F)(F)F was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Cc1cc(I)c(N)cc1C(F)(F)F\", \"reactants\": [\"Cc1ccc(N)cc1C(F)(F)F\", \"ClI\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"Cc1ccc(N)cc1C(F)(F)F\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"ClI\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"JBCDCYFEJQHTTA-UHFFFAOYSA-N.QZRGKCOWNLSUDK-UHFFFAOYSA-N>>OEHDGSONCOREHH-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"Cc1cc(I)c(N)cc1C(F)(F)F\", \"reactants\": [\"Cc1ccc(N)cc1C(F)(F)F\", \"ClI\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"Cc1ccc(N)cc1C(F)(F)F\", \"results\": [{\"inchikey\": \"JBCDCYFEJQHTTA-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Cc1ccc(N)cc1C(F)(F)F\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"ClI\", \"results\": [{\"inchikey\": \"QZRGKCOWNLSUDK-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"ClI\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"Cc1cc(I)c(NC(=O)OC(C)C)cc1C(F)(F)F\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)OC(=O)Cl\": \"precursor\", \"Cc1cc(I)c(N)cc1C(F)(F)F\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)OC(=O)Cl\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"Cc1cc(I)c(N)cc1C(F)(F)F\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"Cc1ccc(N)cc1C(F)(F)F\": \"precursor\", \"ClI\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"Cc1ccc(N)cc1C(F)(F)F\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"ClI\", \"in_stock\": true, \"children\": []}]}]}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"Cc1cc(I)c(NC(=O)OC(C)C)cc1C(F)(F)F","task_id":"retro_70f8e8e6d2bb3e3d5c76","tool_calls":7,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_710fd894bbd1be3b2af0:reference-expert:a0","kind":"single_route","max_steps":4,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target COc1cc(C(=O)c2cnc3ccccc3c2)cc([N+](=O)[O-])c1O in at most 4 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COc1cc(C(=O)c2cnc3ccccc3c2)cc([N+](=O)[O-])c1O\", \"reactants\": [\"COc1cc(C(=O)c2cnc3ccccc3c2)ccc1O\", \"O=[N+]([O-])O\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"COc1cc(C(=O)c2cnc3ccccc3c2)ccc1O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=[N+]([O-])O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"GRYLNZFGIOXLOG-UHFFFAOYSA-N.GUQRQYIIWBFFQU-UHFFFAOYSA-N>>GHSAKBQKJPCTHZ-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"COc1cc(C(=O)c2cnc3ccccc3c2)cc([N+](=O)[O-])c1O\", \"reactants\": [\"COc1cc(C(=O)c2cnc3ccccc3c2)ccc1O\", \"O=[N+]([O-])O\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"COc1cc(C(=O)c2cnc3ccccc3c2)ccc1O\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"O=[N+]([O-])O\", \"results\": [{\"inchikey\": \"GRYLNZFGIOXLOG-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=[N+]([O-])O\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"COc1cc(C(=O)c2cnc3ccccc3c2)ccc1O was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COc1cc(C(=O)c2cnc3ccccc3c2)ccc1O\", \"reactants\": [\"COc1cc(C(=O)c2cnc3ccccc3c2)ccc1OCc1ccccc1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"COc1cc(C(=O)c2cnc3ccccc3c2)ccc1OCc1ccccc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"NFFDZJDWHPFOCP-UHFFFAOYSA-N>>GUQRQYIIWBFFQU-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"COc1cc(C(=O)c2cnc3ccccc3c2)ccc1O\", \"reactants\": [\"COc1cc(C(=O)c2cnc3ccccc3c2)ccc1OCc1ccccc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"COc1cc(C(=O)c2cnc3ccccc3c2)ccc1OCc1ccccc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"COc1cc(C(=O)c2cnc3ccccc3c2)ccc1OCc1ccccc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COc1cc(C(=O)c2cnc3ccccc3c2)ccc1OCc1ccccc1\", \"reactants\": [\"COc1cc(C(O)c2cnc3ccccc3c2)ccc1OCc1ccccc1\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"COc1cc(C(O)c2cnc3ccccc3c2)ccc1OCc1ccccc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_complete\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"XECBSJWCGVYLHB-UHFFFAOYSA-N>>NFFDZJDWHPFOCP-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"COc1cc(C(=O)c2cnc3ccccc3c2)ccc1OCc1ccccc1\", \"reactants\": [\"COc1cc(C(O)c2cnc3ccccc3c2)ccc1OCc1ccccc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"COc1cc(C(O)c2cnc3ccccc3c2)ccc1OCc1ccccc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"COc1cc(C(O)c2cnc3ccccc3c2)ccc1OCc1ccccc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COc1cc(C(O)c2cnc3ccccc3c2)ccc1OCc1ccccc1\", \"reactants\": [\"Brc1cnc2ccccc2c1\", \"COc1cc(C=O)ccc1OCc1ccccc1\"]}","name":"validate_disconnection"},"id":"call_4_0","type":"function"},{"function":{"arguments":"{\"query\": \"Brc1cnc2ccccc2c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_1","type":"function"},{"function":{"arguments":"{\"query\": \"COc1cc(C=O)ccc1OCc1ccccc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"JSHLOPGSDZTEGQ-UHFFFAOYSA-N.ZGIKWINFUGEQEO-UHFFFAOYSA-N>>XECBSJWCGVYLHB-UHFFFAOYSA-N\", \"model_turns_remaining\": 12, \"product\": \"COc1cc(C(O)c2cnc3ccccc3c2)ccc1OCc1ccccc1\", \"reactants\": [\"Brc1cnc2ccccc2c1\", \"COc1cc(C=O)ccc1OCc1ccccc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_4_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"Brc1cnc2ccccc2c1\", \"results\": [{\"inchikey\": \"ZGIKWINFUGEQEO-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Brc1cnc2ccccc2c1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"COc1cc(C=O)ccc1OCc1ccccc1\", \"results\": [{\"inchikey\": \"JSHLOPGSDZTEGQ-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"COc1cc(C=O)ccc1OCc1ccccc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"COc1cc(C(=O)c2cnc3ccccc3c2)cc([N+](=O)[O-])c1O\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COc1cc(C(=O)c2cnc3ccccc3c2)ccc1O\": \"precursor\", \"O=[N+]([O-])O\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COc1cc(C(=O)c2cnc3ccccc3c2)ccc1O\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COc1cc(C(=O)c2cnc3ccccc3c2)ccc1OCc1ccccc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COc1cc(C(=O)c2cnc3ccccc3c2)ccc1OCc1ccccc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COc1cc(C(O)c2cnc3ccccc3c2)ccc1OCc1ccccc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COc1cc(C(O)c2cnc3ccccc3c2)ccc1OCc1ccccc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"Brc1cnc2ccccc2c1\": \"precursor\", \"COc1cc(C=O)ccc1OCc1ccccc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"Brc1cnc2ccccc2c1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"COc1cc(C=O)ccc1OCc1ccccc1\", \"in_stock\": true, \"children\": []}]}]}]}]}]}]}, {\"type\": \"mol\", \"smiles\": \"O=[N+]([O-])O\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_5_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"COc1cc(C(=O)c2cnc3ccccc3c2)cc([N+](=O)[O-])c1O","task_id":"retro_710fd894bbd1be3b2af0","tool_calls":11,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":5}
{"exact_match":true,"id":"retro_7166e3ef57af40728426:reference-expert:a0","kind":"single_route","max_steps":4,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target O=C(CN1CCCC1)Nc1cccc(-c2cnc3ccccc3n2)c1 in at most 4 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"O=C(CN1CCCC1)Nc1cccc(-c2cnc3ccccc3n2)c1\", \"reactants\": [\"C1CCNC1\", \"O=C(CCl)Nc1cccc(-c2cnc3ccccc3n2)c1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"C1CCNC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=C(CCl)Nc1cccc(-c2cnc3ccccc3n2)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"RWRDLPDLKQPQOW-UHFFFAOYSA-N.WBRXCUKAZWEAJZ-UHFFFAOYSA-N>>RVDYQNMCCLFQNH-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"O=C(CN1CCCC1)Nc1cccc(-c2cnc3ccccc3n2)c1\", \"reactants\": [\"C1CCNC1\", \"O=C(CCl)Nc1cccc(-c2cnc3ccccc3n2)c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"C1CCNC1\", \"results\": [{\"inchikey\": \"RWRDLPDLKQPQOW-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"C1CCNC1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"O=C(CCl)Nc1cccc(-c2cnc3ccccc3n2)c1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"O=C(CCl)Nc1cccc(-c2cnc3ccccc3n2)c1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"O=C(CCl)Nc1cccc(-c2cnc3ccccc3n2)c1\", \"reactants\": [\"Nc1cccc(-c2cnc3ccccc3n2)c1\", \"O=C(Cl)CCl\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"Nc1cccc(-c2cnc3ccccc3n2)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=C(Cl)CCl\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"FTKCJWKPAZRHTL-UHFFFAOYSA-N.VGCXGMAHQTYDJK-UHFFFAOYSA-N>>WBRXCUKAZWEAJZ-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"O=C(CCl)Nc1cccc(-c2cnc3ccccc3n2)c1\", \"reactants\": [\"Nc1cccc(-c2cnc3ccccc3n2)c1\", \"O=C(Cl)CCl\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"Nc1cccc(-c2cnc3ccccc3n2)c1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"O=C(Cl)CCl\", \"results\": [{\"inchikey\": \"VGCXGMAHQTYDJK-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=C(Cl)CCl\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Nc1cccc(-c2cnc3ccccc3n2)c1 was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Nc1cccc(-c2cnc3ccccc3n2)c1\", \"reactants\": [\"O=[N+]([O-])c1cccc(-c2cnc3ccccc3n2)c1\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"O=[N+]([O-])c1cccc(-c2cnc3ccccc3n2)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"XTBOWTFVCVWSTE-UHFFFAOYSA-N>>FTKCJWKPAZRHTL-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"Nc1cccc(-c2cnc3ccccc3n2)c1\", \"reactants\": [\"O=[N+]([O-])c1cccc(-c2cnc3ccccc3n2)c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"O=[N+]([O-])c1cccc(-c2cnc3ccccc3n2)c1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"O=[N+]([O-])c1cccc(-c2cnc3ccccc3n2)c1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"O=[N+]([O-])c1cccc(-c2cnc3ccccc3n2)c1\", \"reactants\": [\"Nc1ccccc1N\", \"O=C(CBr)c1cccc([N+](=O)[O-])c1\"]}","name":"validate_disconnection"},"id":"call_4_0","type":"function"},{"function":{"arguments":"{\"query\": \"Nc1ccccc1N\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=C(CBr)c1cccc([N+](=O)[O-])c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"GEYOCULIXLDCMW-UHFFFAOYSA-N.GZHPNIQBPGUSSX-UHFFFAOYSA-N>>XTBOWTFVCVWSTE-UHFFFAOYSA-N\", \"model_turns_remaining\": 12, \"product\": \"O=[N+]([O-])c1cccc(-c2cnc3ccccc3n2)c1\", \"reactants\": [\"Nc1ccccc1N\", \"O=C(CBr)c1cccc([N+](=O)[O-])c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_4_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"Nc1ccccc1N\", \"results\": [{\"inchikey\": \"GEYOCULIXLDCMW-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Nc1ccccc1N\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"O=C(CBr)c1cccc([N+](=O)[O-])c1\", \"results\": [{\"inchikey\": \"GZHPNIQBPGUSSX-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=C(CBr)c1cccc([N+](=O)[O-])c1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"O=C(CN1CCCC1)Nc1cccc(-c2cnc3ccccc3n2)c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"C1CCNC1\": \"precursor\", \"O=C(CCl)Nc1cccc(-c2cnc3ccccc3n2)c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"C1CCNC1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=C(CCl)Nc1cccc(-c2cnc3ccccc3n2)c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"Nc1cccc(-c2cnc3ccccc3n2)c1\": \"precursor\", \"O=C(Cl)CCl\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"Nc1cccc(-c2cnc3ccccc3n2)c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"O=[N+]([O-])c1cccc(-c2cnc3ccccc3n2)c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"O=[N+]([O-])c1cccc(-c2cnc3ccccc3n2)c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"Nc1ccccc1N\": \"precursor\", \"O=C(CBr)c1cccc([N+](=O)[O-])c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"Nc1ccccc1N\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=C(CBr)c1cccc([N+](=O)[O-])c1\", \"in_stock\": true, \"children\": []}]}]}]}]}, {\"type\": \"mol\", \"smiles\": \"O=C(Cl)CCl\", \"in_stock\": true, \"children\": []}]}]}]}]}]}}","name":"emit_routes"},"id":"call_5_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"O=C(CN1CCCC1)Nc1cccc(-c2cnc3ccccc3n2)c1","task_id":"retro_7166e3ef57af40728426","tool_calls":12,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":5}
{"exact_match":true,"id":"retro_72d31a0b0c3074ba93c6:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target COC(=O)c1ccccc1NC(=O)C1CCNCC1 in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COC(=O)c1ccccc1NC(=O)C1CCNCC1\", \"reactants\": [\"COC(=O)c1ccccc1NC(=O)C1CCN(C(=O)OC(C)(C)C)CC1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"COC(=O)c1ccccc1NC(=O)C1CCN(C(=O)OC(C)(C)C)CC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"CATTZDKTHUUQJY-UHFFFAOYSA-N>>BUQVQVPEMPNOAB-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"COC(=O)c1ccccc1NC(=O)C1CCNCC1\", \"reactants\": [\"COC(=O)c1ccccc1NC(=O)C1CCN(C(=O)OC(C)(C)C)CC1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"COC(=O)c1ccccc1NC(=O)C1CCN(C(=O)OC(C)(C)C)CC1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"COC(=O)c1ccccc1NC(=O)C1CCN(C(=O)OC(C)(C)C)CC1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COC(=O)c1ccccc1NC(=O)C1CCN(C(=O)OC(C)(C)C)CC1\", \"reactants\": [\"CC(C)(C)OC(=O)N1CCC(C(=O)O)CC1\", \"COC(=O)c1ccccc1N\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)OC(=O)N1CCC(C(=O)O)CC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"COC(=O)c1ccccc1N\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"JWOHBPPVVDQMKB-UHFFFAOYSA-N.VAMXMNNIEUEQDV-UHFFFAOYSA-N>>CATTZDKTHUUQJY-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"COC(=O)c1ccccc1NC(=O)C1CCN(C(=O)OC(C)(C)C)CC1\", \"reactants\": [\"CC(C)(C)OC(=O)N1CCC(C(=O)O)CC1\", \"COC(=O)c1ccccc1N\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CC(C)(C)OC(=O)N1CCC(C(=O)O)CC1\", \"results\": [{\"inchikey\": \"JWOHBPPVVDQMKB-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CC(C)(C)OC(=O)N1CCC(C(=O)O)CC1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"COC(=O)c1ccccc1N\", \"results\": [{\"inchikey\": \"VAMXMNNIEUEQDV-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"COC(=O)c1ccccc1N\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"COC(=O)c1ccccc1NC(=O)C1CCNCC1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COC(=O)c1ccccc1NC(=O)C1CCN(C(=O)OC(C)(C)C)CC1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COC(=O)c1ccccc1NC(=O)C1CCN(C(=O)OC(C)(C)C)CC1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)(C)OC(=O)N1CCC(C(=O)O)CC1\": \"precursor\", \"COC(=O)c1ccccc1N\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)OC(=O)N1CCC(C(=O)O)CC1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"COC(=O)c1ccccc1N\", \"in_stock\": true, \"children\": []}]}]}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"COC(=O)c1ccccc1NC(=O)C1CCNCC1","task_id":"retro_72d31a0b0c3074ba93c6","tool_calls":6,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_73ccd38d786e811d1faf:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target Cn1c(CC(F)(F)F)nc2cc(Cl)c(Cl)cc21 in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Cn1c(CC(F)(F)F)nc2cc(Cl)c(Cl)cc21\", \"reactants\": [\"CI\", \"FC(F)(F)Cc1nc2cc(Cl)c(Cl)cc2[nH]1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CI\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"FC(F)(F)Cc1nc2cc(Cl)c(Cl)cc2[nH]1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"INQOMBQAUSQDDS-UHFFFAOYSA-N.WTPSGAGGBLVYRS-UHFFFAOYSA-N>>HTNLPUSERVHLOV-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"Cn1c(CC(F)(F)F)nc2cc(Cl)c(Cl)cc21\", \"reactants\": [\"CI\", \"FC(F)(F)Cc1nc2cc(Cl)c(Cl)cc2[nH]1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CI\", \"results\": [{\"inchikey\": \"INQOMBQAUSQDDS-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CI\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"FC(F)(F)Cc1nc2cc(Cl)c(Cl)cc2[nH]1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"FC(F)(F)Cc1nc2cc(Cl)c(Cl)cc2[nH]1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"FC(F)(F)Cc1nc2cc(Cl)c(Cl)cc2[nH]1\", \"reactants\": [\"Nc1cc(Cl)c(Cl)cc1N\", \"O=C(O)CC(F)(F)F\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"Nc1cc(Cl)c(Cl)cc1N\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=C(O)CC(F)(F)F\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"IWFHBRFJOHTIPU-UHFFFAOYSA-N.KSNKQSPJFRQSEI-UHFFFAOYSA-N>>WTPSGAGGBLVYRS-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"FC(F)(F)Cc1nc2cc(Cl)c(Cl)cc2[nH]1\", \"reactants\": [\"Nc1cc(Cl)c(Cl)cc1N\", \"O=C(O)CC(F)(F)F\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"Nc1cc(Cl)c(Cl)cc1N\", \"results\": [{\"inchikey\": \"IWFHBRFJOHTIPU-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Nc1cc(Cl)c(Cl)cc1N\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"O=C(O)CC(F)(F)F\", \"results\": [{\"inchikey\": \"KSNKQSPJFRQSEI-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=C(O)CC(F)(F)F\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"Cn1c(CC(F)(F)F)nc2cc(Cl)c(Cl)cc21\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CI\": \"precursor\", \"FC(F)(F)Cc1nc2cc(Cl)c(Cl)cc2[nH]1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CI\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"FC(F)(F)Cc1nc2cc(Cl)c(Cl)cc2[nH]1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"Nc1cc(Cl)c(Cl)cc1N\": \"precursor\", \"O=C(O)CC(F)(F)F\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"Nc1cc(Cl)c(Cl)cc1N\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=C(O)CC(F)(F)F\", \"in_stock\": true, \"children\": []}]}]}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"Cn1c(CC(F)(F)F)nc2cc(Cl)c(Cl)cc21","task_id":"retro_73ccd38d786e811d1faf","tool_calls":7,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_743417702bbe591607ed:reference-expert:a0","kind":"single_route","max_steps":5,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CCC(CC)(c1ccc(OCC(=O)C(C)(C)C)c(C)c1)c1nc2ccc(C(=O)N(C)C)cc2o1 in at most 5 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCC(CC)(c1ccc(OCC(=O)C(C)(C)C)c(C)c1)c1nc2ccc(C(=O)N(C)C)cc2o1\", \"reactants\": [\"CCC(CC)(c1ccc(OCC(=O)C(C)(C)C)c(C)c1)c1nc2ccc(C(=O)O)cc2o1\", \"CNC\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCC(CC)(c1ccc(OCC(=O)C(C)(C)C)c(C)c1)c1nc2ccc(C(=O)O)cc2o1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"CNC\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"LEDWRPKMFJPZMP-UHFFFAOYSA-N.ROSDSFDQCJNGOL-UHFFFAOYSA-N>>SWZPGNUXSFQNRC-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"CCC(CC)(c1ccc(OCC(=O)C(C)(C)C)c(C)c1)c1nc2ccc(C(=O)N(C)C)cc2o1\", \"reactants\": [\"CCC(CC)(c1ccc(OCC(=O)C(C)(C)C)c(C)c1)c1nc2ccc(C(=O)O)cc2o1\", \"CNC\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CCC(CC)(c1ccc(OCC(=O)C(C)(C)C)c(C)c1)c1nc2ccc(C(=O)O)cc2o1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CNC\", \"results\": [{\"inchikey\": \"ROSDSFDQCJNGOL-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CNC\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"CCC(CC)(c1ccc(OCC(=O)C(C)(C)C)c(C)c1)c1nc2ccc(C(=O)O)cc2o1 was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCC(CC)(c1ccc(OCC(=O)C(C)(C)C)c(C)c1)c1nc2ccc(C(=O)O)cc2o1\", \"reactants\": [\"CCC(CC)(c1ccc(OCC(=O)C(C)(C)C)c(C)c1)c1nc2ccc(C(=O)OC)cc2o1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCC(CC)(c1ccc(OCC(=O)C(C)(C)C)c(C)c1)c1nc2ccc(C(=O)OC)cc2o1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"WKQFPLUMMBKENV-UHFFFAOYSA-N>>LEDWRPKMFJPZMP-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"CCC(CC)(c1ccc(OCC(=O)C(C)(C)C)c(C)c1)c1nc2ccc(C(=O)O)cc2o1\", \"reactants\": [\"CCC(CC)(c1ccc(OCC(=O)C(C)(C)C)c(C)c1)c1nc2ccc(C(=O)OC)cc2o1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CCC(CC)(c1ccc(OCC(=O)C(C)(C)C)c(C)c1)c1nc2ccc(C(=O)OC)cc2o1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"CCC(CC)(c1ccc(OCC(=O)C(C)(C)C)c(C)c1)c1nc2ccc(C(=O)OC)cc2o1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCC(CC)(c1ccc(OCC(=O)C(C)(C)C)c(C)c1)c1nc2ccc(C(=O)OC)cc2o1\", \"reactants\": [\"CC(C)(C)C(=O)CBr\", \"CCC(CC)(c1ccc(O)c(C)c1)c1nc2ccc(C(=O)OC)cc2o1\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)C(=O)CBr\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"CCC(CC)(c1ccc(O)c(C)c1)c1nc2ccc(C(=O)OC)cc2o1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"QBINYHIIXVVFLP-UHFFFAOYSA-N.SAIRZMWXVJEBMO-UHFFFAOYSA-N>>WKQFPLUMMBKENV-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"CCC(CC)(c1ccc(OCC(=O)C(C)(C)C)c(C)c1)c1nc2ccc(C(=O)OC)cc2o1\", \"reactants\": [\"CC(C)(C)C(=O)CBr\", \"CCC(CC)(c1ccc(O)c(C)c1)c1nc2ccc(C(=O)OC)cc2o1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"CC(C)(C)C(=O)CBr\", \"results\": [{\"inchikey\": \"SAIRZMWXVJEBMO-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CC(C)(C)C(=O)CBr\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"CCC(CC)(c1ccc(O)c(C)c1)c1nc2ccc(C(=O)OC)cc2o1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"CCC(CC)(c1ccc(O)c(C)c1)c1nc2ccc(C(=O)OC)cc2o1 was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCC(CC)(c1ccc(O)c(C)c1)c1nc2ccc(C(=O)OC)cc2o1\", \"reactants\": [\"CCC(CC)(c1ccc(OCc2ccccc2)c(C)c1)c1nc2ccc(C(=O)OC)cc2o1\"]}","name":"validate_disconnection"},"id":"call_4_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCC(CC)(c1ccc(OCc2ccccc2)c(C)c1)c1nc2ccc(C(=O)OC)cc2o1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"MOAFRJLHEUNFEV-UHFFFAOYSA-N>>QBINYHIIXVVFLP-UHFFFAOYSA-N\", \"model_turns_remaining\": 12, \"product\": \"CCC(CC)(c1ccc(O)c(C)c1)c1nc2ccc(C(=O)OC)cc2o1\", \"reactants\": [\"CCC(CC)(c1ccc(OCc2ccccc2)c(C)c1)c1nc2ccc(C(=O)OC)cc2o1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_4_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"CCC(CC)(c1ccc(OCc2ccccc2)c(C)c1)c1nc2ccc(C(=O)OC)cc2o1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_1"},{"content":"CCC(CC)(c1ccc(OCc2ccccc2)c(C)c1)c1nc2ccc(C(=O)OC)cc2o1 was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCC(CC)(c1ccc(OCc2ccccc2)c(C)c1)c1nc2ccc(C(=O)OC)cc2o1\", \"reactants\": [\"CCC(CC)(C(=O)Nc1ccc(C(=O)OC)cc1O)c1ccc(OCc2ccccc2)c(C)c1\"]}","name":"validate_disconnection"},"id":"call_5_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCC(CC)(C(=O)Nc1ccc(C(=O)OC)cc1O)c1ccc(OCc2ccccc2)c(C)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_5_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"DHBLVCMSCPGVSM-UHFFFAOYSA-N>>MOAFRJLHEUNFEV-UHFFFAOYSA-N\", \"model_turns_remaining\": 11, \"product\": \"CCC(CC)(c1ccc(OCc2ccccc2)c(C)c1)c1nc2ccc(C(=O)OC)cc2o1\", \"reactants\": [\"CCC(CC)(C(=O)Nc1ccc(C(=O)OC)cc1O)c1ccc(OCc2ccccc2)c(C)c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_5_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 11, \"query\": \"CCC(CC)(C(=O)Nc1ccc(C(=O)OC)cc1O)c1ccc(OCc2ccccc2)c(C)c1\", \"results\": [{\"inchikey\": \"DHBLVCMSCPGVSM-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CCC(CC)(C(=O)Nc1ccc(C(=O)OC)cc1O)c1ccc(OCc2ccccc2)c(C)c1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_5_1"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CCC(CC)(c1ccc(OCC(=O)C(C)(C)C)c(C)c1)c1nc2ccc(C(=O)N(C)C)cc2o1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCC(CC)(c1ccc(OCC(=O)C(C)(C)C)c(C)c1)c1nc2ccc(C(=O)O)cc2o1\": \"precursor\", \"CNC\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCC(CC)(c1ccc(OCC(=O)C(C)(C)C)c(C)c1)c1nc2ccc(C(=O)O)cc2o1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCC(CC)(c1ccc(OCC(=O)C(C)(C)C)c(C)c1)c1nc2ccc(C(=O)OC)cc2o1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCC(CC)(c1ccc(OCC(=O)C(C)(C)C)c(C)c1)c1nc2ccc(C(=O)OC)cc2o1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)(C)C(=O)CBr\": \"precursor\", \"CCC(CC)(c1ccc(O)c(C)c1)c1nc2ccc(C(=O)OC)cc2o1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)C(=O)CBr\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"CCC(CC)(c1ccc(O)c(C)c1)c1nc2ccc(C(=O)OC)cc2o1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCC(CC)(c1ccc(OCc2ccccc2)c(C)c1)c1nc2ccc(C(=O)OC)cc2o1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCC(CC)(c1ccc(OCc2ccccc2)c(C)c1)c1nc2ccc(C(=O)OC)cc2o1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCC(CC)(C(=O)Nc1ccc(C(=O)OC)cc1O)c1ccc(OCc2ccccc2)c(C)c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCC(CC)(C(=O)Nc1ccc(C(=O)OC)cc1O)c1ccc(OCc2ccccc2)c(C)c1\", \"in_stock\": true, \"children\": []}]}]}]}]}]}]}]}]}, {\"type\": \"mol\", \"smiles\": \"CNC\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_6_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"CCC(CC)(c1ccc(OCC(=O)C(C)(C)C)c(C)c1)c1nc2ccc(C(=O)N(C)C)cc2o1","task_id":"retro_743417702bbe591607ed","tool_calls":13,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":6}
{"exact_match":true,"id":"retro_75688017c4345d0c74b8:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target NC(=O)c1ccc(OCCCN2C[C@H]3CCC[C@H]3C2)cc1 in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"NC(=O)c1ccc(OCCCN2C[C@H]3CCC[C@H]3C2)cc1\", \"reactants\": [\"C1C[C@@H]2CNC[C@@H]2C1\", \"NC(=O)c1ccc(OCCCCl)cc1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"C1C[C@@H]2CNC[C@@H]2C1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"NC(=O)c1ccc(OCCCCl)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"CKPWJBXTVZXVHS-UHFFFAOYSA-N.UZHVXJZEHGSWQV-KNVOCYPGSA-N>>MRNMYWNBLVJWKG-GASCZTMLSA-N\", \"model_turns_remaining\": 15, \"product\": \"NC(=O)c1ccc(OCCCN2C[C@H]3CCC[C@H]3C2)cc1\", \"reactants\": [\"C1C[C@@H]2CNC[C@@H]2C1\", \"NC(=O)c1ccc(OCCCCl)cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"C1C[C@@H]2CNC[C@@H]2C1\", \"results\": [{\"inchikey\": \"UZHVXJZEHGSWQV-KNVOCYPGSA-N\", \"similarity\": 1.0, \"smiles\": \"C1C[C@@H]2CNC[C@@H]2C1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"NC(=O)c1ccc(OCCCCl)cc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"NC(=O)c1ccc(OCCCCl)cc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"NC(=O)c1ccc(OCCCCl)cc1\", \"reactants\": [\"ClCCCBr\", \"NC(=O)c1ccc(O)cc1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"ClCCCBr\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"NC(=O)c1ccc(O)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"MFESCIUQSIBMSM-UHFFFAOYSA-N.QXSAKPUBHTZHKW-UHFFFAOYSA-N>>CKPWJBXTVZXVHS-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"NC(=O)c1ccc(OCCCCl)cc1\", \"reactants\": [\"ClCCCBr\", \"NC(=O)c1ccc(O)cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"ClCCCBr\", \"results\": [{\"inchikey\": \"MFESCIUQSIBMSM-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"ClCCCBr\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"NC(=O)c1ccc(O)cc1\", \"results\": [{\"inchikey\": \"QXSAKPUBHTZHKW-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"NC(=O)c1ccc(O)cc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"NC(=O)c1ccc(OCCCN2C[C@H]3CCC[C@H]3C2)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"C1C[C@@H]2CNC[C@@H]2C1\": \"precursor\", \"NC(=O)c1ccc(OCCCCl)cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"C1C[C@@H]2CNC[C@@H]2C1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"NC(=O)c1ccc(OCCCCl)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"ClCCCBr\": \"precursor\", \"NC(=O)c1ccc(O)cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"ClCCCBr\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"NC(=O)c1ccc(O)cc1\", \"in_stock\": true, \"children\": []}]}]}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"NC(=O)c1ccc(OCCCN2C[C@H]3CCC[C@H]3C2)cc1","task_id":"retro_75688017c4345d0c74b8","tool_calls":7,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_75d9678939616f694669:reference-expert:a0","kind":"single_route","max_steps":3,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target COc1ccc(SCc2ccc(F)cc2F)c(Cl)c1Cl in at most 3 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COc1ccc(SCc2ccc(F)cc2F)c(Cl)c1Cl\", \"reactants\": [\"COc1ccc(S)c(Cl)c1Cl\", \"Fc1ccc(CBr)c(F)c1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"COc1ccc(S)c(Cl)c1Cl\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"Fc1ccc(CBr)c(F)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"IBLMYGXJKQIGSN-UHFFFAOYSA-N.YDSLCJAIZJHFTI-UHFFFAOYSA-N>>ULNBBJXIUCFTCW-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"COc1ccc(SCc2ccc(F)cc2F)c(Cl)c1Cl\", \"reactants\": [\"COc1ccc(S)c(Cl)c1Cl\", \"Fc1ccc(CBr)c(F)c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"COc1ccc(S)c(Cl)c1Cl\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"Fc1ccc(CBr)c(F)c1\", \"results\": [{\"inchikey\": \"IBLMYGXJKQIGSN-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Fc1ccc(CBr)c(F)c1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"COc1ccc(S)c(Cl)c1Cl was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COc1ccc(S)c(Cl)c1Cl\", \"reactants\": [\"COc1ccc(S(=O)(=O)Cl)c(Cl)c1Cl\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"COc1ccc(S(=O)(=O)Cl)c(Cl)c1Cl\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"AJHJBAMQCLTOGP-UHFFFAOYSA-N>>YDSLCJAIZJHFTI-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"COc1ccc(S)c(Cl)c1Cl\", \"reactants\": [\"COc1ccc(S(=O)(=O)Cl)c(Cl)c1Cl\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"COc1ccc(S(=O)(=O)Cl)c(Cl)c1Cl\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"COc1ccc(S(=O)(=O)Cl)c(Cl)c1Cl was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COc1ccc(S(=O)(=O)Cl)c(Cl)c1Cl\", \"reactants\": [\"COc1cccc(Cl)c1Cl\", \"O=S(=O)(O)Cl\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"COc1cccc(Cl)c1Cl\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=S(=O)(O)Cl\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"HFEASCCDHUVYKU-UHFFFAOYSA-N.XTHPWXDJESJLNJ-UHFFFAOYSA-N>>AJHJBAMQCLTOGP-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"COc1ccc(S(=O)(=O)Cl)c(Cl)c1Cl\", \"reactants\": [\"COc1cccc(Cl)c1Cl\", \"O=S(=O)(O)Cl\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"COc1cccc(Cl)c1Cl\", \"results\": [{\"inchikey\": \"HFEASCCDHUVYKU-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"COc1cccc(Cl)c1Cl\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"O=S(=O)(O)Cl\", \"results\": [{\"inchikey\": \"XTHPWXDJESJLNJ-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=S(=O)(O)Cl\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"COc1ccc(SCc2ccc(F)cc2F)c(Cl)c1Cl\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COc1ccc(S)c(Cl)c1Cl\": \"precursor\", \"Fc1ccc(CBr)c(F)c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COc1ccc(S)c(Cl)c1Cl\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COc1ccc(S(=O)(=O)Cl)c(Cl)c1Cl\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COc1ccc(S(=O)(=O)Cl)c(Cl)c1Cl\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COc1cccc(Cl)c1Cl\": \"precursor\", \"O=S(=O)(O)Cl\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COc1cccc(Cl)c1Cl\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=S(=O)(O)Cl\", \"in_stock\": true, \"children\": []}]}]}]}]}, {\"type\": \"mol\", \"smiles\": \"Fc1ccc(CBr)c(F)c1\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_4_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"COc1ccc(SCc2ccc(F)cc2F)c(Cl)c1Cl","task_id":"retro_75d9678939616f694669","tool_calls":9,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":4}
{"exact_match":true,"id":"retro_75ece8f42943e6cb8b7d:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target COc1ccc(CC2CCC2)cc1 in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COc1ccc(CC2CCC2)cc1\", \"reactants\": [\"COc1ccc(C(=O)C2CCC2)cc1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"COc1ccc(C(=O)C2CCC2)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"ZFYOOJLCJQTVHL-UHFFFAOYSA-N>>LTUOAKZAEVRZQA-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"COc1ccc(CC2CCC2)cc1\", \"reactants\": [\"COc1ccc(C(=O)C2CCC2)cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"COc1ccc(C(=O)C2CCC2)cc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"COc1ccc(C(=O)C2CCC2)cc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COc1ccc(C(=O)C2CCC2)cc1\", \"reactants\": [\"COc1ccccc1\", \"O=C(O)C1CCC1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"COc1ccccc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=C(O)C1CCC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"RDOXTESZEPMUJZ-UHFFFAOYSA-N.TXWOGHSRPAYOML-UHFFFAOYSA-N>>ZFYOOJLCJQTVHL-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"COc1ccc(C(=O)C2CCC2)cc1\", \"reactants\": [\"COc1ccccc1\", \"O=C(O)C1CCC1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"COc1ccccc1\", \"results\": [{\"inchikey\": \"RDOXTESZEPMUJZ-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"COc1ccccc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"O=C(O)C1CCC1\", \"results\": [{\"inchikey\": \"TXWOGHSRPAYOML-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=C(O)C1CCC1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"COc1ccc(CC2CCC2)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COc1ccc(C(=O)C2CCC2)cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COc1ccc(C(=O)C2CCC2)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COc1ccccc1\": \"precursor\", \"O=C(O)C1CCC1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COc1ccccc1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=C(O)C1CCC1\", \"in_stock\": true, \"children\": []}]}]}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"COc1ccc(CC2CCC2)cc1","task_id":"retro_75ece8f42943e6cb8b7d","tool_calls":6,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_77b57cd625db65a093fd:reference-expert:a0","kind":"single_route","max_steps":5,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target Cc1cc(OS(=O)(=O)c2ccccc2)cc2c(C3CCN(C)CC3)cn(C)c12 in at most 5 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Cc1cc(OS(=O)(=O)c2ccccc2)cc2c(C3CCN(C)CC3)cn(C)c12\", \"reactants\": [\"Cc1cc(O)cc2c(C3CCN(C)CC3)cn(C)c12\", \"O=S(=O)(Cl)c1ccccc1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"Cc1cc(O)cc2c(C3CCN(C)CC3)cn(C)c12\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=S(=O)(Cl)c1ccccc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"CSKNSYBAZOQPLR-UHFFFAOYSA-N.DGRLPBVZZXUQNU-UHFFFAOYSA-N>>GFJSINCJLPAEBP-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"Cc1cc(OS(=O)(=O)c2ccccc2)cc2c(C3CCN(C)CC3)cn(C)c12\", \"reactants\": [\"Cc1cc(O)cc2c(C3CCN(C)CC3)cn(C)c12\", \"O=S(=O)(Cl)c1ccccc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"Cc1cc(O)cc2c(C3CCN(C)CC3)cn(C)c12\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"O=S(=O)(Cl)c1ccccc1\", \"results\": [{\"inchikey\": \"CSKNSYBAZOQPLR-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=S(=O)(Cl)c1ccccc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"Cc1cc(O)cc2c(C3CCN(C)CC3)cn(C)c12 was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Cc1cc(O)cc2c(C3CCN(C)CC3)cn(C)c12\", \"reactants\": [\"COc1cc(C)c2c(c1)c(C1CCN(C)CC1)cn2C\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"COc1cc(C)c2c(c1)c(C1CCN(C)CC1)cn2C\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"GUJOCYGHAMPXTP-UHFFFAOYSA-N>>DGRLPBVZZXUQNU-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"Cc1cc(O)cc2c(C3CCN(C)CC3)cn(C)c12\", \"reactants\": [\"COc1cc(C)c2c(c1)c(C1CCN(C)CC1)cn2C\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"COc1cc(C)c2c(c1)c(C1CCN(C)CC1)cn2C\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"COc1cc(C)c2c(c1)c(C1CCN(C)CC1)cn2C was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COc1cc(C)c2c(c1)c(C1CCN(C)CC1)cn2C\", \"reactants\": [\"CI\", \"COc1cc(C)c2[nH]cc(C3CCN(C)CC3)c2c1\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"CI\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"COc1cc(C)c2[nH]cc(C3CCN(C)CC3)c2c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"INQOMBQAUSQDDS-UHFFFAOYSA-N.IVLXLWQMKWGZJO-UHFFFAOYSA-N>>GUJOCYGHAMPXTP-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"COc1cc(C)c2c(c1)c(C1CCN(C)CC1)cn2C\", \"reactants\": [\"CI\", \"COc1cc(C)c2[nH]cc(C3CCN(C)CC3)c2c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"CI\", \"results\": [{\"inchikey\": \"INQOMBQAUSQDDS-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CI\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"COc1cc(C)c2[nH]cc(C3CCN(C)CC3)c2c1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"COc1cc(C)c2[nH]cc(C3CCN(C)CC3)c2c1 was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COc1cc(C)c2[nH]cc(C3CCN(C)CC3)c2c1\", \"reactants\": [\"COc1cc(C)c2[nH]cc(C3=CCN(C)CC3)c2c1\"]}","name":"validate_disconnection"},"id":"call_4_0","type":"function"},{"function":{"arguments":"{\"query\": \"COc1cc(C)c2[nH]cc(C3=CCN(C)CC3)c2c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_complete\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"POLLWUBKYBKASK-UHFFFAOYSA-N>>IVLXLWQMKWGZJO-UHFFFAOYSA-N\", \"model_turns_remaining\": 12, \"product\": \"COc1cc(C)c2[nH]cc(C3CCN(C)CC3)c2c1\", \"reactants\": [\"COc1cc(C)c2[nH]cc(C3=CCN(C)CC3)c2c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_4_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"COc1cc(C)c2[nH]cc(C3=CCN(C)CC3)c2c1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_1"},{"content":"COc1cc(C)c2[nH]cc(C3=CCN(C)CC3)c2c1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COc1cc(C)c2[nH]cc(C3=CCN(C)CC3)c2c1\", \"reactants\": [\"CN1CCC(=O)CC1\", \"COc1cc(C)c2[nH]ccc2c1\"]}","name":"validate_disconnection"},"id":"call_5_0","type":"function"},{"function":{"arguments":"{\"query\": \"CN1CCC(=O)CC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_5_1","type":"function"},{"function":{"arguments":"{\"query\": \"COc1cc(C)c2[nH]ccc2c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_5_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"HUUPVABNAQUEJW-UHFFFAOYSA-N.YGPVRHHGKCQSIL-UHFFFAOYSA-N>>POLLWUBKYBKASK-UHFFFAOYSA-N\", \"model_turns_remaining\": 11, \"product\": \"COc1cc(C)c2[nH]cc(C3=CCN(C)CC3)c2c1\", \"reactants\": [\"CN1CCC(=O)CC1\", \"COc1cc(C)c2[nH]ccc2c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_5_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 11, \"query\": \"CN1CCC(=O)CC1\", \"results\": [{\"inchikey\": \"HUUPVABNAQUEJW-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CN1CCC(=O)CC1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_5_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 11, \"query\": \"COc1cc(C)c2[nH]ccc2c1\", \"results\": [{\"inchikey\": \"YGPVRHHGKCQSIL-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"COc1cc(C)c2[nH]ccc2c1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_5_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"Cc1cc(OS(=O)(=O)c2ccccc2)cc2c(C3CCN(C)CC3)cn(C)c12\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"Cc1cc(O)cc2c(C3CCN(C)CC3)cn(C)c12\": \"precursor\", \"O=S(=O)(Cl)c1ccccc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"Cc1cc(O)cc2c(C3CCN(C)CC3)cn(C)c12\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COc1cc(C)c2c(c1)c(C1CCN(C)CC1)cn2C\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COc1cc(C)c2c(c1)c(C1CCN(C)CC1)cn2C\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CI\": \"precursor\", \"COc1cc(C)c2[nH]cc(C3CCN(C)CC3)c2c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CI\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"COc1cc(C)c2[nH]cc(C3CCN(C)CC3)c2c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COc1cc(C)c2[nH]cc(C3=CCN(C)CC3)c2c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COc1cc(C)c2[nH]cc(C3=CCN(C)CC3)c2c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CN1CCC(=O)CC1\": \"precursor\", \"COc1cc(C)c2[nH]ccc2c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CN1CCC(=O)CC1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"COc1cc(C)c2[nH]ccc2c1\", \"in_stock\": true, \"children\": []}]}]}]}]}]}]}]}]}, {\"type\": \"mol\", \"smiles\": \"O=S(=O)(Cl)c1ccccc1\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_6_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"Cc1cc(OS(=O)(=O)c2ccccc2)cc2c(C3CCN(C)CC3)cn(C)c12","task_id":"retro_77b57cd625db65a093fd","tool_calls":14,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":6}
{"exact_match":true,"id":"retro_77b9802639e014b1994e:reference-expert:a0","kind":"single_route","max_steps":3,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target FC(F)(F)Oc1cccc(SC2CCOC(c3ccc(Cl)cc3)C2)c1 in at most 3 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"FC(F)(F)Oc1cccc(SC2CCOC(c3ccc(Cl)cc3)C2)c1\", \"reactants\": [\"CS(=O)(=O)OC1CCOC(c2ccc(Cl)cc2)C1\", \"FC(F)(F)Oc1cccc(S)c1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CS(=O)(=O)OC1CCOC(c2ccc(Cl)cc2)C1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"FC(F)(F)Oc1cccc(S)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"GEJGGOYNWFQKKH-UHFFFAOYSA-N.JQCUGOGTRJTGNS-UHFFFAOYSA-N>>LRQZEYRVXTTZNC-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"FC(F)(F)Oc1cccc(SC2CCOC(c3ccc(Cl)cc3)C2)c1\", \"reactants\": [\"CS(=O)(=O)OC1CCOC(c2ccc(Cl)cc2)C1\", \"FC(F)(F)Oc1cccc(S)c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CS(=O)(=O)OC1CCOC(c2ccc(Cl)cc2)C1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"FC(F)(F)Oc1cccc(S)c1\", \"results\": [{\"inchikey\": \"GEJGGOYNWFQKKH-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"FC(F)(F)Oc1cccc(S)c1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"CS(=O)(=O)OC1CCOC(c2ccc(Cl)cc2)C1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CS(=O)(=O)OC1CCOC(c2ccc(Cl)cc2)C1\", \"reactants\": [\"CS(=O)(=O)Cl\", \"OC1CCOC(c2ccc(Cl)cc2)C1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CS(=O)(=O)Cl\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"OC1CCOC(c2ccc(Cl)cc2)C1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"QARBMVPHQWIHKH-UHFFFAOYSA-N.SMDAPVBKEBEABV-UHFFFAOYSA-N>>JQCUGOGTRJTGNS-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"CS(=O)(=O)OC1CCOC(c2ccc(Cl)cc2)C1\", \"reactants\": [\"CS(=O)(=O)Cl\", \"OC1CCOC(c2ccc(Cl)cc2)C1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CS(=O)(=O)Cl\", \"results\": [{\"inchikey\": \"QARBMVPHQWIHKH-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CS(=O)(=O)Cl\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"OC1CCOC(c2ccc(Cl)cc2)C1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"OC1CCOC(c2ccc(Cl)cc2)C1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"OC1CCOC(c2ccc(Cl)cc2)C1\", \"reactants\": [\"C=CCCO\", \"O=Cc1ccc(Cl)cc1\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"C=CCCO\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=Cc1ccc(Cl)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_complete\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"AVPYQKSLYISFPO-UHFFFAOYSA-N.ZSPTYLOMNJNZNG-UHFFFAOYSA-N>>SMDAPVBKEBEABV-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"OC1CCOC(c2ccc(Cl)cc2)C1\", \"reactants\": [\"C=CCCO\", \"O=Cc1ccc(Cl)cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"C=CCCO\", \"results\": [{\"inchikey\": \"ZSPTYLOMNJNZNG-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"C=CCCO\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"O=Cc1ccc(Cl)cc1\", \"results\": [{\"inchikey\": \"AVPYQKSLYISFPO-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=Cc1ccc(Cl)cc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"FC(F)(F)Oc1cccc(SC2CCOC(c3ccc(Cl)cc3)C2)c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CS(=O)(=O)OC1CCOC(c2ccc(Cl)cc2)C1\": \"precursor\", \"FC(F)(F)Oc1cccc(S)c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CS(=O)(=O)OC1CCOC(c2ccc(Cl)cc2)C1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CS(=O)(=O)Cl\": \"precursor\", \"OC1CCOC(c2ccc(Cl)cc2)C1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CS(=O)(=O)Cl\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"OC1CCOC(c2ccc(Cl)cc2)C1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"C=CCCO\": \"precursor\", \"O=Cc1ccc(Cl)cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"C=CCCO\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=Cc1ccc(Cl)cc1\", \"in_stock\": true, \"children\": []}]}]}]}]}, {\"type\": \"mol\", \"smiles\": \"FC(F)(F)Oc1cccc(S)c1\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_4_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"FC(F)(F)Oc1cccc(SC2CCOC(c3ccc(Cl)cc3)C2)c1","task_id":"retro_77b9802639e014b1994e","tool_calls":10,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":4}
{"exact_match":true,"id":"retro_77d9238681b679f11025:reference-expert:a0","kind":"single_route","max_steps":5,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target Cc1ccccc1N1CCc2c(ncnc2Nc2ccc(C(F)(F)F)cc2)C1 in at most 5 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Cc1ccccc1N1CCc2c(ncnc2Nc2ccc(C(F)(F)F)cc2)C1\", \"reactants\": [\"Cc1ccccc1Br\", \"FC(F)(F)c1ccc(Nc2ncnc3c2CCNC3)cc1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"Cc1ccccc1Br\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"FC(F)(F)c1ccc(Nc2ncnc3c2CCNC3)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"QSSXJPIWXQTSIX-UHFFFAOYSA-N.YHFLYGLLHVDOJO-UHFFFAOYSA-N>>YRSRXBIIOPPTKI-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"Cc1ccccc1N1CCc2c(ncnc2Nc2ccc(C(F)(F)F)cc2)C1\", \"reactants\": [\"Cc1ccccc1Br\", \"FC(F)(F)c1ccc(Nc2ncnc3c2CCNC3)cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"Cc1ccccc1Br\", \"results\": [{\"inchikey\": \"QSSXJPIWXQTSIX-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Cc1ccccc1Br\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"FC(F)(F)c1ccc(Nc2ncnc3c2CCNC3)cc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"FC(F)(F)c1ccc(Nc2ncnc3c2CCNC3)cc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"FC(F)(F)c1ccc(Nc2ncnc3c2CCNC3)cc1\", \"reactants\": [\"FC(F)(F)c1ccc(Nc2ncnc3c2CCN(Cc2ccccc2)C3)cc1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"FC(F)(F)c1ccc(Nc2ncnc3c2CCN(Cc2ccccc2)C3)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"OJPLZSMABGZDTB-UHFFFAOYSA-N>>YHFLYGLLHVDOJO-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"FC(F)(F)c1ccc(Nc2ncnc3c2CCNC3)cc1\", \"reactants\": [\"FC(F)(F)c1ccc(Nc2ncnc3c2CCN(Cc2ccccc2)C3)cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"FC(F)(F)c1ccc(Nc2ncnc3c2CCN(Cc2ccccc2)C3)cc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"FC(F)(F)c1ccc(Nc2ncnc3c2CCN(Cc2ccccc2)C3)cc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"FC(F)(F)c1ccc(Nc2ncnc3c2CCN(Cc2ccccc2)C3)cc1\", \"reactants\": [\"Clc1ncnc2c1CCN(Cc1ccccc1)C2\", \"Nc1ccc(C(F)(F)F)cc1\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"Clc1ncnc2c1CCN(Cc1ccccc1)C2\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"Nc1ccc(C(F)(F)F)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"ODGIMMLDVSWADK-UHFFFAOYSA-N.ZUDXEFPMOWJJQK-UHFFFAOYSA-N>>OJPLZSMABGZDTB-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"FC(F)(F)c1ccc(Nc2ncnc3c2CCN(Cc2ccccc2)C3)cc1\", \"reactants\": [\"Clc1ncnc2c1CCN(Cc1ccccc1)C2\", \"Nc1ccc(C(F)(F)F)cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"Clc1ncnc2c1CCN(Cc1ccccc1)C2\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"Nc1ccc(C(F)(F)F)cc1\", \"results\": [{\"inchikey\": \"ODGIMMLDVSWADK-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Nc1ccc(C(F)(F)F)cc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"Clc1ncnc2c1CCN(Cc1ccccc1)C2 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Clc1ncnc2c1CCN(Cc1ccccc1)C2\", \"reactants\": [\"O=P(Cl)(Cl)Cl\", \"O=c1[nH]cnc2c1CCN(Cc1ccccc1)C2\"]}","name":"validate_disconnection"},"id":"call_4_0","type":"function"},{"function":{"arguments":"{\"query\": \"O=P(Cl)(Cl)Cl\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=c1[nH]cnc2c1CCN(Cc1ccccc1)C2\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"NBOPLUXBZUJFHI-UHFFFAOYSA-N.XHXFXVLFKHQFAL-UHFFFAOYSA-N>>ZUDXEFPMOWJJQK-UHFFFAOYSA-N\", \"model_turns_remaining\": 12, \"product\": \"Clc1ncnc2c1CCN(Cc1ccccc1)C2\", \"reactants\": [\"O=P(Cl)(Cl)Cl\", \"O=c1[nH]cnc2c1CCN(Cc1ccccc1)C2\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_4_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"O=P(Cl)(Cl)Cl\", \"results\": [{\"inchikey\": \"XHXFXVLFKHQFAL-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=P(Cl)(Cl)Cl\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"O=c1[nH]cnc2c1CCN(Cc1ccccc1)C2\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_2"},{"content":"O=c1[nH]cnc2c1CCN(Cc1ccccc1)C2 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"O=c1[nH]cnc2c1CCN(Cc1ccccc1)C2\", \"reactants\": [\"CCOC(=O)C1CCN(Cc2ccccc2)CC1=O\", \"N=CN\"]}","name":"validate_disconnection"},"id":"call_5_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCOC(=O)C1CCN(Cc2ccccc2)CC1=O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_5_1","type":"function"},{"function":{"arguments":"{\"query\": \"N=CN\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_5_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"JYFGIESQUYQLGM-UHFFFAOYSA-N.PNKUSGQVOMIXLU-UHFFFAOYSA-N>>NBOPLUXBZUJFHI-UHFFFAOYSA-N\", \"model_turns_remaining\": 11, \"product\": \"O=c1[nH]cnc2c1CCN(Cc1ccccc1)C2\", \"reactants\": [\"CCOC(=O)C1CCN(Cc2ccccc2)CC1=O\", \"N=CN\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_5_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 11, \"query\": \"CCOC(=O)C1CCN(Cc2ccccc2)CC1=O\", \"results\": [{\"inchikey\": \"JYFGIESQUYQLGM-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CCOC(=O)C1CCN(Cc2ccccc2)CC1=O\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_5_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 11, \"query\": \"N=CN\", \"results\": [{\"inchikey\": \"PNKUSGQVOMIXLU-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"N=CN\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_5_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"Cc1ccccc1N1CCc2c(ncnc2Nc2ccc(C(F)(F)F)cc2)C1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"Cc1ccccc1Br\": \"precursor\", \"FC(F)(F)c1ccc(Nc2ncnc3c2CCNC3)cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"Cc1ccccc1Br\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"FC(F)(F)c1ccc(Nc2ncnc3c2CCNC3)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"FC(F)(F)c1ccc(Nc2ncnc3c2CCN(Cc2ccccc2)C3)cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"FC(F)(F)c1ccc(Nc2ncnc3c2CCN(Cc2ccccc2)C3)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"Clc1ncnc2c1CCN(Cc1ccccc1)C2\": \"precursor\", \"Nc1ccc(C(F)(F)F)cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"Clc1ncnc2c1CCN(Cc1ccccc1)C2\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"O=P(Cl)(Cl)Cl\": \"precursor\", \"O=c1[nH]cnc2c1CCN(Cc1ccccc1)C2\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"O=P(Cl)(Cl)Cl\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=c1[nH]cnc2c1CCN(Cc1ccccc1)C2\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCOC(=O)C1CCN(Cc2ccccc2)CC1=O\": \"precursor\", \"N=CN\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCOC(=O)C1CCN(Cc2ccccc2)CC1=O\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"N=CN\", \"in_stock\": true, \"children\": []}]}]}]}]}, {\"type\": \"mol\", \"smiles\": \"Nc1ccc(C(F)(F)F)cc1\", \"in_stock\": true, \"children\": []}]}]}]}]}]}]}]}}","name":"emit_routes"},"id":"call_6_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"Cc1ccccc1N1CCc2c(ncnc2Nc2ccc(C(F)(F)F)cc2)C1","task_id":"retro_77d9238681b679f11025","tool_calls":15,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":6}
{"exact_match":true,"id":"retro_78429a2bf750cd506474:reference-expert:a0","kind":"single_route","max_steps":3,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CC(F)(F)[C@H]1OC[C@]2(c3cc(NC(=O)c4cnc(-n5cncn5)cn4)ccc3F)N=C(N)SC[C@H]12 in at most 3 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(F)(F)[C@H]1OC[C@]2(c3cc(NC(=O)c4cnc(-n5cncn5)cn4)ccc3F)N=C(N)SC[C@H]12\", \"reactants\": [\"CC(F)(F)[C@H]1OC[C@]2(c3cc(NC(=O)c4cnc(-n5cncn5)cn4)ccc3F)N=C(NC(=O)c3ccccc3)SC[C@H]12\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(F)(F)[C@H]1OC[C@]2(c3cc(NC(=O)c4cnc(-n5cncn5)cn4)ccc3F)N=C(NC(=O)c3ccccc3)SC[C@H]12\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"XVTCSUHZNMUDRM-BUVJYCSZSA-N>>XANIWDNIBGABPW-GQNMWPQZSA-N\", \"model_turns_remaining\": 15, \"product\": \"CC(F)(F)[C@H]1OC[C@]2(c3cc(NC(=O)c4cnc(-n5cncn5)cn4)ccc3F)N=C(N)SC[C@H]12\", \"reactants\": [\"CC(F)(F)[C@H]1OC[C@]2(c3cc(NC(=O)c4cnc(-n5cncn5)cn4)ccc3F)N=C(NC(=O)c3ccccc3)SC[C@H]12\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CC(F)(F)[C@H]1OC[C@]2(c3cc(NC(=O)c4cnc(-n5cncn5)cn4)ccc3F)N=C(NC(=O)c3ccccc3)SC[C@H]12\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"CC(F)(F)[C@H]1OC[C@]2(c3cc(NC(=O)c4cnc(-n5cncn5)cn4)ccc3F)N=C(NC(=O)c3ccccc3)SC[C@H]12 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(F)(F)[C@H]1OC[C@]2(c3cc(NC(=O)c4cnc(-n5cncn5)cn4)ccc3F)N=C(NC(=O)c3ccccc3)SC[C@H]12\", \"reactants\": [\"CC(F)(F)[C@H]1OC[C@]2(c3cc(N)ccc3F)N=C(NC(=O)c3ccccc3)SC[C@H]12\", \"O=C(O)c1cnc(-n2cncn2)cn1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(F)(F)[C@H]1OC[C@]2(c3cc(N)ccc3F)N=C(NC(=O)c3ccccc3)SC[C@H]12\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=C(O)c1cnc(-n2cncn2)cn1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"FJNAHISQPZDAEP-UHFFFAOYSA-N.LEAHIJJHDFNHPV-LDBYXDLTSA-N>>XVTCSUHZNMUDRM-BUVJYCSZSA-N\", \"model_turns_remaining\": 14, \"product\": \"CC(F)(F)[C@H]1OC[C@]2(c3cc(NC(=O)c4cnc(-n5cncn5)cn4)ccc3F)N=C(NC(=O)c3ccccc3)SC[C@H]12\", \"reactants\": [\"CC(F)(F)[C@H]1OC[C@]2(c3cc(N)ccc3F)N=C(NC(=O)c3ccccc3)SC[C@H]12\", \"O=C(O)c1cnc(-n2cncn2)cn1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CC(F)(F)[C@H]1OC[C@]2(c3cc(N)ccc3F)N=C(NC(=O)c3ccccc3)SC[C@H]12\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"O=C(O)c1cnc(-n2cncn2)cn1\", \"results\": [{\"inchikey\": \"FJNAHISQPZDAEP-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=C(O)c1cnc(-n2cncn2)cn1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"CC(F)(F)[C@H]1OC[C@]2(c3cc(N)ccc3F)N=C(NC(=O)c3ccccc3)SC[C@H]12 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(F)(F)[C@H]1OC[C@]2(c3cc(N)ccc3F)N=C(NC(=O)c3ccccc3)SC[C@H]12\", \"reactants\": [\"CC(F)(F)[C@H]1OC[C@]2(c3cc(Br)ccc3F)N=C(NC(=O)c3ccccc3)SC[C@H]12\", \"[N-]=[N+]=[N-]\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(F)(F)[C@H]1OC[C@]2(c3cc(Br)ccc3F)N=C(NC(=O)c3ccccc3)SC[C@H]12\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"[N-]=[N+]=[N-]\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"BUDUJOGZZIOHKL-LDBYXDLTSA-N.IVRMZWNICZWHMI-UHFFFAOYSA-N>>LEAHIJJHDFNHPV-LDBYXDLTSA-N\", \"model_turns_remaining\": 13, \"product\": \"CC(F)(F)[C@H]1OC[C@]2(c3cc(N)ccc3F)N=C(NC(=O)c3ccccc3)SC[C@H]12\", \"reactants\": [\"CC(F)(F)[C@H]1OC[C@]2(c3cc(Br)ccc3F)N=C(NC(=O)c3ccccc3)SC[C@H]12\", \"[N-]=[N+]=[N-]\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"CC(F)(F)[C@H]1OC[C@]2(c3cc(Br)ccc3F)N=C(NC(=O)c3ccccc3)SC[C@H]12\", \"results\": [{\"inchikey\": \"BUDUJOGZZIOHKL-LDBYXDLTSA-N\", \"similarity\": 1.0, \"smiles\": \"CC(F)(F)[C@H]1OC[C@]2(c3cc(Br)ccc3F)N=C(NC(=O)c3ccccc3)SC[C@H]12\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"[N-]=[N+]=[N-]\", \"results\": [{\"inchikey\": \"IVRMZWNICZWHMI-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"[N-]=[N+]=[N-]\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CC(F)(F)[C@H]1OC[C@]2(c3cc(NC(=O)c4cnc(-n5cncn5)cn4)ccc3F)N=C(N)SC[C@H]12\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(F)(F)[C@H]1OC[C@]2(c3cc(NC(=O)c4cnc(-n5cncn5)cn4)ccc3F)N=C(NC(=O)c3ccccc3)SC[C@H]12\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(F)(F)[C@H]1OC[C@]2(c3cc(NC(=O)c4cnc(-n5cncn5)cn4)ccc3F)N=C(NC(=O)c3ccccc3)SC[C@H]12\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(F)(F)[C@H]1OC[C@]2(c3cc(N)ccc3F)N=C(NC(=O)c3ccccc3)SC[C@H]12\": \"precursor\", \"O=C(O)c1cnc(-n2cncn2)cn1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(F)(F)[C@H]1OC[C@]2(c3cc(N)ccc3F)N=C(NC(=O)c3ccccc3)SC[C@H]12\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(F)(F)[C@H]1OC[C@]2(c3cc(Br)ccc3F)N=C(NC(=O)c3ccccc3)SC[C@H]12\": \"precursor\", \"[N-]=[N+]=[N-]\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(F)(F)[C@H]1OC[C@]2(c3cc(Br)ccc3F)N=C(NC(=O)c3ccccc3)SC[C@H]12\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"[N-]=[N+]=[N-]\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"O=C(O)c1cnc(-n2cncn2)cn1\", \"in_stock\": true, \"children\": []}]}]}]}]}]}}","name":"emit_routes"},"id":"call_4_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"CC(F)(F)[C@H]1OC[C@]2(c3cc(NC(=O)c4cnc(-n5cncn5)cn4)ccc3F)N=C(N)SC[C@H]12","task_id":"retro_78429a2bf750cd506474","tool_calls":9,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":4}
{"exact_match":true,"id":"retro_78c09921433795d0cd1d:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target O=Cc1ccc(Oc2ccccc2)nc1 in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"O=Cc1ccc(Oc2ccccc2)nc1\", \"reactants\": [\"Brc1ccc(Oc2ccccc2)nc1\", \"CN(C)C=O\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"Brc1ccc(Oc2ccccc2)nc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"CN(C)C=O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"ZHIHQFMWBOTCQR-UHFFFAOYSA-N.ZMXDDKWLCZADIW-UHFFFAOYSA-N>>SOPOQXNWJNVZMI-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"O=Cc1ccc(Oc2ccccc2)nc1\", \"reactants\": [\"Brc1ccc(Oc2ccccc2)nc1\", \"CN(C)C=O\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"Brc1ccc(Oc2ccccc2)nc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CN(C)C=O\", \"results\": [{\"inchikey\": \"ZMXDDKWLCZADIW-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CN(C)C=O\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"Brc1ccc(Oc2ccccc2)nc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Brc1ccc(Oc2ccccc2)nc1\", \"reactants\": [\"Brc1ccc(Br)nc1\", \"Oc1ccccc1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"Brc1ccc(Br)nc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"Oc1ccccc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"ISWSIDIOOBJBQZ-UHFFFAOYSA-N.ZHXUWDPHUQHFOV-UHFFFAOYSA-N>>ZHIHQFMWBOTCQR-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"Brc1ccc(Oc2ccccc2)nc1\", \"reactants\": [\"Brc1ccc(Br)nc1\", \"Oc1ccccc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"Brc1ccc(Br)nc1\", \"results\": [{\"inchikey\": \"ZHXUWDPHUQHFOV-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Brc1ccc(Br)nc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"Oc1ccccc1\", \"results\": [{\"inchikey\": \"ISWSIDIOOBJBQZ-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Oc1ccccc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"O=Cc1ccc(Oc2ccccc2)nc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"Brc1ccc(Oc2ccccc2)nc1\": \"precursor\", \"CN(C)C=O\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"Brc1ccc(Oc2ccccc2)nc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"Brc1ccc(Br)nc1\": \"precursor\", \"Oc1ccccc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"Brc1ccc(Br)nc1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"Oc1ccccc1\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"CN(C)C=O\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"O=Cc1ccc(Oc2ccccc2)nc1","task_id":"retro_78c09921433795d0cd1d","tool_calls":7,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_7929a8db65efdc8bcad9:reference-expert:a0","kind":"single_route","max_steps":3,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target COC(=O)c1ccc(Nc2nc(-c3ccccc3)c3ccccc3n2)c(C)c1 in at most 3 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COC(=O)c1ccc(Nc2nc(-c3ccccc3)c3ccccc3n2)c(C)c1\", \"reactants\": [\"COC(=O)c1ccc(N)c(C)c1\", \"Clc1nc(-c2ccccc2)c2ccccc2n1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"COC(=O)c1ccc(N)c(C)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"Clc1nc(-c2ccccc2)c2ccccc2n1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"SFKMVPQJJGJCMI-UHFFFAOYSA-N.ZHIPSMIKSRYZFV-UHFFFAOYSA-N>>VVWZPLLVBRCTNC-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"COC(=O)c1ccc(Nc2nc(-c3ccccc3)c3ccccc3n2)c(C)c1\", \"reactants\": [\"COC(=O)c1ccc(N)c(C)c1\", \"Clc1nc(-c2ccccc2)c2ccccc2n1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"COC(=O)c1ccc(N)c(C)c1\", \"results\": [{\"inchikey\": \"ZHIPSMIKSRYZFV-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"COC(=O)c1ccc(N)c(C)c1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"Clc1nc(-c2ccccc2)c2ccccc2n1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"Clc1nc(-c2ccccc2)c2ccccc2n1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Clc1nc(-c2ccccc2)c2ccccc2n1\", \"reactants\": [\"O=P(Cl)(Cl)Cl\", \"O=c1nc(-c2ccccc2)c2ccccc2[nH]1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"O=P(Cl)(Cl)Cl\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=c1nc(-c2ccccc2)c2ccccc2[nH]1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"FHUBTSLLILWICW-UHFFFAOYSA-N.XHXFXVLFKHQFAL-UHFFFAOYSA-N>>SFKMVPQJJGJCMI-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"Clc1nc(-c2ccccc2)c2ccccc2n1\", \"reactants\": [\"O=P(Cl)(Cl)Cl\", \"O=c1nc(-c2ccccc2)c2ccccc2[nH]1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"O=P(Cl)(Cl)Cl\", \"results\": [{\"inchikey\": \"XHXFXVLFKHQFAL-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=P(Cl)(Cl)Cl\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"O=c1nc(-c2ccccc2)c2ccccc2[nH]1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"O=c1nc(-c2ccccc2)c2ccccc2[nH]1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"O=c1nc(-c2ccccc2)c2ccccc2[nH]1\", \"reactants\": [\"NC(N)=O\", \"Nc1ccccc1C(=O)c1ccccc1\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"NC(N)=O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"Nc1ccccc1C(=O)c1ccccc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"MAOBFOXLCJIFLV-UHFFFAOYSA-N.XSQUKJJJFZCRTK-UHFFFAOYSA-N>>FHUBTSLLILWICW-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"O=c1nc(-c2ccccc2)c2ccccc2[nH]1\", \"reactants\": [\"NC(N)=O\", \"Nc1ccccc1C(=O)c1ccccc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"NC(N)=O\", \"results\": [{\"inchikey\": \"XSQUKJJJFZCRTK-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"NC(N)=O\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"Nc1ccccc1C(=O)c1ccccc1\", \"results\": [{\"inchikey\": \"MAOBFOXLCJIFLV-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Nc1ccccc1C(=O)c1ccccc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"COC(=O)c1ccc(Nc2nc(-c3ccccc3)c3ccccc3n2)c(C)c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COC(=O)c1ccc(N)c(C)c1\": \"precursor\", \"Clc1nc(-c2ccccc2)c2ccccc2n1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COC(=O)c1ccc(N)c(C)c1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"Clc1nc(-c2ccccc2)c2ccccc2n1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"O=P(Cl)(Cl)Cl\": \"precursor\", \"O=c1nc(-c2ccccc2)c2ccccc2[nH]1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"O=P(Cl)(Cl)Cl\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=c1nc(-c2ccccc2)c2ccccc2[nH]1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"NC(N)=O\": \"precursor\", \"Nc1ccccc1C(=O)c1ccccc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"NC(N)=O\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"Nc1ccccc1C(=O)c1ccccc1\", \"in_stock\": true, \"children\": []}]}]}]}]}]}]}]}}","name":"emit_routes"},"id":"call_4_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"COC(=O)c1ccc(Nc2nc(-c3ccccc3)c3ccccc3n2)c(C)c1","task_id":"retro_7929a8db65efdc8bcad9","tool_calls":10,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":4}
{"exact_match":true,"id":"retro_79757aeb79e51fdc6085:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target C=CC(=O)OCCCCCCOc1ccc(C=CC(=O)O)cc1 in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"C=CC(=O)OCCCCCCOc1ccc(C=CC(=O)O)cc1\", \"reactants\": [\"C=CC(=O)Cl\", \"O=C(O)C=Cc1ccc(OCCCCCCO)cc1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"C=CC(=O)Cl\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=C(O)C=Cc1ccc(OCCCCCCO)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"HFBMWMNUJJDEQZ-UHFFFAOYSA-N.OOUIOHASXNAAAE-UHFFFAOYSA-N>>ROPFOQCOQALTKZ-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"C=CC(=O)OCCCCCCOc1ccc(C=CC(=O)O)cc1\", \"reactants\": [\"C=CC(=O)Cl\", \"O=C(O)C=Cc1ccc(OCCCCCCO)cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"C=CC(=O)Cl\", \"results\": [{\"inchikey\": \"HFBMWMNUJJDEQZ-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"C=CC(=O)Cl\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"O=C(O)C=Cc1ccc(OCCCCCCO)cc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"O=C(O)C=Cc1ccc(OCCCCCCO)cc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"O=C(O)C=Cc1ccc(OCCCCCCO)cc1\", \"reactants\": [\"O=C(O)C=Cc1ccc(O)cc1\", \"OCCCCCCCl\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"O=C(O)C=Cc1ccc(O)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"OCCCCCCCl\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"JNTPTNNCGDAGEJ-UHFFFAOYSA-N.NGSWKAQJJWESNS-UHFFFAOYSA-N>>OOUIOHASXNAAAE-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"O=C(O)C=Cc1ccc(OCCCCCCO)cc1\", \"reactants\": [\"O=C(O)C=Cc1ccc(O)cc1\", \"OCCCCCCCl\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"O=C(O)C=Cc1ccc(O)cc1\", \"results\": [{\"inchikey\": \"NGSWKAQJJWESNS-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=C(O)C=Cc1ccc(O)cc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"OCCCCCCCl\", \"results\": [{\"inchikey\": \"JNTPTNNCGDAGEJ-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"OCCCCCCCl\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"C=CC(=O)OCCCCCCOc1ccc(C=CC(=O)O)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"C=CC(=O)Cl\": \"precursor\", \"O=C(O)C=Cc1ccc(OCCCCCCO)cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"C=CC(=O)Cl\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=C(O)C=Cc1ccc(OCCCCCCO)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"O=C(O)C=Cc1ccc(O)cc1\": \"precursor\", \"OCCCCCCCl\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"O=C(O)C=Cc1ccc(O)cc1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"OCCCCCCCl\", \"in_stock\": true, \"children\": []}]}]}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"C=CC(=O)OCCCCCCOc1ccc(C=CC(=O)O)cc1","task_id":"retro_79757aeb79e51fdc6085","tool_calls":7,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_79df1fb9af037dea99ae:reference-expert:a0","kind":"single_route","max_steps":3,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target c1cc(-c2ccc(Cn3ccnc3)cn2)ccn1 in at most 3 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"c1cc(-c2ccc(Cn3ccnc3)cn2)ccn1\", \"reactants\": [\"Brc1ccc(Cn2ccnc2)cn1\", \"OB(O)c1ccncc1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"Brc1ccc(Cn2ccnc2)cn1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"OB(O)c1ccncc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"QLULGIRFKAWHOJ-UHFFFAOYSA-N.RMVSKVIWDJAADC-UHFFFAOYSA-N>>MBAVDMJPGMKVTG-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"c1cc(-c2ccc(Cn3ccnc3)cn2)ccn1\", \"reactants\": [\"Brc1ccc(Cn2ccnc2)cn1\", \"OB(O)c1ccncc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"Brc1ccc(Cn2ccnc2)cn1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"OB(O)c1ccncc1\", \"results\": [{\"inchikey\": \"QLULGIRFKAWHOJ-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"OB(O)c1ccncc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"Brc1ccc(Cn2ccnc2)cn1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Brc1ccc(Cn2ccnc2)cn1\", \"reactants\": [\"BrCc1ccc(Br)nc1\", \"c1c[nH]cn1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"BrCc1ccc(Br)nc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"c1c[nH]cn1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"CRRMIKBAPPOPNW-UHFFFAOYSA-N.RAXXELZNTBOGNW-UHFFFAOYSA-N>>RMVSKVIWDJAADC-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"Brc1ccc(Cn2ccnc2)cn1\", \"reactants\": [\"BrCc1ccc(Br)nc1\", \"c1c[nH]cn1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"BrCc1ccc(Br)nc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"c1c[nH]cn1\", \"results\": [{\"inchikey\": \"RAXXELZNTBOGNW-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"c1c[nH]cn1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"BrCc1ccc(Br)nc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"BrCc1ccc(Br)nc1\", \"reactants\": [\"Cc1ccc(Br)nc1\", \"O=C1CCC(=O)N1Br\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"Cc1ccc(Br)nc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=C1CCC(=O)N1Br\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"PCLIMKBDDGJMGD-UHFFFAOYSA-N.YWNJQQNBJQUKME-UHFFFAOYSA-N>>CRRMIKBAPPOPNW-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"BrCc1ccc(Br)nc1\", \"reactants\": [\"Cc1ccc(Br)nc1\", \"O=C1CCC(=O)N1Br\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"Cc1ccc(Br)nc1\", \"results\": [{\"inchikey\": \"YWNJQQNBJQUKME-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Cc1ccc(Br)nc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"O=C1CCC(=O)N1Br\", \"results\": [{\"inchikey\": \"PCLIMKBDDGJMGD-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=C1CCC(=O)N1Br\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"c1cc(-c2ccc(Cn3ccnc3)cn2)ccn1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"Brc1ccc(Cn2ccnc2)cn1\": \"precursor\", \"OB(O)c1ccncc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"Brc1ccc(Cn2ccnc2)cn1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"BrCc1ccc(Br)nc1\": \"precursor\", \"c1c[nH]cn1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"BrCc1ccc(Br)nc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"Cc1ccc(Br)nc1\": \"precursor\", \"O=C1CCC(=O)N1Br\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"Cc1ccc(Br)nc1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=C1CCC(=O)N1Br\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"c1c[nH]cn1\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"OB(O)c1ccncc1\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_4_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"c1cc(-c2ccc(Cn3ccnc3)cn2)ccn1","task_id":"retro_79df1fb9af037dea99ae","tool_calls":10,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":4}
{"exact_match":true,"id":"retro_7be513818a9d3533b427:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CC(=O)N(C)c1ccc(Br)cc1 in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(=O)N(C)c1ccc(Br)cc1\", \"reactants\": [\"CC(=O)Nc1ccc(Br)cc1\", \"CI\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(=O)Nc1ccc(Br)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"CI\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"INQOMBQAUSQDDS-UHFFFAOYSA-N.MSLICLMCQYQNPK-UHFFFAOYSA-N>>JDWFXKUASRMYEO-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"CC(=O)N(C)c1ccc(Br)cc1\", \"reactants\": [\"CC(=O)Nc1ccc(Br)cc1\", \"CI\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CC(=O)Nc1ccc(Br)cc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CI\", \"results\": [{\"inchikey\": \"INQOMBQAUSQDDS-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CI\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"CC(=O)Nc1ccc(Br)cc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(=O)Nc1ccc(Br)cc1\", \"reactants\": [\"CC(=O)Cl\", \"Nc1ccc(Br)cc1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(=O)Cl\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"Nc1ccc(Br)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"WDFQBORIUYODSI-UHFFFAOYSA-N.WETWJCDKMRHUPV-UHFFFAOYSA-N>>MSLICLMCQYQNPK-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"CC(=O)Nc1ccc(Br)cc1\", \"reactants\": [\"CC(=O)Cl\", \"Nc1ccc(Br)cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CC(=O)Cl\", \"results\": [{\"inchikey\": \"WETWJCDKMRHUPV-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CC(=O)Cl\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"Nc1ccc(Br)cc1\", \"results\": [{\"inchikey\": \"WDFQBORIUYODSI-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Nc1ccc(Br)cc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CC(=O)N(C)c1ccc(Br)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(=O)Nc1ccc(Br)cc1\": \"precursor\", \"CI\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(=O)Nc1ccc(Br)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(=O)Cl\": \"precursor\", \"Nc1ccc(Br)cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(=O)Cl\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"Nc1ccc(Br)cc1\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"CI\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"CC(=O)N(C)c1ccc(Br)cc1","task_id":"retro_7be513818a9d3533b427","tool_calls":7,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_7d944e316df8deb3bdce:reference-expert:a0","kind":"single_route","max_steps":3,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CSc1nc(N)c(C#N)c(-c2cccc([N+](=O)[O-])c2)n1 in at most 3 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CSc1nc(N)c(C#N)c(-c2cccc([N+](=O)[O-])c2)n1\", \"reactants\": [\"CSc1nc(Cl)c(C#N)c(-c2cccc([N+](=O)[O-])c2)n1\", \"N\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CSc1nc(Cl)c(C#N)c(-c2cccc([N+](=O)[O-])c2)n1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"N\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"AHEJTRNLCOGEEL-UHFFFAOYSA-N.QGZKDVFQNNGYKY-UHFFFAOYSA-N>>ZZDPNHWSACUSSH-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"CSc1nc(N)c(C#N)c(-c2cccc([N+](=O)[O-])c2)n1\", \"reactants\": [\"CSc1nc(Cl)c(C#N)c(-c2cccc([N+](=O)[O-])c2)n1\", \"N\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CSc1nc(Cl)c(C#N)c(-c2cccc([N+](=O)[O-])c2)n1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"N\", \"results\": [{\"inchikey\": \"QGZKDVFQNNGYKY-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"N\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"CSc1nc(Cl)c(C#N)c(-c2cccc([N+](=O)[O-])c2)n1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CSc1nc(Cl)c(C#N)c(-c2cccc([N+](=O)[O-])c2)n1\", \"reactants\": [\"CSc1nc(O)c(C#N)c(-c2cccc([N+](=O)[O-])c2)n1\", \"O=P(Cl)(Cl)Cl\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CSc1nc(O)c(C#N)c(-c2cccc([N+](=O)[O-])c2)n1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=P(Cl)(Cl)Cl\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"BERKBNAVADPOTQ-UHFFFAOYSA-N.XHXFXVLFKHQFAL-UHFFFAOYSA-N>>AHEJTRNLCOGEEL-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"CSc1nc(Cl)c(C#N)c(-c2cccc([N+](=O)[O-])c2)n1\", \"reactants\": [\"CSc1nc(O)c(C#N)c(-c2cccc([N+](=O)[O-])c2)n1\", \"O=P(Cl)(Cl)Cl\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CSc1nc(O)c(C#N)c(-c2cccc([N+](=O)[O-])c2)n1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"O=P(Cl)(Cl)Cl\", \"results\": [{\"inchikey\": \"XHXFXVLFKHQFAL-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=P(Cl)(Cl)Cl\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"CSc1nc(O)c(C#N)c(-c2cccc([N+](=O)[O-])c2)n1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CSc1nc(O)c(C#N)c(-c2cccc([N+](=O)[O-])c2)n1\", \"reactants\": [\"CCOC(=O)CC#N\", \"CSC(=N)N\", \"O=Cc1cccc([N+](=O)[O-])c1\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCOC(=O)CC#N\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"CSC(=N)N\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"},{"function":{"arguments":"{\"query\": \"O=Cc1cccc([N+](=O)[O-])c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_3","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"SDDKIZNHOCEXTF-UHFFFAOYSA-N.ZETIVVHRRQLWFW-UHFFFAOYSA-N.ZIUSEGSNTOUIPT-UHFFFAOYSA-N>>BERKBNAVADPOTQ-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"CSc1nc(O)c(C#N)c(-c2cccc([N+](=O)[O-])c2)n1\", \"reactants\": [\"CCOC(=O)CC#N\", \"CSC(=N)N\", \"O=Cc1cccc([N+](=O)[O-])c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"CCOC(=O)CC#N\", \"results\": [{\"inchikey\": \"ZIUSEGSNTOUIPT-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CCOC(=O)CC#N\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"CSC(=N)N\", \"results\": [{\"inchikey\": \"SDDKIZNHOCEXTF-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CSC(=N)N\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"O=Cc1cccc([N+](=O)[O-])c1\", \"results\": [{\"inchikey\": \"ZETIVVHRRQLWFW-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=Cc1cccc([N+](=O)[O-])c1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_3"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CSc1nc(N)c(C#N)c(-c2cccc([N+](=O)[O-])c2)n1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CSc1nc(Cl)c(C#N)c(-c2cccc([N+](=O)[O-])c2)n1\": \"precursor\", \"N\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CSc1nc(Cl)c(C#N)c(-c2cccc([N+](=O)[O-])c2)n1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CSc1nc(O)c(C#N)c(-c2cccc([N+](=O)[O-])c2)n1\": \"precursor\", \"O=P(Cl)(Cl)Cl\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CSc1nc(O)c(C#N)c(-c2cccc([N+](=O)[O-])c2)n1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCOC(=O)CC#N\": \"precursor\", \"CSC(=N)N\": \"precursor\", \"O=Cc1cccc([N+](=O)[O-])c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCOC(=O)CC#N\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"CSC(=N)N\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=Cc1cccc([N+](=O)[O-])c1\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"O=P(Cl)(Cl)Cl\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"N\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_4_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"CSc1nc(N)c(C#N)c(-c2cccc([N+](=O)[O-])c2)n1","task_id":"retro_7d944e316df8deb3bdce","tool_calls":11,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":4}
{"exact_match":true,"id":"retro_7d9d85c791cb0b02b26d:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target O=C(c1ccc(F)cc1)c1ccc(CBr)cc1 in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"O=C(c1ccc(F)cc1)c1ccc(CBr)cc1\", \"reactants\": [\"Cc1ccc(C(=O)c2ccc(F)cc2)cc1\", \"O=C1CCC(=O)N1Br\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"Cc1ccc(C(=O)c2ccc(F)cc2)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=C1CCC(=O)N1Br\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"PCLIMKBDDGJMGD-UHFFFAOYSA-N.SLMBDAUYJQQTRF-UHFFFAOYSA-N>>WXLLULZQLLBAAU-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"O=C(c1ccc(F)cc1)c1ccc(CBr)cc1\", \"reactants\": [\"Cc1ccc(C(=O)c2ccc(F)cc2)cc1\", \"O=C1CCC(=O)N1Br\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"Cc1ccc(C(=O)c2ccc(F)cc2)cc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"O=C1CCC(=O)N1Br\", \"results\": [{\"inchikey\": \"PCLIMKBDDGJMGD-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=C1CCC(=O)N1Br\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"Cc1ccc(C(=O)c2ccc(F)cc2)cc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Cc1ccc(C(=O)c2ccc(F)cc2)cc1\", \"reactants\": [\"Cc1ccccc1\", \"O=C(Cl)c1ccc(F)cc1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"Cc1ccccc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=C(Cl)c1ccc(F)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"CZKLEJHVLCMVQR-UHFFFAOYSA-N.YXFVVABEGXRONW-UHFFFAOYSA-N>>SLMBDAUYJQQTRF-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"Cc1ccc(C(=O)c2ccc(F)cc2)cc1\", \"reactants\": [\"Cc1ccccc1\", \"O=C(Cl)c1ccc(F)cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"Cc1ccccc1\", \"results\": [{\"inchikey\": \"YXFVVABEGXRONW-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Cc1ccccc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"O=C(Cl)c1ccc(F)cc1\", \"results\": [{\"inchikey\": \"CZKLEJHVLCMVQR-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=C(Cl)c1ccc(F)cc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"O=C(c1ccc(F)cc1)c1ccc(CBr)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"Cc1ccc(C(=O)c2ccc(F)cc2)cc1\": \"precursor\", \"O=C1CCC(=O)N1Br\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"Cc1ccc(C(=O)c2ccc(F)cc2)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"Cc1ccccc1\": \"precursor\", \"O=C(Cl)c1ccc(F)cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"Cc1ccccc1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=C(Cl)c1ccc(F)cc1\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"O=C1CCC(=O)N1Br\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"O=C(c1ccc(F)cc1)c1ccc(CBr)cc1","task_id":"retro_7d9d85c791cb0b02b26d","tool_calls":7,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_7db421a4845d4735d5e5:reference-expert:a0","kind":"single_route","max_steps":5,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target Nc1nc(NCc2ccc(C(=O)Nc3ccccc3N)cc2)nc(NC2Cc3ccccc3C2)n1 in at most 5 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Nc1nc(NCc2ccc(C(=O)Nc3ccccc3N)cc2)nc(NC2Cc3ccccc3C2)n1\", \"reactants\": [\"Nc1ccccc1N\", \"Nc1nc(NCc2ccc(C(=O)O)cc2)nc(NC2Cc3ccccc3C2)n1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"Nc1ccccc1N\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"Nc1nc(NCc2ccc(C(=O)O)cc2)nc(NC2Cc3ccccc3C2)n1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"GEYOCULIXLDCMW-UHFFFAOYSA-N.IHAHLZZNQXZSBK-UHFFFAOYSA-N>>WEGZAQQQNAZHTD-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"Nc1nc(NCc2ccc(C(=O)Nc3ccccc3N)cc2)nc(NC2Cc3ccccc3C2)n1\", \"reactants\": [\"Nc1ccccc1N\", \"Nc1nc(NCc2ccc(C(=O)O)cc2)nc(NC2Cc3ccccc3C2)n1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"Nc1ccccc1N\", \"results\": [{\"inchikey\": \"GEYOCULIXLDCMW-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Nc1ccccc1N\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"Nc1nc(NCc2ccc(C(=O)O)cc2)nc(NC2Cc3ccccc3C2)n1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"Nc1nc(NCc2ccc(C(=O)O)cc2)nc(NC2Cc3ccccc3C2)n1 was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Nc1nc(NCc2ccc(C(=O)O)cc2)nc(NC2Cc3ccccc3C2)n1\", \"reactants\": [\"COC(=O)c1ccc(CNc2nc(N)nc(NC3Cc4ccccc4C3)n2)cc1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"COC(=O)c1ccc(CNc2nc(N)nc(NC3Cc4ccccc4C3)n2)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"ZRSKCJZDDBRNCN-UHFFFAOYSA-N>>IHAHLZZNQXZSBK-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"Nc1nc(NCc2ccc(C(=O)O)cc2)nc(NC2Cc3ccccc3C2)n1\", \"reactants\": [\"COC(=O)c1ccc(CNc2nc(N)nc(NC3Cc4ccccc4C3)n2)cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"COC(=O)c1ccc(CNc2nc(N)nc(NC3Cc4ccccc4C3)n2)cc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"COC(=O)c1ccc(CNc2nc(N)nc(NC3Cc4ccccc4C3)n2)cc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COC(=O)c1ccc(CNc2nc(N)nc(NC3Cc4ccccc4C3)n2)cc1\", \"reactants\": [\"COC(=O)c1ccc(CNc2nc(Cl)nc(NC3Cc4ccccc4C3)n2)cc1\", \"N\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"COC(=O)c1ccc(CNc2nc(Cl)nc(NC3Cc4ccccc4C3)n2)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"N\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"BFIYMUOUENDNRF-UHFFFAOYSA-N.QGZKDVFQNNGYKY-UHFFFAOYSA-N>>ZRSKCJZDDBRNCN-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"COC(=O)c1ccc(CNc2nc(N)nc(NC3Cc4ccccc4C3)n2)cc1\", \"reactants\": [\"COC(=O)c1ccc(CNc2nc(Cl)nc(NC3Cc4ccccc4C3)n2)cc1\", \"N\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"COC(=O)c1ccc(CNc2nc(Cl)nc(NC3Cc4ccccc4C3)n2)cc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"N\", \"results\": [{\"inchikey\": \"QGZKDVFQNNGYKY-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"N\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"COC(=O)c1ccc(CNc2nc(Cl)nc(NC3Cc4ccccc4C3)n2)cc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COC(=O)c1ccc(CNc2nc(Cl)nc(NC3Cc4ccccc4C3)n2)cc1\", \"reactants\": [\"COC(=O)c1ccc(CNc2nc(Cl)nc(Cl)n2)cc1\", \"NC1Cc2ccccc2C1\"]}","name":"validate_disconnection"},"id":"call_4_0","type":"function"},{"function":{"arguments":"{\"query\": \"COC(=O)c1ccc(CNc2nc(Cl)nc(Cl)n2)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_1","type":"function"},{"function":{"arguments":"{\"query\": \"NC1Cc2ccccc2C1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"DCAKEZDWADNLJJ-UHFFFAOYSA-N.LMHHFZAXSANGGM-UHFFFAOYSA-N>>BFIYMUOUENDNRF-UHFFFAOYSA-N\", \"model_turns_remaining\": 12, \"product\": \"COC(=O)c1ccc(CNc2nc(Cl)nc(NC3Cc4ccccc4C3)n2)cc1\", \"reactants\": [\"COC(=O)c1ccc(CNc2nc(Cl)nc(Cl)n2)cc1\", \"NC1Cc2ccccc2C1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_4_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"COC(=O)c1ccc(CNc2nc(Cl)nc(Cl)n2)cc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"NC1Cc2ccccc2C1\", \"results\": [{\"inchikey\": \"LMHHFZAXSANGGM-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"NC1Cc2ccccc2C1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_2"},{"content":"COC(=O)c1ccc(CNc2nc(Cl)nc(Cl)n2)cc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COC(=O)c1ccc(CNc2nc(Cl)nc(Cl)n2)cc1\", \"reactants\": [\"COC(=O)c1ccc(CN)cc1\", \"Clc1nc(Cl)nc(Cl)n1\"]}","name":"validate_disconnection"},"id":"call_5_0","type":"function"},{"function":{"arguments":"{\"query\": \"COC(=O)c1ccc(CN)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_5_1","type":"function"},{"function":{"arguments":"{\"query\": \"Clc1nc(Cl)nc(Cl)n1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_5_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"AQBJGAUQEJFPKZ-UHFFFAOYSA-N.MGNCLNQXLYJVJD-UHFFFAOYSA-N>>DCAKEZDWADNLJJ-UHFFFAOYSA-N\", \"model_turns_remaining\": 11, \"product\": \"COC(=O)c1ccc(CNc2nc(Cl)nc(Cl)n2)cc1\", \"reactants\": [\"COC(=O)c1ccc(CN)cc1\", \"Clc1nc(Cl)nc(Cl)n1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_5_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 11, \"query\": \"COC(=O)c1ccc(CN)cc1\", \"results\": [{\"inchikey\": \"AQBJGAUQEJFPKZ-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"COC(=O)c1ccc(CN)cc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_5_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 11, \"query\": \"Clc1nc(Cl)nc(Cl)n1\", \"results\": [{\"inchikey\": \"MGNCLNQXLYJVJD-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Clc1nc(Cl)nc(Cl)n1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_5_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"Nc1nc(NCc2ccc(C(=O)Nc3ccccc3N)cc2)nc(NC2Cc3ccccc3C2)n1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"Nc1ccccc1N\": \"precursor\", \"Nc1nc(NCc2ccc(C(=O)O)cc2)nc(NC2Cc3ccccc3C2)n1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"Nc1ccccc1N\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"Nc1nc(NCc2ccc(C(=O)O)cc2)nc(NC2Cc3ccccc3C2)n1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COC(=O)c1ccc(CNc2nc(N)nc(NC3Cc4ccccc4C3)n2)cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COC(=O)c1ccc(CNc2nc(N)nc(NC3Cc4ccccc4C3)n2)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COC(=O)c1ccc(CNc2nc(Cl)nc(NC3Cc4ccccc4C3)n2)cc1\": \"precursor\", \"N\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COC(=O)c1ccc(CNc2nc(Cl)nc(NC3Cc4ccccc4C3)n2)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COC(=O)c1ccc(CNc2nc(Cl)nc(Cl)n2)cc1\": \"precursor\", \"NC1Cc2ccccc2C1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COC(=O)c1ccc(CNc2nc(Cl)nc(Cl)n2)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COC(=O)c1ccc(CN)cc1\": \"precursor\", \"Clc1nc(Cl)nc(Cl)n1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COC(=O)c1ccc(CN)cc1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"Clc1nc(Cl)nc(Cl)n1\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"NC1Cc2ccccc2C1\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"N\", \"in_stock\": true, \"children\": []}]}]}]}]}]}]}]}}","name":"emit_routes"},"id":"call_6_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"Nc1nc(NCc2ccc(C(=O)Nc3ccccc3N)cc2)nc(NC2Cc3ccccc3C2)n1","task_id":"retro_7db421a4845d4735d5e5","tool_calls":15,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":6}
{"exact_match":true,"id":"retro_7e39aa5d2b2fdf1461a5:reference-expert:a0","kind":"single_route","max_steps":4,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CCOC=C(C(=O)OCC)C(=O)c1cc(F)c(F)cc1Br in at most 4 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCOC=C(C(=O)OCC)C(=O)c1cc(F)c(F)cc1Br\", \"reactants\": [\"CCOC(=O)CC(=O)c1cc(F)c(F)cc1Br\", \"CCOC(O)O\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCOC(=O)CC(=O)c1cc(F)c(F)cc1Br\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"CCOC(O)O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"FGCLOJOLJQDQOG-UHFFFAOYSA-N.WRUMCLTUEABERX-UHFFFAOYSA-N>>QJKUMQAWKZGQBS-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"CCOC=C(C(=O)OCC)C(=O)c1cc(F)c(F)cc1Br\", \"reactants\": [\"CCOC(=O)CC(=O)c1cc(F)c(F)cc1Br\", \"CCOC(O)O\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CCOC(=O)CC(=O)c1cc(F)c(F)cc1Br\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CCOC(O)O\", \"results\": [{\"inchikey\": \"FGCLOJOLJQDQOG-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CCOC(O)O\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"CCOC(=O)CC(=O)c1cc(F)c(F)cc1Br was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCOC(=O)CC(=O)c1cc(F)c(F)cc1Br\", \"reactants\": [\"CCOC(=O)C(C(=O)OCC)C(=O)c1cc(F)c(F)cc1Br\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCOC(=O)C(C(=O)OCC)C(=O)c1cc(F)c(F)cc1Br\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"CHTRZUBNDPFPOB-UHFFFAOYSA-N>>WRUMCLTUEABERX-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"CCOC(=O)CC(=O)c1cc(F)c(F)cc1Br\", \"reactants\": [\"CCOC(=O)C(C(=O)OCC)C(=O)c1cc(F)c(F)cc1Br\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CCOC(=O)C(C(=O)OCC)C(=O)c1cc(F)c(F)cc1Br\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"CCOC(=O)C(C(=O)OCC)C(=O)c1cc(F)c(F)cc1Br was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCOC(=O)C(C(=O)OCC)C(=O)c1cc(F)c(F)cc1Br\", \"reactants\": [\"CCOC(=O)CC(=O)OCC\", \"O=C(Cl)c1cc(F)c(F)cc1Br\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCOC(=O)CC(=O)OCC\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=C(Cl)c1cc(F)c(F)cc1Br\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"IYXGSMUGOJNHAZ-UHFFFAOYSA-N.UFZYNSSKIDMEDS-UHFFFAOYSA-N>>CHTRZUBNDPFPOB-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"CCOC(=O)C(C(=O)OCC)C(=O)c1cc(F)c(F)cc1Br\", \"reactants\": [\"CCOC(=O)CC(=O)OCC\", \"O=C(Cl)c1cc(F)c(F)cc1Br\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"CCOC(=O)CC(=O)OCC\", \"results\": [{\"inchikey\": \"IYXGSMUGOJNHAZ-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CCOC(=O)CC(=O)OCC\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"O=C(Cl)c1cc(F)c(F)cc1Br\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"O=C(Cl)c1cc(F)c(F)cc1Br was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"O=C(Cl)c1cc(F)c(F)cc1Br\", \"reactants\": [\"O=C(O)c1cc(F)c(F)cc1Br\", \"O=S(Cl)Cl\"]}","name":"validate_disconnection"},"id":"call_4_0","type":"function"},{"function":{"arguments":"{\"query\": \"O=C(O)c1cc(F)c(F)cc1Br\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=S(Cl)Cl\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"DGCBGBZYTNTZJH-UHFFFAOYSA-N.FYSNRJHAOHDILO-UHFFFAOYSA-N>>UFZYNSSKIDMEDS-UHFFFAOYSA-N\", \"model_turns_remaining\": 12, \"product\": \"O=C(Cl)c1cc(F)c(F)cc1Br\", \"reactants\": [\"O=C(O)c1cc(F)c(F)cc1Br\", \"O=S(Cl)Cl\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_4_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"O=C(O)c1cc(F)c(F)cc1Br\", \"results\": [{\"inchikey\": \"DGCBGBZYTNTZJH-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=C(O)c1cc(F)c(F)cc1Br\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"O=S(Cl)Cl\", \"results\": [{\"inchikey\": \"FYSNRJHAOHDILO-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=S(Cl)Cl\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CCOC=C(C(=O)OCC)C(=O)c1cc(F)c(F)cc1Br\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCOC(=O)CC(=O)c1cc(F)c(F)cc1Br\": \"precursor\", \"CCOC(O)O\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCOC(=O)CC(=O)c1cc(F)c(F)cc1Br\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCOC(=O)C(C(=O)OCC)C(=O)c1cc(F)c(F)cc1Br\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCOC(=O)C(C(=O)OCC)C(=O)c1cc(F)c(F)cc1Br\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCOC(=O)CC(=O)OCC\": \"precursor\", \"O=C(Cl)c1cc(F)c(F)cc1Br\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCOC(=O)CC(=O)OCC\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=C(Cl)c1cc(F)c(F)cc1Br\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"O=C(O)c1cc(F)c(F)cc1Br\": \"precursor\", \"O=S(Cl)Cl\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"O=C(O)c1cc(F)c(F)cc1Br\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=S(Cl)Cl\", \"in_stock\": true, \"children\": []}]}]}]}]}]}]}, {\"type\": \"mol\", \"smiles\": \"CCOC(O)O\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_5_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"CCOC=C(C(=O)OCC)C(=O)c1cc(F)c(F)cc1Br","task_id":"retro_7e39aa5d2b2fdf1461a5","tool_calls":12,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":5}
{"exact_match":true,"id":"retro_7f3772ef51f7e28dd136:reference-expert:a0","kind":"single_route","max_steps":3,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target COCOc1ccc2ccc(CO)nc2c1[N+](=O)[O-] in at most 3 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COCOc1ccc2ccc(CO)nc2c1[N+](=O)[O-]\", \"reactants\": [\"COCOc1ccc2ccc(C=O)nc2c1[N+](=O)[O-]\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"COCOc1ccc2ccc(C=O)nc2c1[N+](=O)[O-]\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_complete\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"VGFQCXUVBJVWIQ-UHFFFAOYSA-N>>VEAWENQRXNMMQP-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"COCOc1ccc2ccc(CO)nc2c1[N+](=O)[O-]\", \"reactants\": [\"COCOc1ccc2ccc(C=O)nc2c1[N+](=O)[O-]\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"COCOc1ccc2ccc(C=O)nc2c1[N+](=O)[O-]\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"COCOc1ccc2ccc(C=O)nc2c1[N+](=O)[O-] was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COCOc1ccc2ccc(C=O)nc2c1[N+](=O)[O-]\", \"reactants\": [\"COCOc1ccc2ccc(C)nc2c1[N+](=O)[O-]\", \"O=[Se]=O\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"COCOc1ccc2ccc(C)nc2c1[N+](=O)[O-]\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=[Se]=O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"GAPXJSQRFMWOPI-UHFFFAOYSA-N.JPJALAQPGMAKDF-UHFFFAOYSA-N>>VGFQCXUVBJVWIQ-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"COCOc1ccc2ccc(C=O)nc2c1[N+](=O)[O-]\", \"reactants\": [\"COCOc1ccc2ccc(C)nc2c1[N+](=O)[O-]\", \"O=[Se]=O\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"COCOc1ccc2ccc(C)nc2c1[N+](=O)[O-]\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"O=[Se]=O\", \"results\": [{\"inchikey\": \"JPJALAQPGMAKDF-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=[Se]=O\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"COCOc1ccc2ccc(C)nc2c1[N+](=O)[O-] was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COCOc1ccc2ccc(C)nc2c1[N+](=O)[O-]\", \"reactants\": [\"COCCl\", \"Cc1ccc2ccc(O)c([N+](=O)[O-])c2n1\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"COCCl\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"Cc1ccc2ccc(O)c([N+](=O)[O-])c2n1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"QDVAIZGDGVWQJR-UHFFFAOYSA-N.XJUZRXYOEPSWMB-UHFFFAOYSA-N>>GAPXJSQRFMWOPI-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"COCOc1ccc2ccc(C)nc2c1[N+](=O)[O-]\", \"reactants\": [\"COCCl\", \"Cc1ccc2ccc(O)c([N+](=O)[O-])c2n1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"COCCl\", \"results\": [{\"inchikey\": \"XJUZRXYOEPSWMB-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"COCCl\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"Cc1ccc2ccc(O)c([N+](=O)[O-])c2n1\", \"results\": [{\"inchikey\": \"QDVAIZGDGVWQJR-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Cc1ccc2ccc(O)c([N+](=O)[O-])c2n1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"COCOc1ccc2ccc(CO)nc2c1[N+](=O)[O-]\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COCOc1ccc2ccc(C=O)nc2c1[N+](=O)[O-]\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COCOc1ccc2ccc(C=O)nc2c1[N+](=O)[O-]\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COCOc1ccc2ccc(C)nc2c1[N+](=O)[O-]\": \"precursor\", \"O=[Se]=O\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COCOc1ccc2ccc(C)nc2c1[N+](=O)[O-]\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COCCl\": \"precursor\", \"Cc1ccc2ccc(O)c([N+](=O)[O-])c2n1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COCCl\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"Cc1ccc2ccc(O)c([N+](=O)[O-])c2n1\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"O=[Se]=O\", \"in_stock\": true, \"children\": []}]}]}]}]}]}}","name":"emit_routes"},"id":"call_4_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"COCOc1ccc2ccc(CO)nc2c1[N+](=O)[O-]","task_id":"retro_7f3772ef51f7e28dd136","tool_calls":9,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":4}
{"exact_match":true,"id":"retro_7f4a74b8a44d514b153e:reference-expert:a0","kind":"single_route","max_steps":4,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CCN1C(=O)C(C)(C)C(=O)N(C)c2cc(OCCCNS(=O)(=O)c3ccccc3[N+](=O)[O-])ccc21 in at most 4 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCN1C(=O)C(C)(C)C(=O)N(C)c2cc(OCCCNS(=O)(=O)c3ccccc3[N+](=O)[O-])ccc21\", \"reactants\": [\"CCN1C(=O)C(C)(C)C(=O)N(C)c2cc(OCCCN)ccc21\", \"O=[N+]([O-])c1ccccc1S(=O)(=O)Cl\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCN1C(=O)C(C)(C)C(=O)N(C)c2cc(OCCCN)ccc21\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=[N+]([O-])c1ccccc1S(=O)(=O)Cl\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"LGXUUPQEGHNLMV-UHFFFAOYSA-N.WPHUUIODWRNJLO-UHFFFAOYSA-N>>ADIPEWDLPLYCLM-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"CCN1C(=O)C(C)(C)C(=O)N(C)c2cc(OCCCNS(=O)(=O)c3ccccc3[N+](=O)[O-])ccc21\", \"reactants\": [\"CCN1C(=O)C(C)(C)C(=O)N(C)c2cc(OCCCN)ccc21\", \"O=[N+]([O-])c1ccccc1S(=O)(=O)Cl\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CCN1C(=O)C(C)(C)C(=O)N(C)c2cc(OCCCN)ccc21\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"O=[N+]([O-])c1ccccc1S(=O)(=O)Cl\", \"results\": [{\"inchikey\": \"WPHUUIODWRNJLO-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=[N+]([O-])c1ccccc1S(=O)(=O)Cl\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"CCN1C(=O)C(C)(C)C(=O)N(C)c2cc(OCCCN)ccc21 was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCN1C(=O)C(C)(C)C(=O)N(C)c2cc(OCCCN)ccc21\", \"reactants\": [\"CCN1C(=O)C(C)(C)C(=O)N(C)c2cc(OCCCN3C(=O)c4ccccc4C3=O)ccc21\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCN1C(=O)C(C)(C)C(=O)N(C)c2cc(OCCCN3C(=O)c4ccccc4C3=O)ccc21\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"PUYKWRISRCARFB-UHFFFAOYSA-N>>LGXUUPQEGHNLMV-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"CCN1C(=O)C(C)(C)C(=O)N(C)c2cc(OCCCN)ccc21\", \"reactants\": [\"CCN1C(=O)C(C)(C)C(=O)N(C)c2cc(OCCCN3C(=O)c4ccccc4C3=O)ccc21\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CCN1C(=O)C(C)(C)C(=O)N(C)c2cc(OCCCN3C(=O)c4ccccc4C3=O)ccc21\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"CCN1C(=O)C(C)(C)C(=O)N(C)c2cc(OCCCN3C(=O)c4ccccc4C3=O)ccc21 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCN1C(=O)C(C)(C)C(=O)N(C)c2cc(OCCCN3C(=O)c4ccccc4C3=O)ccc21\", \"reactants\": [\"CCN1C(=O)C(C)(C)C(=O)N(C)c2cc(O)ccc21\", \"O=C1c2ccccc2C(=O)N1CCCBr\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCN1C(=O)C(C)(C)C(=O)N(C)c2cc(O)ccc21\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=C1c2ccccc2C(=O)N1CCCBr\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"VKJCJJYNVIYVQR-UHFFFAOYSA-N.ZHBMOURQWKNAOL-UHFFFAOYSA-N>>PUYKWRISRCARFB-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"CCN1C(=O)C(C)(C)C(=O)N(C)c2cc(OCCCN3C(=O)c4ccccc4C3=O)ccc21\", \"reactants\": [\"CCN1C(=O)C(C)(C)C(=O)N(C)c2cc(O)ccc21\", \"O=C1c2ccccc2C(=O)N1CCCBr\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"CCN1C(=O)C(C)(C)C(=O)N(C)c2cc(O)ccc21\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"O=C1c2ccccc2C(=O)N1CCCBr\", \"results\": [{\"inchikey\": \"VKJCJJYNVIYVQR-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=C1c2ccccc2C(=O)N1CCCBr\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"CCN1C(=O)C(C)(C)C(=O)N(C)c2cc(O)ccc21 was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCN1C(=O)C(C)(C)C(=O)N(C)c2cc(O)ccc21\", \"reactants\": [\"CCN1C(=O)C(C)(C)C(=O)N(C)c2cc(OC)ccc21\"]}","name":"validate_disconnection"},"id":"call_4_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCN1C(=O)C(C)(C)C(=O)N(C)c2cc(OC)ccc21\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"YVCXCIVSLRSIMZ-UHFFFAOYSA-N>>ZHBMOURQWKNAOL-UHFFFAOYSA-N\", \"model_turns_remaining\": 12, \"product\": \"CCN1C(=O)C(C)(C)C(=O)N(C)c2cc(O)ccc21\", \"reactants\": [\"CCN1C(=O)C(C)(C)C(=O)N(C)c2cc(OC)ccc21\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_4_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"CCN1C(=O)C(C)(C)C(=O)N(C)c2cc(OC)ccc21\", \"results\": [{\"inchikey\": \"YVCXCIVSLRSIMZ-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CCN1C(=O)C(C)(C)C(=O)N(C)c2cc(OC)ccc21\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_1"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CCN1C(=O)C(C)(C)C(=O)N(C)c2cc(OCCCNS(=O)(=O)c3ccccc3[N+](=O)[O-])ccc21\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCN1C(=O)C(C)(C)C(=O)N(C)c2cc(OCCCN)ccc21\": \"precursor\", \"O=[N+]([O-])c1ccccc1S(=O)(=O)Cl\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCN1C(=O)C(C)(C)C(=O)N(C)c2cc(OCCCN)ccc21\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCN1C(=O)C(C)(C)C(=O)N(C)c2cc(OCCCN3C(=O)c4ccccc4C3=O)ccc21\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCN1C(=O)C(C)(C)C(=O)N(C)c2cc(OCCCN3C(=O)c4ccccc4C3=O)ccc21\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCN1C(=O)C(C)(C)C(=O)N(C)c2cc(O)ccc21\": \"precursor\", \"O=C1c2ccccc2C(=O)N1CCCBr\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCN1C(=O)C(C)(C)C(=O)N(C)c2cc(O)ccc21\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCN1C(=O)C(C)(C)C(=O)N(C)c2cc(OC)ccc21\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCN1C(=O)C(C)(C)C(=O)N(C)c2cc(OC)ccc21\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"O=C1c2ccccc2C(=O)N1CCCBr\", \"in_stock\": true, \"children\": []}]}]}]}]}, {\"type\": \"mol\", \"smiles\": \"O=[N+]([O-])c1ccccc1S(=O)(=O)Cl\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_5_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"CCN1C(=O)C(C)(C)C(=O)N(C)c2cc(OCCCNS(=O)(=O)c3ccccc3[N+](=O)[O-])ccc21","task_id":"retro_7f4a74b8a44d514b153e","tool_calls":11,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":5}
{"exact_match":true,"id":"retro_7f9c8c4bc7c42787795e:reference-expert:a0","kind":"single_route","max_steps":4,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target Cc1n[nH]c(N)c1C#Cc1ccccc1 in at most 4 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Cc1n[nH]c(N)c1C#Cc1ccccc1\", \"reactants\": [\"CC(=O)Nc1[nH]nc(C)c1C#Cc1ccccc1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(=O)Nc1[nH]nc(C)c1C#Cc1ccccc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"KNTQUIPJASOVLZ-UHFFFAOYSA-N>>SVTKJFAMEAQRED-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"Cc1n[nH]c(N)c1C#Cc1ccccc1\", \"reactants\": [\"CC(=O)Nc1[nH]nc(C)c1C#Cc1ccccc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CC(=O)Nc1[nH]nc(C)c1C#Cc1ccccc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"CC(=O)Nc1[nH]nc(C)c1C#Cc1ccccc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(=O)Nc1[nH]nc(C)c1C#Cc1ccccc1\", \"reactants\": [\"C#Cc1ccccc1\", \"CC(=O)Nc1[nH]nc(C)c1I\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"C#Cc1ccccc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"CC(=O)Nc1[nH]nc(C)c1I\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"ABIXSBKLTOUOHS-UHFFFAOYSA-N.UEXCJVNBTNXOEH-UHFFFAOYSA-N>>KNTQUIPJASOVLZ-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"CC(=O)Nc1[nH]nc(C)c1C#Cc1ccccc1\", \"reactants\": [\"C#Cc1ccccc1\", \"CC(=O)Nc1[nH]nc(C)c1I\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"C#Cc1ccccc1\", \"results\": [{\"inchikey\": \"UEXCJVNBTNXOEH-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"C#Cc1ccccc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CC(=O)Nc1[nH]nc(C)c1I\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"CC(=O)Nc1[nH]nc(C)c1I was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(=O)Nc1[nH]nc(C)c1I\", \"reactants\": [\"CC(=O)Nc1cc(C)n[nH]1\", \"II\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(=O)Nc1cc(C)n[nH]1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"II\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"LUFRABHJXNJTNZ-UHFFFAOYSA-N.PNDPGZBMCMUPRI-UHFFFAOYSA-N>>ABIXSBKLTOUOHS-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"CC(=O)Nc1[nH]nc(C)c1I\", \"reactants\": [\"CC(=O)Nc1cc(C)n[nH]1\", \"II\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"CC(=O)Nc1cc(C)n[nH]1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"II\", \"results\": [{\"inchikey\": \"PNDPGZBMCMUPRI-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"II\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"CC(=O)Nc1cc(C)n[nH]1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(=O)Nc1cc(C)n[nH]1\", \"reactants\": [\"CC(=O)Cl\", \"Cc1cc(N)[nH]n1\"]}","name":"validate_disconnection"},"id":"call_4_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(=O)Cl\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_1","type":"function"},{"function":{"arguments":"{\"query\": \"Cc1cc(N)[nH]n1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"FYTLHYRDGXRYEY-UHFFFAOYSA-N.WETWJCDKMRHUPV-UHFFFAOYSA-N>>LUFRABHJXNJTNZ-UHFFFAOYSA-N\", \"model_turns_remaining\": 12, \"product\": \"CC(=O)Nc1cc(C)n[nH]1\", \"reactants\": [\"CC(=O)Cl\", \"Cc1cc(N)[nH]n1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_4_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"CC(=O)Cl\", \"results\": [{\"inchikey\": \"WETWJCDKMRHUPV-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CC(=O)Cl\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"Cc1cc(N)[nH]n1\", \"results\": [{\"inchikey\": \"FYTLHYRDGXRYEY-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Cc1cc(N)[nH]n1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"Cc1n[nH]c(N)c1C#Cc1ccccc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(=O)Nc1[nH]nc(C)c1C#Cc1ccccc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(=O)Nc1[nH]nc(C)c1C#Cc1ccccc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"C#Cc1ccccc1\": \"precursor\", \"CC(=O)Nc1[nH]nc(C)c1I\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"C#Cc1ccccc1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"CC(=O)Nc1[nH]nc(C)c1I\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(=O)Nc1cc(C)n[nH]1\": \"precursor\", \"II\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(=O)Nc1cc(C)n[nH]1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(=O)Cl\": \"precursor\", \"Cc1cc(N)[nH]n1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(=O)Cl\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"Cc1cc(N)[nH]n1\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"II\", \"in_stock\": true, \"children\": []}]}]}]}]}]}]}]}}","name":"emit_routes"},"id":"call_5_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"Cc1n[nH]c(N)c1C#Cc1ccccc1","task_id":"retro_7f9c8c4bc7c42787795e","tool_calls":12,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":5}
{"exact_match":true,"id":"retro_7fd0692d57d052c4754e:reference-expert:a0","kind":"single_route","max_steps":3,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CC1=C(C#N)[C@@H](c2ccc(C#N)cc2N)NC(=O)N1c1cccc(C(F)(F)F)c1 in at most 3 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC1=C(C#N)[C@@H](c2ccc(C#N)cc2N)NC(=O)N1c1cccc(C(F)(F)F)c1\", \"reactants\": [\"CC1=C(C#N)[C@@H](c2ccc(C#N)cc2[N+](=O)[O-])NC(=O)N1c1cccc(C(F)(F)F)c1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC1=C(C#N)[C@@H](c2ccc(C#N)cc2[N+](=O)[O-])NC(=O)N1c1cccc(C(F)(F)F)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"AWXWJJYXJXVEEI-GOSISDBHSA-N>>FRSZIWJZNYKQCQ-GOSISDBHSA-N\", \"model_turns_remaining\": 15, \"product\": \"CC1=C(C#N)[C@@H](c2ccc(C#N)cc2N)NC(=O)N1c1cccc(C(F)(F)F)c1\", \"reactants\": [\"CC1=C(C#N)[C@@H](c2ccc(C#N)cc2[N+](=O)[O-])NC(=O)N1c1cccc(C(F)(F)F)c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CC1=C(C#N)[C@@H](c2ccc(C#N)cc2[N+](=O)[O-])NC(=O)N1c1cccc(C(F)(F)F)c1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"CC1=C(C#N)[C@@H](c2ccc(C#N)cc2[N+](=O)[O-])NC(=O)N1c1cccc(C(F)(F)F)c1 was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC1=C(C#N)[C@@H](c2ccc(C#N)cc2[N+](=O)[O-])NC(=O)N1c1cccc(C(F)(F)F)c1\", \"reactants\": [\"CC1=C(C(N)=O)[C@@H](c2ccc(C#N)cc2[N+](=O)[O-])NC(=O)N1c1cccc(C(F)(F)F)c1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC1=C(C(N)=O)[C@@H](c2ccc(C#N)cc2[N+](=O)[O-])NC(=O)N1c1cccc(C(F)(F)F)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"UZJDLSKHZZSRNH-QGZVFWFLSA-N>>AWXWJJYXJXVEEI-GOSISDBHSA-N\", \"model_turns_remaining\": 14, \"product\": \"CC1=C(C#N)[C@@H](c2ccc(C#N)cc2[N+](=O)[O-])NC(=O)N1c1cccc(C(F)(F)F)c1\", \"reactants\": [\"CC1=C(C(N)=O)[C@@H](c2ccc(C#N)cc2[N+](=O)[O-])NC(=O)N1c1cccc(C(F)(F)F)c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CC1=C(C(N)=O)[C@@H](c2ccc(C#N)cc2[N+](=O)[O-])NC(=O)N1c1cccc(C(F)(F)F)c1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"CC1=C(C(N)=O)[C@@H](c2ccc(C#N)cc2[N+](=O)[O-])NC(=O)N1c1cccc(C(F)(F)F)c1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC1=C(C(N)=O)[C@@H](c2ccc(C#N)cc2[N+](=O)[O-])NC(=O)N1c1cccc(C(F)(F)F)c1\", \"reactants\": [\"CC1=C(C(=O)O)[C@@H](c2ccc(C#N)cc2[N+](=O)[O-])NC(=O)N1c1cccc(C(F)(F)F)c1\", \"N\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC1=C(C(=O)O)[C@@H](c2ccc(C#N)cc2[N+](=O)[O-])NC(=O)N1c1cccc(C(F)(F)F)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"N\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"ASYFGFVBEYMGAM-QGZVFWFLSA-N.QGZKDVFQNNGYKY-UHFFFAOYSA-N>>UZJDLSKHZZSRNH-QGZVFWFLSA-N\", \"model_turns_remaining\": 13, \"product\": \"CC1=C(C(N)=O)[C@@H](c2ccc(C#N)cc2[N+](=O)[O-])NC(=O)N1c1cccc(C(F)(F)F)c1\", \"reactants\": [\"CC1=C(C(=O)O)[C@@H](c2ccc(C#N)cc2[N+](=O)[O-])NC(=O)N1c1cccc(C(F)(F)F)c1\", \"N\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"CC1=C(C(=O)O)[C@@H](c2ccc(C#N)cc2[N+](=O)[O-])NC(=O)N1c1cccc(C(F)(F)F)c1\", \"results\": [{\"inchikey\": \"ASYFGFVBEYMGAM-QGZVFWFLSA-N\", \"similarity\": 1.0, \"smiles\": \"CC1=C(C(=O)O)[C@@H](c2ccc(C#N)cc2[N+](=O)[O-])NC(=O)N1c1cccc(C(F)(F)F)c1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"N\", \"results\": [{\"inchikey\": \"QGZKDVFQNNGYKY-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"N\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CC1=C(C#N)[C@@H](c2ccc(C#N)cc2N)NC(=O)N1c1cccc(C(F)(F)F)c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC1=C(C#N)[C@@H](c2ccc(C#N)cc2[N+](=O)[O-])NC(=O)N1c1cccc(C(F)(F)F)c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC1=C(C#N)[C@@H](c2ccc(C#N)cc2[N+](=O)[O-])NC(=O)N1c1cccc(C(F)(F)F)c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC1=C(C(N)=O)[C@@H](c2ccc(C#N)cc2[N+](=O)[O-])NC(=O)N1c1cccc(C(F)(F)F)c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC1=C(C(N)=O)[C@@H](c2ccc(C#N)cc2[N+](=O)[O-])NC(=O)N1c1cccc(C(F)(F)F)c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC1=C(C(=O)O)[C@@H](c2ccc(C#N)cc2[N+](=O)[O-])NC(=O)N1c1cccc(C(F)(F)F)c1\": \"precursor\", \"N\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC1=C(C(=O)O)[C@@H](c2ccc(C#N)cc2[N+](=O)[O-])NC(=O)N1c1cccc(C(F)(F)F)c1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"N\", \"in_stock\": true, \"children\": []}]}]}]}]}]}]}]}}","name":"emit_routes"},"id":"call_4_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"CC1=C(C#N)[C@@H](c2ccc(C#N)cc2N)NC(=O)N1c1cccc(C(F)(F)F)c1","task_id":"retro_7fd0692d57d052c4754e","tool_calls":8,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":4}
{"exact_match":true,"id":"retro_81e0d3267abfc4209a56:reference-expert:a0","kind":"single_route","max_steps":3,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CC(Nc1ncc(Cl)c(Nc2cc(C3CC3)[nH]n2)n1)c1ccc(F)cn1 in at most 3 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(Nc1ncc(Cl)c(Nc2cc(C3CC3)[nH]n2)n1)c1ccc(F)cn1\", \"reactants\": [\"CC(N)c1ccc(F)cn1\", \"Clc1ncc(Cl)c(Nc2cc(C3CC3)[nH]n2)n1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(N)c1ccc(F)cn1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"Clc1ncc(Cl)c(Nc2cc(C3CC3)[nH]n2)n1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"FXEBKOLHJOHTAY-UHFFFAOYSA-N.KNKRMCSSVBSDNL-UHFFFAOYSA-N>>OJZRYNOBGQMTOS-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"CC(Nc1ncc(Cl)c(Nc2cc(C3CC3)[nH]n2)n1)c1ccc(F)cn1\", \"reactants\": [\"CC(N)c1ccc(F)cn1\", \"Clc1ncc(Cl)c(Nc2cc(C3CC3)[nH]n2)n1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CC(N)c1ccc(F)cn1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"Clc1ncc(Cl)c(Nc2cc(C3CC3)[nH]n2)n1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"CC(N)c1ccc(F)cn1 was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(N)c1ccc(F)cn1\", \"reactants\": [\"CC(N=[N+]=[N-])c1ccc(F)cn1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(N=[N+]=[N-])c1ccc(F)cn1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"XPVSJVOKPDXFTD-UHFFFAOYSA-N>>KNKRMCSSVBSDNL-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"CC(N)c1ccc(F)cn1\", \"reactants\": [\"CC(N=[N+]=[N-])c1ccc(F)cn1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CC(N=[N+]=[N-])c1ccc(F)cn1\", \"results\": [{\"inchikey\": \"XPVSJVOKPDXFTD-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CC(N=[N+]=[N-])c1ccc(F)cn1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"Clc1ncc(Cl)c(Nc2cc(C3CC3)[nH]n2)n1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Clc1ncc(Cl)c(Nc2cc(C3CC3)[nH]n2)n1\", \"reactants\": [\"Clc1ncc(Cl)c(Cl)n1\", \"Nc1cc(C2CC2)[nH]n1\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"Clc1ncc(Cl)c(Cl)n1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"Nc1cc(C2CC2)[nH]n1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"GIKMWFAAEIACRF-UHFFFAOYSA-N.MXVAGCQKBDMKPG-UHFFFAOYSA-N>>FXEBKOLHJOHTAY-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"Clc1ncc(Cl)c(Nc2cc(C3CC3)[nH]n2)n1\", \"reactants\": [\"Clc1ncc(Cl)c(Cl)n1\", \"Nc1cc(C2CC2)[nH]n1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"Clc1ncc(Cl)c(Cl)n1\", \"results\": [{\"inchikey\": \"GIKMWFAAEIACRF-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Clc1ncc(Cl)c(Cl)n1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"Nc1cc(C2CC2)[nH]n1\", \"results\": [{\"inchikey\": \"MXVAGCQKBDMKPG-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Nc1cc(C2CC2)[nH]n1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CC(Nc1ncc(Cl)c(Nc2cc(C3CC3)[nH]n2)n1)c1ccc(F)cn1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(N)c1ccc(F)cn1\": \"precursor\", \"Clc1ncc(Cl)c(Nc2cc(C3CC3)[nH]n2)n1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(N)c1ccc(F)cn1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(N=[N+]=[N-])c1ccc(F)cn1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(N=[N+]=[N-])c1ccc(F)cn1\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"Clc1ncc(Cl)c(Nc2cc(C3CC3)[nH]n2)n1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"Clc1ncc(Cl)c(Cl)n1\": \"precursor\", \"Nc1cc(C2CC2)[nH]n1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"Clc1ncc(Cl)c(Cl)n1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"Nc1cc(C2CC2)[nH]n1\", \"in_stock\": true, \"children\": []}]}]}]}]}]}}","name":"emit_routes"},"id":"call_4_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"CC(Nc1ncc(Cl)c(Nc2cc(C3CC3)[nH]n2)n1)c1ccc(F)cn1","task_id":"retro_81e0d3267abfc4209a56","tool_calls":9,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":4}
{"exact_match":true,"id":"retro_82810530022340bf99f5:reference-expert:a0","kind":"single_route","max_steps":3,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target Cc1ncccc1Oc1ncnc2c1cnn2C1CCN(C(=O)OCc2ccccc2)CC1 in at most 3 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Cc1ncccc1Oc1ncnc2c1cnn2C1CCN(C(=O)OCc2ccccc2)CC1\", \"reactants\": [\"Cc1ncccc1Oc1ncnc2c1cnn2C1CCN(C(=O)OC(C)(C)C)CC1\", \"O=C(Cl)OCc1ccccc1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"Cc1ncccc1Oc1ncnc2c1cnn2C1CCN(C(=O)OC(C)(C)C)CC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=C(Cl)OCc1ccccc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"HSDAJNMJOMSNEV-UHFFFAOYSA-N.IOGGTWTZCOUVJP-UHFFFAOYSA-N>>ZEQXHQYHJVVFLK-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"Cc1ncccc1Oc1ncnc2c1cnn2C1CCN(C(=O)OCc2ccccc2)CC1\", \"reactants\": [\"Cc1ncccc1Oc1ncnc2c1cnn2C1CCN(C(=O)OC(C)(C)C)CC1\", \"O=C(Cl)OCc1ccccc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"Cc1ncccc1Oc1ncnc2c1cnn2C1CCN(C(=O)OC(C)(C)C)CC1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"O=C(Cl)OCc1ccccc1\", \"results\": [{\"inchikey\": \"HSDAJNMJOMSNEV-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=C(Cl)OCc1ccccc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"Cc1ncccc1Oc1ncnc2c1cnn2C1CCN(C(=O)OC(C)(C)C)CC1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Cc1ncccc1Oc1ncnc2c1cnn2C1CCN(C(=O)OC(C)(C)C)CC1\", \"reactants\": [\"CC(C)(C)OC(=O)N1CCC(n2ncc3c(Cl)ncnc32)CC1\", \"Cc1ncccc1O\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)OC(=O)N1CCC(n2ncc3c(Cl)ncnc32)CC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"Cc1ncccc1O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"AQSRRZGQRFFFGS-UHFFFAOYSA-N.BNXIZPZXSBYUQT-UHFFFAOYSA-N>>IOGGTWTZCOUVJP-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"Cc1ncccc1Oc1ncnc2c1cnn2C1CCN(C(=O)OC(C)(C)C)CC1\", \"reactants\": [\"CC(C)(C)OC(=O)N1CCC(n2ncc3c(Cl)ncnc32)CC1\", \"Cc1ncccc1O\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CC(C)(C)OC(=O)N1CCC(n2ncc3c(Cl)ncnc32)CC1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"Cc1ncccc1O\", \"results\": [{\"inchikey\": \"AQSRRZGQRFFFGS-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Cc1ncccc1O\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"CC(C)(C)OC(=O)N1CCC(n2ncc3c(Cl)ncnc32)CC1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(C)(C)OC(=O)N1CCC(n2ncc3c(Cl)ncnc32)CC1\", \"reactants\": [\"CC(C)(C)OC(=O)N1CCC(NN)CC1\", \"O=Cc1c(Cl)ncnc1Cl\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)OC(=O)N1CCC(NN)CC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=Cc1c(Cl)ncnc1Cl\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"HZHVNRRMSFVLSH-UHFFFAOYSA-N.XQSJHQXYQAUDFC-UHFFFAOYSA-N>>BNXIZPZXSBYUQT-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"CC(C)(C)OC(=O)N1CCC(n2ncc3c(Cl)ncnc32)CC1\", \"reactants\": [\"CC(C)(C)OC(=O)N1CCC(NN)CC1\", \"O=Cc1c(Cl)ncnc1Cl\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"CC(C)(C)OC(=O)N1CCC(NN)CC1\", \"results\": [{\"inchikey\": \"HZHVNRRMSFVLSH-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CC(C)(C)OC(=O)N1CCC(NN)CC1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"O=Cc1c(Cl)ncnc1Cl\", \"results\": [{\"inchikey\": \"XQSJHQXYQAUDFC-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=Cc1c(Cl)ncnc1Cl\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"Cc1ncccc1Oc1ncnc2c1cnn2C1CCN(C(=O)OCc2ccccc2)CC1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"Cc1ncccc1Oc1ncnc2c1cnn2C1CCN(C(=O)OC(C)(C)C)CC1\": \"precursor\", \"O=C(Cl)OCc1ccccc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"Cc1ncccc1Oc1ncnc2c1cnn2C1CCN(C(=O)OC(C)(C)C)CC1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)(C)OC(=O)N1CCC(n2ncc3c(Cl)ncnc32)CC1\": \"precursor\", \"Cc1ncccc1O\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)OC(=O)N1CCC(n2ncc3c(Cl)ncnc32)CC1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)(C)OC(=O)N1CCC(NN)CC1\": \"precursor\", \"O=Cc1c(Cl)ncnc1Cl\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)OC(=O)N1CCC(NN)CC1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=Cc1c(Cl)ncnc1Cl\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"Cc1ncccc1O\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"O=C(Cl)OCc1ccccc1\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_4_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"Cc1ncccc1Oc1ncnc2c1cnn2C1CCN(C(=O)OCc2ccccc2)CC1","task_id":"retro_82810530022340bf99f5","tool_calls":10,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":4}
{"exact_match":true,"id":"retro_82f91e726b009e6de21f:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CCCc1c(OCc2ccc(N)cc2)ccc(C(C)=O)c1O in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCCc1c(OCc2ccc(N)cc2)ccc(C(C)=O)c1O\", \"reactants\": [\"CCCc1c(OCc2ccc([N+](=O)[O-])cc2)ccc(C(C)=O)c1O\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCCc1c(OCc2ccc([N+](=O)[O-])cc2)ccc(C(C)=O)c1O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"ZDBAOTAWDVMJKU-UHFFFAOYSA-N>>SFPFNLGEVKUWIO-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"CCCc1c(OCc2ccc(N)cc2)ccc(C(C)=O)c1O\", \"reactants\": [\"CCCc1c(OCc2ccc([N+](=O)[O-])cc2)ccc(C(C)=O)c1O\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CCCc1c(OCc2ccc([N+](=O)[O-])cc2)ccc(C(C)=O)c1O\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"CCCc1c(OCc2ccc([N+](=O)[O-])cc2)ccc(C(C)=O)c1O was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCCc1c(OCc2ccc([N+](=O)[O-])cc2)ccc(C(C)=O)c1O\", \"reactants\": [\"CCCc1c(O)ccc(C(C)=O)c1O\", \"O=[N+]([O-])c1ccc(CBr)cc1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCCc1c(O)ccc(C(C)=O)c1O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=[N+]([O-])c1ccc(CBr)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"QGGRBWUQXAFYEC-UHFFFAOYSA-N.VOLRSQPSJGXRNJ-UHFFFAOYSA-N>>ZDBAOTAWDVMJKU-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"CCCc1c(OCc2ccc([N+](=O)[O-])cc2)ccc(C(C)=O)c1O\", \"reactants\": [\"CCCc1c(O)ccc(C(C)=O)c1O\", \"O=[N+]([O-])c1ccc(CBr)cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CCCc1c(O)ccc(C(C)=O)c1O\", \"results\": [{\"inchikey\": \"QGGRBWUQXAFYEC-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CCCc1c(O)ccc(C(C)=O)c1O\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"O=[N+]([O-])c1ccc(CBr)cc1\", \"results\": [{\"inchikey\": \"VOLRSQPSJGXRNJ-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=[N+]([O-])c1ccc(CBr)cc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CCCc1c(OCc2ccc(N)cc2)ccc(C(C)=O)c1O\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCCc1c(OCc2ccc([N+](=O)[O-])cc2)ccc(C(C)=O)c1O\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCCc1c(OCc2ccc([N+](=O)[O-])cc2)ccc(C(C)=O)c1O\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCCc1c(O)ccc(C(C)=O)c1O\": \"precursor\", \"O=[N+]([O-])c1ccc(CBr)cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCCc1c(O)ccc(C(C)=O)c1O\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=[N+]([O-])c1ccc(CBr)cc1\", \"in_stock\": true, \"children\": []}]}]}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"CCCc1c(OCc2ccc(N)cc2)ccc(C(C)=O)c1O","task_id":"retro_82f91e726b009e6de21f","tool_calls":6,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_837833021514235eb541:reference-expert:a0","kind":"single_route","max_steps":5,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CC(=O)N(C)[C@H](C)COc1cccc2ncnc(Nc3ccc(Oc4ccc(C)nc4)c(C)c3)c12 in at most 5 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(=O)N(C)[C@H](C)COc1cccc2ncnc(Nc3ccc(Oc4ccc(C)nc4)c(C)c3)c12\", \"reactants\": [\"CC(=O)OC(C)=O\", \"CN[C@H](C)COc1cccc2ncnc(Nc3ccc(Oc4ccc(C)nc4)c(C)c3)c12\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(=O)OC(C)=O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"CN[C@H](C)COc1cccc2ncnc(Nc3ccc(Oc4ccc(C)nc4)c(C)c3)c12\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"PAKBXQOBZMIKSR-GOSISDBHSA-N.WFDIJRYMOXRFFG-UHFFFAOYSA-N>>LAAYSIJTDUWVJU-LJQANCHMSA-N\", \"model_turns_remaining\": 15, \"product\": \"CC(=O)N(C)[C@H](C)COc1cccc2ncnc(Nc3ccc(Oc4ccc(C)nc4)c(C)c3)c12\", \"reactants\": [\"CC(=O)OC(C)=O\", \"CN[C@H](C)COc1cccc2ncnc(Nc3ccc(Oc4ccc(C)nc4)c(C)c3)c12\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CC(=O)OC(C)=O\", \"results\": [{\"inchikey\": \"WFDIJRYMOXRFFG-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CC(=O)OC(C)=O\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CN[C@H](C)COc1cccc2ncnc(Nc3ccc(Oc4ccc(C)nc4)c(C)c3)c12\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"CN[C@H](C)COc1cccc2ncnc(Nc3ccc(Oc4ccc(C)nc4)c(C)c3)c12 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CN[C@H](C)COc1cccc2ncnc(Nc3ccc(Oc4ccc(C)nc4)c(C)c3)c12\", \"reactants\": [\"CN[C@H](C)CO\", \"Cc1ccc(Oc2ccc(Nc3ncnc4cccc(F)c34)cc2C)cn1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CN[C@H](C)CO\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"Cc1ccc(Oc2ccc(Nc3ncnc4cccc(F)c34)cc2C)cn1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"PXWASTUQOKUFKY-SCSAIBSYSA-N.ZWIANDNCAFFXOZ-UHFFFAOYSA-N>>PAKBXQOBZMIKSR-GOSISDBHSA-N\", \"model_turns_remaining\": 14, \"product\": \"CN[C@H](C)COc1cccc2ncnc(Nc3ccc(Oc4ccc(C)nc4)c(C)c3)c12\", \"reactants\": [\"CN[C@H](C)CO\", \"Cc1ccc(Oc2ccc(Nc3ncnc4cccc(F)c34)cc2C)cn1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CN[C@H](C)CO\", \"results\": [{\"inchikey\": \"PXWASTUQOKUFKY-SCSAIBSYSA-N\", \"similarity\": 1.0, \"smiles\": \"CN[C@H](C)CO\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"Cc1ccc(Oc2ccc(Nc3ncnc4cccc(F)c34)cc2C)cn1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Cc1ccc(Oc2ccc(Nc3ncnc4cccc(F)c34)cc2C)cn1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Cc1ccc(Oc2ccc(Nc3ncnc4cccc(F)c34)cc2C)cn1\", \"reactants\": [\"Cc1ccc(Oc2ccc(N)cc2C)cn1\", \"Fc1cccc2ncnc(Cl)c12\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"Cc1ccc(Oc2ccc(N)cc2C)cn1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"Fc1cccc2ncnc(Cl)c12\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"GBMQBBQKWXOOJZ-UHFFFAOYSA-N.NRVNUZHSKMEHOT-UHFFFAOYSA-N>>ZWIANDNCAFFXOZ-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"Cc1ccc(Oc2ccc(Nc3ncnc4cccc(F)c34)cc2C)cn1\", \"reactants\": [\"Cc1ccc(Oc2ccc(N)cc2C)cn1\", \"Fc1cccc2ncnc(Cl)c12\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"Cc1ccc(Oc2ccc(N)cc2C)cn1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"Fc1cccc2ncnc(Cl)c12\", \"results\": [{\"inchikey\": \"NRVNUZHSKMEHOT-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Fc1cccc2ncnc(Cl)c12\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"Cc1ccc(Oc2ccc(N)cc2C)cn1 was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Cc1ccc(Oc2ccc(N)cc2C)cn1\", \"reactants\": [\"Cc1ccc(Oc2ccc([N+](=O)[O-])cc2C)cn1\"]}","name":"validate_disconnection"},"id":"call_4_0","type":"function"},{"function":{"arguments":"{\"query\": \"Cc1ccc(Oc2ccc([N+](=O)[O-])cc2C)cn1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"BTMOLGOJGLILQV-UHFFFAOYSA-N>>GBMQBBQKWXOOJZ-UHFFFAOYSA-N\", \"model_turns_remaining\": 12, \"product\": \"Cc1ccc(Oc2ccc(N)cc2C)cn1\", \"reactants\": [\"Cc1ccc(Oc2ccc([N+](=O)[O-])cc2C)cn1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_4_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"Cc1ccc(Oc2ccc([N+](=O)[O-])cc2C)cn1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_1"},{"content":"Cc1ccc(Oc2ccc([N+](=O)[O-])cc2C)cn1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Cc1ccc(Oc2ccc([N+](=O)[O-])cc2C)cn1\", \"reactants\": [\"Cc1cc([N+](=O)[O-])ccc1F\", \"Cc1ccc(O)cn1\"]}","name":"validate_disconnection"},"id":"call_5_0","type":"function"},{"function":{"arguments":"{\"query\": \"Cc1cc([N+](=O)[O-])ccc1F\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_5_1","type":"function"},{"function":{"arguments":"{\"query\": \"Cc1ccc(O)cn1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_5_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"DHLUJPLHLZJUBW-UHFFFAOYSA-N.XUCYJGMIICONES-UHFFFAOYSA-N>>BTMOLGOJGLILQV-UHFFFAOYSA-N\", \"model_turns_remaining\": 11, \"product\": \"Cc1ccc(Oc2ccc([N+](=O)[O-])cc2C)cn1\", \"reactants\": [\"Cc1cc([N+](=O)[O-])ccc1F\", \"Cc1ccc(O)cn1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_5_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 11, \"query\": \"Cc1cc([N+](=O)[O-])ccc1F\", \"results\": [{\"inchikey\": \"XUCYJGMIICONES-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Cc1cc([N+](=O)[O-])ccc1F\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_5_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 11, \"query\": \"Cc1ccc(O)cn1\", \"results\": [{\"inchikey\": \"DHLUJPLHLZJUBW-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Cc1ccc(O)cn1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_5_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CC(=O)N(C)[C@H](C)COc1cccc2ncnc(Nc3ccc(Oc4ccc(C)nc4)c(C)c3)c12\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(=O)OC(C)=O\": \"precursor\", \"CN[C@H](C)COc1cccc2ncnc(Nc3ccc(Oc4ccc(C)nc4)c(C)c3)c12\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(=O)OC(C)=O\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"CN[C@H](C)COc1cccc2ncnc(Nc3ccc(Oc4ccc(C)nc4)c(C)c3)c12\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CN[C@H](C)CO\": \"precursor\", \"Cc1ccc(Oc2ccc(Nc3ncnc4cccc(F)c34)cc2C)cn1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CN[C@H](C)CO\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"Cc1ccc(Oc2ccc(Nc3ncnc4cccc(F)c34)cc2C)cn1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"Cc1ccc(Oc2ccc(N)cc2C)cn1\": \"precursor\", \"Fc1cccc2ncnc(Cl)c12\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"Cc1ccc(Oc2ccc(N)cc2C)cn1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"Cc1ccc(Oc2ccc([N+](=O)[O-])cc2C)cn1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"Cc1ccc(Oc2ccc([N+](=O)[O-])cc2C)cn1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"Cc1cc([N+](=O)[O-])ccc1F\": \"precursor\", \"Cc1ccc(O)cn1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"Cc1cc([N+](=O)[O-])ccc1F\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"Cc1ccc(O)cn1\", \"in_stock\": true, \"children\": []}]}]}]}]}, {\"type\": \"mol\", \"smiles\": \"Fc1cccc2ncnc(Cl)c12\", \"in_stock\": true, \"children\": []}]}]}]}]}]}]}]}}","name":"emit_routes"},"id":"call_6_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"CC(=O)N(C)[C@H](C)COc1cccc2ncnc(Nc3ccc(Oc4ccc(C)nc4)c(C)c3)c12","task_id":"retro_837833021514235eb541","tool_calls":15,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":6}
{"exact_match":true,"id":"retro_8582661b4be35cd29cf0:reference-expert:a0","kind":"single_route","max_steps":3,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CC(C)(C)OC(=O)N1CCC(C#N)(c2ncccc2Br)CC1 in at most 3 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(C)(C)OC(=O)N1CCC(C#N)(c2ncccc2Br)CC1\", \"reactants\": [\"CC(C)(C)OC(=O)N(CCCl)CCCl\", \"N#CCc1ncccc1Br\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)OC(=O)N(CCCl)CCCl\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"N#CCc1ncccc1Br\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"FQZLNQAUUMSUHT-UHFFFAOYSA-N.TYSWNHWAGMAOJF-UHFFFAOYSA-N>>QEAAPUNMNUIJAZ-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"CC(C)(C)OC(=O)N1CCC(C#N)(c2ncccc2Br)CC1\", \"reactants\": [\"CC(C)(C)OC(=O)N(CCCl)CCCl\", \"N#CCc1ncccc1Br\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CC(C)(C)OC(=O)N(CCCl)CCCl\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"N#CCc1ncccc1Br\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"CC(C)(C)OC(=O)N(CCCl)CCCl was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(C)(C)OC(=O)N(CCCl)CCCl\", \"reactants\": [\"CC(C)(C)OC(=O)OC(=O)OC(C)(C)C\", \"ClCCNCCCl\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)OC(=O)OC(=O)OC(C)(C)C\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"ClCCNCCCl\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"DYHSDKLCOJIUFX-UHFFFAOYSA-N.TXFLGZOGNOOEFZ-UHFFFAOYSA-N>>FQZLNQAUUMSUHT-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"CC(C)(C)OC(=O)N(CCCl)CCCl\", \"reactants\": [\"CC(C)(C)OC(=O)OC(=O)OC(C)(C)C\", \"ClCCNCCCl\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CC(C)(C)OC(=O)OC(=O)OC(C)(C)C\", \"results\": [{\"inchikey\": \"DYHSDKLCOJIUFX-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CC(C)(C)OC(=O)OC(=O)OC(C)(C)C\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"ClCCNCCCl\", \"results\": [{\"inchikey\": \"TXFLGZOGNOOEFZ-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"ClCCNCCCl\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"N#CCc1ncccc1Br was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"N#CCc1ncccc1Br\", \"reactants\": [\"BrCc1ncccc1Br\", \"C#N\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"BrCc1ncccc1Br\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"C#N\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"FVIZOBDAEIFYGH-UHFFFAOYSA-N.LELOWRISYMNNSU-UHFFFAOYSA-N>>TYSWNHWAGMAOJF-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"N#CCc1ncccc1Br\", \"reactants\": [\"BrCc1ncccc1Br\", \"C#N\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"BrCc1ncccc1Br\", \"results\": [{\"inchikey\": \"FVIZOBDAEIFYGH-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"BrCc1ncccc1Br\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"C#N\", \"results\": [{\"inchikey\": \"LELOWRISYMNNSU-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"C#N\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)OC(=O)N1CCC(C#N)(c2ncccc2Br)CC1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)(C)OC(=O)N(CCCl)CCCl\": \"precursor\", \"N#CCc1ncccc1Br\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)OC(=O)N(CCCl)CCCl\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)(C)OC(=O)OC(=O)OC(C)(C)C\": \"precursor\", \"ClCCNCCCl\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)OC(=O)OC(=O)OC(C)(C)C\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"ClCCNCCCl\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"N#CCc1ncccc1Br\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"BrCc1ncccc1Br\": \"precursor\", \"C#N\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"BrCc1ncccc1Br\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"C#N\", \"in_stock\": true, \"children\": []}]}]}]}]}]}}","name":"emit_routes"},"id":"call_4_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"CC(C)(C)OC(=O)N1CCC(C#N)(c2ncccc2Br)CC1","task_id":"retro_8582661b4be35cd29cf0","tool_calls":10,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":4}
{"exact_match":true,"id":"retro_8781eec7becaa53ca051:reference-expert:a0","kind":"single_route","max_steps":4,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CC(C)S(=O)(=O)c1ccc2c(c1)nc(CC(C)(C)C)n2CCN1CCCC1 in at most 4 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(C)S(=O)(=O)c1ccc2c(c1)nc(CC(C)(C)C)n2CCN1CCCC1\", \"reactants\": [\"CC(C)(C)CC(=O)Cl\", \"CC(C)S(=O)(=O)c1ccc(NCCN2CCCC2)c(N)c1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)CC(=O)Cl\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)S(=O)(=O)c1ccc(NCCN2CCCC2)c(N)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"BUTKIHRNYUEGKB-UHFFFAOYSA-N.RHWGMEQXKWKBGT-UHFFFAOYSA-N>>RZBRHMJPJZUQHQ-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"CC(C)S(=O)(=O)c1ccc2c(c1)nc(CC(C)(C)C)n2CCN1CCCC1\", \"reactants\": [\"CC(C)(C)CC(=O)Cl\", \"CC(C)S(=O)(=O)c1ccc(NCCN2CCCC2)c(N)c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CC(C)(C)CC(=O)Cl\", \"results\": [{\"inchikey\": \"BUTKIHRNYUEGKB-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CC(C)(C)CC(=O)Cl\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CC(C)S(=O)(=O)c1ccc(NCCN2CCCC2)c(N)c1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"CC(C)S(=O)(=O)c1ccc(NCCN2CCCC2)c(N)c1 was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(C)S(=O)(=O)c1ccc(NCCN2CCCC2)c(N)c1\", \"reactants\": [\"CC(C)S(=O)(=O)c1ccc(NCCN2CCCC2)c([N+](=O)[O-])c1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)S(=O)(=O)c1ccc(NCCN2CCCC2)c([N+](=O)[O-])c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"QYLWDSRULXNNJJ-UHFFFAOYSA-N>>RHWGMEQXKWKBGT-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"CC(C)S(=O)(=O)c1ccc(NCCN2CCCC2)c(N)c1\", \"reactants\": [\"CC(C)S(=O)(=O)c1ccc(NCCN2CCCC2)c([N+](=O)[O-])c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CC(C)S(=O)(=O)c1ccc(NCCN2CCCC2)c([N+](=O)[O-])c1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"CC(C)S(=O)(=O)c1ccc(NCCN2CCCC2)c([N+](=O)[O-])c1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(C)S(=O)(=O)c1ccc(NCCN2CCCC2)c([N+](=O)[O-])c1\", \"reactants\": [\"CC(C)S(=O)(=O)c1ccc(Cl)c([N+](=O)[O-])c1\", \"NCCN1CCCC1\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)S(=O)(=O)c1ccc(Cl)c([N+](=O)[O-])c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"NCCN1CCCC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"RUWLFSCBPCABKC-UHFFFAOYSA-N.WRXNJTBODVGDRY-UHFFFAOYSA-N>>QYLWDSRULXNNJJ-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"CC(C)S(=O)(=O)c1ccc(NCCN2CCCC2)c([N+](=O)[O-])c1\", \"reactants\": [\"CC(C)S(=O)(=O)c1ccc(Cl)c([N+](=O)[O-])c1\", \"NCCN1CCCC1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"CC(C)S(=O)(=O)c1ccc(Cl)c([N+](=O)[O-])c1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"NCCN1CCCC1\", \"results\": [{\"inchikey\": \"WRXNJTBODVGDRY-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"NCCN1CCCC1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"CC(C)S(=O)(=O)c1ccc(Cl)c([N+](=O)[O-])c1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(C)S(=O)(=O)c1ccc(Cl)c([N+](=O)[O-])c1\", \"reactants\": [\"CC(C)S(=O)(=O)c1ccc(Cl)cc1\", \"O=[N+]([O-])O\"]}","name":"validate_disconnection"},"id":"call_4_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)S(=O)(=O)c1ccc(Cl)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=[N+]([O-])O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"GRYLNZFGIOXLOG-UHFFFAOYSA-N.ZKVPUWNTECRZSQ-UHFFFAOYSA-N>>RUWLFSCBPCABKC-UHFFFAOYSA-N\", \"model_turns_remaining\": 12, \"product\": \"CC(C)S(=O)(=O)c1ccc(Cl)c([N+](=O)[O-])c1\", \"reactants\": [\"CC(C)S(=O)(=O)c1ccc(Cl)cc1\", \"O=[N+]([O-])O\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_4_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"CC(C)S(=O)(=O)c1ccc(Cl)cc1\", \"results\": [{\"inchikey\": \"ZKVPUWNTECRZSQ-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CC(C)S(=O)(=O)c1ccc(Cl)cc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"O=[N+]([O-])O\", \"results\": [{\"inchikey\": \"GRYLNZFGIOXLOG-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=[N+]([O-])O\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CC(C)S(=O)(=O)c1ccc2c(c1)nc(CC(C)(C)C)n2CCN1CCCC1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)(C)CC(=O)Cl\": \"precursor\", \"CC(C)S(=O)(=O)c1ccc(NCCN2CCCC2)c(N)c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)CC(=O)Cl\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"CC(C)S(=O)(=O)c1ccc(NCCN2CCCC2)c(N)c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)S(=O)(=O)c1ccc(NCCN2CCCC2)c([N+](=O)[O-])c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)S(=O)(=O)c1ccc(NCCN2CCCC2)c([N+](=O)[O-])c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)S(=O)(=O)c1ccc(Cl)c([N+](=O)[O-])c1\": \"precursor\", \"NCCN1CCCC1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)S(=O)(=O)c1ccc(Cl)c([N+](=O)[O-])c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)S(=O)(=O)c1ccc(Cl)cc1\": \"precursor\", \"O=[N+]([O-])O\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)S(=O)(=O)c1ccc(Cl)cc1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=[N+]([O-])O\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"NCCN1CCCC1\", \"in_stock\": true, \"children\": []}]}]}]}]}]}]}]}}","name":"emit_routes"},"id":"call_5_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"CC(C)S(=O)(=O)c1ccc2c(c1)nc(CC(C)(C)C)n2CCN1CCCC1","task_id":"retro_8781eec7becaa53ca051","tool_calls":12,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":5}
{"exact_match":true,"id":"retro_8a678d96fd54532769e5:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target COc1cccc(C2(O)CCCN(C(=O)c3ccc([N+](=O)[O-])cc3)C2)c1 in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COc1cccc(C2(O)CCCN(C(=O)c3ccc([N+](=O)[O-])cc3)C2)c1\", \"reactants\": [\"COc1cccc(C2(O)CCCNC2)c1\", \"O=C(Cl)c1ccc([N+](=O)[O-])cc1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"COc1cccc(C2(O)CCCNC2)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=C(Cl)c1ccc([N+](=O)[O-])cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"SKDHHIUENRGTHK-UHFFFAOYSA-N.ZHVVKZZITMJIDF-UHFFFAOYSA-N>>CZFDAWWUKRGLDB-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"COc1cccc(C2(O)CCCN(C(=O)c3ccc([N+](=O)[O-])cc3)C2)c1\", \"reactants\": [\"COc1cccc(C2(O)CCCNC2)c1\", \"O=C(Cl)c1ccc([N+](=O)[O-])cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"COc1cccc(C2(O)CCCNC2)c1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"O=C(Cl)c1ccc([N+](=O)[O-])cc1\", \"results\": [{\"inchikey\": \"SKDHHIUENRGTHK-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=C(Cl)c1ccc([N+](=O)[O-])cc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"COc1cccc(C2(O)CCCNC2)c1 was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COc1cccc(C2(O)CCCNC2)c1\", \"reactants\": [\"COc1cccc(C2(O)CCCN(Cc3ccccc3)C2)c1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"COc1cccc(C2(O)CCCN(Cc3ccccc3)C2)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"LNHMXWVXOYXBNZ-UHFFFAOYSA-N>>ZHVVKZZITMJIDF-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"COc1cccc(C2(O)CCCNC2)c1\", \"reactants\": [\"COc1cccc(C2(O)CCCN(Cc3ccccc3)C2)c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"COc1cccc(C2(O)CCCN(Cc3ccccc3)C2)c1\", \"results\": [{\"inchikey\": \"LNHMXWVXOYXBNZ-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"COc1cccc(C2(O)CCCN(Cc3ccccc3)C2)c1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"COc1cccc(C2(O)CCCN(C(=O)c3ccc([N+](=O)[O-])cc3)C2)c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COc1cccc(C2(O)CCCNC2)c1\": \"precursor\", \"O=C(Cl)c1ccc([N+](=O)[O-])cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COc1cccc(C2(O)CCCNC2)c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COc1cccc(C2(O)CCCN(Cc3ccccc3)C2)c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COc1cccc(C2(O)CCCN(Cc3ccccc3)C2)c1\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"O=C(Cl)c1ccc([N+](=O)[O-])cc1\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"COc1cccc(C2(O)CCCN(C(=O)c3ccc([N+](=O)[O-])cc3)C2)c1","task_id":"retro_8a678d96fd54532769e5","tool_calls":6,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_8b3a4624eee78bfc9c73:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target O=C(O)Cn1c(=O)n(-c2ccccn2)c2ccccc21 in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"O=C(O)Cn1c(=O)n(-c2ccccn2)c2ccccc21\", \"reactants\": [\"CC(C)(C)OC(=O)Cn1c(=O)n(-c2ccccn2)c2ccccc21\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)OC(=O)Cn1c(=O)n(-c2ccccn2)c2ccccc21\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"AMKFTJVTRZWNLE-UHFFFAOYSA-N>>ZNRVGLMGJSWZKM-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"O=C(O)Cn1c(=O)n(-c2ccccn2)c2ccccc21\", \"reactants\": [\"CC(C)(C)OC(=O)Cn1c(=O)n(-c2ccccn2)c2ccccc21\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CC(C)(C)OC(=O)Cn1c(=O)n(-c2ccccn2)c2ccccc21\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"CC(C)(C)OC(=O)Cn1c(=O)n(-c2ccccn2)c2ccccc21 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(C)(C)OC(=O)Cn1c(=O)n(-c2ccccn2)c2ccccc21\", \"reactants\": [\"Brc1ccccn1\", \"CC(C)(C)OC(=O)Cn1c(=O)[nH]c2ccccc21\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"Brc1ccccn1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)OC(=O)Cn1c(=O)[nH]c2ccccc21\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"FCJFZOJBOUYYMU-UHFFFAOYSA-N.IMRWILPUOVGIMU-UHFFFAOYSA-N>>AMKFTJVTRZWNLE-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"CC(C)(C)OC(=O)Cn1c(=O)n(-c2ccccn2)c2ccccc21\", \"reactants\": [\"Brc1ccccn1\", \"CC(C)(C)OC(=O)Cn1c(=O)[nH]c2ccccc21\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"Brc1ccccn1\", \"results\": [{\"inchikey\": \"IMRWILPUOVGIMU-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Brc1ccccn1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CC(C)(C)OC(=O)Cn1c(=O)[nH]c2ccccc21\", \"results\": [{\"inchikey\": \"FCJFZOJBOUYYMU-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CC(C)(C)OC(=O)Cn1c(=O)[nH]c2ccccc21\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"O=C(O)Cn1c(=O)n(-c2ccccn2)c2ccccc21\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)(C)OC(=O)Cn1c(=O)n(-c2ccccn2)c2ccccc21\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)OC(=O)Cn1c(=O)n(-c2ccccn2)c2ccccc21\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"Brc1ccccn1\": \"precursor\", \"CC(C)(C)OC(=O)Cn1c(=O)[nH]c2ccccc21\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"Brc1ccccn1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"CC(C)(C)OC(=O)Cn1c(=O)[nH]c2ccccc21\", \"in_stock\": true, \"children\": []}]}]}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"O=C(O)Cn1c(=O)n(-c2ccccn2)c2ccccc21","task_id":"retro_8b3a4624eee78bfc9c73","tool_calls":6,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_8b5aadde61facb9fd79a:reference-expert:a0","kind":"single_route","max_steps":5,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CNc1ncc2c(C(=O)NCc3c(C)cc(C)nc3O)c(C)n([C@H](C)c3ccccc3)c2n1 in at most 5 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CNc1ncc2c(C(=O)NCc3c(C)cc(C)nc3O)c(C)n([C@H](C)c3ccccc3)c2n1\", \"reactants\": [\"CN\", \"Cc1cc(C)c(CNC(=O)c2c(C)n([C@H](C)c3ccccc3)c3nc(Cl)ncc23)c(O)n1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CN\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"Cc1cc(C)c(CNC(=O)c2c(C)n([C@H](C)c3ccccc3)c3nc(Cl)ncc23)c(O)n1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"BAVYZALUXZFZLV-UHFFFAOYSA-N.OXGOXSJWLFYVKQ-OAHLLOKOSA-N>>YYTJTSIZXQBNSK-MRXNPFEDSA-N\", \"model_turns_remaining\": 15, \"product\": \"CNc1ncc2c(C(=O)NCc3c(C)cc(C)nc3O)c(C)n([C@H](C)c3ccccc3)c2n1\", \"reactants\": [\"CN\", \"Cc1cc(C)c(CNC(=O)c2c(C)n([C@H](C)c3ccccc3)c3nc(Cl)ncc23)c(O)n1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CN\", \"results\": [{\"inchikey\": \"BAVYZALUXZFZLV-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CN\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"Cc1cc(C)c(CNC(=O)c2c(C)n([C@H](C)c3ccccc3)c3nc(Cl)ncc23)c(O)n1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"Cc1cc(C)c(CNC(=O)c2c(C)n([C@H](C)c3ccccc3)c3nc(Cl)ncc23)c(O)n1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Cc1cc(C)c(CNC(=O)c2c(C)n([C@H](C)c3ccccc3)c3nc(Cl)ncc23)c(O)n1\", \"reactants\": [\"Cc1c(C(=O)O)c2cnc(Cl)nc2n1[C@H](C)c1ccccc1\", \"Cc1cc(C)c(CN)c(O)n1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"Cc1c(C(=O)O)c2cnc(Cl)nc2n1[C@H](C)c1ccccc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"Cc1cc(C)c(CN)c(O)n1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"PCJPGNCABBDNJU-UHFFFAOYSA-N.QRRJXNOZOUFOAH-SECBINFHSA-N>>OXGOXSJWLFYVKQ-OAHLLOKOSA-N\", \"model_turns_remaining\": 14, \"product\": \"Cc1cc(C)c(CNC(=O)c2c(C)n([C@H](C)c3ccccc3)c3nc(Cl)ncc23)c(O)n1\", \"reactants\": [\"Cc1c(C(=O)O)c2cnc(Cl)nc2n1[C@H](C)c1ccccc1\", \"Cc1cc(C)c(CN)c(O)n1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"Cc1c(C(=O)O)c2cnc(Cl)nc2n1[C@H](C)c1ccccc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"Cc1cc(C)c(CN)c(O)n1\", \"results\": [{\"inchikey\": \"PCJPGNCABBDNJU-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Cc1cc(C)c(CN)c(O)n1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Cc1c(C(=O)O)c2cnc(Cl)nc2n1[C@H](C)c1ccccc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Cc1c(C(=O)O)c2cnc(Cl)nc2n1[C@H](C)c1ccccc1\", \"reactants\": [\"COC(=O)c1c(C)n([C@H](C)c2ccccc2)c2nc(Cl)ncc12\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"COC(=O)c1c(C)n([C@H](C)c2ccccc2)c2nc(Cl)ncc12\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"JVRFZYSSZMGRCA-SNVBAGLBSA-N>>QRRJXNOZOUFOAH-SECBINFHSA-N\", \"model_turns_remaining\": 13, \"product\": \"Cc1c(C(=O)O)c2cnc(Cl)nc2n1[C@H](C)c1ccccc1\", \"reactants\": [\"COC(=O)c1c(C)n([C@H](C)c2ccccc2)c2nc(Cl)ncc12\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"COC(=O)c1c(C)n([C@H](C)c2ccccc2)c2nc(Cl)ncc12\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"COC(=O)c1c(C)n([C@H](C)c2ccccc2)c2nc(Cl)ncc12 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COC(=O)c1c(C)n([C@H](C)c2ccccc2)c2nc(Cl)ncc12\", \"reactants\": [\"CC#CC(=O)OC\", \"C[C@@H](Nc1nc(Cl)ncc1Br)c1ccccc1\"]}","name":"validate_disconnection"},"id":"call_4_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC#CC(=O)OC\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_1","type":"function"},{"function":{"arguments":"{\"query\": \"C[C@@H](Nc1nc(Cl)ncc1Br)c1ccccc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"KPRCJWWQFYWTOK-MRVPVSSYSA-N.UJQCANQILFWSDJ-UHFFFAOYSA-N>>JVRFZYSSZMGRCA-SNVBAGLBSA-N\", \"model_turns_remaining\": 12, \"product\": \"COC(=O)c1c(C)n([C@H](C)c2ccccc2)c2nc(Cl)ncc12\", \"reactants\": [\"CC#CC(=O)OC\", \"C[C@@H](Nc1nc(Cl)ncc1Br)c1ccccc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_4_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"CC#CC(=O)OC\", \"results\": [{\"inchikey\": \"UJQCANQILFWSDJ-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CC#CC(=O)OC\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"C[C@@H](Nc1nc(Cl)ncc1Br)c1ccccc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_2"},{"content":"C[C@@H](Nc1nc(Cl)ncc1Br)c1ccccc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"C[C@@H](Nc1nc(Cl)ncc1Br)c1ccccc1\", \"reactants\": [\"C[C@@H](N)c1ccccc1\", \"Clc1ncc(Br)c(Cl)n1\"]}","name":"validate_disconnection"},"id":"call_5_0","type":"function"},{"function":{"arguments":"{\"query\": \"C[C@@H](N)c1ccccc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_5_1","type":"function"},{"function":{"arguments":"{\"query\": \"Clc1ncc(Br)c(Cl)n1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_5_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"RQEUFEKYXDPUSK-SSDOTTSWSA-N.SIKXIUWKPGWBBF-UHFFFAOYSA-N>>KPRCJWWQFYWTOK-MRVPVSSYSA-N\", \"model_turns_remaining\": 11, \"product\": \"C[C@@H](Nc1nc(Cl)ncc1Br)c1ccccc1\", \"reactants\": [\"C[C@@H](N)c1ccccc1\", \"Clc1ncc(Br)c(Cl)n1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_5_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 11, \"query\": \"C[C@@H](N)c1ccccc1\", \"results\": [{\"inchikey\": \"RQEUFEKYXDPUSK-SSDOTTSWSA-N\", \"similarity\": 1.0, \"smiles\": \"C[C@@H](N)c1ccccc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_5_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 11, \"query\": \"Clc1ncc(Br)c(Cl)n1\", \"results\": [{\"inchikey\": \"SIKXIUWKPGWBBF-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Clc1ncc(Br)c(Cl)n1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_5_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CNc1ncc2c(C(=O)NCc3c(C)cc(C)nc3O)c(C)n([C@H](C)c3ccccc3)c2n1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CN\": \"precursor\", \"Cc1cc(C)c(CNC(=O)c2c(C)n([C@H](C)c3ccccc3)c3nc(Cl)ncc23)c(O)n1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CN\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"Cc1cc(C)c(CNC(=O)c2c(C)n([C@H](C)c3ccccc3)c3nc(Cl)ncc23)c(O)n1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"Cc1c(C(=O)O)c2cnc(Cl)nc2n1[C@H](C)c1ccccc1\": \"precursor\", \"Cc1cc(C)c(CN)c(O)n1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"Cc1c(C(=O)O)c2cnc(Cl)nc2n1[C@H](C)c1ccccc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COC(=O)c1c(C)n([C@H](C)c2ccccc2)c2nc(Cl)ncc12\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COC(=O)c1c(C)n([C@H](C)c2ccccc2)c2nc(Cl)ncc12\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC#CC(=O)OC\": \"precursor\", \"C[C@@H](Nc1nc(Cl)ncc1Br)c1ccccc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC#CC(=O)OC\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"C[C@@H](Nc1nc(Cl)ncc1Br)c1ccccc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"C[C@@H](N)c1ccccc1\": \"precursor\", \"Clc1ncc(Br)c(Cl)n1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"C[C@@H](N)c1ccccc1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"Clc1ncc(Br)c(Cl)n1\", \"in_stock\": true, \"children\": []}]}]}]}]}]}]}, {\"type\": \"mol\", \"smiles\": \"Cc1cc(C)c(CN)c(O)n1\", \"in_stock\": true, \"children\": []}]}]}]}]}]}}","name":"emit_routes"},"id":"call_6_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"CNc1ncc2c(C(=O)NCc3c(C)cc(C)nc3O)c(C)n([C@H](C)c3ccccc3)c2n1","task_id":"retro_8b5aadde61facb9fd79a","tool_calls":15,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":6}
{"exact_match":true,"id":"retro_8c31173d5f6197b83a93:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CCOC(=O)C(C#N)c1ccc(OC)c(OC)c1CCCCl in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCOC(=O)C(C#N)c1ccc(OC)c(OC)c1CCCCl\", \"reactants\": [\"CCOC(=O)C(C#N)c1ccc(OC)c(OC)c1\", \"ClCCCBr\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCOC(=O)C(C#N)c1ccc(OC)c(OC)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"ClCCCBr\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"MFESCIUQSIBMSM-UHFFFAOYSA-N.YHESBDUINPOZFB-UHFFFAOYSA-N>>CFYMTOZRHDCXBB-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"CCOC(=O)C(C#N)c1ccc(OC)c(OC)c1CCCCl\", \"reactants\": [\"CCOC(=O)C(C#N)c1ccc(OC)c(OC)c1\", \"ClCCCBr\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CCOC(=O)C(C#N)c1ccc(OC)c(OC)c1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"ClCCCBr\", \"results\": [{\"inchikey\": \"MFESCIUQSIBMSM-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"ClCCCBr\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"CCOC(=O)C(C#N)c1ccc(OC)c(OC)c1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCOC(=O)C(C#N)c1ccc(OC)c(OC)c1\", \"reactants\": [\"CCOC(=O)OCC\", \"COc1ccc(CC#N)cc1OC\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCOC(=O)OCC\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"COc1ccc(CC#N)cc1OC\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"ASLSUMISAQDOOB-UHFFFAOYSA-N.OIFBSDVPJOWBCH-UHFFFAOYSA-N>>YHESBDUINPOZFB-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"CCOC(=O)C(C#N)c1ccc(OC)c(OC)c1\", \"reactants\": [\"CCOC(=O)OCC\", \"COc1ccc(CC#N)cc1OC\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CCOC(=O)OCC\", \"results\": [{\"inchikey\": \"OIFBSDVPJOWBCH-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CCOC(=O)OCC\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"COc1ccc(CC#N)cc1OC\", \"results\": [{\"inchikey\": \"ASLSUMISAQDOOB-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"COc1ccc(CC#N)cc1OC\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CCOC(=O)C(C#N)c1ccc(OC)c(OC)c1CCCCl\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCOC(=O)C(C#N)c1ccc(OC)c(OC)c1\": \"precursor\", \"ClCCCBr\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCOC(=O)C(C#N)c1ccc(OC)c(OC)c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCOC(=O)OCC\": \"precursor\", \"COc1ccc(CC#N)cc1OC\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCOC(=O)OCC\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"COc1ccc(CC#N)cc1OC\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"ClCCCBr\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"CCOC(=O)C(C#N)c1ccc(OC)c(OC)c1CCCCl","task_id":"retro_8c31173d5f6197b83a93","tool_calls":7,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_8c3b6cc56c616398531b:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target COC(C)(C)c1cc2c(N3CCOCC3)nc(-c3cnc(N)nc3)nc2s1 in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COC(C)(C)c1cc2c(N3CCOCC3)nc(-c3cnc(N)nc3)nc2s1\", \"reactants\": [\"CC1(C)OB(c2cnc(N)nc2)OC1(C)C\", \"COC(C)(C)c1cc2c(N3CCOCC3)nc(Cl)nc2s1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC1(C)OB(c2cnc(N)nc2)OC1(C)C\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"COC(C)(C)c1cc2c(N3CCOCC3)nc(Cl)nc2s1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"BPQVMIDUTRJYSC-UHFFFAOYSA-N.MFMCCMIDMNTXFH-UHFFFAOYSA-N>>CBLOVEBQPRPWJT-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"COC(C)(C)c1cc2c(N3CCOCC3)nc(-c3cnc(N)nc3)nc2s1\", \"reactants\": [\"CC1(C)OB(c2cnc(N)nc2)OC1(C)C\", \"COC(C)(C)c1cc2c(N3CCOCC3)nc(Cl)nc2s1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CC1(C)OB(c2cnc(N)nc2)OC1(C)C\", \"results\": [{\"inchikey\": \"BPQVMIDUTRJYSC-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CC1(C)OB(c2cnc(N)nc2)OC1(C)C\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"COC(C)(C)c1cc2c(N3CCOCC3)nc(Cl)nc2s1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"COC(C)(C)c1cc2c(N3CCOCC3)nc(Cl)nc2s1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COC(C)(C)c1cc2c(N3CCOCC3)nc(Cl)nc2s1\", \"reactants\": [\"CC(C)(O)c1cc2c(N3CCOCC3)nc(Cl)nc2s1\", \"CI\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(O)c1cc2c(N3CCOCC3)nc(Cl)nc2s1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"CI\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"INQOMBQAUSQDDS-UHFFFAOYSA-N.WGZMBOOUEDABRP-UHFFFAOYSA-N>>MFMCCMIDMNTXFH-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"COC(C)(C)c1cc2c(N3CCOCC3)nc(Cl)nc2s1\", \"reactants\": [\"CC(C)(O)c1cc2c(N3CCOCC3)nc(Cl)nc2s1\", \"CI\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CC(C)(O)c1cc2c(N3CCOCC3)nc(Cl)nc2s1\", \"results\": [{\"inchikey\": \"WGZMBOOUEDABRP-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CC(C)(O)c1cc2c(N3CCOCC3)nc(Cl)nc2s1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CI\", \"results\": [{\"inchikey\": \"INQOMBQAUSQDDS-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CI\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"COC(C)(C)c1cc2c(N3CCOCC3)nc(-c3cnc(N)nc3)nc2s1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC1(C)OB(c2cnc(N)nc2)OC1(C)C\": \"precursor\", \"COC(C)(C)c1cc2c(N3CCOCC3)nc(Cl)nc2s1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC1(C)OB(c2cnc(N)nc2)OC1(C)C\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"COC(C)(C)c1cc2c(N3CCOCC3)nc(Cl)nc2s1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)(O)c1cc2c(N3CCOCC3)nc(Cl)nc2s1\": \"precursor\", \"CI\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(O)c1cc2c(N3CCOCC3)nc(Cl)nc2s1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"CI\", \"in_stock\": true, \"children\": []}]}]}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"COC(C)(C)c1cc2c(N3CCOCC3)nc(-c3cnc(N)nc3)nc2s1","task_id":"retro_8c3b6cc56c616398531b","tool_calls":7,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_8c509681d3d5c88096fd:reference-expert:a0","kind":"single_route","max_steps":3,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target OCc1ccc(CCC(O)(c2ccccc2)C2CN3CCC2CC3)cc1 in at most 3 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"OCc1ccc(CCC(O)(c2ccccc2)C2CN3CCC2CC3)cc1\", \"reactants\": [\"COC(=O)c1ccc(CCC(O)(c2ccccc2)C2CN3CCC2CC3)cc1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"COC(=O)c1ccc(CCC(O)(c2ccccc2)C2CN3CCC2CC3)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"ZKAZKFDNIAFVAA-UHFFFAOYSA-N>>GNTSAMPEWOPQSH-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"OCc1ccc(CCC(O)(c2ccccc2)C2CN3CCC2CC3)cc1\", \"reactants\": [\"COC(=O)c1ccc(CCC(O)(c2ccccc2)C2CN3CCC2CC3)cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"COC(=O)c1ccc(CCC(O)(c2ccccc2)C2CN3CCC2CC3)cc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"COC(=O)c1ccc(CCC(O)(c2ccccc2)C2CN3CCC2CC3)cc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COC(=O)c1ccc(CCC(O)(c2ccccc2)C2CN3CCC2CC3)cc1\", \"reactants\": [\"COC(=O)c1ccc(C#CC(O)(c2ccccc2)C2CN3CCC2CC3)cc1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"COC(=O)c1ccc(C#CC(O)(c2ccccc2)C2CN3CCC2CC3)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_complete\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"FIMOCVHJQIXXNI-UHFFFAOYSA-N>>ZKAZKFDNIAFVAA-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"COC(=O)c1ccc(CCC(O)(c2ccccc2)C2CN3CCC2CC3)cc1\", \"reactants\": [\"COC(=O)c1ccc(C#CC(O)(c2ccccc2)C2CN3CCC2CC3)cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"COC(=O)c1ccc(C#CC(O)(c2ccccc2)C2CN3CCC2CC3)cc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"COC(=O)c1ccc(C#CC(O)(c2ccccc2)C2CN3CCC2CC3)cc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COC(=O)c1ccc(C#CC(O)(c2ccccc2)C2CN3CCC2CC3)cc1\", \"reactants\": [\"C#CC(O)(c1ccccc1)C1CN2CCC1CC2\", \"COC(=O)c1ccc(Br)cc1\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"C#CC(O)(c1ccccc1)C1CN2CCC1CC2\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"COC(=O)c1ccc(Br)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"CZNGTXVOZOWWKM-UHFFFAOYSA-N.TTYHZAJTEFVPAO-UHFFFAOYSA-N>>FIMOCVHJQIXXNI-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"COC(=O)c1ccc(C#CC(O)(c2ccccc2)C2CN3CCC2CC3)cc1\", \"reactants\": [\"C#CC(O)(c1ccccc1)C1CN2CCC1CC2\", \"COC(=O)c1ccc(Br)cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"C#CC(O)(c1ccccc1)C1CN2CCC1CC2\", \"results\": [{\"inchikey\": \"TTYHZAJTEFVPAO-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"C#CC(O)(c1ccccc1)C1CN2CCC1CC2\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"COC(=O)c1ccc(Br)cc1\", \"results\": [{\"inchikey\": \"CZNGTXVOZOWWKM-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"COC(=O)c1ccc(Br)cc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"OCc1ccc(CCC(O)(c2ccccc2)C2CN3CCC2CC3)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COC(=O)c1ccc(CCC(O)(c2ccccc2)C2CN3CCC2CC3)cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COC(=O)c1ccc(CCC(O)(c2ccccc2)C2CN3CCC2CC3)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COC(=O)c1ccc(C#CC(O)(c2ccccc2)C2CN3CCC2CC3)cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COC(=O)c1ccc(C#CC(O)(c2ccccc2)C2CN3CCC2CC3)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"C#CC(O)(c1ccccc1)C1CN2CCC1CC2\": \"precursor\", \"COC(=O)c1ccc(Br)cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"C#CC(O)(c1ccccc1)C1CN2CCC1CC2\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"COC(=O)c1ccc(Br)cc1\", \"in_stock\": true, \"children\": []}]}]}]}]}]}]}]}}","name":"emit_routes"},"id":"call_4_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"OCc1ccc(CCC(O)(c2ccccc2)C2CN3CCC2CC3)cc1","task_id":"retro_8c509681d3d5c88096fd","tool_calls":8,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":4}
{"exact_match":true,"id":"retro_8cb21590d7eb09b3cb64:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target c1ccc(CNCCCCCOCCc2ccccn2)cc1 in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"c1ccc(CNCCCCCOCCc2ccccn2)cc1\", \"reactants\": [\"BrCCCCCOCCc1ccccn1\", \"NCc1ccccc1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"BrCCCCCOCCc1ccccn1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"NCc1ccccc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"IIJXKJWWEKNFRS-UHFFFAOYSA-N.WGQKYBSKWIADBV-UHFFFAOYSA-N>>PBVMVTXWYZXRBE-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"c1ccc(CNCCCCCOCCc2ccccn2)cc1\", \"reactants\": [\"BrCCCCCOCCc1ccccn1\", \"NCc1ccccc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"BrCCCCCOCCc1ccccn1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"NCc1ccccc1\", \"results\": [{\"inchikey\": \"WGQKYBSKWIADBV-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"NCc1ccccc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"BrCCCCCOCCc1ccccn1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"BrCCCCCOCCc1ccccn1\", \"reactants\": [\"BrCCCCCBr\", \"OCCc1ccccn1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"BrCCCCCBr\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"OCCc1ccccn1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"BXGYBSJAZFGIPX-UHFFFAOYSA-N.IBODDUNKEPPBKW-UHFFFAOYSA-N>>IIJXKJWWEKNFRS-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"BrCCCCCOCCc1ccccn1\", \"reactants\": [\"BrCCCCCBr\", \"OCCc1ccccn1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"BrCCCCCBr\", \"results\": [{\"inchikey\": \"IBODDUNKEPPBKW-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"BrCCCCCBr\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"OCCc1ccccn1\", \"results\": [{\"inchikey\": \"BXGYBSJAZFGIPX-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"OCCc1ccccn1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"c1ccc(CNCCCCCOCCc2ccccn2)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"BrCCCCCOCCc1ccccn1\": \"precursor\", \"NCc1ccccc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"BrCCCCCOCCc1ccccn1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"BrCCCCCBr\": \"precursor\", \"OCCc1ccccn1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"BrCCCCCBr\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"OCCc1ccccn1\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"NCc1ccccc1\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"c1ccc(CNCCCCCOCCc2ccccn2)cc1","task_id":"retro_8cb21590d7eb09b3cb64","tool_calls":7,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_8d0e4f54c3ae420f6e2d:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CC(C)(C)OC(=O)NCCCCCI in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(C)(C)OC(=O)NCCCCCI\", \"reactants\": [\"CC(C)(C)OC(=O)NCCCCCOS(C)(=O)=O\", \"I\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)OC(=O)NCCCCCOS(C)(=O)=O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"I\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"BMDRTAQNZSCQKT-UHFFFAOYSA-N.XMBWDFGMSWQBCA-UHFFFAOYSA-N>>ARXOWAUDEJFDNC-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"CC(C)(C)OC(=O)NCCCCCI\", \"reactants\": [\"CC(C)(C)OC(=O)NCCCCCOS(C)(=O)=O\", \"I\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CC(C)(C)OC(=O)NCCCCCOS(C)(=O)=O\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"I\", \"results\": [{\"inchikey\": \"XMBWDFGMSWQBCA-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"I\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"CC(C)(C)OC(=O)NCCCCCOS(C)(=O)=O was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(C)(C)OC(=O)NCCCCCOS(C)(=O)=O\", \"reactants\": [\"CC(C)(C)OC(=O)NCCCCCO\", \"CS(=O)(=O)Cl\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)OC(=O)NCCCCCO\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"CS(=O)(=O)Cl\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"DDGNGFVNTZJMMZ-UHFFFAOYSA-N.QARBMVPHQWIHKH-UHFFFAOYSA-N>>BMDRTAQNZSCQKT-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"CC(C)(C)OC(=O)NCCCCCOS(C)(=O)=O\", \"reactants\": [\"CC(C)(C)OC(=O)NCCCCCO\", \"CS(=O)(=O)Cl\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CC(C)(C)OC(=O)NCCCCCO\", \"results\": [{\"inchikey\": \"DDGNGFVNTZJMMZ-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CC(C)(C)OC(=O)NCCCCCO\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CS(=O)(=O)Cl\", \"results\": [{\"inchikey\": \"QARBMVPHQWIHKH-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CS(=O)(=O)Cl\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)OC(=O)NCCCCCI\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)(C)OC(=O)NCCCCCOS(C)(=O)=O\": \"precursor\", \"I\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)OC(=O)NCCCCCOS(C)(=O)=O\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)(C)OC(=O)NCCCCCO\": \"precursor\", \"CS(=O)(=O)Cl\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)OC(=O)NCCCCCO\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"CS(=O)(=O)Cl\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"I\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"CC(C)(C)OC(=O)NCCCCCI","task_id":"retro_8d0e4f54c3ae420f6e2d","tool_calls":7,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_8d302761e10205aacfd0:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target COC(=O)c1ccc(C#N)cc1Cl in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COC(=O)c1ccc(C#N)cc1Cl\", \"reactants\": [\"C#N\", \"COC(=O)c1ccc(Br)cc1Cl\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"C#N\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"COC(=O)c1ccc(Br)cc1Cl\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"JSNXIWYWUKTWAX-UHFFFAOYSA-N.LELOWRISYMNNSU-UHFFFAOYSA-N>>GLZBUNHGODEJPT-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"COC(=O)c1ccc(C#N)cc1Cl\", \"reactants\": [\"C#N\", \"COC(=O)c1ccc(Br)cc1Cl\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"C#N\", \"results\": [{\"inchikey\": \"LELOWRISYMNNSU-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"C#N\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"COC(=O)c1ccc(Br)cc1Cl\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"COC(=O)c1ccc(Br)cc1Cl was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COC(=O)c1ccc(Br)cc1Cl\", \"reactants\": [\"CO\", \"O=C(O)c1ccc(Br)cc1Cl\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CO\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=C(O)c1ccc(Br)cc1Cl\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"JAVZWSOFJKYSDY-UHFFFAOYSA-N.OKKJLVBELUTLKV-UHFFFAOYSA-N>>JSNXIWYWUKTWAX-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"COC(=O)c1ccc(Br)cc1Cl\", \"reactants\": [\"CO\", \"O=C(O)c1ccc(Br)cc1Cl\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CO\", \"results\": [{\"inchikey\": \"OKKJLVBELUTLKV-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CO\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"O=C(O)c1ccc(Br)cc1Cl\", \"results\": [{\"inchikey\": \"JAVZWSOFJKYSDY-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=C(O)c1ccc(Br)cc1Cl\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"COC(=O)c1ccc(C#N)cc1Cl\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"C#N\": \"precursor\", \"COC(=O)c1ccc(Br)cc1Cl\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"C#N\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"COC(=O)c1ccc(Br)cc1Cl\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CO\": \"precursor\", \"O=C(O)c1ccc(Br)cc1Cl\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CO\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=C(O)c1ccc(Br)cc1Cl\", \"in_stock\": true, \"children\": []}]}]}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"COC(=O)c1ccc(C#N)cc1Cl","task_id":"retro_8d302761e10205aacfd0","tool_calls":7,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_8e335edbb4fa93f74dc5:reference-expert:a0","kind":"single_route","max_steps":4,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target NC(=O)c1cnc2cncc(-c3ccc(F)cc3)c2c1 in at most 4 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"NC(=O)c1cnc2cncc(-c3ccc(F)cc3)c2c1\", \"reactants\": [\"NC(=O)c1cnc2cncc(Br)c2c1\", \"OB(O)c1ccc(F)cc1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"NC(=O)c1cnc2cncc(Br)c2c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"OB(O)c1ccc(F)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"LBUNNMJLXWQQBY-UHFFFAOYSA-N.NZRDVBIOQZATNT-UHFFFAOYSA-N>>FDJLRNUCVWESJO-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"NC(=O)c1cnc2cncc(-c3ccc(F)cc3)c2c1\", \"reactants\": [\"NC(=O)c1cnc2cncc(Br)c2c1\", \"OB(O)c1ccc(F)cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"NC(=O)c1cnc2cncc(Br)c2c1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"OB(O)c1ccc(F)cc1\", \"results\": [{\"inchikey\": \"LBUNNMJLXWQQBY-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"OB(O)c1ccc(F)cc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"NC(=O)c1cnc2cncc(Br)c2c1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"NC(=O)c1cnc2cncc(Br)c2c1\", \"reactants\": [\"N\", \"O=C(O)c1cnc2cncc(Br)c2c1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"N\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=C(O)c1cnc2cncc(Br)c2c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"QGZKDVFQNNGYKY-UHFFFAOYSA-N.UTTFLGYXIKJWNC-UHFFFAOYSA-N>>NZRDVBIOQZATNT-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"NC(=O)c1cnc2cncc(Br)c2c1\", \"reactants\": [\"N\", \"O=C(O)c1cnc2cncc(Br)c2c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"N\", \"results\": [{\"inchikey\": \"QGZKDVFQNNGYKY-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"N\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"O=C(O)c1cnc2cncc(Br)c2c1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"O=C(O)c1cnc2cncc(Br)c2c1 was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"O=C(O)c1cnc2cncc(Br)c2c1\", \"reactants\": [\"CCOC(=O)c1cnc2cncc(Br)c2c1\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCOC(=O)c1cnc2cncc(Br)c2c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"ULSIPBXASHTKBH-UHFFFAOYSA-N>>UTTFLGYXIKJWNC-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"O=C(O)c1cnc2cncc(Br)c2c1\", \"reactants\": [\"CCOC(=O)c1cnc2cncc(Br)c2c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"CCOC(=O)c1cnc2cncc(Br)c2c1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"CCOC(=O)c1cnc2cncc(Br)c2c1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCOC(=O)c1cnc2cncc(Br)c2c1\", \"reactants\": [\"CCOC(=O)c1cnc2cnccc2c1\", \"O=C1CCC(=O)N1Br\"]}","name":"validate_disconnection"},"id":"call_4_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCOC(=O)c1cnc2cnccc2c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=C1CCC(=O)N1Br\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"NZKOQKBFFCBTDU-UHFFFAOYSA-N.PCLIMKBDDGJMGD-UHFFFAOYSA-N>>ULSIPBXASHTKBH-UHFFFAOYSA-N\", \"model_turns_remaining\": 12, \"product\": \"CCOC(=O)c1cnc2cncc(Br)c2c1\", \"reactants\": [\"CCOC(=O)c1cnc2cnccc2c1\", \"O=C1CCC(=O)N1Br\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_4_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"CCOC(=O)c1cnc2cnccc2c1\", \"results\": [{\"inchikey\": \"NZKOQKBFFCBTDU-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CCOC(=O)c1cnc2cnccc2c1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"O=C1CCC(=O)N1Br\", \"results\": [{\"inchikey\": \"PCLIMKBDDGJMGD-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=C1CCC(=O)N1Br\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"NC(=O)c1cnc2cncc(-c3ccc(F)cc3)c2c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"NC(=O)c1cnc2cncc(Br)c2c1\": \"precursor\", \"OB(O)c1ccc(F)cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"NC(=O)c1cnc2cncc(Br)c2c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"N\": \"precursor\", \"O=C(O)c1cnc2cncc(Br)c2c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"N\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=C(O)c1cnc2cncc(Br)c2c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCOC(=O)c1cnc2cncc(Br)c2c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCOC(=O)c1cnc2cncc(Br)c2c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCOC(=O)c1cnc2cnccc2c1\": \"precursor\", \"O=C1CCC(=O)N1Br\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCOC(=O)c1cnc2cnccc2c1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=C1CCC(=O)N1Br\", \"in_stock\": true, \"children\": []}]}]}]}]}]}]}, {\"type\": \"mol\", \"smiles\": \"OB(O)c1ccc(F)cc1\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_5_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"NC(=O)c1cnc2cncc(-c3ccc(F)cc3)c2c1","task_id":"retro_8e335edbb4fa93f74dc5","tool_calls":12,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":5}
{"exact_match":true,"id":"retro_8e37545fe0b4c7bdfb85:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target C=CCOc1ccc(Cl)cc1C=NS(=O)C(C)(C)C in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"C=CCOc1ccc(Cl)cc1C=NS(=O)C(C)(C)C\", \"reactants\": [\"C=CCOc1ccc(Cl)cc1C=O\", \"CC(C)(C)S(N)=O\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"C=CCOc1ccc(Cl)cc1C=O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)S(N)=O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"CESUXLKAADQNTB-UHFFFAOYSA-N.GWIGVDNGOWNOJL-UHFFFAOYSA-N>>KFMLMRDTRMVDDS-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"C=CCOc1ccc(Cl)cc1C=NS(=O)C(C)(C)C\", \"reactants\": [\"C=CCOc1ccc(Cl)cc1C=O\", \"CC(C)(C)S(N)=O\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"C=CCOc1ccc(Cl)cc1C=O\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CC(C)(C)S(N)=O\", \"results\": [{\"inchikey\": \"CESUXLKAADQNTB-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CC(C)(C)S(N)=O\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"C=CCOc1ccc(Cl)cc1C=O was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"C=CCOc1ccc(Cl)cc1C=O\", \"reactants\": [\"C=CCBr\", \"O=Cc1cc(Cl)ccc1O\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"C=CCBr\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=Cc1cc(Cl)ccc1O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"BHELZAPQIKSEDF-UHFFFAOYSA-N.FUGKCSRLAQKUHG-UHFFFAOYSA-N>>GWIGVDNGOWNOJL-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"C=CCOc1ccc(Cl)cc1C=O\", \"reactants\": [\"C=CCBr\", \"O=Cc1cc(Cl)ccc1O\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"C=CCBr\", \"results\": [{\"inchikey\": \"BHELZAPQIKSEDF-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"C=CCBr\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"O=Cc1cc(Cl)ccc1O\", \"results\": [{\"inchikey\": \"FUGKCSRLAQKUHG-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=Cc1cc(Cl)ccc1O\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"C=CCOc1ccc(Cl)cc1C=NS(=O)C(C)(C)C\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"C=CCOc1ccc(Cl)cc1C=O\": \"precursor\", \"CC(C)(C)S(N)=O\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"C=CCOc1ccc(Cl)cc1C=O\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"C=CCBr\": \"precursor\", \"O=Cc1cc(Cl)ccc1O\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"C=CCBr\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=Cc1cc(Cl)ccc1O\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"CC(C)(C)S(N)=O\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"C=CCOc1ccc(Cl)cc1C=NS(=O)C(C)(C)C","task_id":"retro_8e37545fe0b4c7bdfb85","tool_calls":7,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_8ed70fb8de79407eb9e8:reference-expert:a0","kind":"single_route","max_steps":5,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CC(C)(CN1CCCC1)S(=O)(=O)c1ccc2nc(N)sc2c1 in at most 5 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(C)(CN1CCCC1)S(=O)(=O)c1ccc2nc(N)sc2c1\", \"reactants\": [\"CC(C)(CN1CCCC1)Sc1ccc2nc(N)sc2c1\", \"OO\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(CN1CCCC1)Sc1ccc2nc(N)sc2c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"OO\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_complete\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"LEDJVIJOQROENK-UHFFFAOYSA-N.MHAJPDPJQMAIIY-UHFFFAOYSA-N>>SNBXYEXHXPHONG-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"CC(C)(CN1CCCC1)S(=O)(=O)c1ccc2nc(N)sc2c1\", \"reactants\": [\"CC(C)(CN1CCCC1)Sc1ccc2nc(N)sc2c1\", \"OO\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CC(C)(CN1CCCC1)Sc1ccc2nc(N)sc2c1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"OO\", \"results\": [{\"inchikey\": \"MHAJPDPJQMAIIY-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"OO\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"CC(C)(CN1CCCC1)Sc1ccc2nc(N)sc2c1 was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(C)(CN1CCCC1)Sc1ccc2nc(N)sc2c1\", \"reactants\": [\"CC(C)(Sc1ccc2nc(N)sc2c1)C(=O)N1CCCC1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(Sc1ccc2nc(N)sc2c1)C(=O)N1CCCC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"IIIJWOUKWQAYTC-UHFFFAOYSA-N>>LEDJVIJOQROENK-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"CC(C)(CN1CCCC1)Sc1ccc2nc(N)sc2c1\", \"reactants\": [\"CC(C)(Sc1ccc2nc(N)sc2c1)C(=O)N1CCCC1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CC(C)(Sc1ccc2nc(N)sc2c1)C(=O)N1CCCC1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"CC(C)(Sc1ccc2nc(N)sc2c1)C(=O)N1CCCC1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(C)(Sc1ccc2nc(N)sc2c1)C(=O)N1CCCC1\", \"reactants\": [\"C1CCNC1\", \"CC(C)(Sc1ccc2nc(N)sc2c1)C(=O)O\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"C1CCNC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(Sc1ccc2nc(N)sc2c1)C(=O)O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"OIPQBIJDVPFVCE-UHFFFAOYSA-N.RWRDLPDLKQPQOW-UHFFFAOYSA-N>>IIIJWOUKWQAYTC-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"CC(C)(Sc1ccc2nc(N)sc2c1)C(=O)N1CCCC1\", \"reactants\": [\"C1CCNC1\", \"CC(C)(Sc1ccc2nc(N)sc2c1)C(=O)O\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"C1CCNC1\", \"results\": [{\"inchikey\": \"RWRDLPDLKQPQOW-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"C1CCNC1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"CC(C)(Sc1ccc2nc(N)sc2c1)C(=O)O\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"CC(C)(Sc1ccc2nc(N)sc2c1)C(=O)O was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(C)(Sc1ccc2nc(N)sc2c1)C(=O)O\", \"reactants\": [\"CCOC(=O)C(C)(C)Sc1ccc2nc(N)sc2c1\"]}","name":"validate_disconnection"},"id":"call_4_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCOC(=O)C(C)(C)Sc1ccc2nc(N)sc2c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"NRQKKJMTRGMANP-UHFFFAOYSA-N>>OIPQBIJDVPFVCE-UHFFFAOYSA-N\", \"model_turns_remaining\": 12, \"product\": \"CC(C)(Sc1ccc2nc(N)sc2c1)C(=O)O\", \"reactants\": [\"CCOC(=O)C(C)(C)Sc1ccc2nc(N)sc2c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_4_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"CCOC(=O)C(C)(C)Sc1ccc2nc(N)sc2c1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_1"},{"content":"CCOC(=O)C(C)(C)Sc1ccc2nc(N)sc2c1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCOC(=O)C(C)(C)Sc1ccc2nc(N)sc2c1\", \"reactants\": [\"CCOC(=O)C(C)(C)Br\", \"Nc1nc2ccc(S)cc2s1\"]}","name":"validate_disconnection"},"id":"call_5_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCOC(=O)C(C)(C)Br\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_5_1","type":"function"},{"function":{"arguments":"{\"query\": \"Nc1nc2ccc(S)cc2s1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_5_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"FJPCGRWFXJAOOH-UHFFFAOYSA-N.IOLQWGVDEFWYNP-UHFFFAOYSA-N>>NRQKKJMTRGMANP-UHFFFAOYSA-N\", \"model_turns_remaining\": 11, \"product\": \"CCOC(=O)C(C)(C)Sc1ccc2nc(N)sc2c1\", \"reactants\": [\"CCOC(=O)C(C)(C)Br\", \"Nc1nc2ccc(S)cc2s1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_5_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 11, \"query\": \"CCOC(=O)C(C)(C)Br\", \"results\": [{\"inchikey\": \"IOLQWGVDEFWYNP-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CCOC(=O)C(C)(C)Br\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_5_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 11, \"query\": \"Nc1nc2ccc(S)cc2s1\", \"results\": [{\"inchikey\": \"FJPCGRWFXJAOOH-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Nc1nc2ccc(S)cc2s1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_5_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(CN1CCCC1)S(=O)(=O)c1ccc2nc(N)sc2c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)(CN1CCCC1)Sc1ccc2nc(N)sc2c1\": \"precursor\", \"OO\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(CN1CCCC1)Sc1ccc2nc(N)sc2c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)(Sc1ccc2nc(N)sc2c1)C(=O)N1CCCC1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(Sc1ccc2nc(N)sc2c1)C(=O)N1CCCC1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"C1CCNC1\": \"precursor\", \"CC(C)(Sc1ccc2nc(N)sc2c1)C(=O)O\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"C1CCNC1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"CC(C)(Sc1ccc2nc(N)sc2c1)C(=O)O\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCOC(=O)C(C)(C)Sc1ccc2nc(N)sc2c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCOC(=O)C(C)(C)Sc1ccc2nc(N)sc2c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCOC(=O)C(C)(C)Br\": \"precursor\", \"Nc1nc2ccc(S)cc2s1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCOC(=O)C(C)(C)Br\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"Nc1nc2ccc(S)cc2s1\", \"in_stock\": true, \"children\": []}]}]}]}]}]}]}]}]}, {\"type\": \"mol\", \"smiles\": \"OO\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_6_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"CC(C)(CN1CCCC1)S(=O)(=O)c1ccc2nc(N)sc2c1","task_id":"retro_8ed70fb8de79407eb9e8","tool_calls":14,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":6}
{"exact_match":true,"id":"retro_8fffabae6eee1e5717c6:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target Cc1cc(NC(=O)NCCN2CCN(C(=O)OC(C)(C)C)CC2)c2ccccc2n1 in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Cc1cc(NC(=O)NCCN2CCN(C(=O)OC(C)(C)C)CC2)c2ccccc2n1\", \"reactants\": [\"CC(C)(C)OC(=O)N1CCNCC1\", \"Cc1cc(NC(=O)NCCCl)c2ccccc2n1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)OC(=O)N1CCNCC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"Cc1cc(NC(=O)NCCCl)c2ccccc2n1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"CWXPZXBSDSIRCS-UHFFFAOYSA-N.KDQTVKCVJSCFKG-UHFFFAOYSA-N>>DWDOABZOIGUBGC-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"Cc1cc(NC(=O)NCCN2CCN(C(=O)OC(C)(C)C)CC2)c2ccccc2n1\", \"reactants\": [\"CC(C)(C)OC(=O)N1CCNCC1\", \"Cc1cc(NC(=O)NCCCl)c2ccccc2n1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CC(C)(C)OC(=O)N1CCNCC1\", \"results\": [{\"inchikey\": \"CWXPZXBSDSIRCS-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CC(C)(C)OC(=O)N1CCNCC1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"Cc1cc(NC(=O)NCCCl)c2ccccc2n1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"Cc1cc(NC(=O)NCCCl)c2ccccc2n1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Cc1cc(NC(=O)NCCCl)c2ccccc2n1\", \"reactants\": [\"Cc1cc(N)c2ccccc2n1\", \"O=C=NCCCl\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"Cc1cc(N)c2ccccc2n1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=C=NCCCl\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_complete\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"BCMYXYHEMGPZJN-UHFFFAOYSA-N.COCFIBRMFPWUDW-UHFFFAOYSA-N>>KDQTVKCVJSCFKG-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"Cc1cc(NC(=O)NCCCl)c2ccccc2n1\", \"reactants\": [\"Cc1cc(N)c2ccccc2n1\", \"O=C=NCCCl\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"Cc1cc(N)c2ccccc2n1\", \"results\": [{\"inchikey\": \"COCFIBRMFPWUDW-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Cc1cc(N)c2ccccc2n1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"O=C=NCCCl\", \"results\": [{\"inchikey\": \"BCMYXYHEMGPZJN-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=C=NCCCl\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"Cc1cc(NC(=O)NCCN2CCN(C(=O)OC(C)(C)C)CC2)c2ccccc2n1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)(C)OC(=O)N1CCNCC1\": \"precursor\", \"Cc1cc(NC(=O)NCCCl)c2ccccc2n1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)OC(=O)N1CCNCC1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"Cc1cc(NC(=O)NCCCl)c2ccccc2n1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"Cc1cc(N)c2ccccc2n1\": \"precursor\", \"O=C=NCCCl\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"Cc1cc(N)c2ccccc2n1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=C=NCCCl\", \"in_stock\": true, \"children\": []}]}]}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"Cc1cc(NC(=O)NCCN2CCN(C(=O)OC(C)(C)C)CC2)c2ccccc2n1","task_id":"retro_8fffabae6eee1e5717c6","tool_calls":7,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_90df3effe07f9733c337:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CCN(C(=O)OC(C)(C)C)c1cccc(Br)c1 in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCN(C(=O)OC(C)(C)C)c1cccc(Br)c1\", \"reactants\": [\"CC(C)(C)OC(=O)Nc1cccc(Br)c1\", \"CCI\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)OC(=O)Nc1cccc(Br)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"CCI\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"HVTICUPFWKNHNG-UHFFFAOYSA-N.VDFBCTSISJDKNW-UHFFFAOYSA-N>>APOIFUDCOFYIIX-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"CCN(C(=O)OC(C)(C)C)c1cccc(Br)c1\", \"reactants\": [\"CC(C)(C)OC(=O)Nc1cccc(Br)c1\", \"CCI\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CC(C)(C)OC(=O)Nc1cccc(Br)c1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CCI\", \"results\": [{\"inchikey\": \"HVTICUPFWKNHNG-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CCI\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"CC(C)(C)OC(=O)Nc1cccc(Br)c1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(C)(C)OC(=O)Nc1cccc(Br)c1\", \"reactants\": [\"CC(C)(C)OC(=O)OC(=O)OC(C)(C)C\", \"Nc1cccc(Br)c1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)OC(=O)OC(=O)OC(C)(C)C\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"Nc1cccc(Br)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"DHYHYLGCQVVLOQ-UHFFFAOYSA-N.DYHSDKLCOJIUFX-UHFFFAOYSA-N>>VDFBCTSISJDKNW-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"CC(C)(C)OC(=O)Nc1cccc(Br)c1\", \"reactants\": [\"CC(C)(C)OC(=O)OC(=O)OC(C)(C)C\", \"Nc1cccc(Br)c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CC(C)(C)OC(=O)OC(=O)OC(C)(C)C\", \"results\": [{\"inchikey\": \"DYHSDKLCOJIUFX-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CC(C)(C)OC(=O)OC(=O)OC(C)(C)C\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"Nc1cccc(Br)c1\", \"results\": [{\"inchikey\": \"DHYHYLGCQVVLOQ-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Nc1cccc(Br)c1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CCN(C(=O)OC(C)(C)C)c1cccc(Br)c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)(C)OC(=O)Nc1cccc(Br)c1\": \"precursor\", \"CCI\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)OC(=O)Nc1cccc(Br)c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)(C)OC(=O)OC(=O)OC(C)(C)C\": \"precursor\", \"Nc1cccc(Br)c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)OC(=O)OC(=O)OC(C)(C)C\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"Nc1cccc(Br)c1\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"CCI\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"CCN(C(=O)OC(C)(C)C)c1cccc(Br)c1","task_id":"retro_90df3effe07f9733c337","tool_calls":7,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_926d09b76b45fad9298b:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CCN(CC)C(=O)CCC#Cc1cn(Cc2ncc(C)c(OC)c2C)c2nc(N)nc(Cl)c12 in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCN(CC)C(=O)CCC#Cc1cn(Cc2ncc(C)c(OC)c2C)c2nc(N)nc(Cl)c12\", \"reactants\": [\"CCNCC\", \"COc1c(C)cnc(Cn2cc(C#CCCC(=O)O)c3c(Cl)nc(N)nc32)c1C\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCNCC\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"COc1c(C)cnc(Cn2cc(C#CCCC(=O)O)c3c(Cl)nc(N)nc32)c1C\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"HPNMFZURTQLUMO-UHFFFAOYSA-N.WBZZVDPPBISSKB-UHFFFAOYSA-N>>NIDWBEZSVJTECR-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"CCN(CC)C(=O)CCC#Cc1cn(Cc2ncc(C)c(OC)c2C)c2nc(N)nc(Cl)c12\", \"reactants\": [\"CCNCC\", \"COc1c(C)cnc(Cn2cc(C#CCCC(=O)O)c3c(Cl)nc(N)nc32)c1C\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CCNCC\", \"results\": [{\"inchikey\": \"HPNMFZURTQLUMO-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CCNCC\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"COc1c(C)cnc(Cn2cc(C#CCCC(=O)O)c3c(Cl)nc(N)nc32)c1C\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"COc1c(C)cnc(Cn2cc(C#CCCC(=O)O)c3c(Cl)nc(N)nc32)c1C was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COc1c(C)cnc(Cn2cc(C#CCCC(=O)O)c3c(Cl)nc(N)nc32)c1C\", \"reactants\": [\"C#CCCC(=O)O\", \"COc1c(C)cnc(Cn2cc(I)c3c(Cl)nc(N)nc32)c1C\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"C#CCCC(=O)O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"COc1c(C)cnc(Cn2cc(I)c3c(Cl)nc(N)nc32)c1C\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"CEZDADICECYSPS-UHFFFAOYSA-N.MLBYLEUJXUBIJJ-UHFFFAOYSA-N>>WBZZVDPPBISSKB-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"COc1c(C)cnc(Cn2cc(C#CCCC(=O)O)c3c(Cl)nc(N)nc32)c1C\", \"reactants\": [\"C#CCCC(=O)O\", \"COc1c(C)cnc(Cn2cc(I)c3c(Cl)nc(N)nc32)c1C\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"C#CCCC(=O)O\", \"results\": [{\"inchikey\": \"MLBYLEUJXUBIJJ-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"C#CCCC(=O)O\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"COc1c(C)cnc(Cn2cc(I)c3c(Cl)nc(N)nc32)c1C\", \"results\": [{\"inchikey\": \"CEZDADICECYSPS-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"COc1c(C)cnc(Cn2cc(I)c3c(Cl)nc(N)nc32)c1C\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CCN(CC)C(=O)CCC#Cc1cn(Cc2ncc(C)c(OC)c2C)c2nc(N)nc(Cl)c12\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCNCC\": \"precursor\", \"COc1c(C)cnc(Cn2cc(C#CCCC(=O)O)c3c(Cl)nc(N)nc32)c1C\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCNCC\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"COc1c(C)cnc(Cn2cc(C#CCCC(=O)O)c3c(Cl)nc(N)nc32)c1C\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"C#CCCC(=O)O\": \"precursor\", \"COc1c(C)cnc(Cn2cc(I)c3c(Cl)nc(N)nc32)c1C\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"C#CCCC(=O)O\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"COc1c(C)cnc(Cn2cc(I)c3c(Cl)nc(N)nc32)c1C\", \"in_stock\": true, \"children\": []}]}]}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"CCN(CC)C(=O)CCC#Cc1cn(Cc2ncc(C)c(OC)c2C)c2nc(N)nc(Cl)c12","task_id":"retro_926d09b76b45fad9298b","tool_calls":7,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_93769490702618033878:reference-expert:a0","kind":"single_route","max_steps":5,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CN(C)C(=O)c1cc2cnc(Nc3ccc(N4CCN(C(=O)OC(C)(C)C)CC4)nn3)nc2n1C1CCCC1 in at most 5 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CN(C)C(=O)c1cc2cnc(Nc3ccc(N4CCN(C(=O)OC(C)(C)C)CC4)nn3)nc2n1C1CCCC1\", \"reactants\": [\"CC(C)(C)OC(=O)N1CCN(c2ccc(N)nn2)CC1\", \"CN(C)C(=O)c1cc2cnc(Cl)nc2n1C1CCCC1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)OC(=O)N1CCN(c2ccc(N)nn2)CC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"CN(C)C(=O)c1cc2cnc(Cl)nc2n1C1CCCC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"PMDDQOHZLBZUSO-UHFFFAOYSA-N.QBQVUQPRZYYTGL-UHFFFAOYSA-N>>BMBFWSJTQOPTEI-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"CN(C)C(=O)c1cc2cnc(Nc3ccc(N4CCN(C(=O)OC(C)(C)C)CC4)nn3)nc2n1C1CCCC1\", \"reactants\": [\"CC(C)(C)OC(=O)N1CCN(c2ccc(N)nn2)CC1\", \"CN(C)C(=O)c1cc2cnc(Cl)nc2n1C1CCCC1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CC(C)(C)OC(=O)N1CCN(c2ccc(N)nn2)CC1\", \"results\": [{\"inchikey\": \"QBQVUQPRZYYTGL-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CC(C)(C)OC(=O)N1CCN(c2ccc(N)nn2)CC1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CN(C)C(=O)c1cc2cnc(Cl)nc2n1C1CCCC1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"CN(C)C(=O)c1cc2cnc(Cl)nc2n1C1CCCC1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CN(C)C(=O)c1cc2cnc(Cl)nc2n1C1CCCC1\", \"reactants\": [\"CNC\", \"O=C(O)c1cc2cnc(Cl)nc2n1C1CCCC1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CNC\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=C(O)c1cc2cnc(Cl)nc2n1C1CCCC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"LXCZVGKSFJMLRO-UHFFFAOYSA-N.ROSDSFDQCJNGOL-UHFFFAOYSA-N>>PMDDQOHZLBZUSO-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"CN(C)C(=O)c1cc2cnc(Cl)nc2n1C1CCCC1\", \"reactants\": [\"CNC\", \"O=C(O)c1cc2cnc(Cl)nc2n1C1CCCC1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CNC\", \"results\": [{\"inchikey\": \"ROSDSFDQCJNGOL-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CNC\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"O=C(O)c1cc2cnc(Cl)nc2n1C1CCCC1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"O=C(O)c1cc2cnc(Cl)nc2n1C1CCCC1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"O=C(O)c1cc2cnc(Cl)nc2n1C1CCCC1\", \"reactants\": [\"O=Cc1cc2cnc(Cl)nc2n1C1CCCC1\", \"O=S(O)OO\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"O=Cc1cc2cnc(Cl)nc2n1C1CCCC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=S(O)OO\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"AYSIGUCDFZQVQT-UHFFFAOYSA-N.SOXVKQLLJZHYTL-UHFFFAOYSA-N>>LXCZVGKSFJMLRO-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"O=C(O)c1cc2cnc(Cl)nc2n1C1CCCC1\", \"reactants\": [\"O=Cc1cc2cnc(Cl)nc2n1C1CCCC1\", \"O=S(O)OO\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"O=Cc1cc2cnc(Cl)nc2n1C1CCCC1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"O=S(O)OO\", \"results\": [{\"inchikey\": \"AYSIGUCDFZQVQT-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=S(O)OO\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"O=Cc1cc2cnc(Cl)nc2n1C1CCCC1 was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"O=Cc1cc2cnc(Cl)nc2n1C1CCCC1\", \"reactants\": [\"CCOC(OCC)c1cc2cnc(Cl)nc2n1C1CCCC1\"]}","name":"validate_disconnection"},"id":"call_4_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCOC(OCC)c1cc2cnc(Cl)nc2n1C1CCCC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"YWICPKUTHUYIHQ-UHFFFAOYSA-N>>SOXVKQLLJZHYTL-UHFFFAOYSA-N\", \"model_turns_remaining\": 12, \"product\": \"O=Cc1cc2cnc(Cl)nc2n1C1CCCC1\", \"reactants\": [\"CCOC(OCC)c1cc2cnc(Cl)nc2n1C1CCCC1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_4_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"CCOC(OCC)c1cc2cnc(Cl)nc2n1C1CCCC1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_1"},{"content":"CCOC(OCC)c1cc2cnc(Cl)nc2n1C1CCCC1 was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCOC(OCC)c1cc2cnc(Cl)nc2n1C1CCCC1\", \"reactants\": [\"CCOC(C#Cc1cnc(Cl)nc1NC1CCCC1)OCC\"]}","name":"validate_disconnection"},"id":"call_5_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCOC(C#Cc1cnc(Cl)nc1NC1CCCC1)OCC\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_5_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_complete\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"NPWHRGNZZPOQJN-UHFFFAOYSA-N>>YWICPKUTHUYIHQ-UHFFFAOYSA-N\", \"model_turns_remaining\": 11, \"product\": \"CCOC(OCC)c1cc2cnc(Cl)nc2n1C1CCCC1\", \"reactants\": [\"CCOC(C#Cc1cnc(Cl)nc1NC1CCCC1)OCC\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_5_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 11, \"query\": \"CCOC(C#Cc1cnc(Cl)nc1NC1CCCC1)OCC\", \"results\": [{\"inchikey\": \"NPWHRGNZZPOQJN-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CCOC(C#Cc1cnc(Cl)nc1NC1CCCC1)OCC\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_5_1"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CN(C)C(=O)c1cc2cnc(Nc3ccc(N4CCN(C(=O)OC(C)(C)C)CC4)nn3)nc2n1C1CCCC1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)(C)OC(=O)N1CCN(c2ccc(N)nn2)CC1\": \"precursor\", \"CN(C)C(=O)c1cc2cnc(Cl)nc2n1C1CCCC1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)OC(=O)N1CCN(c2ccc(N)nn2)CC1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"CN(C)C(=O)c1cc2cnc(Cl)nc2n1C1CCCC1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CNC\": \"precursor\", \"O=C(O)c1cc2cnc(Cl)nc2n1C1CCCC1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CNC\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=C(O)c1cc2cnc(Cl)nc2n1C1CCCC1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"O=Cc1cc2cnc(Cl)nc2n1C1CCCC1\": \"precursor\", \"O=S(O)OO\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"O=Cc1cc2cnc(Cl)nc2n1C1CCCC1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCOC(OCC)c1cc2cnc(Cl)nc2n1C1CCCC1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCOC(OCC)c1cc2cnc(Cl)nc2n1C1CCCC1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCOC(C#Cc1cnc(Cl)nc1NC1CCCC1)OCC\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCOC(C#Cc1cnc(Cl)nc1NC1CCCC1)OCC\", \"in_stock\": true, \"children\": []}]}]}]}]}, {\"type\": \"mol\", \"smiles\": \"O=S(O)OO\", \"in_stock\": true, \"children\": []}]}]}]}]}]}]}]}}","name":"emit_routes"},"id":"call_6_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"CN(C)C(=O)c1cc2cnc(Nc3ccc(N4CCN(C(=O)OC(C)(C)C)CC4)nn3)nc2n1C1CCCC1","task_id":"retro_93769490702618033878","tool_calls":14,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":6}
{"exact_match":true,"id":"retro_93c76a925a353564cba8:reference-expert:a0","kind":"single_route","max_steps":3,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CC(C)(C)OC(=O)N[C@H](Cc1ccccc1)[C@@H](O)CN1CCCC1 in at most 3 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(C)(C)OC(=O)N[C@H](Cc1ccccc1)[C@@H](O)CN1CCCC1\", \"reactants\": [\"C1CCNC1\", \"CC(C)(C)OC(=O)N[C@H](Cc1ccccc1)[C@@H]1CO1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"C1CCNC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)OC(=O)N[C@H](Cc1ccccc1)[C@@H]1CO1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_complete\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"NVPOUMXZERMIJK-OLZOCXBDSA-N.RWRDLPDLKQPQOW-UHFFFAOYSA-N>>OFAHSHKXSPOFGM-SJORKVTESA-N\", \"model_turns_remaining\": 15, \"product\": \"CC(C)(C)OC(=O)N[C@H](Cc1ccccc1)[C@@H](O)CN1CCCC1\", \"reactants\": [\"C1CCNC1\", \"CC(C)(C)OC(=O)N[C@H](Cc1ccccc1)[C@@H]1CO1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"C1CCNC1\", \"results\": [{\"inchikey\": \"RWRDLPDLKQPQOW-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"C1CCNC1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CC(C)(C)OC(=O)N[C@H](Cc1ccccc1)[C@@H]1CO1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"CC(C)(C)OC(=O)N[C@H](Cc1ccccc1)[C@@H]1CO1 was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(C)(C)OC(=O)N[C@H](Cc1ccccc1)[C@@H]1CO1\", \"reactants\": [\"CC(C)(C)OC(=O)N[C@H](Cc1ccccc1)[C@@H](O)CCl\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)OC(=O)N[C@H](Cc1ccccc1)[C@@H](O)CCl\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"GFGQSTIUFXHAJS-OLZOCXBDSA-N>>NVPOUMXZERMIJK-OLZOCXBDSA-N\", \"model_turns_remaining\": 14, \"product\": \"CC(C)(C)OC(=O)N[C@H](Cc1ccccc1)[C@@H]1CO1\", \"reactants\": [\"CC(C)(C)OC(=O)N[C@H](Cc1ccccc1)[C@@H](O)CCl\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CC(C)(C)OC(=O)N[C@H](Cc1ccccc1)[C@@H](O)CCl\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"CC(C)(C)OC(=O)N[C@H](Cc1ccccc1)[C@@H](O)CCl was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(C)(C)OC(=O)N[C@H](Cc1ccccc1)[C@@H](O)CCl\", \"reactants\": [\"CC(C)(C)OC(=O)N[C@H](Cc1ccccc1)C(=O)CCl\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)OC(=O)N[C@H](Cc1ccccc1)C(=O)CCl\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_complete\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"JAKDNFBATYIEIE-GFCCVEGCSA-N>>GFGQSTIUFXHAJS-OLZOCXBDSA-N\", \"model_turns_remaining\": 13, \"product\": \"CC(C)(C)OC(=O)N[C@H](Cc1ccccc1)[C@@H](O)CCl\", \"reactants\": [\"CC(C)(C)OC(=O)N[C@H](Cc1ccccc1)C(=O)CCl\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"CC(C)(C)OC(=O)N[C@H](Cc1ccccc1)C(=O)CCl\", \"results\": [{\"inchikey\": \"JAKDNFBATYIEIE-GFCCVEGCSA-N\", \"similarity\": 1.0, \"smiles\": \"CC(C)(C)OC(=O)N[C@H](Cc1ccccc1)C(=O)CCl\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)OC(=O)N[C@H](Cc1ccccc1)[C@@H](O)CN1CCCC1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"C1CCNC1\": \"precursor\", \"CC(C)(C)OC(=O)N[C@H](Cc1ccccc1)[C@@H]1CO1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"C1CCNC1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"CC(C)(C)OC(=O)N[C@H](Cc1ccccc1)[C@@H]1CO1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)(C)OC(=O)N[C@H](Cc1ccccc1)[C@@H](O)CCl\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)OC(=O)N[C@H](Cc1ccccc1)[C@@H](O)CCl\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)(C)OC(=O)N[C@H](Cc1ccccc1)C(=O)CCl\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)OC(=O)N[C@H](Cc1ccccc1)C(=O)CCl\", \"in_stock\": true, \"children\": []}]}]}]}]}]}]}]}}","name":"emit_routes"},"id":"call_4_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"CC(C)(C)OC(=O)N[C@H](Cc1ccccc1)[C@@H](O)CN1CCCC1","task_id":"retro_93c76a925a353564cba8","tool_calls":8,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":4}
{"exact_match":true,"id":"retro_9477d2ef93b8c5285e78:reference-expert:a0","kind":"single_route","max_steps":3,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target Nc1cc(-c2ccncc2)ccc1OCc1ccccc1 in at most 3 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Nc1cc(-c2ccncc2)ccc1OCc1ccccc1\", \"reactants\": [\"O=[N+]([O-])c1cc(-c2ccncc2)ccc1OCc1ccccc1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"O=[N+]([O-])c1cc(-c2ccncc2)ccc1OCc1ccccc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"KRKUXAVADOOZJX-UHFFFAOYSA-N>>XXLYVLANMOFYAK-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"Nc1cc(-c2ccncc2)ccc1OCc1ccccc1\", \"reactants\": [\"O=[N+]([O-])c1cc(-c2ccncc2)ccc1OCc1ccccc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"O=[N+]([O-])c1cc(-c2ccncc2)ccc1OCc1ccccc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"O=[N+]([O-])c1cc(-c2ccncc2)ccc1OCc1ccccc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"O=[N+]([O-])c1cc(-c2ccncc2)ccc1OCc1ccccc1\", \"reactants\": [\"O=[N+]([O-])c1cc(Br)ccc1OCc1ccccc1\", \"OB(O)c1ccncc1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"O=[N+]([O-])c1cc(Br)ccc1OCc1ccccc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"OB(O)c1ccncc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"HUELJXGNXNSEQJ-UHFFFAOYSA-N.QLULGIRFKAWHOJ-UHFFFAOYSA-N>>KRKUXAVADOOZJX-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"O=[N+]([O-])c1cc(-c2ccncc2)ccc1OCc1ccccc1\", \"reactants\": [\"O=[N+]([O-])c1cc(Br)ccc1OCc1ccccc1\", \"OB(O)c1ccncc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"O=[N+]([O-])c1cc(Br)ccc1OCc1ccccc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"OB(O)c1ccncc1\", \"results\": [{\"inchikey\": \"QLULGIRFKAWHOJ-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"OB(O)c1ccncc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"O=[N+]([O-])c1cc(Br)ccc1OCc1ccccc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"O=[N+]([O-])c1cc(Br)ccc1OCc1ccccc1\", \"reactants\": [\"BrCc1ccccc1\", \"O=[N+]([O-])c1cc(Br)ccc1O\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"BrCc1ccccc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=[N+]([O-])c1cc(Br)ccc1O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"AGEZXYOZHKGVCM-UHFFFAOYSA-N.CUTFAPGINUFNQM-UHFFFAOYSA-N>>HUELJXGNXNSEQJ-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"O=[N+]([O-])c1cc(Br)ccc1OCc1ccccc1\", \"reactants\": [\"BrCc1ccccc1\", \"O=[N+]([O-])c1cc(Br)ccc1O\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"BrCc1ccccc1\", \"results\": [{\"inchikey\": \"AGEZXYOZHKGVCM-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"BrCc1ccccc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"O=[N+]([O-])c1cc(Br)ccc1O\", \"results\": [{\"inchikey\": \"CUTFAPGINUFNQM-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=[N+]([O-])c1cc(Br)ccc1O\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"Nc1cc(-c2ccncc2)ccc1OCc1ccccc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"O=[N+]([O-])c1cc(-c2ccncc2)ccc1OCc1ccccc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"O=[N+]([O-])c1cc(-c2ccncc2)ccc1OCc1ccccc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"O=[N+]([O-])c1cc(Br)ccc1OCc1ccccc1\": \"precursor\", \"OB(O)c1ccncc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"O=[N+]([O-])c1cc(Br)ccc1OCc1ccccc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"BrCc1ccccc1\": \"precursor\", \"O=[N+]([O-])c1cc(Br)ccc1O\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"BrCc1ccccc1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=[N+]([O-])c1cc(Br)ccc1O\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"OB(O)c1ccncc1\", \"in_stock\": true, \"children\": []}]}]}]}]}]}}","name":"emit_routes"},"id":"call_4_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"Nc1cc(-c2ccncc2)ccc1OCc1ccccc1","task_id":"retro_9477d2ef93b8c5285e78","tool_calls":9,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":4}
{"exact_match":true,"id":"retro_97f95e8d69200c6fc72b:reference-expert:a0","kind":"single_route","max_steps":4,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target Cc1c(F)cc(C(=O)NC2CC2)cc1-c1ccc2c(=O)n(CC3CC3)cc(CN3CCNC[C@@H]3C)c2c1 in at most 4 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Cc1c(F)cc(C(=O)NC2CC2)cc1-c1ccc2c(=O)n(CC3CC3)cc(CN3CCNC[C@@H]3C)c2c1\", \"reactants\": [\"C[C@H]1CN(C(=O)OC(C)(C)C)CCN1\", \"Cc1c(F)cc(C(=O)NC2CC2)cc1-c1ccc2c(=O)n(CC3CC3)cc(C=O)c2c1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"C[C@H]1CN(C(=O)OC(C)(C)C)CCN1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"Cc1c(F)cc(C(=O)NC2CC2)cc1-c1ccc2c(=O)n(CC3CC3)cc(C=O)c2c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"FMLPQHJYUZTHQS-QMMMGPOBSA-N.GBCBQBSMQRMEQE-UHFFFAOYSA-N>>FOHSBRAHUYDFLX-SFHVURJKSA-N\", \"model_turns_remaining\": 15, \"product\": \"Cc1c(F)cc(C(=O)NC2CC2)cc1-c1ccc2c(=O)n(CC3CC3)cc(CN3CCNC[C@@H]3C)c2c1\", \"reactants\": [\"C[C@H]1CN(C(=O)OC(C)(C)C)CCN1\", \"Cc1c(F)cc(C(=O)NC2CC2)cc1-c1ccc2c(=O)n(CC3CC3)cc(C=O)c2c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"C[C@H]1CN(C(=O)OC(C)(C)C)CCN1\", \"results\": [{\"inchikey\": \"FMLPQHJYUZTHQS-QMMMGPOBSA-N\", \"similarity\": 1.0, \"smiles\": \"C[C@H]1CN(C(=O)OC(C)(C)C)CCN1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"Cc1c(F)cc(C(=O)NC2CC2)cc1-c1ccc2c(=O)n(CC3CC3)cc(C=O)c2c1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"Cc1c(F)cc(C(=O)NC2CC2)cc1-c1ccc2c(=O)n(CC3CC3)cc(C=O)c2c1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Cc1c(F)cc(C(=O)NC2CC2)cc1-c1ccc2c(=O)n(CC3CC3)cc(C=O)c2c1\", \"reactants\": [\"Cc1c(F)cc(C(=O)NC2CC2)cc1B1OC(C)(C)C(C)(C)O1\", \"O=Cc1cn(CC2CC2)c(=O)c2ccc(Br)cc12\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"Cc1c(F)cc(C(=O)NC2CC2)cc1B1OC(C)(C)C(C)(C)O1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=Cc1cn(CC2CC2)c(=O)c2ccc(Br)cc12\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"VXKIGPDDANOPJU-UHFFFAOYSA-N.YQOKHFYXTCCFBL-UHFFFAOYSA-N>>GBCBQBSMQRMEQE-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"Cc1c(F)cc(C(=O)NC2CC2)cc1-c1ccc2c(=O)n(CC3CC3)cc(C=O)c2c1\", \"reactants\": [\"Cc1c(F)cc(C(=O)NC2CC2)cc1B1OC(C)(C)C(C)(C)O1\", \"O=Cc1cn(CC2CC2)c(=O)c2ccc(Br)cc12\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"Cc1c(F)cc(C(=O)NC2CC2)cc1B1OC(C)(C)C(C)(C)O1\", \"results\": [{\"inchikey\": \"YQOKHFYXTCCFBL-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Cc1c(F)cc(C(=O)NC2CC2)cc1B1OC(C)(C)C(C)(C)O1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"O=Cc1cn(CC2CC2)c(=O)c2ccc(Br)cc12\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"O=Cc1cn(CC2CC2)c(=O)c2ccc(Br)cc12 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"O=Cc1cn(CC2CC2)c(=O)c2ccc(Br)cc12\", \"reactants\": [\"CN(C)C=O\", \"O=c1c2ccc(Br)cc2ccn1CC1CC1\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"CN(C)C=O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=c1c2ccc(Br)cc2ccn1CC1CC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"XTIUXAYOAXOAAG-UHFFFAOYSA-N.ZMXDDKWLCZADIW-UHFFFAOYSA-N>>VXKIGPDDANOPJU-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"O=Cc1cn(CC2CC2)c(=O)c2ccc(Br)cc12\", \"reactants\": [\"CN(C)C=O\", \"O=c1c2ccc(Br)cc2ccn1CC1CC1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"CN(C)C=O\", \"results\": [{\"inchikey\": \"ZMXDDKWLCZADIW-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CN(C)C=O\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"O=c1c2ccc(Br)cc2ccn1CC1CC1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"O=c1c2ccc(Br)cc2ccn1CC1CC1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"O=c1c2ccc(Br)cc2ccn1CC1CC1\", \"reactants\": [\"BrCC1CC1\", \"O=c1[nH]ccc2cc(Br)ccc12\"]}","name":"validate_disconnection"},"id":"call_4_0","type":"function"},{"function":{"arguments":"{\"query\": \"BrCC1CC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=c1[nH]ccc2cc(Br)ccc12\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"AEILLAXRDHDKDY-UHFFFAOYSA-N.ZDYXSEQHOVSTPA-UHFFFAOYSA-N>>XTIUXAYOAXOAAG-UHFFFAOYSA-N\", \"model_turns_remaining\": 12, \"product\": \"O=c1c2ccc(Br)cc2ccn1CC1CC1\", \"reactants\": [\"BrCC1CC1\", \"O=c1[nH]ccc2cc(Br)ccc12\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_4_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"BrCC1CC1\", \"results\": [{\"inchikey\": \"AEILLAXRDHDKDY-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"BrCC1CC1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"O=c1[nH]ccc2cc(Br)ccc12\", \"results\": [{\"inchikey\": \"ZDYXSEQHOVSTPA-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=c1[nH]ccc2cc(Br)ccc12\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"Cc1c(F)cc(C(=O)NC2CC2)cc1-c1ccc2c(=O)n(CC3CC3)cc(CN3CCNC[C@@H]3C)c2c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"C[C@H]1CN(C(=O)OC(C)(C)C)CCN1\": \"precursor\", \"Cc1c(F)cc(C(=O)NC2CC2)cc1-c1ccc2c(=O)n(CC3CC3)cc(C=O)c2c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"C[C@H]1CN(C(=O)OC(C)(C)C)CCN1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"Cc1c(F)cc(C(=O)NC2CC2)cc1-c1ccc2c(=O)n(CC3CC3)cc(C=O)c2c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"Cc1c(F)cc(C(=O)NC2CC2)cc1B1OC(C)(C)C(C)(C)O1\": \"precursor\", \"O=Cc1cn(CC2CC2)c(=O)c2ccc(Br)cc12\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"Cc1c(F)cc(C(=O)NC2CC2)cc1B1OC(C)(C)C(C)(C)O1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=Cc1cn(CC2CC2)c(=O)c2ccc(Br)cc12\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CN(C)C=O\": \"precursor\", \"O=c1c2ccc(Br)cc2ccn1CC1CC1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CN(C)C=O\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=c1c2ccc(Br)cc2ccn1CC1CC1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"BrCC1CC1\": \"precursor\", \"O=c1[nH]ccc2cc(Br)ccc12\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"BrCC1CC1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=c1[nH]ccc2cc(Br)ccc12\", \"in_stock\": true, \"children\": []}]}]}]}]}]}]}]}]}]}}","name":"emit_routes"},"id":"call_5_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"Cc1c(F)cc(C(=O)NC2CC2)cc1-c1ccc2c(=O)n(CC3CC3)cc(CN3CCNC[C@@H]3C)c2c1","task_id":"retro_97f95e8d69200c6fc72b","tool_calls":13,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":5}
{"exact_match":true,"id":"retro_986a29ea7719c00ff90f:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CC(C)(C)OC(=O)n1cc(CCCCCc2cn(CCNC(=O)c3ccc(C(C)(C)C)cc3)nn2)nc1N in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(C)(C)OC(=O)n1cc(CCCCCc2cn(CCNC(=O)c3ccc(C(C)(C)C)cc3)nn2)nc1N\", \"reactants\": [\"C#CCCCCCc1cn(C(=O)OC(C)(C)C)c(N)n1\", \"CC(C)(C)c1ccc(C(=O)NCCN=[N+]=[N-])cc1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"C#CCCCCCc1cn(C(=O)OC(C)(C)C)c(N)n1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)c1ccc(C(=O)NCCN=[N+]=[N-])cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_complete\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"FPGSQLKBGUEUQD-UHFFFAOYSA-N.SPVQBBRBVAZWKR-UHFFFAOYSA-N>>KGVWILJQXBUXKP-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"CC(C)(C)OC(=O)n1cc(CCCCCc2cn(CCNC(=O)c3ccc(C(C)(C)C)cc3)nn2)nc1N\", \"reactants\": [\"C#CCCCCCc1cn(C(=O)OC(C)(C)C)c(N)n1\", \"CC(C)(C)c1ccc(C(=O)NCCN=[N+]=[N-])cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"C#CCCCCCc1cn(C(=O)OC(C)(C)C)c(N)n1\", \"results\": [{\"inchikey\": \"FPGSQLKBGUEUQD-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"C#CCCCCCc1cn(C(=O)OC(C)(C)C)c(N)n1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CC(C)(C)c1ccc(C(=O)NCCN=[N+]=[N-])cc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"CC(C)(C)c1ccc(C(=O)NCCN=[N+]=[N-])cc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(C)(C)c1ccc(C(=O)NCCN=[N+]=[N-])cc1\", \"reactants\": [\"CC(C)(C)c1ccc(C(=O)Cl)cc1\", \"[N-]=[N+]=NCCN\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)c1ccc(C(=O)Cl)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"[N-]=[N+]=NCCN\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"CSTIZSQKHUSKHU-UHFFFAOYSA-N.WNLMYNASWOULQY-UHFFFAOYSA-N>>SPVQBBRBVAZWKR-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"CC(C)(C)c1ccc(C(=O)NCCN=[N+]=[N-])cc1\", \"reactants\": [\"CC(C)(C)c1ccc(C(=O)Cl)cc1\", \"[N-]=[N+]=NCCN\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CC(C)(C)c1ccc(C(=O)Cl)cc1\", \"results\": [{\"inchikey\": \"WNLMYNASWOULQY-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CC(C)(C)c1ccc(C(=O)Cl)cc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"[N-]=[N+]=NCCN\", \"results\": [{\"inchikey\": \"CSTIZSQKHUSKHU-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"[N-]=[N+]=NCCN\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)OC(=O)n1cc(CCCCCc2cn(CCNC(=O)c3ccc(C(C)(C)C)cc3)nn2)nc1N\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"C#CCCCCCc1cn(C(=O)OC(C)(C)C)c(N)n1\": \"precursor\", \"CC(C)(C)c1ccc(C(=O)NCCN=[N+]=[N-])cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"C#CCCCCCc1cn(C(=O)OC(C)(C)C)c(N)n1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"CC(C)(C)c1ccc(C(=O)NCCN=[N+]=[N-])cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)(C)c1ccc(C(=O)Cl)cc1\": \"precursor\", \"[N-]=[N+]=NCCN\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)c1ccc(C(=O)Cl)cc1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"[N-]=[N+]=NCCN\", \"in_stock\": true, \"children\": []}]}]}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"CC(C)(C)OC(=O)n1cc(CCCCCc2cn(CCNC(=O)c3ccc(C(C)(C)C)cc3)nn2)nc1N","task_id":"retro_986a29ea7719c00ff90f","tool_calls":7,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_9884ad6a405d15adb529:reference-expert:a0","kind":"single_route","max_steps":3,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target Nc1nc2cc(B(O)O)ccc2s1 in at most 3 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Nc1nc2cc(B(O)O)ccc2s1\", \"reactants\": [\"CC(C)OB(OC(C)C)OC(C)C\", \"Nc1nc2cc(Br)ccc2s1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)OB(OC(C)C)OC(C)C\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"Nc1nc2cc(Br)ccc2s1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"NHDIQVFFNDKAQU-UHFFFAOYSA-N.ZPUJTWBWSOOMRP-UHFFFAOYSA-N>>IVLSCLRCPUOHLX-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"Nc1nc2cc(B(O)O)ccc2s1\", \"reactants\": [\"CC(C)OB(OC(C)C)OC(C)C\", \"Nc1nc2cc(Br)ccc2s1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CC(C)OB(OC(C)C)OC(C)C\", \"results\": [{\"inchikey\": \"NHDIQVFFNDKAQU-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CC(C)OB(OC(C)C)OC(C)C\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"Nc1nc2cc(Br)ccc2s1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"Nc1nc2cc(Br)ccc2s1 was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Nc1nc2cc(Br)ccc2s1\", \"reactants\": [\"NC(=S)Nc1cccc(Br)c1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"NC(=S)Nc1cccc(Br)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_complete\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"XBRVSIPVHYWULW-UHFFFAOYSA-N>>ZPUJTWBWSOOMRP-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"Nc1nc2cc(Br)ccc2s1\", \"reactants\": [\"NC(=S)Nc1cccc(Br)c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"NC(=S)Nc1cccc(Br)c1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"NC(=S)Nc1cccc(Br)c1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"NC(=S)Nc1cccc(Br)c1\", \"reactants\": [\"N#CS\", \"Nc1cccc(Br)c1\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"N#CS\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"Nc1cccc(Br)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_complete\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"DHYHYLGCQVVLOQ-UHFFFAOYSA-N.ZMZDMBWJUHKJPS-UHFFFAOYSA-N>>XBRVSIPVHYWULW-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"NC(=S)Nc1cccc(Br)c1\", \"reactants\": [\"N#CS\", \"Nc1cccc(Br)c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"N#CS\", \"results\": [{\"inchikey\": \"ZMZDMBWJUHKJPS-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"N#CS\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"Nc1cccc(Br)c1\", \"results\": [{\"inchikey\": \"DHYHYLGCQVVLOQ-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Nc1cccc(Br)c1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"Nc1nc2cc(B(O)O)ccc2s1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)OB(OC(C)C)OC(C)C\": \"precursor\", \"Nc1nc2cc(Br)ccc2s1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)OB(OC(C)C)OC(C)C\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"Nc1nc2cc(Br)ccc2s1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"NC(=S)Nc1cccc(Br)c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"NC(=S)Nc1cccc(Br)c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"N#CS\": \"precursor\", \"Nc1cccc(Br)c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"N#CS\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"Nc1cccc(Br)c1\", \"in_stock\": true, \"children\": []}]}]}]}]}]}]}]}}","name":"emit_routes"},"id":"call_4_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"Nc1nc2cc(B(O)O)ccc2s1","task_id":"retro_9884ad6a405d15adb529","tool_calls":9,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":4}
{"exact_match":true,"id":"retro_9a33ff21eb3e45e15710:reference-expert:a0","kind":"single_route","max_steps":3,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target COC[C@H](C)Oc1cc(Oc2ccc(C(C)O)cc2)cc(-c2ccc(-c3nccs3)[nH]2)c1 in at most 3 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COC[C@H](C)Oc1cc(Oc2ccc(C(C)O)cc2)cc(-c2ccc(-c3nccs3)[nH]2)c1\", \"reactants\": [\"COC[C@H](C)Oc1cc(Oc2ccc(C(C)=O)cc2)cc(-c2ccc(-c3nccs3)[nH]2)c1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"COC[C@H](C)Oc1cc(Oc2ccc(C(C)=O)cc2)cc(-c2ccc(-c3nccs3)[nH]2)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_complete\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"BWRLEAICAVUCEG-INIZCTEOSA-N>>HTQYQIKBVDFTAP-BHWOMJMDSA-N\", \"model_turns_remaining\": 15, \"product\": \"COC[C@H](C)Oc1cc(Oc2ccc(C(C)O)cc2)cc(-c2ccc(-c3nccs3)[nH]2)c1\", \"reactants\": [\"COC[C@H](C)Oc1cc(Oc2ccc(C(C)=O)cc2)cc(-c2ccc(-c3nccs3)[nH]2)c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"COC[C@H](C)Oc1cc(Oc2ccc(C(C)=O)cc2)cc(-c2ccc(-c3nccs3)[nH]2)c1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"COC[C@H](C)Oc1cc(Oc2ccc(C(C)=O)cc2)cc(-c2ccc(-c3nccs3)[nH]2)c1 was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COC[C@H](C)Oc1cc(Oc2ccc(C(C)=O)cc2)cc(-c2ccc(-c3nccs3)[nH]2)c1\", \"reactants\": [\"COC[C@H](C)Oc1cc(Oc2ccc(C(C)=O)cc2)cc(-c2ccc(-c3nccs3)n2C(=O)OC(C)(C)C)c1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"COC[C@H](C)Oc1cc(Oc2ccc(C(C)=O)cc2)cc(-c2ccc(-c3nccs3)n2C(=O)OC(C)(C)C)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"FQMCLBPEKZMPAB-IBGZPJMESA-N>>BWRLEAICAVUCEG-INIZCTEOSA-N\", \"model_turns_remaining\": 14, \"product\": \"COC[C@H](C)Oc1cc(Oc2ccc(C(C)=O)cc2)cc(-c2ccc(-c3nccs3)[nH]2)c1\", \"reactants\": [\"COC[C@H](C)Oc1cc(Oc2ccc(C(C)=O)cc2)cc(-c2ccc(-c3nccs3)n2C(=O)OC(C)(C)C)c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"COC[C@H](C)Oc1cc(Oc2ccc(C(C)=O)cc2)cc(-c2ccc(-c3nccs3)n2C(=O)OC(C)(C)C)c1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"COC[C@H](C)Oc1cc(Oc2ccc(C(C)=O)cc2)cc(-c2ccc(-c3nccs3)n2C(=O)OC(C)(C)C)c1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COC[C@H](C)Oc1cc(Oc2ccc(C(C)=O)cc2)cc(-c2ccc(-c3nccs3)n2C(=O)OC(C)(C)C)c1\", \"reactants\": [\"CC(=O)c1ccc(B(O)O)cc1\", \"COC[C@H](C)Oc1cc(O)cc(-c2ccc(-c3nccs3)n2C(=O)OC(C)(C)C)c1\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(=O)c1ccc(B(O)O)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"COC[C@H](C)Oc1cc(O)cc(-c2ccc(-c3nccs3)n2C(=O)OC(C)(C)C)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"IMDXWFATKFCMJS-AWEZNQCLSA-N.OBQRODBYVNIZJU-UHFFFAOYSA-N>>FQMCLBPEKZMPAB-IBGZPJMESA-N\", \"model_turns_remaining\": 13, \"product\": \"COC[C@H](C)Oc1cc(Oc2ccc(C(C)=O)cc2)cc(-c2ccc(-c3nccs3)n2C(=O)OC(C)(C)C)c1\", \"reactants\": [\"CC(=O)c1ccc(B(O)O)cc1\", \"COC[C@H](C)Oc1cc(O)cc(-c2ccc(-c3nccs3)n2C(=O)OC(C)(C)C)c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"CC(=O)c1ccc(B(O)O)cc1\", \"results\": [{\"inchikey\": \"OBQRODBYVNIZJU-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CC(=O)c1ccc(B(O)O)cc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"COC[C@H](C)Oc1cc(O)cc(-c2ccc(-c3nccs3)n2C(=O)OC(C)(C)C)c1\", \"results\": [{\"inchikey\": \"IMDXWFATKFCMJS-AWEZNQCLSA-N\", \"similarity\": 1.0, \"smiles\": \"COC[C@H](C)Oc1cc(O)cc(-c2ccc(-c3nccs3)n2C(=O)OC(C)(C)C)c1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"COC[C@H](C)Oc1cc(Oc2ccc(C(C)O)cc2)cc(-c2ccc(-c3nccs3)[nH]2)c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COC[C@H](C)Oc1cc(Oc2ccc(C(C)=O)cc2)cc(-c2ccc(-c3nccs3)[nH]2)c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COC[C@H](C)Oc1cc(Oc2ccc(C(C)=O)cc2)cc(-c2ccc(-c3nccs3)[nH]2)c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COC[C@H](C)Oc1cc(Oc2ccc(C(C)=O)cc2)cc(-c2ccc(-c3nccs3)n2C(=O)OC(C)(C)C)c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COC[C@H](C)Oc1cc(Oc2ccc(C(C)=O)cc2)cc(-c2ccc(-c3nccs3)n2C(=O)OC(C)(C)C)c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(=O)c1ccc(B(O)O)cc1\": \"precursor\", \"COC[C@H](C)Oc1cc(O)cc(-c2ccc(-c3nccs3)n2C(=O)OC(C)(C)C)c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(=O)c1ccc(B(O)O)cc1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"COC[C@H](C)Oc1cc(O)cc(-c2ccc(-c3nccs3)n2C(=O)OC(C)(C)C)c1\", \"in_stock\": true, \"children\": []}]}]}]}]}]}]}]}}","name":"emit_routes"},"id":"call_4_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"COC[C@H](C)Oc1cc(Oc2ccc(C(C)O)cc2)cc(-c2ccc(-c3nccs3)[nH]2)c1","task_id":"retro_9a33ff21eb3e45e15710","tool_calls":8,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":4}
{"exact_match":true,"id":"retro_9a649287a2816d00d444:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CNc1cc(F)cc(F)c1 in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CNc1cc(F)cc(F)c1\", \"reactants\": [\"O=CNc1cc(F)cc(F)c1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"O=CNc1cc(F)cc(F)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"ZYDUAODJWDWHKD-UHFFFAOYSA-N>>RVLAHRBSGLXXPZ-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"CNc1cc(F)cc(F)c1\", \"reactants\": [\"O=CNc1cc(F)cc(F)c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"O=CNc1cc(F)cc(F)c1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"O=CNc1cc(F)cc(F)c1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"O=CNc1cc(F)cc(F)c1\", \"reactants\": [\"Nc1cc(F)cc(F)c1\", \"O=CO\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"Nc1cc(F)cc(F)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=CO\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"BDAGIHXWWSANSR-UHFFFAOYSA-N.KQOIBXZRCYFZSO-UHFFFAOYSA-N>>ZYDUAODJWDWHKD-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"O=CNc1cc(F)cc(F)c1\", \"reactants\": [\"Nc1cc(F)cc(F)c1\", \"O=CO\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"Nc1cc(F)cc(F)c1\", \"results\": [{\"inchikey\": \"KQOIBXZRCYFZSO-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Nc1cc(F)cc(F)c1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"O=CO\", \"results\": [{\"inchikey\": \"BDAGIHXWWSANSR-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=CO\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CNc1cc(F)cc(F)c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"O=CNc1cc(F)cc(F)c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"O=CNc1cc(F)cc(F)c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"Nc1cc(F)cc(F)c1\": \"precursor\", \"O=CO\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"Nc1cc(F)cc(F)c1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=CO\", \"in_stock\": true, \"children\": []}]}]}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"CNc1cc(F)cc(F)c1","task_id":"retro_9a649287a2816d00d444","tool_calls":6,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_9f67a9b9fab33c2e97de:reference-expert:a0","kind":"single_route","max_steps":5,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target N#Cc1ccc2ccn(C3CCN(CCc4ccc(F)cc4)CC3)c2c1 in at most 5 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"N#Cc1ccc2ccn(C3CCN(CCc4ccc(F)cc4)CC3)c2c1\", \"reactants\": [\"N#Cc1ccc2c(c1)N(C1CCN(CCc3ccc(F)cc3)CC1)CC2\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"N#Cc1ccc2c(c1)N(C1CCN(CCc3ccc(F)cc3)CC1)CC2\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_complete\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"SXUOSQOMIZYDIN-UHFFFAOYSA-N>>RBNZDXGJONEAPP-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"N#Cc1ccc2ccn(C3CCN(CCc4ccc(F)cc4)CC3)c2c1\", \"reactants\": [\"N#Cc1ccc2c(c1)N(C1CCN(CCc3ccc(F)cc3)CC1)CC2\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"N#Cc1ccc2c(c1)N(C1CCN(CCc3ccc(F)cc3)CC1)CC2\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"N#Cc1ccc2c(c1)N(C1CCN(CCc3ccc(F)cc3)CC1)CC2 was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"N#Cc1ccc2c(c1)N(C1CCN(CCc3ccc(F)cc3)CC1)CC2\", \"reactants\": [\"ON=Cc1ccc2c(c1)N(C1CCN(CCc3ccc(F)cc3)CC1)CC2\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"ON=Cc1ccc2c(c1)N(C1CCN(CCc3ccc(F)cc3)CC1)CC2\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"YRXICQHTJANEIJ-UHFFFAOYSA-N>>SXUOSQOMIZYDIN-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"N#Cc1ccc2c(c1)N(C1CCN(CCc3ccc(F)cc3)CC1)CC2\", \"reactants\": [\"ON=Cc1ccc2c(c1)N(C1CCN(CCc3ccc(F)cc3)CC1)CC2\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"ON=Cc1ccc2c(c1)N(C1CCN(CCc3ccc(F)cc3)CC1)CC2\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"ON=Cc1ccc2c(c1)N(C1CCN(CCc3ccc(F)cc3)CC1)CC2 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"ON=Cc1ccc2c(c1)N(C1CCN(CCc3ccc(F)cc3)CC1)CC2\", \"reactants\": [\"NO\", \"O=Cc1ccc2c(c1)N(C1CCN(CCc3ccc(F)cc3)CC1)CC2\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"NO\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=Cc1ccc2c(c1)N(C1CCN(CCc3ccc(F)cc3)CC1)CC2\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"ABHNJAJFVWIUOX-UHFFFAOYSA-N.AVXURJPOCDRRFD-UHFFFAOYSA-N>>YRXICQHTJANEIJ-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"ON=Cc1ccc2c(c1)N(C1CCN(CCc3ccc(F)cc3)CC1)CC2\", \"reactants\": [\"NO\", \"O=Cc1ccc2c(c1)N(C1CCN(CCc3ccc(F)cc3)CC1)CC2\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"NO\", \"results\": [{\"inchikey\": \"AVXURJPOCDRRFD-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"NO\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"O=Cc1ccc2c(c1)N(C1CCN(CCc3ccc(F)cc3)CC1)CC2\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"O=Cc1ccc2c(c1)N(C1CCN(CCc3ccc(F)cc3)CC1)CC2 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"O=Cc1ccc2c(c1)N(C1CCN(CCc3ccc(F)cc3)CC1)CC2\", \"reactants\": [\"CN(C)C=O\", \"Fc1ccc(CCN2CCC(N3CCc4ccc(Br)cc43)CC2)cc1\"]}","name":"validate_disconnection"},"id":"call_4_0","type":"function"},{"function":{"arguments":"{\"query\": \"CN(C)C=O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_1","type":"function"},{"function":{"arguments":"{\"query\": \"Fc1ccc(CCN2CCC(N3CCc4ccc(Br)cc43)CC2)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"PRVRAPGFIBKDHO-UHFFFAOYSA-N.ZMXDDKWLCZADIW-UHFFFAOYSA-N>>ABHNJAJFVWIUOX-UHFFFAOYSA-N\", \"model_turns_remaining\": 12, \"product\": \"O=Cc1ccc2c(c1)N(C1CCN(CCc3ccc(F)cc3)CC1)CC2\", \"reactants\": [\"CN(C)C=O\", \"Fc1ccc(CCN2CCC(N3CCc4ccc(Br)cc43)CC2)cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_4_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"CN(C)C=O\", \"results\": [{\"inchikey\": \"ZMXDDKWLCZADIW-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CN(C)C=O\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"Fc1ccc(CCN2CCC(N3CCc4ccc(Br)cc43)CC2)cc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_2"},{"content":"Fc1ccc(CCN2CCC(N3CCc4ccc(Br)cc43)CC2)cc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Fc1ccc(CCN2CCC(N3CCc4ccc(Br)cc43)CC2)cc1\", \"reactants\": [\"Brc1ccc2c(c1)NCC2\", \"O=C1CCN(CCc2ccc(F)cc2)CC1\"]}","name":"validate_disconnection"},"id":"call_5_0","type":"function"},{"function":{"arguments":"{\"query\": \"Brc1ccc2c(c1)NCC2\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_5_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=C1CCN(CCc2ccc(F)cc2)CC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_5_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"MTSYZAHZABCWMS-UHFFFAOYSA-N.RLCBASWXFBEVKY-UHFFFAOYSA-N>>PRVRAPGFIBKDHO-UHFFFAOYSA-N\", \"model_turns_remaining\": 11, \"product\": \"Fc1ccc(CCN2CCC(N3CCc4ccc(Br)cc43)CC2)cc1\", \"reactants\": [\"Brc1ccc2c(c1)NCC2\", \"O=C1CCN(CCc2ccc(F)cc2)CC1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_5_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 11, \"query\": \"Brc1ccc2c(c1)NCC2\", \"results\": [{\"inchikey\": \"MTSYZAHZABCWMS-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Brc1ccc2c(c1)NCC2\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_5_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 11, \"query\": \"O=C1CCN(CCc2ccc(F)cc2)CC1\", \"results\": [{\"inchikey\": \"RLCBASWXFBEVKY-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=C1CCN(CCc2ccc(F)cc2)CC1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_5_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"N#Cc1ccc2ccn(C3CCN(CCc4ccc(F)cc4)CC3)c2c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"N#Cc1ccc2c(c1)N(C1CCN(CCc3ccc(F)cc3)CC1)CC2\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"N#Cc1ccc2c(c1)N(C1CCN(CCc3ccc(F)cc3)CC1)CC2\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"ON=Cc1ccc2c(c1)N(C1CCN(CCc3ccc(F)cc3)CC1)CC2\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"ON=Cc1ccc2c(c1)N(C1CCN(CCc3ccc(F)cc3)CC1)CC2\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"NO\": \"precursor\", \"O=Cc1ccc2c(c1)N(C1CCN(CCc3ccc(F)cc3)CC1)CC2\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"NO\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=Cc1ccc2c(c1)N(C1CCN(CCc3ccc(F)cc3)CC1)CC2\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CN(C)C=O\": \"precursor\", \"Fc1ccc(CCN2CCC(N3CCc4ccc(Br)cc43)CC2)cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CN(C)C=O\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"Fc1ccc(CCN2CCC(N3CCc4ccc(Br)cc43)CC2)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"Brc1ccc2c(c1)NCC2\": \"precursor\", \"O=C1CCN(CCc2ccc(F)cc2)CC1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"Brc1ccc2c(c1)NCC2\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=C1CCN(CCc2ccc(F)cc2)CC1\", \"in_stock\": true, \"children\": []}]}]}]}]}]}]}]}]}]}]}]}}","name":"emit_routes"},"id":"call_6_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"N#Cc1ccc2ccn(C3CCN(CCc4ccc(F)cc4)CC3)c2c1","task_id":"retro_9f67a9b9fab33c2e97de","tool_calls":14,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":6}
{"exact_match":true,"id":"retro_a080db09675ec34d2e42:reference-expert:a0","kind":"single_route","max_steps":3,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target COc1cc(OCc2sc(-c3ccc(C(F)(F)F)cc3)nc2CCCN2CCC2)ccc1-c1noc(=O)[nH]1 in at most 3 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COc1cc(OCc2sc(-c3ccc(C(F)(F)F)cc3)nc2CCCN2CCC2)ccc1-c1noc(=O)[nH]1\", \"reactants\": [\"C1CNC1\", \"COc1cc(OCc2sc(-c3ccc(C(F)(F)F)cc3)nc2CCCOS(C)(=O)=O)ccc1-c1noc(=O)[nH]1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"C1CNC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"COc1cc(OCc2sc(-c3ccc(C(F)(F)F)cc3)nc2CCCOS(C)(=O)=O)ccc1-c1noc(=O)[nH]1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"HONIICLYMWZJFZ-UHFFFAOYSA-N.JIAVKTSSCWJUOA-UHFFFAOYSA-N>>TXTGAFKYDNEWIO-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"COc1cc(OCc2sc(-c3ccc(C(F)(F)F)cc3)nc2CCCN2CCC2)ccc1-c1noc(=O)[nH]1\", \"reactants\": [\"C1CNC1\", \"COc1cc(OCc2sc(-c3ccc(C(F)(F)F)cc3)nc2CCCOS(C)(=O)=O)ccc1-c1noc(=O)[nH]1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"C1CNC1\", \"results\": [{\"inchikey\": \"HONIICLYMWZJFZ-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"C1CNC1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"COc1cc(OCc2sc(-c3ccc(C(F)(F)F)cc3)nc2CCCOS(C)(=O)=O)ccc1-c1noc(=O)[nH]1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"COc1cc(OCc2sc(-c3ccc(C(F)(F)F)cc3)nc2CCCOS(C)(=O)=O)ccc1-c1noc(=O)[nH]1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COc1cc(OCc2sc(-c3ccc(C(F)(F)F)cc3)nc2CCCOS(C)(=O)=O)ccc1-c1noc(=O)[nH]1\", \"reactants\": [\"COc1cc(OCc2sc(-c3ccc(C(F)(F)F)cc3)nc2CCCO)ccc1-c1noc(=O)[nH]1\", \"CS(=O)(=O)OS(C)(=O)=O\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"COc1cc(OCc2sc(-c3ccc(C(F)(F)F)cc3)nc2CCCO)ccc1-c1noc(=O)[nH]1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"CS(=O)(=O)OS(C)(=O)=O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"IZDROVVXIHRYMH-UHFFFAOYSA-N.NRARFNUZBDJKMI-UHFFFAOYSA-N>>JIAVKTSSCWJUOA-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"COc1cc(OCc2sc(-c3ccc(C(F)(F)F)cc3)nc2CCCOS(C)(=O)=O)ccc1-c1noc(=O)[nH]1\", \"reactants\": [\"COc1cc(OCc2sc(-c3ccc(C(F)(F)F)cc3)nc2CCCO)ccc1-c1noc(=O)[nH]1\", \"CS(=O)(=O)OS(C)(=O)=O\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"COc1cc(OCc2sc(-c3ccc(C(F)(F)F)cc3)nc2CCCO)ccc1-c1noc(=O)[nH]1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CS(=O)(=O)OS(C)(=O)=O\", \"results\": [{\"inchikey\": \"IZDROVVXIHRYMH-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CS(=O)(=O)OS(C)(=O)=O\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"COc1cc(OCc2sc(-c3ccc(C(F)(F)F)cc3)nc2CCCO)ccc1-c1noc(=O)[nH]1 was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COc1cc(OCc2sc(-c3ccc(C(F)(F)F)cc3)nc2CCCO)ccc1-c1noc(=O)[nH]1\", \"reactants\": [\"COc1cc(OCc2sc(-c3ccc(C(F)(F)F)cc3)nc2CCCOCc2ccccc2)ccc1-c1noc(=O)[nH]1\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"COc1cc(OCc2sc(-c3ccc(C(F)(F)F)cc3)nc2CCCOCc2ccccc2)ccc1-c1noc(=O)[nH]1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"JYJIKSJNSANEHU-UHFFFAOYSA-N>>NRARFNUZBDJKMI-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"COc1cc(OCc2sc(-c3ccc(C(F)(F)F)cc3)nc2CCCO)ccc1-c1noc(=O)[nH]1\", \"reactants\": [\"COc1cc(OCc2sc(-c3ccc(C(F)(F)F)cc3)nc2CCCOCc2ccccc2)ccc1-c1noc(=O)[nH]1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"COc1cc(OCc2sc(-c3ccc(C(F)(F)F)cc3)nc2CCCOCc2ccccc2)ccc1-c1noc(=O)[nH]1\", \"results\": [{\"inchikey\": \"JYJIKSJNSANEHU-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"COc1cc(OCc2sc(-c3ccc(C(F)(F)F)cc3)nc2CCCOCc2ccccc2)ccc1-c1noc(=O)[nH]1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"COc1cc(OCc2sc(-c3ccc(C(F)(F)F)cc3)nc2CCCN2CCC2)ccc1-c1noc(=O)[nH]1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"C1CNC1\": \"precursor\", \"COc1cc(OCc2sc(-c3ccc(C(F)(F)F)cc3)nc2CCCOS(C)(=O)=O)ccc1-c1noc(=O)[nH]1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"C1CNC1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"COc1cc(OCc2sc(-c3ccc(C(F)(F)F)cc3)nc2CCCOS(C)(=O)=O)ccc1-c1noc(=O)[nH]1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COc1cc(OCc2sc(-c3ccc(C(F)(F)F)cc3)nc2CCCO)ccc1-c1noc(=O)[nH]1\": \"precursor\", \"CS(=O)(=O)OS(C)(=O)=O\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COc1cc(OCc2sc(-c3ccc(C(F)(F)F)cc3)nc2CCCO)ccc1-c1noc(=O)[nH]1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COc1cc(OCc2sc(-c3ccc(C(F)(F)F)cc3)nc2CCCOCc2ccccc2)ccc1-c1noc(=O)[nH]1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COc1cc(OCc2sc(-c3ccc(C(F)(F)F)cc3)nc2CCCOCc2ccccc2)ccc1-c1noc(=O)[nH]1\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"CS(=O)(=O)OS(C)(=O)=O\", \"in_stock\": true, \"children\": []}]}]}]}]}]}}","name":"emit_routes"},"id":"call_4_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"COc1cc(OCc2sc(-c3ccc(C(F)(F)F)cc3)nc2CCCN2CCC2)ccc1-c1noc(=O)[nH]1","task_id":"retro_a080db09675ec34d2e42","tool_calls":9,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":4}
{"exact_match":true,"id":"retro_a17cc713554cb302b942:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CC[C@H]1CC[C@H](COc2ccc(O)c(F)c2F)CC1 in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC[C@H]1CC[C@H](COc2ccc(O)c(F)c2F)CC1\", \"reactants\": [\"CC[C@H]1CC[C@H](COc2cccc(F)c2F)CC1\", \"OO\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC[C@H]1CC[C@H](COc2cccc(F)c2F)CC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"OO\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"FDMJBSNXXWAOQD-HAQNSBGRSA-N.MHAJPDPJQMAIIY-UHFFFAOYSA-N>>NRZOBTUJAICNFD-XYPYZODXSA-N\", \"model_turns_remaining\": 15, \"product\": \"CC[C@H]1CC[C@H](COc2ccc(O)c(F)c2F)CC1\", \"reactants\": [\"CC[C@H]1CC[C@H](COc2cccc(F)c2F)CC1\", \"OO\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CC[C@H]1CC[C@H](COc2cccc(F)c2F)CC1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"OO\", \"results\": [{\"inchikey\": \"MHAJPDPJQMAIIY-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"OO\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"CC[C@H]1CC[C@H](COc2cccc(F)c2F)CC1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC[C@H]1CC[C@H](COc2cccc(F)c2F)CC1\", \"reactants\": [\"CC[C@H]1CC[C@H](CBr)CC1\", \"Oc1cccc(F)c1F\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC[C@H]1CC[C@H](CBr)CC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"Oc1cccc(F)c1F\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"GTTAKDFRWSHWKT-KYZUINATSA-N.RPEPGIOVXBBUMJ-UHFFFAOYSA-N>>FDMJBSNXXWAOQD-HAQNSBGRSA-N\", \"model_turns_remaining\": 14, \"product\": \"CC[C@H]1CC[C@H](COc2cccc(F)c2F)CC1\", \"reactants\": [\"CC[C@H]1CC[C@H](CBr)CC1\", \"Oc1cccc(F)c1F\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CC[C@H]1CC[C@H](CBr)CC1\", \"results\": [{\"inchikey\": \"GTTAKDFRWSHWKT-KYZUINATSA-N\", \"similarity\": 1.0, \"smiles\": \"CC[C@H]1CC[C@H](CBr)CC1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"Oc1cccc(F)c1F\", \"results\": [{\"inchikey\": \"RPEPGIOVXBBUMJ-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Oc1cccc(F)c1F\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CC[C@H]1CC[C@H](COc2ccc(O)c(F)c2F)CC1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC[C@H]1CC[C@H](COc2cccc(F)c2F)CC1\": \"precursor\", \"OO\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC[C@H]1CC[C@H](COc2cccc(F)c2F)CC1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC[C@H]1CC[C@H](CBr)CC1\": \"precursor\", \"Oc1cccc(F)c1F\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC[C@H]1CC[C@H](CBr)CC1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"Oc1cccc(F)c1F\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"OO\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"CC[C@H]1CC[C@H](COc2ccc(O)c(F)c2F)CC1","task_id":"retro_a17cc713554cb302b942","tool_calls":7,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_a36734b7aa6b8afef777:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CCOC(=O)CNc1ccc(C=O)cc1 in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCOC(=O)CNc1ccc(C=O)cc1\", \"reactants\": [\"CCOC(=O)CNc1ccc(C)cc1\", \"CO\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCOC(=O)CNc1ccc(C)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"CO\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"OKKJLVBELUTLKV-UHFFFAOYSA-N.RFCHXXFHULMCDW-UHFFFAOYSA-N>>KIAPTEQXIVHCOL-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"CCOC(=O)CNc1ccc(C=O)cc1\", \"reactants\": [\"CCOC(=O)CNc1ccc(C)cc1\", \"CO\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CCOC(=O)CNc1ccc(C)cc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CO\", \"results\": [{\"inchikey\": \"OKKJLVBELUTLKV-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CO\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"CCOC(=O)CNc1ccc(C)cc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCOC(=O)CNc1ccc(C)cc1\", \"reactants\": [\"CCOC(=O)CBr\", \"Cc1ccc(N)cc1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCOC(=O)CBr\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"Cc1ccc(N)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"PQJJJMRNHATNKG-UHFFFAOYSA-N.RZXMPPFPUUCRFN-UHFFFAOYSA-N>>RFCHXXFHULMCDW-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"CCOC(=O)CNc1ccc(C)cc1\", \"reactants\": [\"CCOC(=O)CBr\", \"Cc1ccc(N)cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CCOC(=O)CBr\", \"results\": [{\"inchikey\": \"PQJJJMRNHATNKG-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CCOC(=O)CBr\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"Cc1ccc(N)cc1\", \"results\": [{\"inchikey\": \"RZXMPPFPUUCRFN-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Cc1ccc(N)cc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CCOC(=O)CNc1ccc(C=O)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCOC(=O)CNc1ccc(C)cc1\": \"precursor\", \"CO\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCOC(=O)CNc1ccc(C)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCOC(=O)CBr\": \"precursor\", \"Cc1ccc(N)cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCOC(=O)CBr\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"Cc1ccc(N)cc1\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"CO\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"CCOC(=O)CNc1ccc(C=O)cc1","task_id":"retro_a36734b7aa6b8afef777","tool_calls":7,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_a406683757522f0502a5:reference-expert:a0","kind":"single_route","max_steps":4,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target N#Cc1cccc(Oc2nc(-c3cccnc3)ncc2N)c1 in at most 4 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"N#Cc1cccc(Oc2nc(-c3cccnc3)ncc2N)c1\", \"reactants\": [\"CC(C)(C)OC(=O)Nc1cnc(-c2cccnc2)nc1Oc1cccc(C#N)c1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)OC(=O)Nc1cnc(-c2cccnc2)nc1Oc1cccc(C#N)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"KIMHQPVCSMKIEU-UHFFFAOYSA-N>>PKFJPCSKZBLQTR-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"N#Cc1cccc(Oc2nc(-c3cccnc3)ncc2N)c1\", \"reactants\": [\"CC(C)(C)OC(=O)Nc1cnc(-c2cccnc2)nc1Oc1cccc(C#N)c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CC(C)(C)OC(=O)Nc1cnc(-c2cccnc2)nc1Oc1cccc(C#N)c1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"CC(C)(C)OC(=O)Nc1cnc(-c2cccnc2)nc1Oc1cccc(C#N)c1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(C)(C)OC(=O)Nc1cnc(-c2cccnc2)nc1Oc1cccc(C#N)c1\", \"reactants\": [\"CC(C)(C)O\", \"N#Cc1cccc(Oc2nc(-c3cccnc3)ncc2C(=O)O)c1\", \"[N-]=[N+]=NP(=O)(c1ccccc1)c1ccccc1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"N#Cc1cccc(Oc2nc(-c3cccnc3)ncc2C(=O)O)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"},{"function":{"arguments":"{\"query\": \"[N-]=[N+]=NP(=O)(c1ccccc1)c1ccccc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_3","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"DKGAVHZHDRPRBM-UHFFFAOYSA-N.MKRTXPORKIRPDG-UHFFFAOYSA-N.NFKUPVPYCDPSCQ-UHFFFAOYSA-N>>KIMHQPVCSMKIEU-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"CC(C)(C)OC(=O)Nc1cnc(-c2cccnc2)nc1Oc1cccc(C#N)c1\", \"reactants\": [\"CC(C)(C)O\", \"N#Cc1cccc(Oc2nc(-c3cccnc3)ncc2C(=O)O)c1\", \"[N-]=[N+]=NP(=O)(c1ccccc1)c1ccccc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CC(C)(C)O\", \"results\": [{\"inchikey\": \"DKGAVHZHDRPRBM-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CC(C)(C)O\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"N#Cc1cccc(Oc2nc(-c3cccnc3)ncc2C(=O)O)c1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"[N-]=[N+]=NP(=O)(c1ccccc1)c1ccccc1\", \"results\": [{\"inchikey\": \"MKRTXPORKIRPDG-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"[N-]=[N+]=NP(=O)(c1ccccc1)c1ccccc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_3"},{"content":"N#Cc1cccc(Oc2nc(-c3cccnc3)ncc2C(=O)O)c1 was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"N#Cc1cccc(Oc2nc(-c3cccnc3)ncc2C(=O)O)c1\", \"reactants\": [\"CCOC(=O)c1cnc(-c2cccnc2)nc1Oc1cccc(C#N)c1\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCOC(=O)c1cnc(-c2cccnc2)nc1Oc1cccc(C#N)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"GMTAUMVHHDWIPY-UHFFFAOYSA-N>>NFKUPVPYCDPSCQ-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"N#Cc1cccc(Oc2nc(-c3cccnc3)ncc2C(=O)O)c1\", \"reactants\": [\"CCOC(=O)c1cnc(-c2cccnc2)nc1Oc1cccc(C#N)c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"CCOC(=O)c1cnc(-c2cccnc2)nc1Oc1cccc(C#N)c1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"CCOC(=O)c1cnc(-c2cccnc2)nc1Oc1cccc(C#N)c1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCOC(=O)c1cnc(-c2cccnc2)nc1Oc1cccc(C#N)c1\", \"reactants\": [\"CCOC(=O)c1cnc(-c2cccnc2)nc1Cl\", \"N#Cc1cccc(O)c1\"]}","name":"validate_disconnection"},"id":"call_4_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCOC(=O)c1cnc(-c2cccnc2)nc1Cl\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_1","type":"function"},{"function":{"arguments":"{\"query\": \"N#Cc1cccc(O)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"BGZFNCGOWTUOAD-UHFFFAOYSA-N.SGHBRHKBCLLVCI-UHFFFAOYSA-N>>GMTAUMVHHDWIPY-UHFFFAOYSA-N\", \"model_turns_remaining\": 12, \"product\": \"CCOC(=O)c1cnc(-c2cccnc2)nc1Oc1cccc(C#N)c1\", \"reactants\": [\"CCOC(=O)c1cnc(-c2cccnc2)nc1Cl\", \"N#Cc1cccc(O)c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_4_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"CCOC(=O)c1cnc(-c2cccnc2)nc1Cl\", \"results\": [{\"inchikey\": \"BGZFNCGOWTUOAD-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CCOC(=O)c1cnc(-c2cccnc2)nc1Cl\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"N#Cc1cccc(O)c1\", \"results\": [{\"inchikey\": \"SGHBRHKBCLLVCI-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"N#Cc1cccc(O)c1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"N#Cc1cccc(Oc2nc(-c3cccnc3)ncc2N)c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)(C)OC(=O)Nc1cnc(-c2cccnc2)nc1Oc1cccc(C#N)c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)OC(=O)Nc1cnc(-c2cccnc2)nc1Oc1cccc(C#N)c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)(C)O\": \"precursor\", \"N#Cc1cccc(Oc2nc(-c3cccnc3)ncc2C(=O)O)c1\": \"precursor\", \"[N-]=[N+]=NP(=O)(c1ccccc1)c1ccccc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)O\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"N#Cc1cccc(Oc2nc(-c3cccnc3)ncc2C(=O)O)c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCOC(=O)c1cnc(-c2cccnc2)nc1Oc1cccc(C#N)c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCOC(=O)c1cnc(-c2cccnc2)nc1Oc1cccc(C#N)c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCOC(=O)c1cnc(-c2cccnc2)nc1Cl\": \"precursor\", \"N#Cc1cccc(O)c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCOC(=O)c1cnc(-c2cccnc2)nc1Cl\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"N#Cc1cccc(O)c1\", \"in_stock\": true, \"children\": []}]}]}]}]}, {\"type\": \"mol\", \"smiles\": \"[N-]=[N+]=NP(=O)(c1ccccc1)c1ccccc1\", \"in_stock\": true, \"children\": []}]}]}]}]}]}}","name":"emit_routes"},"id":"call_5_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"N#Cc1cccc(Oc2nc(-c3cccnc3)ncc2N)c1","task_id":"retro_a406683757522f0502a5","tool_calls":12,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":5}
{"exact_match":true,"id":"retro_a4754b645d0c71e074a9:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target N[C@@H]1CCCN(c2ccc(Br)cc2)C1 in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"N[C@@H]1CCCN(c2ccc(Br)cc2)C1\", \"reactants\": [\"CC(C)(C)OC(=O)N[C@@H]1CCCN(c2ccc(Br)cc2)C1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)OC(=O)N[C@@H]1CCCN(c2ccc(Br)cc2)C1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"ZMOZNWPWWWKMKG-CYBMUJFWSA-N>>XNOMIDUMMMWUEZ-SNVBAGLBSA-N\", \"model_turns_remaining\": 15, \"product\": \"N[C@@H]1CCCN(c2ccc(Br)cc2)C1\", \"reactants\": [\"CC(C)(C)OC(=O)N[C@@H]1CCCN(c2ccc(Br)cc2)C1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CC(C)(C)OC(=O)N[C@@H]1CCCN(c2ccc(Br)cc2)C1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"CC(C)(C)OC(=O)N[C@@H]1CCCN(c2ccc(Br)cc2)C1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(C)(C)OC(=O)N[C@@H]1CCCN(c2ccc(Br)cc2)C1\", \"reactants\": [\"Brc1ccc(I)cc1\", \"CC(C)(C)OC(=O)N[C@@H]1CCCNC1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"Brc1ccc(I)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)OC(=O)N[C@@H]1CCCNC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"UCCUXODGPMAHRL-UHFFFAOYSA-N.WUOQXNWMYLFAHT-MRVPVSSYSA-N>>ZMOZNWPWWWKMKG-CYBMUJFWSA-N\", \"model_turns_remaining\": 14, \"product\": \"CC(C)(C)OC(=O)N[C@@H]1CCCN(c2ccc(Br)cc2)C1\", \"reactants\": [\"Brc1ccc(I)cc1\", \"CC(C)(C)OC(=O)N[C@@H]1CCCNC1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"Brc1ccc(I)cc1\", \"results\": [{\"inchikey\": \"UCCUXODGPMAHRL-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Brc1ccc(I)cc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CC(C)(C)OC(=O)N[C@@H]1CCCNC1\", \"results\": [{\"inchikey\": \"WUOQXNWMYLFAHT-MRVPVSSYSA-N\", \"similarity\": 1.0, \"smiles\": \"CC(C)(C)OC(=O)N[C@@H]1CCCNC1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"N[C@@H]1CCCN(c2ccc(Br)cc2)C1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)(C)OC(=O)N[C@@H]1CCCN(c2ccc(Br)cc2)C1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)OC(=O)N[C@@H]1CCCN(c2ccc(Br)cc2)C1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"Brc1ccc(I)cc1\": \"precursor\", \"CC(C)(C)OC(=O)N[C@@H]1CCCNC1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"Brc1ccc(I)cc1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"CC(C)(C)OC(=O)N[C@@H]1CCCNC1\", \"in_stock\": true, \"children\": []}]}]}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"N[C@@H]1CCCN(c2ccc(Br)cc2)C1","task_id":"retro_a4754b645d0c71e074a9","tool_calls":6,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_a562ef2a0af59380c64a:reference-expert:a0","kind":"single_route","max_steps":3,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CCOC(=O)c1ccc(NC(=O)OC(C)(C)C)c(N)c1 in at most 3 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCOC(=O)c1ccc(NC(=O)OC(C)(C)C)c(N)c1\", \"reactants\": [\"CCOC(=O)c1ccc(NC(=O)OC(C)(C)C)c([N+](=O)[O-])c1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCOC(=O)c1ccc(NC(=O)OC(C)(C)C)c([N+](=O)[O-])c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"FMDQZDKSQVGLTI-UHFFFAOYSA-N>>IFBQJWYHROHSLG-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"CCOC(=O)c1ccc(NC(=O)OC(C)(C)C)c(N)c1\", \"reactants\": [\"CCOC(=O)c1ccc(NC(=O)OC(C)(C)C)c([N+](=O)[O-])c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CCOC(=O)c1ccc(NC(=O)OC(C)(C)C)c([N+](=O)[O-])c1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"CCOC(=O)c1ccc(NC(=O)OC(C)(C)C)c([N+](=O)[O-])c1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCOC(=O)c1ccc(NC(=O)OC(C)(C)C)c([N+](=O)[O-])c1\", \"reactants\": [\"CC(C)(C)OC(=O)OC(=O)OC(C)(C)C\", \"CCOC(=O)c1ccc(N)c([N+](=O)[O-])c1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)OC(=O)OC(=O)OC(C)(C)C\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"CCOC(=O)c1ccc(N)c([N+](=O)[O-])c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"DYHSDKLCOJIUFX-UHFFFAOYSA-N.HPCYANYWTUCLMH-UHFFFAOYSA-N>>FMDQZDKSQVGLTI-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"CCOC(=O)c1ccc(NC(=O)OC(C)(C)C)c([N+](=O)[O-])c1\", \"reactants\": [\"CC(C)(C)OC(=O)OC(=O)OC(C)(C)C\", \"CCOC(=O)c1ccc(N)c([N+](=O)[O-])c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CC(C)(C)OC(=O)OC(=O)OC(C)(C)C\", \"results\": [{\"inchikey\": \"DYHSDKLCOJIUFX-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CC(C)(C)OC(=O)OC(=O)OC(C)(C)C\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CCOC(=O)c1ccc(N)c([N+](=O)[O-])c1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"CCOC(=O)c1ccc(N)c([N+](=O)[O-])c1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCOC(=O)c1ccc(N)c([N+](=O)[O-])c1\", \"reactants\": [\"CCO\", \"Nc1ccc(C(=O)O)cc1[N+](=O)[O-]\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCO\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"Nc1ccc(C(=O)O)cc1[N+](=O)[O-]\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"LFQSCWFLJHTTHZ-UHFFFAOYSA-N.ZZNAYFWAXZJITH-UHFFFAOYSA-N>>HPCYANYWTUCLMH-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"CCOC(=O)c1ccc(N)c([N+](=O)[O-])c1\", \"reactants\": [\"CCO\", \"Nc1ccc(C(=O)O)cc1[N+](=O)[O-]\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"CCO\", \"results\": [{\"inchikey\": \"LFQSCWFLJHTTHZ-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CCO\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"Nc1ccc(C(=O)O)cc1[N+](=O)[O-]\", \"results\": [{\"inchikey\": \"ZZNAYFWAXZJITH-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Nc1ccc(C(=O)O)cc1[N+](=O)[O-]\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CCOC(=O)c1ccc(NC(=O)OC(C)(C)C)c(N)c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCOC(=O)c1ccc(NC(=O)OC(C)(C)C)c([N+](=O)[O-])c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCOC(=O)c1ccc(NC(=O)OC(C)(C)C)c([N+](=O)[O-])c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)(C)OC(=O)OC(=O)OC(C)(C)C\": \"precursor\", \"CCOC(=O)c1ccc(N)c([N+](=O)[O-])c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)OC(=O)OC(=O)OC(C)(C)C\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"CCOC(=O)c1ccc(N)c([N+](=O)[O-])c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCO\": \"precursor\", \"Nc1ccc(C(=O)O)cc1[N+](=O)[O-]\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCO\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"Nc1ccc(C(=O)O)cc1[N+](=O)[O-]\", \"in_stock\": true, \"children\": []}]}]}]}]}]}]}]}}","name":"emit_routes"},"id":"call_4_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"CCOC(=O)c1ccc(NC(=O)OC(C)(C)C)c(N)c1","task_id":"retro_a562ef2a0af59380c64a","tool_calls":9,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":4}
{"exact_match":true,"id":"retro_a6c923ea1fcf78733073:reference-expert:a0","kind":"single_route","max_steps":3,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target COc1ccc(-c2cccs2)cc1CC(=O)c1ccc(N2CCCC2)cc1 in at most 3 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COc1ccc(-c2cccs2)cc1CC(=O)c1ccc(N2CCCC2)cc1\", \"reactants\": [\"C1CCNC1\", \"COc1ccc(-c2cccs2)cc1CC(=O)c1ccc(F)cc1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"C1CCNC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"COc1ccc(-c2cccs2)cc1CC(=O)c1ccc(F)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"BWRSMVYYPAREPL-UHFFFAOYSA-N.RWRDLPDLKQPQOW-UHFFFAOYSA-N>>FFVCKNRTEVGHKD-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"COc1ccc(-c2cccs2)cc1CC(=O)c1ccc(N2CCCC2)cc1\", \"reactants\": [\"C1CCNC1\", \"COc1ccc(-c2cccs2)cc1CC(=O)c1ccc(F)cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"C1CCNC1\", \"results\": [{\"inchikey\": \"RWRDLPDLKQPQOW-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"C1CCNC1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"COc1ccc(-c2cccs2)cc1CC(=O)c1ccc(F)cc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"COc1ccc(-c2cccs2)cc1CC(=O)c1ccc(F)cc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COc1ccc(-c2cccs2)cc1CC(=O)c1ccc(F)cc1\", \"reactants\": [\"COc1ccc(-c2cccs2)cc1CC(O)c1ccc(F)cc1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"COc1ccc(-c2cccs2)cc1CC(O)c1ccc(F)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_complete\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"MHTKQEKVTKAYTD-UHFFFAOYSA-N>>BWRSMVYYPAREPL-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"COc1ccc(-c2cccs2)cc1CC(=O)c1ccc(F)cc1\", \"reactants\": [\"COc1ccc(-c2cccs2)cc1CC(O)c1ccc(F)cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"COc1ccc(-c2cccs2)cc1CC(O)c1ccc(F)cc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"COc1ccc(-c2cccs2)cc1CC(O)c1ccc(F)cc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COc1ccc(-c2cccs2)cc1CC(O)c1ccc(F)cc1\", \"reactants\": [\"COc1ccc(-c2cccs2)cc1CC=O\", \"Fc1cc[c]([Mg][Br])cc1\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"COc1ccc(-c2cccs2)cc1CC=O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"Fc1cc[c]([Mg][Br])cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"QYBFFRXNNFXREA-UHFFFAOYSA-M.ZHLNRPWHETUSHM-UHFFFAOYSA-N>>MHTKQEKVTKAYTD-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"COc1ccc(-c2cccs2)cc1CC(O)c1ccc(F)cc1\", \"reactants\": [\"COc1ccc(-c2cccs2)cc1CC=O\", \"Fc1cc[c]([Mg][Br])cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"COc1ccc(-c2cccs2)cc1CC=O\", \"results\": [{\"inchikey\": \"ZHLNRPWHETUSHM-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"COc1ccc(-c2cccs2)cc1CC=O\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"Fc1cc[c]([Mg][Br])cc1\", \"results\": [{\"inchikey\": \"QYBFFRXNNFXREA-UHFFFAOYSA-M\", \"similarity\": 1.0, \"smiles\": \"Fc1cc[c]([Mg][Br])cc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"COc1ccc(-c2cccs2)cc1CC(=O)c1ccc(N2CCCC2)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"C1CCNC1\": \"precursor\", \"COc1ccc(-c2cccs2)cc1CC(=O)c1ccc(F)cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"C1CCNC1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"COc1ccc(-c2cccs2)cc1CC(=O)c1ccc(F)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COc1ccc(-c2cccs2)cc1CC(O)c1ccc(F)cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COc1ccc(-c2cccs2)cc1CC(O)c1ccc(F)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COc1ccc(-c2cccs2)cc1CC=O\": \"precursor\", \"Fc1cc[c]([Mg][Br])cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COc1ccc(-c2cccs2)cc1CC=O\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"Fc1cc[c]([Mg][Br])cc1\", \"in_stock\": true, \"children\": []}]}]}]}]}]}]}]}}","name":"emit_routes"},"id":"call_4_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"COc1ccc(-c2cccs2)cc1CC(=O)c1ccc(N2CCCC2)cc1","task_id":"retro_a6c923ea1fcf78733073","tool_calls":9,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":4}
{"exact_match":true,"id":"retro_a7b8c024cc8703b237a8:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target C#CCCCCCC12OCC(C(C)(C)C)(CO1)CO2 in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"C#CCCCCCC12OCC(C(C)(C)C)(CO1)CO2\", \"reactants\": [\"C#CCCCCCC(=O)O\", \"CC(C)(C)C1(CO)COC1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"C#CCCCCCC(=O)O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)C1(CO)COC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"AMONDPRIVREWOC-UHFFFAOYSA-N.WJBHDZBQZOMDFF-UHFFFAOYSA-N>>JFDKXAYFEOLEBV-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"C#CCCCCCC12OCC(C(C)(C)C)(CO1)CO2\", \"reactants\": [\"C#CCCCCCC(=O)O\", \"CC(C)(C)C1(CO)COC1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"C#CCCCCCC(=O)O\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CC(C)(C)C1(CO)COC1\", \"results\": [{\"inchikey\": \"AMONDPRIVREWOC-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CC(C)(C)C1(CO)COC1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"C#CCCCCCC(=O)O was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"C#CCCCCCC(=O)O\", \"reactants\": [\"C#CCCCCC(C(=O)O)C(=O)O\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"C#CCCCCC(C(=O)O)C(=O)O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"MBIWPCBZQHRBIE-UHFFFAOYSA-N>>WJBHDZBQZOMDFF-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"C#CCCCCCC(=O)O\", \"reactants\": [\"C#CCCCCC(C(=O)O)C(=O)O\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"C#CCCCCC(C(=O)O)C(=O)O\", \"results\": [{\"inchikey\": \"MBIWPCBZQHRBIE-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"C#CCCCCC(C(=O)O)C(=O)O\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"C#CCCCCCC12OCC(C(C)(C)C)(CO1)CO2\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"C#CCCCCCC(=O)O\": \"precursor\", \"CC(C)(C)C1(CO)COC1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"C#CCCCCCC(=O)O\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"C#CCCCCC(C(=O)O)C(=O)O\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"C#CCCCCC(C(=O)O)C(=O)O\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"CC(C)(C)C1(CO)COC1\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"C#CCCCCCC12OCC(C(C)(C)C)(CO1)CO2","task_id":"retro_a7b8c024cc8703b237a8","tool_calls":6,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_a92a7df935424dc9b299:reference-expert:a0","kind":"single_route","max_steps":3,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target Cc1cccc(C#Cc2nc(C)n(-c3ccn(C)c(=O)c3)c2C)c1 in at most 3 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Cc1cccc(C#Cc2nc(C)n(-c3ccn(C)c(=O)c3)c2C)c1\", \"reactants\": [\"CI\", \"Cc1cccc(C#Cc2nc(C)n(-c3cc[nH]c(=O)c3)c2C)c1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CI\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"Cc1cccc(C#Cc2nc(C)n(-c3cc[nH]c(=O)c3)c2C)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"DBGHTLCTEAZBTG-UHFFFAOYSA-N.INQOMBQAUSQDDS-UHFFFAOYSA-N>>CCTRVXCLHDJPNO-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"Cc1cccc(C#Cc2nc(C)n(-c3ccn(C)c(=O)c3)c2C)c1\", \"reactants\": [\"CI\", \"Cc1cccc(C#Cc2nc(C)n(-c3cc[nH]c(=O)c3)c2C)c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CI\", \"results\": [{\"inchikey\": \"INQOMBQAUSQDDS-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CI\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"Cc1cccc(C#Cc2nc(C)n(-c3cc[nH]c(=O)c3)c2C)c1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"Cc1cccc(C#Cc2nc(C)n(-c3cc[nH]c(=O)c3)c2C)c1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Cc1cccc(C#Cc2nc(C)n(-c3cc[nH]c(=O)c3)c2C)c1\", \"reactants\": [\"C#Cc1cccc(C)c1\", \"Cc1nc(I)c(C)n1-c1cc[nH]c(=O)c1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"C#Cc1cccc(C)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"Cc1nc(I)c(C)n1-c1cc[nH]c(=O)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"CXDVWFCIKMCEJZ-UHFFFAOYSA-N.RENYIDZOAFFNHC-UHFFFAOYSA-N>>DBGHTLCTEAZBTG-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"Cc1cccc(C#Cc2nc(C)n(-c3cc[nH]c(=O)c3)c2C)c1\", \"reactants\": [\"C#Cc1cccc(C)c1\", \"Cc1nc(I)c(C)n1-c1cc[nH]c(=O)c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"C#Cc1cccc(C)c1\", \"results\": [{\"inchikey\": \"RENYIDZOAFFNHC-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"C#Cc1cccc(C)c1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"Cc1nc(I)c(C)n1-c1cc[nH]c(=O)c1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Cc1nc(I)c(C)n1-c1cc[nH]c(=O)c1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Cc1nc(I)c(C)n1-c1cc[nH]c(=O)c1\", \"reactants\": [\"Cc1nc(I)c(C)n1-c1ccnc(Cl)c1\", \"O\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"Cc1nc(I)c(C)n1-c1ccnc(Cl)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"CGVKIWALSUXLMD-UHFFFAOYSA-N.XLYOFNOQVPJJNP-UHFFFAOYSA-N>>CXDVWFCIKMCEJZ-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"Cc1nc(I)c(C)n1-c1cc[nH]c(=O)c1\", \"reactants\": [\"Cc1nc(I)c(C)n1-c1ccnc(Cl)c1\", \"O\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"Cc1nc(I)c(C)n1-c1ccnc(Cl)c1\", \"results\": [{\"inchikey\": \"CGVKIWALSUXLMD-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Cc1nc(I)c(C)n1-c1ccnc(Cl)c1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"O\", \"results\": [{\"inchikey\": \"XLYOFNOQVPJJNP-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"Cc1cccc(C#Cc2nc(C)n(-c3ccn(C)c(=O)c3)c2C)c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CI\": \"precursor\", \"Cc1cccc(C#Cc2nc(C)n(-c3cc[nH]c(=O)c3)c2C)c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CI\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"Cc1cccc(C#Cc2nc(C)n(-c3cc[nH]c(=O)c3)c2C)c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"C#Cc1cccc(C)c1\": \"precursor\", \"Cc1nc(I)c(C)n1-c1cc[nH]c(=O)c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"C#Cc1cccc(C)c1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"Cc1nc(I)c(C)n1-c1cc[nH]c(=O)c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"Cc1nc(I)c(C)n1-c1ccnc(Cl)c1\": \"precursor\", \"O\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"Cc1nc(I)c(C)n1-c1ccnc(Cl)c1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O\", \"in_stock\": true, \"children\": []}]}]}]}]}]}]}]}}","name":"emit_routes"},"id":"call_4_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"Cc1cccc(C#Cc2nc(C)n(-c3ccn(C)c(=O)c3)c2C)c1","task_id":"retro_a92a7df935424dc9b299","tool_calls":10,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":4}
{"exact_match":true,"id":"retro_a9754e7a364cfb0b0b1a:reference-expert:a0","kind":"single_route","max_steps":3,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target C=Cc1cc(C(N)=O)nc(-c2ccc(Oc3ccc(C#N)c(C(F)(F)F)c3)cc2)n1 in at most 3 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"C=Cc1cc(C(N)=O)nc(-c2ccc(Oc3ccc(C#N)c(C(F)(F)F)c3)cc2)n1\", \"reactants\": [\"C=Cc1cc(C(=O)OC)nc(-c2ccc(Oc3ccc(C#N)c(C(F)(F)F)c3)cc2)n1\", \"N\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"C=Cc1cc(C(=O)OC)nc(-c2ccc(Oc3ccc(C#N)c(C(F)(F)F)c3)cc2)n1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"N\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"LYLUVNCMEABZLX-UHFFFAOYSA-N.QGZKDVFQNNGYKY-UHFFFAOYSA-N>>VCHYRQAPMNJDRI-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"C=Cc1cc(C(N)=O)nc(-c2ccc(Oc3ccc(C#N)c(C(F)(F)F)c3)cc2)n1\", \"reactants\": [\"C=Cc1cc(C(=O)OC)nc(-c2ccc(Oc3ccc(C#N)c(C(F)(F)F)c3)cc2)n1\", \"N\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"C=Cc1cc(C(=O)OC)nc(-c2ccc(Oc3ccc(C#N)c(C(F)(F)F)c3)cc2)n1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"N\", \"results\": [{\"inchikey\": \"QGZKDVFQNNGYKY-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"N\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"C=Cc1cc(C(=O)OC)nc(-c2ccc(Oc3ccc(C#N)c(C(F)(F)F)c3)cc2)n1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"C=Cc1cc(C(=O)OC)nc(-c2ccc(Oc3ccc(C#N)c(C(F)(F)F)c3)cc2)n1\", \"reactants\": [\"C=Cc1cc(C(=O)O)nc(-c2ccc(Oc3ccc(C#N)c(C(F)(F)F)c3)cc2)n1\", \"CI\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"C=Cc1cc(C(=O)O)nc(-c2ccc(Oc3ccc(C#N)c(C(F)(F)F)c3)cc2)n1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"CI\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"INQOMBQAUSQDDS-UHFFFAOYSA-N.YFQZRNNWLNQHKM-UHFFFAOYSA-N>>LYLUVNCMEABZLX-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"C=Cc1cc(C(=O)OC)nc(-c2ccc(Oc3ccc(C#N)c(C(F)(F)F)c3)cc2)n1\", \"reactants\": [\"C=Cc1cc(C(=O)O)nc(-c2ccc(Oc3ccc(C#N)c(C(F)(F)F)c3)cc2)n1\", \"CI\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"C=Cc1cc(C(=O)O)nc(-c2ccc(Oc3ccc(C#N)c(C(F)(F)F)c3)cc2)n1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CI\", \"results\": [{\"inchikey\": \"INQOMBQAUSQDDS-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CI\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"C=Cc1cc(C(=O)O)nc(-c2ccc(Oc3ccc(C#N)c(C(F)(F)F)c3)cc2)n1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"C=Cc1cc(C(=O)O)nc(-c2ccc(Oc3ccc(C#N)c(C(F)(F)F)c3)cc2)n1\", \"reactants\": [\"C=Cc1cc(C(=O)O)nc(Cl)n1\", \"CC1(C)OB(c2ccc(Oc3ccc(C#N)c(C(F)(F)F)c3)cc2)OC1(C)C\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"C=Cc1cc(C(=O)O)nc(Cl)n1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"CC1(C)OB(c2ccc(Oc3ccc(C#N)c(C(F)(F)F)c3)cc2)OC1(C)C\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"LPVWDKKMHFYREI-UHFFFAOYSA-N.WTPHSZPJERUHEK-UHFFFAOYSA-N>>YFQZRNNWLNQHKM-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"C=Cc1cc(C(=O)O)nc(-c2ccc(Oc3ccc(C#N)c(C(F)(F)F)c3)cc2)n1\", \"reactants\": [\"C=Cc1cc(C(=O)O)nc(Cl)n1\", \"CC1(C)OB(c2ccc(Oc3ccc(C#N)c(C(F)(F)F)c3)cc2)OC1(C)C\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"C=Cc1cc(C(=O)O)nc(Cl)n1\", \"results\": [{\"inchikey\": \"WTPHSZPJERUHEK-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"C=Cc1cc(C(=O)O)nc(Cl)n1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"CC1(C)OB(c2ccc(Oc3ccc(C#N)c(C(F)(F)F)c3)cc2)OC1(C)C\", \"results\": [{\"inchikey\": \"LPVWDKKMHFYREI-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CC1(C)OB(c2ccc(Oc3ccc(C#N)c(C(F)(F)F)c3)cc2)OC1(C)C\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"C=Cc1cc(C(N)=O)nc(-c2ccc(Oc3ccc(C#N)c(C(F)(F)F)c3)cc2)n1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"C=Cc1cc(C(=O)OC)nc(-c2ccc(Oc3ccc(C#N)c(C(F)(F)F)c3)cc2)n1\": \"precursor\", \"N\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"C=Cc1cc(C(=O)OC)nc(-c2ccc(Oc3ccc(C#N)c(C(F)(F)F)c3)cc2)n1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"C=Cc1cc(C(=O)O)nc(-c2ccc(Oc3ccc(C#N)c(C(F)(F)F)c3)cc2)n1\": \"precursor\", \"CI\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"C=Cc1cc(C(=O)O)nc(-c2ccc(Oc3ccc(C#N)c(C(F)(F)F)c3)cc2)n1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"C=Cc1cc(C(=O)O)nc(Cl)n1\": \"precursor\", \"CC1(C)OB(c2ccc(Oc3ccc(C#N)c(C(F)(F)F)c3)cc2)OC1(C)C\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"C=Cc1cc(C(=O)O)nc(Cl)n1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"CC1(C)OB(c2ccc(Oc3ccc(C#N)c(C(F)(F)F)c3)cc2)OC1(C)C\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"CI\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"N\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_4_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"C=Cc1cc(C(N)=O)nc(-c2ccc(Oc3ccc(C#N)c(C(F)(F)F)c3)cc2)n1","task_id":"retro_a9754e7a364cfb0b0b1a","tool_calls":10,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":4}
{"exact_match":false,"id":"retro_abef76d664bed5e69244:reference-expert:a0","kind":"single_route","max_steps":3,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CCCCCCOc1cccc(F)c1F in at most 3 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCCCCCOc1cccc(F)c1F\", \"reactants\": [\"CCCCCCBr\", \"Oc1cccc(F)c1F\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCCCCCBr\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"Oc1cccc(F)c1F\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"MNDIARAMWBIKFW-UHFFFAOYSA-N.RPEPGIOVXBBUMJ-UHFFFAOYSA-N>>BJYUARIRPJREFZ-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"CCCCCCOc1cccc(F)c1F\", \"reactants\": [\"CCCCCCBr\", \"Oc1cccc(F)c1F\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CCCCCCBr\", \"results\": [{\"inchikey\": \"MNDIARAMWBIKFW-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CCCCCCBr\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"Oc1cccc(F)c1F\", \"results\": [{\"inchikey\": \"RPEPGIOVXBBUMJ-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Oc1cccc(F)c1F\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CCCCCCOc1cccc(F)c1F\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCCCCCBr\": \"precursor\", \"Oc1cccc(F)c1F\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCCCCCBr\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"Oc1cccc(F)c1F\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_2_0","type":"function"}]}],"provider":"reference","reward":0.833333,"source":"reference-expert","target_smiles":"CCCCCCOc1cccc(F)c1F","task_id":"retro_abef76d664bed5e69244","tool_calls":4,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":2}
{"exact_match":true,"id":"retro_adf2d49a069855db711b:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target Cc1n[nH]c2ccc([N+](=O)[O-])cc12 in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Cc1n[nH]c2ccc([N+](=O)[O-])cc12\", \"reactants\": [\"CC(=O)c1cc([N+](=O)[O-])ccc1O\", \"NN\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(=O)c1cc([N+](=O)[O-])ccc1O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"NN\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"LNCBPUWMGYOISS-UHFFFAOYSA-N.OAKJQQAXSVQMHS-UHFFFAOYSA-N>>ZGDNJFXKELMVLS-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"Cc1n[nH]c2ccc([N+](=O)[O-])cc12\", \"reactants\": [\"CC(=O)c1cc([N+](=O)[O-])ccc1O\", \"NN\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CC(=O)c1cc([N+](=O)[O-])ccc1O\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"NN\", \"results\": [{\"inchikey\": \"OAKJQQAXSVQMHS-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"NN\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"CC(=O)c1cc([N+](=O)[O-])ccc1O was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(=O)c1cc([N+](=O)[O-])ccc1O\", \"reactants\": [\"CC(=O)Cl\", \"O=[N+]([O-])c1ccc(O)cc1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(=O)Cl\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=[N+]([O-])c1ccc(O)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"BTJIUGUIPKRLHP-UHFFFAOYSA-N.WETWJCDKMRHUPV-UHFFFAOYSA-N>>LNCBPUWMGYOISS-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"CC(=O)c1cc([N+](=O)[O-])ccc1O\", \"reactants\": [\"CC(=O)Cl\", \"O=[N+]([O-])c1ccc(O)cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CC(=O)Cl\", \"results\": [{\"inchikey\": \"WETWJCDKMRHUPV-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CC(=O)Cl\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"O=[N+]([O-])c1ccc(O)cc1\", \"results\": [{\"inchikey\": \"BTJIUGUIPKRLHP-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=[N+]([O-])c1ccc(O)cc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"Cc1n[nH]c2ccc([N+](=O)[O-])cc12\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(=O)c1cc([N+](=O)[O-])ccc1O\": \"precursor\", \"NN\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(=O)c1cc([N+](=O)[O-])ccc1O\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(=O)Cl\": \"precursor\", \"O=[N+]([O-])c1ccc(O)cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(=O)Cl\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=[N+]([O-])c1ccc(O)cc1\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"NN\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"Cc1n[nH]c2ccc([N+](=O)[O-])cc12","task_id":"retro_adf2d49a069855db711b","tool_calls":7,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_ae63c46333a4c5fbf314:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CC(C)(C)c1cc([N+](=O)[O-])cc(C=O)c1O in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(C)(C)c1cc([N+](=O)[O-])cc(C=O)c1O\", \"reactants\": [\"CC(C)(C)c1cccc(C=O)c1O\", \"O=[N+]([O-])O\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)c1cccc(C=O)c1O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=[N+]([O-])O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"GRYLNZFGIOXLOG-UHFFFAOYSA-N.ROILLNJICXGZQQ-UHFFFAOYSA-N>>OLYRNMCCQKIUMA-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"CC(C)(C)c1cc([N+](=O)[O-])cc(C=O)c1O\", \"reactants\": [\"CC(C)(C)c1cccc(C=O)c1O\", \"O=[N+]([O-])O\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CC(C)(C)c1cccc(C=O)c1O\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"O=[N+]([O-])O\", \"results\": [{\"inchikey\": \"GRYLNZFGIOXLOG-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=[N+]([O-])O\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"CC(C)(C)c1cccc(C=O)c1O was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(C)(C)c1cccc(C=O)c1O\", \"reactants\": [\"C=O\", \"CC(C)(C)c1ccccc1O\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"C=O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)c1ccccc1O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_complete\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"WJQOZHYUIDYNHM-UHFFFAOYSA-N.WSFSSNUMVMOOMR-UHFFFAOYSA-N>>ROILLNJICXGZQQ-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"CC(C)(C)c1cccc(C=O)c1O\", \"reactants\": [\"C=O\", \"CC(C)(C)c1ccccc1O\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"C=O\", \"results\": [{\"inchikey\": \"WSFSSNUMVMOOMR-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"C=O\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CC(C)(C)c1ccccc1O\", \"results\": [{\"inchikey\": \"WJQOZHYUIDYNHM-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CC(C)(C)c1ccccc1O\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)c1cc([N+](=O)[O-])cc(C=O)c1O\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)(C)c1cccc(C=O)c1O\": \"precursor\", \"O=[N+]([O-])O\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)c1cccc(C=O)c1O\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"C=O\": \"precursor\", \"CC(C)(C)c1ccccc1O\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"C=O\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"CC(C)(C)c1ccccc1O\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"O=[N+]([O-])O\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"CC(C)(C)c1cc([N+](=O)[O-])cc(C=O)c1O","task_id":"retro_ae63c46333a4c5fbf314","tool_calls":7,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_b0cb9e139fc41dd768c5:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CCCCOc1cc(F)c(C(=O)OC(C)(C)C)cc1C1CC1 in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCCCOc1cc(F)c(C(=O)OC(C)(C)C)cc1C1CC1\", \"reactants\": [\"CCCCOc1cc(F)c(C(=O)OC(C)(C)C)cc1Cl\", \"OB(O)C1CC1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCCCOc1cc(F)c(C(=O)OC(C)(C)C)cc1Cl\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"OB(O)C1CC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"DJDASZNKYLAKMP-UHFFFAOYSA-N.WLVKDFJTYKELLQ-UHFFFAOYSA-N>>KGNPYGDDCJOZDP-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"CCCCOc1cc(F)c(C(=O)OC(C)(C)C)cc1C1CC1\", \"reactants\": [\"CCCCOc1cc(F)c(C(=O)OC(C)(C)C)cc1Cl\", \"OB(O)C1CC1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CCCCOc1cc(F)c(C(=O)OC(C)(C)C)cc1Cl\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"OB(O)C1CC1\", \"results\": [{\"inchikey\": \"WLVKDFJTYKELLQ-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"OB(O)C1CC1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"CCCCOc1cc(F)c(C(=O)OC(C)(C)C)cc1Cl was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCCCOc1cc(F)c(C(=O)OC(C)(C)C)cc1Cl\", \"reactants\": [\"CC(C)(C)OC(=O)c1cc(Cl)c(F)cc1F\", \"CCCCO\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)OC(=O)c1cc(Cl)c(F)cc1F\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"CCCCO\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"JXZKTDJNUFYICB-UHFFFAOYSA-N.LRHPLDYGYMQRHN-UHFFFAOYSA-N>>DJDASZNKYLAKMP-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"CCCCOc1cc(F)c(C(=O)OC(C)(C)C)cc1Cl\", \"reactants\": [\"CC(C)(C)OC(=O)c1cc(Cl)c(F)cc1F\", \"CCCCO\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CC(C)(C)OC(=O)c1cc(Cl)c(F)cc1F\", \"results\": [{\"inchikey\": \"JXZKTDJNUFYICB-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CC(C)(C)OC(=O)c1cc(Cl)c(F)cc1F\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CCCCO\", \"results\": [{\"inchikey\": \"LRHPLDYGYMQRHN-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CCCCO\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CCCCOc1cc(F)c(C(=O)OC(C)(C)C)cc1C1CC1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCCCOc1cc(F)c(C(=O)OC(C)(C)C)cc1Cl\": \"precursor\", \"OB(O)C1CC1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCCCOc1cc(F)c(C(=O)OC(C)(C)C)cc1Cl\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)(C)OC(=O)c1cc(Cl)c(F)cc1F\": \"precursor\", \"CCCCO\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)OC(=O)c1cc(Cl)c(F)cc1F\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"CCCCO\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"OB(O)C1CC1\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"CCCCOc1cc(F)c(C(=O)OC(C)(C)C)cc1C1CC1","task_id":"retro_b0cb9e139fc41dd768c5","tool_calls":7,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_b2d06d489428a035590a:reference-expert:a0","kind":"single_route","max_steps":3,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CC(C)NC(=O)OC1CC2CC(N(CC(=O)N3CCCC3C#N)C(=O)OC(C)(C)C)CC2C1 in at most 3 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(C)NC(=O)OC1CC2CC(N(CC(=O)N3CCCC3C#N)C(=O)OC(C)(C)C)CC2C1\", \"reactants\": [\"CC(C)(C)OC(=O)OC(=O)OC(C)(C)C\", \"CC(C)NC(=O)OC1CC2CC(NCC(=O)N3CCCC3C#N)CC2C1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)OC(=O)OC(=O)OC(C)(C)C\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)NC(=O)OC1CC2CC(NCC(=O)N3CCCC3C#N)CC2C1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"DNBGBKMHUQBCON-UHFFFAOYSA-N.DYHSDKLCOJIUFX-UHFFFAOYSA-N>>XBMKTRKXONJOAJ-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"CC(C)NC(=O)OC1CC2CC(N(CC(=O)N3CCCC3C#N)C(=O)OC(C)(C)C)CC2C1\", \"reactants\": [\"CC(C)(C)OC(=O)OC(=O)OC(C)(C)C\", \"CC(C)NC(=O)OC1CC2CC(NCC(=O)N3CCCC3C#N)CC2C1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CC(C)(C)OC(=O)OC(=O)OC(C)(C)C\", \"results\": [{\"inchikey\": \"DYHSDKLCOJIUFX-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CC(C)(C)OC(=O)OC(=O)OC(C)(C)C\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CC(C)NC(=O)OC1CC2CC(NCC(=O)N3CCCC3C#N)CC2C1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"CC(C)NC(=O)OC1CC2CC(NCC(=O)N3CCCC3C#N)CC2C1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(C)NC(=O)OC1CC2CC(NCC(=O)N3CCCC3C#N)CC2C1\", \"reactants\": [\"CC(C)(C)OC(=O)NCC(=O)N1CCCC1C#N\", \"CC(C)NC(=O)OC1CC2CC(=O)CC2C1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)OC(=O)NCC(=O)N1CCCC1C#N\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)NC(=O)OC1CC2CC(=O)CC2C1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"QKUFMUWYDWTTTJ-UHFFFAOYSA-N.SWUOIQQDTSKPJT-UHFFFAOYSA-N>>DNBGBKMHUQBCON-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"CC(C)NC(=O)OC1CC2CC(NCC(=O)N3CCCC3C#N)CC2C1\", \"reactants\": [\"CC(C)(C)OC(=O)NCC(=O)N1CCCC1C#N\", \"CC(C)NC(=O)OC1CC2CC(=O)CC2C1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CC(C)(C)OC(=O)NCC(=O)N1CCCC1C#N\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CC(C)NC(=O)OC1CC2CC(=O)CC2C1\", \"results\": [{\"inchikey\": \"QKUFMUWYDWTTTJ-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CC(C)NC(=O)OC1CC2CC(=O)CC2C1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"CC(C)(C)OC(=O)NCC(=O)N1CCCC1C#N was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(C)(C)OC(=O)NCC(=O)N1CCCC1C#N\", \"reactants\": [\"CC(C)(C)OC(=O)NCC(=O)N1CCCC1C(N)=O\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)OC(=O)NCC(=O)N1CCCC1C(N)=O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"QTNNCICZGXJIAJ-UHFFFAOYSA-N>>SWUOIQQDTSKPJT-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"CC(C)(C)OC(=O)NCC(=O)N1CCCC1C#N\", \"reactants\": [\"CC(C)(C)OC(=O)NCC(=O)N1CCCC1C(N)=O\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"CC(C)(C)OC(=O)NCC(=O)N1CCCC1C(N)=O\", \"results\": [{\"inchikey\": \"QTNNCICZGXJIAJ-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CC(C)(C)OC(=O)NCC(=O)N1CCCC1C(N)=O\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CC(C)NC(=O)OC1CC2CC(N(CC(=O)N3CCCC3C#N)C(=O)OC(C)(C)C)CC2C1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)(C)OC(=O)OC(=O)OC(C)(C)C\": \"precursor\", \"CC(C)NC(=O)OC1CC2CC(NCC(=O)N3CCCC3C#N)CC2C1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)OC(=O)OC(=O)OC(C)(C)C\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"CC(C)NC(=O)OC1CC2CC(NCC(=O)N3CCCC3C#N)CC2C1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)(C)OC(=O)NCC(=O)N1CCCC1C#N\": \"precursor\", \"CC(C)NC(=O)OC1CC2CC(=O)CC2C1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)OC(=O)NCC(=O)N1CCCC1C#N\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)(C)OC(=O)NCC(=O)N1CCCC1C(N)=O\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)OC(=O)NCC(=O)N1CCCC1C(N)=O\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"CC(C)NC(=O)OC1CC2CC(=O)CC2C1\", \"in_stock\": true, \"children\": []}]}]}]}]}]}}","name":"emit_routes"},"id":"call_4_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"CC(C)NC(=O)OC1CC2CC(N(CC(=O)N3CCCC3C#N)C(=O)OC(C)(C)C)CC2C1","task_id":"retro_b2d06d489428a035590a","tool_calls":9,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":4}
{"exact_match":true,"id":"retro_b58a5ac8a20bf89f5f03:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CS(=O)(=O)Nc1ccc2c(c1)S(=O)(=O)N=C(C1=C(O)[C@@H]3[C@H]4CC[C@H](C4)[C@@H]3N(Cc3ccc(F)c(Cl)c3)C1=O)N2 in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CS(=O)(=O)Nc1ccc2c(c1)S(=O)(=O)N=C(C1=C(O)[C@@H]3[C@H]4CC[C@H](C4)[C@@H]3N(Cc3ccc(F)c(Cl)c3)C1=O)N2\", \"reactants\": [\"CCOC(=O)[C@@H]1[C@H]2CC[C@H](C2)[C@@H]1NCc1ccc(F)c(Cl)c1\", \"CS(=O)(=O)Nc1ccc2c(c1)S(=O)(=O)N=C(CC(=O)O)N2\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCOC(=O)[C@@H]1[C@H]2CC[C@H](C2)[C@@H]1NCc1ccc(F)c(Cl)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"CS(=O)(=O)Nc1ccc2c(c1)S(=O)(=O)N=C(CC(=O)O)N2\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"HNUUGLOJRDORBD-OJDYBEQGSA-N.ZCDWNPVNFYEBDG-UHFFFAOYSA-N>>KPAPCAYPFRBKLZ-VQXITPLLSA-N\", \"model_turns_remaining\": 15, \"product\": \"CS(=O)(=O)Nc1ccc2c(c1)S(=O)(=O)N=C(C1=C(O)[C@@H]3[C@H]4CC[C@H](C4)[C@@H]3N(Cc3ccc(F)c(Cl)c3)C1=O)N2\", \"reactants\": [\"CCOC(=O)[C@@H]1[C@H]2CC[C@H](C2)[C@@H]1NCc1ccc(F)c(Cl)c1\", \"CS(=O)(=O)Nc1ccc2c(c1)S(=O)(=O)N=C(CC(=O)O)N2\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CCOC(=O)[C@@H]1[C@H]2CC[C@H](C2)[C@@H]1NCc1ccc(F)c(Cl)c1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CS(=O)(=O)Nc1ccc2c(c1)S(=O)(=O)N=C(CC(=O)O)N2\", \"results\": [{\"inchikey\": \"ZCDWNPVNFYEBDG-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CS(=O)(=O)Nc1ccc2c(c1)S(=O)(=O)N=C(CC(=O)O)N2\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"CCOC(=O)[C@@H]1[C@H]2CC[C@H](C2)[C@@H]1NCc1ccc(F)c(Cl)c1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCOC(=O)[C@@H]1[C@H]2CC[C@H](C2)[C@@H]1NCc1ccc(F)c(Cl)c1\", \"reactants\": [\"CCOC(=O)[C@@H]1[C@H]2CC[C@H](C2)[C@@H]1N\", \"O=Cc1ccc(F)c(Cl)c1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCOC(=O)[C@@H]1[C@H]2CC[C@H](C2)[C@@H]1N\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=Cc1ccc(F)c(Cl)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"GVORVQPNNSASDM-UHFFFAOYSA-N.UIFFSCXLBNDAFP-KDXUFGMBSA-N>>HNUUGLOJRDORBD-OJDYBEQGSA-N\", \"model_turns_remaining\": 14, \"product\": \"CCOC(=O)[C@@H]1[C@H]2CC[C@H](C2)[C@@H]1NCc1ccc(F)c(Cl)c1\", \"reactants\": [\"CCOC(=O)[C@@H]1[C@H]2CC[C@H](C2)[C@@H]1N\", \"O=Cc1ccc(F)c(Cl)c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CCOC(=O)[C@@H]1[C@H]2CC[C@H](C2)[C@@H]1N\", \"results\": [{\"inchikey\": \"UIFFSCXLBNDAFP-KDXUFGMBSA-N\", \"similarity\": 1.0, \"smiles\": \"CCOC(=O)[C@@H]1[C@H]2CC[C@H](C2)[C@@H]1N\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"O=Cc1ccc(F)c(Cl)c1\", \"results\": [{\"inchikey\": \"GVORVQPNNSASDM-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=Cc1ccc(F)c(Cl)c1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CS(=O)(=O)Nc1ccc2c(c1)S(=O)(=O)N=C(C1=C(O)[C@@H]3[C@H]4CC[C@H](C4)[C@@H]3N(Cc3ccc(F)c(Cl)c3)C1=O)N2\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCOC(=O)[C@@H]1[C@H]2CC[C@H](C2)[C@@H]1NCc1ccc(F)c(Cl)c1\": \"precursor\", \"CS(=O)(=O)Nc1ccc2c(c1)S(=O)(=O)N=C(CC(=O)O)N2\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCOC(=O)[C@@H]1[C@H]2CC[C@H](C2)[C@@H]1NCc1ccc(F)c(Cl)c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCOC(=O)[C@@H]1[C@H]2CC[C@H](C2)[C@@H]1N\": \"precursor\", \"O=Cc1ccc(F)c(Cl)c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCOC(=O)[C@@H]1[C@H]2CC[C@H](C2)[C@@H]1N\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=Cc1ccc(F)c(Cl)c1\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"CS(=O)(=O)Nc1ccc2c(c1)S(=O)(=O)N=C(CC(=O)O)N2\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"CS(=O)(=O)Nc1ccc2c(c1)S(=O)(=O)N=C(C1=C(O)[C@@H]3[C@H]4CC[C@H](C4)[C@@H]3N(Cc3ccc(F)c(Cl)c3)C1=O)N2","task_id":"retro_b58a5ac8a20bf89f5f03","tool_calls":7,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_b6e29b4e05090ef5cc30:reference-expert:a0","kind":"single_route","max_steps":4,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target COCn1cc(Br)sc1=Nc1cccc(CN2CCN(C(=O)c3ccccc3)CC2)n1 in at most 4 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COCn1cc(Br)sc1=Nc1cccc(CN2CCN(C(=O)c3ccccc3)CC2)n1\", \"reactants\": [\"COCn1cc(Br)sc1=Nc1cccc(CN2CCNCC2)n1\", \"O=C(Cl)c1ccccc1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"COCn1cc(Br)sc1=Nc1cccc(CN2CCNCC2)n1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=C(Cl)c1ccccc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"CPVAQFYRWBJTJR-UHFFFAOYSA-N.PASDCCFISLVPSO-UHFFFAOYSA-N>>DDXBDCXUVYIQLI-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"COCn1cc(Br)sc1=Nc1cccc(CN2CCN(C(=O)c3ccccc3)CC2)n1\", \"reactants\": [\"COCn1cc(Br)sc1=Nc1cccc(CN2CCNCC2)n1\", \"O=C(Cl)c1ccccc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"COCn1cc(Br)sc1=Nc1cccc(CN2CCNCC2)n1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"O=C(Cl)c1ccccc1\", \"results\": [{\"inchikey\": \"PASDCCFISLVPSO-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=C(Cl)c1ccccc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"COCn1cc(Br)sc1=Nc1cccc(CN2CCNCC2)n1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COCn1cc(Br)sc1=Nc1cccc(CN2CCNCC2)n1\", \"reactants\": [\"C1CNCCN1\", \"COCn1cc(Br)sc1=Nc1cccc(CO)n1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"C1CNCCN1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"COCn1cc(Br)sc1=Nc1cccc(CO)n1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"GLUUGHFHXGJENI-UHFFFAOYSA-N.RFWPWLDEXOTNHE-UHFFFAOYSA-N>>CPVAQFYRWBJTJR-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"COCn1cc(Br)sc1=Nc1cccc(CN2CCNCC2)n1\", \"reactants\": [\"C1CNCCN1\", \"COCn1cc(Br)sc1=Nc1cccc(CO)n1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"C1CNCCN1\", \"results\": [{\"inchikey\": \"GLUUGHFHXGJENI-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"C1CNCCN1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"COCn1cc(Br)sc1=Nc1cccc(CO)n1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"COCn1cc(Br)sc1=Nc1cccc(CO)n1 was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COCn1cc(Br)sc1=Nc1cccc(CO)n1\", \"reactants\": [\"COCn1cc(Br)sc1=Nc1cccc(C(=O)OC)n1\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"COCn1cc(Br)sc1=Nc1cccc(C(=O)OC)n1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"CSSGCZSPZLISHY-UHFFFAOYSA-N>>RFWPWLDEXOTNHE-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"COCn1cc(Br)sc1=Nc1cccc(CO)n1\", \"reactants\": [\"COCn1cc(Br)sc1=Nc1cccc(C(=O)OC)n1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"COCn1cc(Br)sc1=Nc1cccc(C(=O)OC)n1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"COCn1cc(Br)sc1=Nc1cccc(C(=O)OC)n1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COCn1cc(Br)sc1=Nc1cccc(C(=O)OC)n1\", \"reactants\": [\"COCn1ccsc1=Nc1cccc(C(=O)OC)n1\", \"O=C1CCC(=O)N1Br\"]}","name":"validate_disconnection"},"id":"call_4_0","type":"function"},{"function":{"arguments":"{\"query\": \"COCn1ccsc1=Nc1cccc(C(=O)OC)n1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=C1CCC(=O)N1Br\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"LNFRCCCEJYLTPP-UHFFFAOYSA-N.PCLIMKBDDGJMGD-UHFFFAOYSA-N>>CSSGCZSPZLISHY-UHFFFAOYSA-N\", \"model_turns_remaining\": 12, \"product\": \"COCn1cc(Br)sc1=Nc1cccc(C(=O)OC)n1\", \"reactants\": [\"COCn1ccsc1=Nc1cccc(C(=O)OC)n1\", \"O=C1CCC(=O)N1Br\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_4_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"COCn1ccsc1=Nc1cccc(C(=O)OC)n1\", \"results\": [{\"inchikey\": \"LNFRCCCEJYLTPP-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"COCn1ccsc1=Nc1cccc(C(=O)OC)n1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"O=C1CCC(=O)N1Br\", \"results\": [{\"inchikey\": \"PCLIMKBDDGJMGD-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=C1CCC(=O)N1Br\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"COCn1cc(Br)sc1=Nc1cccc(CN2CCN(C(=O)c3ccccc3)CC2)n1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COCn1cc(Br)sc1=Nc1cccc(CN2CCNCC2)n1\": \"precursor\", \"O=C(Cl)c1ccccc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COCn1cc(Br)sc1=Nc1cccc(CN2CCNCC2)n1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"C1CNCCN1\": \"precursor\", \"COCn1cc(Br)sc1=Nc1cccc(CO)n1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"C1CNCCN1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"COCn1cc(Br)sc1=Nc1cccc(CO)n1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COCn1cc(Br)sc1=Nc1cccc(C(=O)OC)n1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COCn1cc(Br)sc1=Nc1cccc(C(=O)OC)n1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COCn1ccsc1=Nc1cccc(C(=O)OC)n1\": \"precursor\", \"O=C1CCC(=O)N1Br\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COCn1ccsc1=Nc1cccc(C(=O)OC)n1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=C1CCC(=O)N1Br\", \"in_stock\": true, \"children\": []}]}]}]}]}]}]}, {\"type\": \"mol\", \"smiles\": \"O=C(Cl)c1ccccc1\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_5_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"COCn1cc(Br)sc1=Nc1cccc(CN2CCN(C(=O)c3ccccc3)CC2)n1","task_id":"retro_b6e29b4e05090ef5cc30","tool_calls":12,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":5}
{"exact_match":true,"id":"retro_b711917eb5a79e5c8aac:reference-expert:a0","kind":"single_route","max_steps":3,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target COc1cc(CCc2cc(NC(=O)c3ccc(N4CCN(C)[C@@H](C)C4)cc3)[nH]n2)cc(OC)c1 in at most 3 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COc1cc(CCc2cc(NC(=O)c3ccc(N4CCN(C)[C@@H](C)C4)cc3)[nH]n2)cc(OC)c1\", \"reactants\": [\"COC(=O)c1ccc(N2CCN(C)[C@@H](C)C2)cc1\", \"COc1cc(CCc2cc(N)[nH]n2)cc(OC)c1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"COC(=O)c1ccc(N2CCN(C)[C@@H](C)C2)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"COc1cc(CCc2cc(N)[nH]n2)cc(OC)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"OYEUPRPCCUJZEP-NSHDSACASA-N.QKEFSZDRDPDTTE-UHFFFAOYSA-N>>PFZTXTPVKAGHPW-SFHVURJKSA-N\", \"model_turns_remaining\": 15, \"product\": \"COc1cc(CCc2cc(NC(=O)c3ccc(N4CCN(C)[C@@H](C)C4)cc3)[nH]n2)cc(OC)c1\", \"reactants\": [\"COC(=O)c1ccc(N2CCN(C)[C@@H](C)C2)cc1\", \"COc1cc(CCc2cc(N)[nH]n2)cc(OC)c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"COC(=O)c1ccc(N2CCN(C)[C@@H](C)C2)cc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"COc1cc(CCc2cc(N)[nH]n2)cc(OC)c1\", \"results\": [{\"inchikey\": \"QKEFSZDRDPDTTE-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"COc1cc(CCc2cc(N)[nH]n2)cc(OC)c1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"COC(=O)c1ccc(N2CCN(C)[C@@H](C)C2)cc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COC(=O)c1ccc(N2CCN(C)[C@@H](C)C2)cc1\", \"reactants\": [\"C=O\", \"COC(=O)c1ccc(N2CCN[C@@H](C)C2)cc1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"C=O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"COC(=O)c1ccc(N2CCN[C@@H](C)C2)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"NHABNVYVQXLSEG-JTQLQIEISA-N.WSFSSNUMVMOOMR-UHFFFAOYSA-N>>OYEUPRPCCUJZEP-NSHDSACASA-N\", \"model_turns_remaining\": 14, \"product\": \"COC(=O)c1ccc(N2CCN(C)[C@@H](C)C2)cc1\", \"reactants\": [\"C=O\", \"COC(=O)c1ccc(N2CCN[C@@H](C)C2)cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"C=O\", \"results\": [{\"inchikey\": \"WSFSSNUMVMOOMR-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"C=O\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"COC(=O)c1ccc(N2CCN[C@@H](C)C2)cc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"COC(=O)c1ccc(N2CCN[C@@H](C)C2)cc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COC(=O)c1ccc(N2CCN[C@@H](C)C2)cc1\", \"reactants\": [\"COC(=O)c1ccc(F)cc1\", \"C[C@H]1CNCCN1\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"COC(=O)c1ccc(F)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"C[C@H]1CNCCN1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"JOMNTHCQHJPVAZ-YFKPBYRVSA-N.MSEBQGULDWDIRW-UHFFFAOYSA-N>>NHABNVYVQXLSEG-JTQLQIEISA-N\", \"model_turns_remaining\": 13, \"product\": \"COC(=O)c1ccc(N2CCN[C@@H](C)C2)cc1\", \"reactants\": [\"COC(=O)c1ccc(F)cc1\", \"C[C@H]1CNCCN1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"COC(=O)c1ccc(F)cc1\", \"results\": [{\"inchikey\": \"MSEBQGULDWDIRW-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"COC(=O)c1ccc(F)cc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"C[C@H]1CNCCN1\", \"results\": [{\"inchikey\": \"JOMNTHCQHJPVAZ-YFKPBYRVSA-N\", \"similarity\": 1.0, \"smiles\": \"C[C@H]1CNCCN1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"COc1cc(CCc2cc(NC(=O)c3ccc(N4CCN(C)[C@@H](C)C4)cc3)[nH]n2)cc(OC)c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COC(=O)c1ccc(N2CCN(C)[C@@H](C)C2)cc1\": \"precursor\", \"COc1cc(CCc2cc(N)[nH]n2)cc(OC)c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COC(=O)c1ccc(N2CCN(C)[C@@H](C)C2)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"C=O\": \"precursor\", \"COC(=O)c1ccc(N2CCN[C@@H](C)C2)cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"C=O\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"COC(=O)c1ccc(N2CCN[C@@H](C)C2)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COC(=O)c1ccc(F)cc1\": \"precursor\", \"C[C@H]1CNCCN1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COC(=O)c1ccc(F)cc1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"C[C@H]1CNCCN1\", \"in_stock\": true, \"children\": []}]}]}]}]}, {\"type\": \"mol\", \"smiles\": \"COc1cc(CCc2cc(N)[nH]n2)cc(OC)c1\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_4_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"COc1cc(CCc2cc(NC(=O)c3ccc(N4CCN(C)[C@@H](C)C4)cc3)[nH]n2)cc(OC)c1","task_id":"retro_b711917eb5a79e5c8aac","tool_calls":10,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":4}
{"exact_match":true,"id":"retro_b732216cf825f8a27eae:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CCCS(=O)(=O)Nc1ccc(F)c(C=O)c1F in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCCS(=O)(=O)Nc1ccc(F)c(C=O)c1F\", \"reactants\": [\"CCCS(=O)(=O)Nc1ccc(F)cc1F\", \"CN(C)C=O\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCCS(=O)(=O)Nc1ccc(F)cc1F\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"CN(C)C=O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"YFZDPIXYOILDMJ-UHFFFAOYSA-N.ZMXDDKWLCZADIW-UHFFFAOYSA-N>>RWAQKKCELAQLHO-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"CCCS(=O)(=O)Nc1ccc(F)c(C=O)c1F\", \"reactants\": [\"CCCS(=O)(=O)Nc1ccc(F)cc1F\", \"CN(C)C=O\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CCCS(=O)(=O)Nc1ccc(F)cc1F\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CN(C)C=O\", \"results\": [{\"inchikey\": \"ZMXDDKWLCZADIW-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CN(C)C=O\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"CCCS(=O)(=O)Nc1ccc(F)cc1F was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCCS(=O)(=O)Nc1ccc(F)cc1F\", \"reactants\": [\"CCCS(=O)(=O)Cl\", \"Nc1ccc(F)cc1F\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCCS(=O)(=O)Cl\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"Nc1ccc(F)cc1F\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"CEPCPXLLFXPZGW-UHFFFAOYSA-N.KPBSJEBFALFJTO-UHFFFAOYSA-N>>YFZDPIXYOILDMJ-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"CCCS(=O)(=O)Nc1ccc(F)cc1F\", \"reactants\": [\"CCCS(=O)(=O)Cl\", \"Nc1ccc(F)cc1F\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CCCS(=O)(=O)Cl\", \"results\": [{\"inchikey\": \"KPBSJEBFALFJTO-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CCCS(=O)(=O)Cl\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"Nc1ccc(F)cc1F\", \"results\": [{\"inchikey\": \"CEPCPXLLFXPZGW-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Nc1ccc(F)cc1F\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CCCS(=O)(=O)Nc1ccc(F)c(C=O)c1F\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCCS(=O)(=O)Nc1ccc(F)cc1F\": \"precursor\", \"CN(C)C=O\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCCS(=O)(=O)Nc1ccc(F)cc1F\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCCS(=O)(=O)Cl\": \"precursor\", \"Nc1ccc(F)cc1F\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCCS(=O)(=O)Cl\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"Nc1ccc(F)cc1F\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"CN(C)C=O\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"CCCS(=O)(=O)Nc1ccc(F)c(C=O)c1F","task_id":"retro_b732216cf825f8a27eae","tool_calls":7,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_b8ed4180b95b750d6aa3:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target O=C(O)c1cc2cc([N+](=O)[O-])ccc2s1 in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"O=C(O)c1cc2cc([N+](=O)[O-])ccc2s1\", \"reactants\": [\"COC(=O)c1cc2cc([N+](=O)[O-])ccc2s1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"COC(=O)c1cc2cc([N+](=O)[O-])ccc2s1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"OSVZEJHBIFIMJF-UHFFFAOYSA-N>>ZGSMHACHDULBBY-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"O=C(O)c1cc2cc([N+](=O)[O-])ccc2s1\", \"reactants\": [\"COC(=O)c1cc2cc([N+](=O)[O-])ccc2s1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"COC(=O)c1cc2cc([N+](=O)[O-])ccc2s1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"COC(=O)c1cc2cc([N+](=O)[O-])ccc2s1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COC(=O)c1cc2cc([N+](=O)[O-])ccc2s1\", \"reactants\": [\"COC(=O)CS\", \"O=Cc1cc([N+](=O)[O-])ccc1F\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"COC(=O)CS\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=Cc1cc([N+](=O)[O-])ccc1F\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"MKIJJIMOAABWGF-UHFFFAOYSA-N.VVXFDFQEIRGULC-UHFFFAOYSA-N>>OSVZEJHBIFIMJF-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"COC(=O)c1cc2cc([N+](=O)[O-])ccc2s1\", \"reactants\": [\"COC(=O)CS\", \"O=Cc1cc([N+](=O)[O-])ccc1F\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"COC(=O)CS\", \"results\": [{\"inchikey\": \"MKIJJIMOAABWGF-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"COC(=O)CS\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"O=Cc1cc([N+](=O)[O-])ccc1F\", \"results\": [{\"inchikey\": \"VVXFDFQEIRGULC-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=Cc1cc([N+](=O)[O-])ccc1F\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"O=C(O)c1cc2cc([N+](=O)[O-])ccc2s1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COC(=O)c1cc2cc([N+](=O)[O-])ccc2s1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COC(=O)c1cc2cc([N+](=O)[O-])ccc2s1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COC(=O)CS\": \"precursor\", \"O=Cc1cc([N+](=O)[O-])ccc1F\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COC(=O)CS\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=Cc1cc([N+](=O)[O-])ccc1F\", \"in_stock\": true, \"children\": []}]}]}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"O=C(O)c1cc2cc([N+](=O)[O-])ccc2s1","task_id":"retro_b8ed4180b95b750d6aa3","tool_calls":6,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_b93a52771364a6b84f01:reference-expert:a0","kind":"single_route","max_steps":4,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CC(C)(C)OC(=O)N(Cc1cn(COCC[Si](C)(C)C)c(C=O)n1)C1CCN(Cc2ccccc2)CC1 in at most 4 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(C)(C)OC(=O)N(Cc1cn(COCC[Si](C)(C)C)c(C=O)n1)C1CCN(Cc2ccccc2)CC1\", \"reactants\": [\"CC(C)(C)OC(=O)N(Cc1cn(COCC[Si](C)(C)C)cn1)C1CCN(Cc2ccccc2)CC1\", \"CN(C)C=O\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)OC(=O)N(Cc1cn(COCC[Si](C)(C)C)cn1)C1CCN(Cc2ccccc2)CC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"CN(C)C=O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"LSEATHAFBVACLW-UHFFFAOYSA-N.ZMXDDKWLCZADIW-UHFFFAOYSA-N>>OFZQRFRHZKQEFL-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"CC(C)(C)OC(=O)N(Cc1cn(COCC[Si](C)(C)C)c(C=O)n1)C1CCN(Cc2ccccc2)CC1\", \"reactants\": [\"CC(C)(C)OC(=O)N(Cc1cn(COCC[Si](C)(C)C)cn1)C1CCN(Cc2ccccc2)CC1\", \"CN(C)C=O\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CC(C)(C)OC(=O)N(Cc1cn(COCC[Si](C)(C)C)cn1)C1CCN(Cc2ccccc2)CC1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CN(C)C=O\", \"results\": [{\"inchikey\": \"ZMXDDKWLCZADIW-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CN(C)C=O\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"CC(C)(C)OC(=O)N(Cc1cn(COCC[Si](C)(C)C)cn1)C1CCN(Cc2ccccc2)CC1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(C)(C)OC(=O)N(Cc1cn(COCC[Si](C)(C)C)cn1)C1CCN(Cc2ccccc2)CC1\", \"reactants\": [\"CC(C)(C)OC(=O)N(Cc1c[nH]cn1)C1CCN(Cc2ccccc2)CC1\", \"C[Si](C)(C)CCOCCl\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)OC(=O)N(Cc1c[nH]cn1)C1CCN(Cc2ccccc2)CC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"C[Si](C)(C)CCOCCl\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"BPXKZEMBEZGUAH-UHFFFAOYSA-N.NCDJAUMBNLVOEZ-UHFFFAOYSA-N>>LSEATHAFBVACLW-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"CC(C)(C)OC(=O)N(Cc1cn(COCC[Si](C)(C)C)cn1)C1CCN(Cc2ccccc2)CC1\", \"reactants\": [\"CC(C)(C)OC(=O)N(Cc1c[nH]cn1)C1CCN(Cc2ccccc2)CC1\", \"C[Si](C)(C)CCOCCl\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CC(C)(C)OC(=O)N(Cc1c[nH]cn1)C1CCN(Cc2ccccc2)CC1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"C[Si](C)(C)CCOCCl\", \"results\": [{\"inchikey\": \"BPXKZEMBEZGUAH-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"C[Si](C)(C)CCOCCl\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"CC(C)(C)OC(=O)N(Cc1c[nH]cn1)C1CCN(Cc2ccccc2)CC1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(C)(C)OC(=O)N(Cc1c[nH]cn1)C1CCN(Cc2ccccc2)CC1\", \"reactants\": [\"CC(C)(C)OC(=O)OC(=O)OC(C)(C)C\", \"c1ccc(CN2CCC(NCc3c[nH]cn3)CC2)cc1\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)OC(=O)OC(=O)OC(C)(C)C\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"c1ccc(CN2CCC(NCc3c[nH]cn3)CC2)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"DYHSDKLCOJIUFX-UHFFFAOYSA-N.RZXDRBOUYGDGKQ-UHFFFAOYSA-N>>NCDJAUMBNLVOEZ-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"CC(C)(C)OC(=O)N(Cc1c[nH]cn1)C1CCN(Cc2ccccc2)CC1\", \"reactants\": [\"CC(C)(C)OC(=O)OC(=O)OC(C)(C)C\", \"c1ccc(CN2CCC(NCc3c[nH]cn3)CC2)cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"CC(C)(C)OC(=O)OC(=O)OC(C)(C)C\", \"results\": [{\"inchikey\": \"DYHSDKLCOJIUFX-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CC(C)(C)OC(=O)OC(=O)OC(C)(C)C\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"c1ccc(CN2CCC(NCc3c[nH]cn3)CC2)cc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"c1ccc(CN2CCC(NCc3c[nH]cn3)CC2)cc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"c1ccc(CN2CCC(NCc3c[nH]cn3)CC2)cc1\", \"reactants\": [\"NC1CCN(Cc2ccccc2)CC1\", \"O=Cc1c[nH]cn1\"]}","name":"validate_disconnection"},"id":"call_4_0","type":"function"},{"function":{"arguments":"{\"query\": \"NC1CCN(Cc2ccccc2)CC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=Cc1c[nH]cn1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"YUBDLZGUSSWQSS-UHFFFAOYSA-N.ZQEXIXXJFSQPNA-UHFFFAOYSA-N>>RZXDRBOUYGDGKQ-UHFFFAOYSA-N\", \"model_turns_remaining\": 12, \"product\": \"c1ccc(CN2CCC(NCc3c[nH]cn3)CC2)cc1\", \"reactants\": [\"NC1CCN(Cc2ccccc2)CC1\", \"O=Cc1c[nH]cn1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_4_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"NC1CCN(Cc2ccccc2)CC1\", \"results\": [{\"inchikey\": \"YUBDLZGUSSWQSS-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"NC1CCN(Cc2ccccc2)CC1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"O=Cc1c[nH]cn1\", \"results\": [{\"inchikey\": \"ZQEXIXXJFSQPNA-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=Cc1c[nH]cn1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)OC(=O)N(Cc1cn(COCC[Si](C)(C)C)c(C=O)n1)C1CCN(Cc2ccccc2)CC1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)(C)OC(=O)N(Cc1cn(COCC[Si](C)(C)C)cn1)C1CCN(Cc2ccccc2)CC1\": \"precursor\", \"CN(C)C=O\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)OC(=O)N(Cc1cn(COCC[Si](C)(C)C)cn1)C1CCN(Cc2ccccc2)CC1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)(C)OC(=O)N(Cc1c[nH]cn1)C1CCN(Cc2ccccc2)CC1\": \"precursor\", \"C[Si](C)(C)CCOCCl\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)OC(=O)N(Cc1c[nH]cn1)C1CCN(Cc2ccccc2)CC1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)(C)OC(=O)OC(=O)OC(C)(C)C\": \"precursor\", \"c1ccc(CN2CCC(NCc3c[nH]cn3)CC2)cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)OC(=O)OC(=O)OC(C)(C)C\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"c1ccc(CN2CCC(NCc3c[nH]cn3)CC2)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"NC1CCN(Cc2ccccc2)CC1\": \"precursor\", \"O=Cc1c[nH]cn1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"NC1CCN(Cc2ccccc2)CC1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=Cc1c[nH]cn1\", \"in_stock\": true, \"children\": []}]}]}]}]}, {\"type\": \"mol\", \"smiles\": \"C[Si](C)(C)CCOCCl\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"CN(C)C=O\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_5_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"CC(C)(C)OC(=O)N(Cc1cn(COCC[Si](C)(C)C)c(C=O)n1)C1CCN(Cc2ccccc2)CC1","task_id":"retro_b93a52771364a6b84f01","tool_calls":13,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":5}
{"exact_match":true,"id":"retro_b9659e8ae970d0348821:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target c1cncc(-c2ccc3[nH]ncc3c2)c1 in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"c1cncc(-c2ccc3[nH]ncc3c2)c1\", \"reactants\": [\"C[Si](C)(C)CCOCn1ncc2cc(-c3cccnc3)ccc21\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"C[Si](C)(C)CCOCn1ncc2cc(-c3cccnc3)ccc21\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"LZOKJJFMTDHXBH-UHFFFAOYSA-N>>RXWLUAHKORPFPY-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"c1cncc(-c2ccc3[nH]ncc3c2)c1\", \"reactants\": [\"C[Si](C)(C)CCOCn1ncc2cc(-c3cccnc3)ccc21\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"C[Si](C)(C)CCOCn1ncc2cc(-c3cccnc3)ccc21\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"C[Si](C)(C)CCOCn1ncc2cc(-c3cccnc3)ccc21 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"C[Si](C)(C)CCOCn1ncc2cc(-c3cccnc3)ccc21\", \"reactants\": [\"C[Si](C)(C)CCOCn1ncc2cc(I)ccc21\", \"OB(O)c1cccnc1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"C[Si](C)(C)CCOCn1ncc2cc(I)ccc21\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"OB(O)c1cccnc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"ABMYEXAYWZJVOV-UHFFFAOYSA-N.PZPDJDIMPYSCHQ-UHFFFAOYSA-N>>LZOKJJFMTDHXBH-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"C[Si](C)(C)CCOCn1ncc2cc(-c3cccnc3)ccc21\", \"reactants\": [\"C[Si](C)(C)CCOCn1ncc2cc(I)ccc21\", \"OB(O)c1cccnc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"C[Si](C)(C)CCOCn1ncc2cc(I)ccc21\", \"results\": [{\"inchikey\": \"PZPDJDIMPYSCHQ-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"C[Si](C)(C)CCOCn1ncc2cc(I)ccc21\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"OB(O)c1cccnc1\", \"results\": [{\"inchikey\": \"ABMYEXAYWZJVOV-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"OB(O)c1cccnc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"c1cncc(-c2ccc3[nH]ncc3c2)c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"C[Si](C)(C)CCOCn1ncc2cc(-c3cccnc3)ccc21\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"C[Si](C)(C)CCOCn1ncc2cc(-c3cccnc3)ccc21\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"C[Si](C)(C)CCOCn1ncc2cc(I)ccc21\": \"precursor\", \"OB(O)c1cccnc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"C[Si](C)(C)CCOCn1ncc2cc(I)ccc21\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"OB(O)c1cccnc1\", \"in_stock\": true, \"children\": []}]}]}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"c1cncc(-c2ccc3[nH]ncc3c2)c1","task_id":"retro_b9659e8ae970d0348821","tool_calls":6,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_b974f999acce883ed0f6:reference-expert:a0","kind":"single_route","max_steps":3,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CC(C)(C)[C@H]1CC[C@H](Oc2ccc3cc(CNC45CCC(C(=O)O)(CC4)C(O)C5)ccc3c2)CC1 in at most 3 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(C)(C)[C@H]1CC[C@H](Oc2ccc3cc(CNC45CCC(C(=O)O)(CC4)C(O)C5)ccc3c2)CC1\", \"reactants\": [\"CCOC(=O)C12CCC(NCc3ccc4cc(O[C@H]5CC[C@H](C(C)(C)C)CC5)ccc4c3)(CC1)CC2O\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCOC(=O)C12CCC(NCc3ccc4cc(O[C@H]5CC[C@H](C(C)(C)C)CC5)ccc4c3)(CC1)CC2O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"NCSBVTGORDYSIY-VQSVEYIPSA-N>>OUCFABRTQVMNNT-PAXVQBFVSA-N\", \"model_turns_remaining\": 15, \"product\": \"CC(C)(C)[C@H]1CC[C@H](Oc2ccc3cc(CNC45CCC(C(=O)O)(CC4)C(O)C5)ccc3c2)CC1\", \"reactants\": [\"CCOC(=O)C12CCC(NCc3ccc4cc(O[C@H]5CC[C@H](C(C)(C)C)CC5)ccc4c3)(CC1)CC2O\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CCOC(=O)C12CCC(NCc3ccc4cc(O[C@H]5CC[C@H](C(C)(C)C)CC5)ccc4c3)(CC1)CC2O\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"CCOC(=O)C12CCC(NCc3ccc4cc(O[C@H]5CC[C@H](C(C)(C)C)CC5)ccc4c3)(CC1)CC2O was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCOC(=O)C12CCC(NCc3ccc4cc(O[C@H]5CC[C@H](C(C)(C)C)CC5)ccc4c3)(CC1)CC2O\", \"reactants\": [\"CC(C)(C)[C@H]1CC[C@H](Oc2ccc3cc(C=O)ccc3c2)CC1\", \"CCOC(=O)C12CCC(N)(CC1)CC2O\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)[C@H]1CC[C@H](Oc2ccc3cc(C=O)ccc3c2)CC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"CCOC(=O)C12CCC(N)(CC1)CC2O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"WHYJZYOAIIOKMI-UHFFFAOYSA-N.ZGQMPGQCFFVDGB-WGSAOQKQSA-N>>NCSBVTGORDYSIY-VQSVEYIPSA-N\", \"model_turns_remaining\": 14, \"product\": \"CCOC(=O)C12CCC(NCc3ccc4cc(O[C@H]5CC[C@H](C(C)(C)C)CC5)ccc4c3)(CC1)CC2O\", \"reactants\": [\"CC(C)(C)[C@H]1CC[C@H](Oc2ccc3cc(C=O)ccc3c2)CC1\", \"CCOC(=O)C12CCC(N)(CC1)CC2O\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CC(C)(C)[C@H]1CC[C@H](Oc2ccc3cc(C=O)ccc3c2)CC1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CCOC(=O)C12CCC(N)(CC1)CC2O\", \"results\": [{\"inchikey\": \"WHYJZYOAIIOKMI-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CCOC(=O)C12CCC(N)(CC1)CC2O\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"CC(C)(C)[C@H]1CC[C@H](Oc2ccc3cc(C=O)ccc3c2)CC1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(C)(C)[C@H]1CC[C@H](Oc2ccc3cc(C=O)ccc3c2)CC1\", \"reactants\": [\"CC(C)(C)[C@H]1CC[C@H](Oc2ccc3cc(Br)ccc3c2)CC1\", \"CN(C)C=O\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)[C@H]1CC[C@H](Oc2ccc3cc(Br)ccc3c2)CC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"CN(C)C=O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"VAQBDDYCCGEUAA-SAABIXHNSA-N.ZMXDDKWLCZADIW-UHFFFAOYSA-N>>ZGQMPGQCFFVDGB-WGSAOQKQSA-N\", \"model_turns_remaining\": 13, \"product\": \"CC(C)(C)[C@H]1CC[C@H](Oc2ccc3cc(C=O)ccc3c2)CC1\", \"reactants\": [\"CC(C)(C)[C@H]1CC[C@H](Oc2ccc3cc(Br)ccc3c2)CC1\", \"CN(C)C=O\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"CC(C)(C)[C@H]1CC[C@H](Oc2ccc3cc(Br)ccc3c2)CC1\", \"results\": [{\"inchikey\": \"VAQBDDYCCGEUAA-SAABIXHNSA-N\", \"similarity\": 1.0, \"smiles\": \"CC(C)(C)[C@H]1CC[C@H](Oc2ccc3cc(Br)ccc3c2)CC1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"CN(C)C=O\", \"results\": [{\"inchikey\": \"ZMXDDKWLCZADIW-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CN(C)C=O\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)[C@H]1CC[C@H](Oc2ccc3cc(CNC45CCC(C(=O)O)(CC4)C(O)C5)ccc3c2)CC1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCOC(=O)C12CCC(NCc3ccc4cc(O[C@H]5CC[C@H](C(C)(C)C)CC5)ccc4c3)(CC1)CC2O\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCOC(=O)C12CCC(NCc3ccc4cc(O[C@H]5CC[C@H](C(C)(C)C)CC5)ccc4c3)(CC1)CC2O\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)(C)[C@H]1CC[C@H](Oc2ccc3cc(C=O)ccc3c2)CC1\": \"precursor\", \"CCOC(=O)C12CCC(N)(CC1)CC2O\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)[C@H]1CC[C@H](Oc2ccc3cc(C=O)ccc3c2)CC1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)(C)[C@H]1CC[C@H](Oc2ccc3cc(Br)ccc3c2)CC1\": \"precursor\", \"CN(C)C=O\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)[C@H]1CC[C@H](Oc2ccc3cc(Br)ccc3c2)CC1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"CN(C)C=O\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"CCOC(=O)C12CCC(N)(CC1)CC2O\", \"in_stock\": true, \"children\": []}]}]}]}]}]}}","name":"emit_routes"},"id":"call_4_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"CC(C)(C)[C@H]1CC[C@H](Oc2ccc3cc(CNC45CCC(C(=O)O)(CC4)C(O)C5)ccc3c2)CC1","task_id":"retro_b974f999acce883ed0f6","tool_calls":9,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":4}
{"exact_match":true,"id":"retro_bae86a6dd6636d2841db:reference-expert:a0","kind":"single_route","max_steps":4,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target COCCOCCOCCOc1ccc(N=C=O)cc1 in at most 4 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COCCOCCOCCOc1ccc(N=C=O)cc1\", \"reactants\": [\"COCCOCCOCCOc1ccc(N)cc1\", \"O=C(Cl)Cl\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"COCCOCCOCCOc1ccc(N)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=C(Cl)Cl\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"YGYAWVDWMABLBF-UHFFFAOYSA-N.ZWTLHSZQFYADME-UHFFFAOYSA-N>>IGLGGYIGRYFKDN-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"COCCOCCOCCOc1ccc(N=C=O)cc1\", \"reactants\": [\"COCCOCCOCCOc1ccc(N)cc1\", \"O=C(Cl)Cl\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"COCCOCCOCCOc1ccc(N)cc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"O=C(Cl)Cl\", \"results\": [{\"inchikey\": \"YGYAWVDWMABLBF-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=C(Cl)Cl\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"COCCOCCOCCOc1ccc(N)cc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COCCOCCOCCOc1ccc(N)cc1\", \"reactants\": [\"COCCOCCOCCOc1ccc([N+](=O)[O-])cc1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"COCCOCCOCCOc1ccc([N+](=O)[O-])cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"RUDKQSRSOJXLSE-UHFFFAOYSA-N>>ZWTLHSZQFYADME-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"COCCOCCOCCOc1ccc(N)cc1\", \"reactants\": [\"COCCOCCOCCOc1ccc([N+](=O)[O-])cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"COCCOCCOCCOc1ccc([N+](=O)[O-])cc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"COCCOCCOCCOc1ccc([N+](=O)[O-])cc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COCCOCCOCCOc1ccc([N+](=O)[O-])cc1\", \"reactants\": [\"COCCOCCOCCOS(=O)(=O)c1ccc(C)cc1\", \"O=[N+]([O-])c1ccc(O)cc1\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"COCCOCCOCCOS(=O)(=O)c1ccc(C)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=[N+]([O-])c1ccc(O)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"BTJIUGUIPKRLHP-UHFFFAOYSA-N.IUDNRKGPFWUYIC-UHFFFAOYSA-N>>RUDKQSRSOJXLSE-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"COCCOCCOCCOc1ccc([N+](=O)[O-])cc1\", \"reactants\": [\"COCCOCCOCCOS(=O)(=O)c1ccc(C)cc1\", \"O=[N+]([O-])c1ccc(O)cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"COCCOCCOCCOS(=O)(=O)c1ccc(C)cc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"O=[N+]([O-])c1ccc(O)cc1\", \"results\": [{\"inchikey\": \"BTJIUGUIPKRLHP-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=[N+]([O-])c1ccc(O)cc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"COCCOCCOCCOS(=O)(=O)c1ccc(C)cc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COCCOCCOCCOS(=O)(=O)c1ccc(C)cc1\", \"reactants\": [\"COCCOCCOCCO\", \"Cc1ccc(S(=O)(=O)Cl)cc1\"]}","name":"validate_disconnection"},"id":"call_4_0","type":"function"},{"function":{"arguments":"{\"query\": \"COCCOCCOCCO\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_1","type":"function"},{"function":{"arguments":"{\"query\": \"Cc1ccc(S(=O)(=O)Cl)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"JLGLQAWTXXGVEM-UHFFFAOYSA-N.YYROPELSRYBVMQ-UHFFFAOYSA-N>>IUDNRKGPFWUYIC-UHFFFAOYSA-N\", \"model_turns_remaining\": 12, \"product\": \"COCCOCCOCCOS(=O)(=O)c1ccc(C)cc1\", \"reactants\": [\"COCCOCCOCCO\", \"Cc1ccc(S(=O)(=O)Cl)cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_4_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"COCCOCCOCCO\", \"results\": [{\"inchikey\": \"JLGLQAWTXXGVEM-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"COCCOCCOCCO\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"Cc1ccc(S(=O)(=O)Cl)cc1\", \"results\": [{\"inchikey\": \"YYROPELSRYBVMQ-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Cc1ccc(S(=O)(=O)Cl)cc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"COCCOCCOCCOc1ccc(N=C=O)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COCCOCCOCCOc1ccc(N)cc1\": \"precursor\", \"O=C(Cl)Cl\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COCCOCCOCCOc1ccc(N)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COCCOCCOCCOc1ccc([N+](=O)[O-])cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COCCOCCOCCOc1ccc([N+](=O)[O-])cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COCCOCCOCCOS(=O)(=O)c1ccc(C)cc1\": \"precursor\", \"O=[N+]([O-])c1ccc(O)cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COCCOCCOCCOS(=O)(=O)c1ccc(C)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COCCOCCOCCO\": \"precursor\", \"Cc1ccc(S(=O)(=O)Cl)cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COCCOCCOCCO\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"Cc1ccc(S(=O)(=O)Cl)cc1\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"O=[N+]([O-])c1ccc(O)cc1\", \"in_stock\": true, \"children\": []}]}]}]}]}, {\"type\": \"mol\", \"smiles\": \"O=C(Cl)Cl\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_5_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"COCCOCCOCCOc1ccc(N=C=O)cc1","task_id":"retro_bae86a6dd6636d2841db","tool_calls":12,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":5}
{"exact_match":true,"id":"retro_bcb22a14773f2078b659:reference-expert:a0","kind":"single_route","max_steps":3,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target C[C@@H]1CN(C(c2ccccc2)c2ccccc2)C[C@H](C)N1CCCN in at most 3 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"C[C@@H]1CN(C(c2ccccc2)c2ccccc2)C[C@H](C)N1CCCN\", \"reactants\": [\"C[C@@H]1CN(C(c2ccccc2)c2ccccc2)C[C@H](C)N1CCCN1C(=O)c2ccccc2C1=O\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"C[C@@H]1CN(C(c2ccccc2)c2ccccc2)C[C@H](C)N1CCCN1C(=O)c2ccccc2C1=O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"IMIQKTJCUIBFJM-ZRZAMGCNSA-N>>UMHZXJMTGGOUJW-KDURUIRLSA-N\", \"model_turns_remaining\": 15, \"product\": \"C[C@@H]1CN(C(c2ccccc2)c2ccccc2)C[C@H](C)N1CCCN\", \"reactants\": [\"C[C@@H]1CN(C(c2ccccc2)c2ccccc2)C[C@H](C)N1CCCN1C(=O)c2ccccc2C1=O\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"C[C@@H]1CN(C(c2ccccc2)c2ccccc2)C[C@H](C)N1CCCN1C(=O)c2ccccc2C1=O\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"C[C@@H]1CN(C(c2ccccc2)c2ccccc2)C[C@H](C)N1CCCN1C(=O)c2ccccc2C1=O was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"C[C@@H]1CN(C(c2ccccc2)c2ccccc2)C[C@H](C)N1CCCN1C(=O)c2ccccc2C1=O\", \"reactants\": [\"C[C@@H]1CN(C(c2ccccc2)c2ccccc2)C[C@H](C)N1\", \"O=C1c2ccccc2C(=O)N1CCCBr\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"C[C@@H]1CN(C(c2ccccc2)c2ccccc2)C[C@H](C)N1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=C1c2ccccc2C(=O)N1CCCBr\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"MRPMOZREZHZBGN-IYBDPMFKSA-N.VKJCJJYNVIYVQR-UHFFFAOYSA-N>>IMIQKTJCUIBFJM-ZRZAMGCNSA-N\", \"model_turns_remaining\": 14, \"product\": \"C[C@@H]1CN(C(c2ccccc2)c2ccccc2)C[C@H](C)N1CCCN1C(=O)c2ccccc2C1=O\", \"reactants\": [\"C[C@@H]1CN(C(c2ccccc2)c2ccccc2)C[C@H](C)N1\", \"O=C1c2ccccc2C(=O)N1CCCBr\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"C[C@@H]1CN(C(c2ccccc2)c2ccccc2)C[C@H](C)N1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"O=C1c2ccccc2C(=O)N1CCCBr\", \"results\": [{\"inchikey\": \"VKJCJJYNVIYVQR-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=C1c2ccccc2C(=O)N1CCCBr\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"C[C@@H]1CN(C(c2ccccc2)c2ccccc2)C[C@H](C)N1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"C[C@@H]1CN(C(c2ccccc2)c2ccccc2)C[C@H](C)N1\", \"reactants\": [\"BrC(c1ccccc1)c1ccccc1\", \"C[C@@H]1CNC[C@H](C)N1\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"BrC(c1ccccc1)c1ccccc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"C[C@@H]1CNC[C@H](C)N1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"IFNWESYYDINUHV-OLQVQODUSA-N.OQROAIRCEOBYJA-UHFFFAOYSA-N>>MRPMOZREZHZBGN-IYBDPMFKSA-N\", \"model_turns_remaining\": 13, \"product\": \"C[C@@H]1CN(C(c2ccccc2)c2ccccc2)C[C@H](C)N1\", \"reactants\": [\"BrC(c1ccccc1)c1ccccc1\", \"C[C@@H]1CNC[C@H](C)N1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"BrC(c1ccccc1)c1ccccc1\", \"results\": [{\"inchikey\": \"OQROAIRCEOBYJA-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"BrC(c1ccccc1)c1ccccc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"C[C@@H]1CNC[C@H](C)N1\", \"results\": [{\"inchikey\": \"IFNWESYYDINUHV-OLQVQODUSA-N\", \"similarity\": 1.0, \"smiles\": \"C[C@@H]1CNC[C@H](C)N1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"C[C@@H]1CN(C(c2ccccc2)c2ccccc2)C[C@H](C)N1CCCN\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"C[C@@H]1CN(C(c2ccccc2)c2ccccc2)C[C@H](C)N1CCCN1C(=O)c2ccccc2C1=O\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"C[C@@H]1CN(C(c2ccccc2)c2ccccc2)C[C@H](C)N1CCCN1C(=O)c2ccccc2C1=O\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"C[C@@H]1CN(C(c2ccccc2)c2ccccc2)C[C@H](C)N1\": \"precursor\", \"O=C1c2ccccc2C(=O)N1CCCBr\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"C[C@@H]1CN(C(c2ccccc2)c2ccccc2)C[C@H](C)N1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"BrC(c1ccccc1)c1ccccc1\": \"precursor\", \"C[C@@H]1CNC[C@H](C)N1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"BrC(c1ccccc1)c1ccccc1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"C[C@@H]1CNC[C@H](C)N1\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"O=C1c2ccccc2C(=O)N1CCCBr\", \"in_stock\": true, \"children\": []}]}]}]}]}]}}","name":"emit_routes"},"id":"call_4_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"C[C@@H]1CN(C(c2ccccc2)c2ccccc2)C[C@H](C)N1CCCN","task_id":"retro_bcb22a14773f2078b659","tool_calls":9,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":4}
{"exact_match":true,"id":"retro_bf07c2cc73d70cf0ebf6:reference-expert:a0","kind":"single_route","max_steps":3,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target Nc1n[nH]c2ccc(C=O)cc12 in at most 3 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Nc1n[nH]c2ccc(C=O)cc12\", \"reactants\": [\"Nc1n[nH]c2ccc(C3OCCO3)cc12\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"Nc1n[nH]c2ccc(C3OCCO3)cc12\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"WRCKKOSZQJWQMO-UHFFFAOYSA-N>>HNXGXWALYGQBSZ-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"Nc1n[nH]c2ccc(C=O)cc12\", \"reactants\": [\"Nc1n[nH]c2ccc(C3OCCO3)cc12\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"Nc1n[nH]c2ccc(C3OCCO3)cc12\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"Nc1n[nH]c2ccc(C3OCCO3)cc12 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Nc1n[nH]c2ccc(C3OCCO3)cc12\", \"reactants\": [\"N#Cc1cc(C2OCCO2)ccc1F\", \"NN\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"N#Cc1cc(C2OCCO2)ccc1F\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"NN\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"JQILWRYPSNJCLL-UHFFFAOYSA-N.OAKJQQAXSVQMHS-UHFFFAOYSA-N>>WRCKKOSZQJWQMO-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"Nc1n[nH]c2ccc(C3OCCO3)cc12\", \"reactants\": [\"N#Cc1cc(C2OCCO2)ccc1F\", \"NN\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"N#Cc1cc(C2OCCO2)ccc1F\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"NN\", \"results\": [{\"inchikey\": \"OAKJQQAXSVQMHS-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"NN\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"N#Cc1cc(C2OCCO2)ccc1F was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"N#Cc1cc(C2OCCO2)ccc1F\", \"reactants\": [\"N#Cc1cc(C=O)ccc1F\", \"OCCO\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"N#Cc1cc(C=O)ccc1F\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"OCCO\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"LYCAIKOWRPUZTN-UHFFFAOYSA-N.MOFRJTLODZILCR-UHFFFAOYSA-N>>JQILWRYPSNJCLL-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"N#Cc1cc(C2OCCO2)ccc1F\", \"reactants\": [\"N#Cc1cc(C=O)ccc1F\", \"OCCO\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"N#Cc1cc(C=O)ccc1F\", \"results\": [{\"inchikey\": \"MOFRJTLODZILCR-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"N#Cc1cc(C=O)ccc1F\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"OCCO\", \"results\": [{\"inchikey\": \"LYCAIKOWRPUZTN-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"OCCO\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"Nc1n[nH]c2ccc(C=O)cc12\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"Nc1n[nH]c2ccc(C3OCCO3)cc12\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"Nc1n[nH]c2ccc(C3OCCO3)cc12\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"N#Cc1cc(C2OCCO2)ccc1F\": \"precursor\", \"NN\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"N#Cc1cc(C2OCCO2)ccc1F\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"N#Cc1cc(C=O)ccc1F\": \"precursor\", \"OCCO\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"N#Cc1cc(C=O)ccc1F\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"OCCO\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"NN\", \"in_stock\": true, \"children\": []}]}]}]}]}]}}","name":"emit_routes"},"id":"call_4_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"Nc1n[nH]c2ccc(C=O)cc12","task_id":"retro_bf07c2cc73d70cf0ebf6","tool_calls":9,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":4}
{"exact_match":true,"id":"retro_bf1362a3e29de115ea88:reference-expert:a0","kind":"single_route","max_steps":5,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CC(=O)NC(C)c1ccc2c(c1)CCN(Cc1ccc(OC(C)C)cc1C)C2 in at most 5 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(=O)NC(C)c1ccc2c(c1)CCN(Cc1ccc(OC(C)C)cc1C)C2\", \"reactants\": [\"CC(=O)NC(C)c1ccc2c(c1)CCNC2\", \"Cc1cc(OC(C)C)ccc1CBr\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(=O)NC(C)c1ccc2c(c1)CCNC2\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"Cc1cc(OC(C)C)ccc1CBr\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"IKAZHJNAUQODLE-UHFFFAOYSA-N.IWWLNRLMXMJGNR-UHFFFAOYSA-N>>VYHUAVZZKUTSQF-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"CC(=O)NC(C)c1ccc2c(c1)CCN(Cc1ccc(OC(C)C)cc1C)C2\", \"reactants\": [\"CC(=O)NC(C)c1ccc2c(c1)CCNC2\", \"Cc1cc(OC(C)C)ccc1CBr\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CC(=O)NC(C)c1ccc2c(c1)CCNC2\", \"results\": [{\"inchikey\": \"IKAZHJNAUQODLE-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CC(=O)NC(C)c1ccc2c(c1)CCNC2\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"Cc1cc(OC(C)C)ccc1CBr\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"Cc1cc(OC(C)C)ccc1CBr was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Cc1cc(OC(C)C)ccc1CBr\", \"reactants\": [\"Br\", \"Cc1cc(OC(C)C)ccc1CO\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"Br\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"Cc1cc(OC(C)C)ccc1CO\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"CPELXLSAUQHCOX-UHFFFAOYSA-N.HEKYVTPIWQQXAF-UHFFFAOYSA-N>>IWWLNRLMXMJGNR-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"Cc1cc(OC(C)C)ccc1CBr\", \"reactants\": [\"Br\", \"Cc1cc(OC(C)C)ccc1CO\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"Br\", \"results\": [{\"inchikey\": \"CPELXLSAUQHCOX-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Br\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"Cc1cc(OC(C)C)ccc1CO\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Cc1cc(OC(C)C)ccc1CO was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Cc1cc(OC(C)C)ccc1CO\", \"reactants\": [\"Cc1cc(OC(C)C)ccc1C=O\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"Cc1cc(OC(C)C)ccc1C=O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_complete\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"HPZOYTGEBKZHCI-UHFFFAOYSA-N>>HEKYVTPIWQQXAF-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"Cc1cc(OC(C)C)ccc1CO\", \"reactants\": [\"Cc1cc(OC(C)C)ccc1C=O\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"Cc1cc(OC(C)C)ccc1C=O\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"Cc1cc(OC(C)C)ccc1C=O was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Cc1cc(OC(C)C)ccc1C=O\", \"reactants\": [\"CN(C)C=O\", \"Cc1cccc(OC(C)C)c1\"]}","name":"validate_disconnection"},"id":"call_4_0","type":"function"},{"function":{"arguments":"{\"query\": \"CN(C)C=O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_1","type":"function"},{"function":{"arguments":"{\"query\": \"Cc1cccc(OC(C)C)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"HZLKLSRFTPNXMY-UHFFFAOYSA-N.ZMXDDKWLCZADIW-UHFFFAOYSA-N>>HPZOYTGEBKZHCI-UHFFFAOYSA-N\", \"model_turns_remaining\": 12, \"product\": \"Cc1cc(OC(C)C)ccc1C=O\", \"reactants\": [\"CN(C)C=O\", \"Cc1cccc(OC(C)C)c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_4_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"CN(C)C=O\", \"results\": [{\"inchikey\": \"ZMXDDKWLCZADIW-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CN(C)C=O\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"Cc1cccc(OC(C)C)c1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_2"},{"content":"Cc1cccc(OC(C)C)c1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Cc1cccc(OC(C)C)c1\", \"reactants\": [\"CC(C)Br\", \"Cc1cccc(O)c1\"]}","name":"validate_disconnection"},"id":"call_5_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)Br\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_5_1","type":"function"},{"function":{"arguments":"{\"query\": \"Cc1cccc(O)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_5_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"NAMYKGVDVNBCFQ-UHFFFAOYSA-N.RLSSMJSEOOYNOY-UHFFFAOYSA-N>>HZLKLSRFTPNXMY-UHFFFAOYSA-N\", \"model_turns_remaining\": 11, \"product\": \"Cc1cccc(OC(C)C)c1\", \"reactants\": [\"CC(C)Br\", \"Cc1cccc(O)c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_5_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 11, \"query\": \"CC(C)Br\", \"results\": [{\"inchikey\": \"NAMYKGVDVNBCFQ-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CC(C)Br\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_5_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 11, \"query\": \"Cc1cccc(O)c1\", \"results\": [{\"inchikey\": \"RLSSMJSEOOYNOY-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Cc1cccc(O)c1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_5_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CC(=O)NC(C)c1ccc2c(c1)CCN(Cc1ccc(OC(C)C)cc1C)C2\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(=O)NC(C)c1ccc2c(c1)CCNC2\": \"precursor\", \"Cc1cc(OC(C)C)ccc1CBr\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(=O)NC(C)c1ccc2c(c1)CCNC2\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"Cc1cc(OC(C)C)ccc1CBr\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"Br\": \"precursor\", \"Cc1cc(OC(C)C)ccc1CO\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"Br\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"Cc1cc(OC(C)C)ccc1CO\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"Cc1cc(OC(C)C)ccc1C=O\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"Cc1cc(OC(C)C)ccc1C=O\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CN(C)C=O\": \"precursor\", \"Cc1cccc(OC(C)C)c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CN(C)C=O\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"Cc1cccc(OC(C)C)c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)Br\": \"precursor\", \"Cc1cccc(O)c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)Br\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"Cc1cccc(O)c1\", \"in_stock\": true, \"children\": []}]}]}]}]}]}]}]}]}]}]}]}}","name":"emit_routes"},"id":"call_6_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"CC(=O)NC(C)c1ccc2c(c1)CCN(Cc1ccc(OC(C)C)cc1C)C2","task_id":"retro_bf1362a3e29de115ea88","tool_calls":15,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":6}
{"exact_match":true,"id":"retro_bf4dd37995e83b65e131:reference-expert:a0","kind":"single_route","max_steps":3,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target Cc1cc(CN(CCC(C)C)C(=O)OC(C)(C)C)ccc1-c1ccc(NS(C)(=O)=O)cc1 in at most 3 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Cc1cc(CN(CCC(C)C)C(=O)OC(C)(C)C)ccc1-c1ccc(NS(C)(=O)=O)cc1\", \"reactants\": [\"CS(=O)(=O)Cl\", \"Cc1cc(CN(CCC(C)C)C(=O)OC(C)(C)C)ccc1-c1ccc(N)cc1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CS(=O)(=O)Cl\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"Cc1cc(CN(CCC(C)C)C(=O)OC(C)(C)C)ccc1-c1ccc(N)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"QARBMVPHQWIHKH-UHFFFAOYSA-N.YDFLSEBOUOMLLZ-UHFFFAOYSA-N>>UCSJVFXBQXXHFN-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"Cc1cc(CN(CCC(C)C)C(=O)OC(C)(C)C)ccc1-c1ccc(NS(C)(=O)=O)cc1\", \"reactants\": [\"CS(=O)(=O)Cl\", \"Cc1cc(CN(CCC(C)C)C(=O)OC(C)(C)C)ccc1-c1ccc(N)cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CS(=O)(=O)Cl\", \"results\": [{\"inchikey\": \"QARBMVPHQWIHKH-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CS(=O)(=O)Cl\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"Cc1cc(CN(CCC(C)C)C(=O)OC(C)(C)C)ccc1-c1ccc(N)cc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"Cc1cc(CN(CCC(C)C)C(=O)OC(C)(C)C)ccc1-c1ccc(N)cc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Cc1cc(CN(CCC(C)C)C(=O)OC(C)(C)C)ccc1-c1ccc(N)cc1\", \"reactants\": [\"Cc1cc(CN(CCC(C)C)C(=O)OC(C)(C)C)ccc1-c1ccc([N+](=O)[O-])cc1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"Cc1cc(CN(CCC(C)C)C(=O)OC(C)(C)C)ccc1-c1ccc([N+](=O)[O-])cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"SNBCCMBSDDOORG-UHFFFAOYSA-N>>YDFLSEBOUOMLLZ-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"Cc1cc(CN(CCC(C)C)C(=O)OC(C)(C)C)ccc1-c1ccc(N)cc1\", \"reactants\": [\"Cc1cc(CN(CCC(C)C)C(=O)OC(C)(C)C)ccc1-c1ccc([N+](=O)[O-])cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"Cc1cc(CN(CCC(C)C)C(=O)OC(C)(C)C)ccc1-c1ccc([N+](=O)[O-])cc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"Cc1cc(CN(CCC(C)C)C(=O)OC(C)(C)C)ccc1-c1ccc([N+](=O)[O-])cc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Cc1cc(CN(CCC(C)C)C(=O)OC(C)(C)C)ccc1-c1ccc([N+](=O)[O-])cc1\", \"reactants\": [\"Cc1cc(CN(CCC(C)C)C(=O)OC(C)(C)C)ccc1Br\", \"O=[N+]([O-])c1ccc(B(O)O)cc1\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"Cc1cc(CN(CCC(C)C)C(=O)OC(C)(C)C)ccc1Br\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=[N+]([O-])c1ccc(B(O)O)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"NSFJAFZHYOAMHL-UHFFFAOYSA-N.QZQYQXINEZIYBM-UHFFFAOYSA-N>>SNBCCMBSDDOORG-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"Cc1cc(CN(CCC(C)C)C(=O)OC(C)(C)C)ccc1-c1ccc([N+](=O)[O-])cc1\", \"reactants\": [\"Cc1cc(CN(CCC(C)C)C(=O)OC(C)(C)C)ccc1Br\", \"O=[N+]([O-])c1ccc(B(O)O)cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"Cc1cc(CN(CCC(C)C)C(=O)OC(C)(C)C)ccc1Br\", \"results\": [{\"inchikey\": \"QZQYQXINEZIYBM-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Cc1cc(CN(CCC(C)C)C(=O)OC(C)(C)C)ccc1Br\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"O=[N+]([O-])c1ccc(B(O)O)cc1\", \"results\": [{\"inchikey\": \"NSFJAFZHYOAMHL-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=[N+]([O-])c1ccc(B(O)O)cc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"Cc1cc(CN(CCC(C)C)C(=O)OC(C)(C)C)ccc1-c1ccc(NS(C)(=O)=O)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CS(=O)(=O)Cl\": \"precursor\", \"Cc1cc(CN(CCC(C)C)C(=O)OC(C)(C)C)ccc1-c1ccc(N)cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CS(=O)(=O)Cl\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"Cc1cc(CN(CCC(C)C)C(=O)OC(C)(C)C)ccc1-c1ccc(N)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"Cc1cc(CN(CCC(C)C)C(=O)OC(C)(C)C)ccc1-c1ccc([N+](=O)[O-])cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"Cc1cc(CN(CCC(C)C)C(=O)OC(C)(C)C)ccc1-c1ccc([N+](=O)[O-])cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"Cc1cc(CN(CCC(C)C)C(=O)OC(C)(C)C)ccc1Br\": \"precursor\", \"O=[N+]([O-])c1ccc(B(O)O)cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"Cc1cc(CN(CCC(C)C)C(=O)OC(C)(C)C)ccc1Br\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=[N+]([O-])c1ccc(B(O)O)cc1\", \"in_stock\": true, \"children\": []}]}]}]}]}]}]}]}}","name":"emit_routes"},"id":"call_4_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"Cc1cc(CN(CCC(C)C)C(=O)OC(C)(C)C)ccc1-c1ccc(NS(C)(=O)=O)cc1","task_id":"retro_bf4dd37995e83b65e131","tool_calls":9,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":4}
{"exact_match":true,"id":"retro_bf71fca3190406442e18:reference-expert:a0","kind":"single_route","max_steps":3,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target Cn1c(=O)n(C)c2cc(Oc3cccc(OCC4CCN(C(=O)OC(C)(C)C)CC4)c3)c(N)cc21 in at most 3 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Cn1c(=O)n(C)c2cc(Oc3cccc(OCC4CCN(C(=O)OC(C)(C)C)CC4)c3)c(N)cc21\", \"reactants\": [\"CC(C)(C)OC(=O)N1CCC(CBr)CC1\", \"Cn1c(=O)n(C)c2cc(Oc3cccc(O)c3)c(N)cc21\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)OC(=O)N1CCC(CBr)CC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"Cn1c(=O)n(C)c2cc(Oc3cccc(O)c3)c(N)cc21\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"ILTFHEUCZSGPQB-UHFFFAOYSA-N.YGJXBTRLYHCWGD-UHFFFAOYSA-N>>LUJXUEXMVWWISJ-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"Cn1c(=O)n(C)c2cc(Oc3cccc(OCC4CCN(C(=O)OC(C)(C)C)CC4)c3)c(N)cc21\", \"reactants\": [\"CC(C)(C)OC(=O)N1CCC(CBr)CC1\", \"Cn1c(=O)n(C)c2cc(Oc3cccc(O)c3)c(N)cc21\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CC(C)(C)OC(=O)N1CCC(CBr)CC1\", \"results\": [{\"inchikey\": \"YGJXBTRLYHCWGD-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CC(C)(C)OC(=O)N1CCC(CBr)CC1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"Cn1c(=O)n(C)c2cc(Oc3cccc(O)c3)c(N)cc21\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"Cn1c(=O)n(C)c2cc(Oc3cccc(O)c3)c(N)cc21 was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Cn1c(=O)n(C)c2cc(Oc3cccc(O)c3)c(N)cc21\", \"reactants\": [\"Cn1c(=O)n(C)c2cc(Oc3cccc(OCc4ccccc4)c3)c(N)cc21\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"Cn1c(=O)n(C)c2cc(Oc3cccc(OCc4ccccc4)c3)c(N)cc21\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"RQUXTWCPAXSCSP-UHFFFAOYSA-N>>ILTFHEUCZSGPQB-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"Cn1c(=O)n(C)c2cc(Oc3cccc(O)c3)c(N)cc21\", \"reactants\": [\"Cn1c(=O)n(C)c2cc(Oc3cccc(OCc4ccccc4)c3)c(N)cc21\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"Cn1c(=O)n(C)c2cc(Oc3cccc(OCc4ccccc4)c3)c(N)cc21\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"Cn1c(=O)n(C)c2cc(Oc3cccc(OCc4ccccc4)c3)c(N)cc21 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Cn1c(=O)n(C)c2cc(Oc3cccc(OCc4ccccc4)c3)c(N)cc21\", \"reactants\": [\"Cn1c(=O)n(C)c2cc(Br)c(N)cc21\", \"Oc1cccc(OCc2ccccc2)c1\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"Cn1c(=O)n(C)c2cc(Br)c(N)cc21\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"Oc1cccc(OCc2ccccc2)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"FOTVZLOJAIEAOY-UHFFFAOYSA-N.SXPRALARBJCCIH-UHFFFAOYSA-N>>RQUXTWCPAXSCSP-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"Cn1c(=O)n(C)c2cc(Oc3cccc(OCc4ccccc4)c3)c(N)cc21\", \"reactants\": [\"Cn1c(=O)n(C)c2cc(Br)c(N)cc21\", \"Oc1cccc(OCc2ccccc2)c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"Cn1c(=O)n(C)c2cc(Br)c(N)cc21\", \"results\": [{\"inchikey\": \"SXPRALARBJCCIH-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Cn1c(=O)n(C)c2cc(Br)c(N)cc21\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"Oc1cccc(OCc2ccccc2)c1\", \"results\": [{\"inchikey\": \"FOTVZLOJAIEAOY-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Oc1cccc(OCc2ccccc2)c1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"Cn1c(=O)n(C)c2cc(Oc3cccc(OCC4CCN(C(=O)OC(C)(C)C)CC4)c3)c(N)cc21\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)(C)OC(=O)N1CCC(CBr)CC1\": \"precursor\", \"Cn1c(=O)n(C)c2cc(Oc3cccc(O)c3)c(N)cc21\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)OC(=O)N1CCC(CBr)CC1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"Cn1c(=O)n(C)c2cc(Oc3cccc(O)c3)c(N)cc21\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"Cn1c(=O)n(C)c2cc(Oc3cccc(OCc4ccccc4)c3)c(N)cc21\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"Cn1c(=O)n(C)c2cc(Oc3cccc(OCc4ccccc4)c3)c(N)cc21\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"Cn1c(=O)n(C)c2cc(Br)c(N)cc21\": \"precursor\", \"Oc1cccc(OCc2ccccc2)c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"Cn1c(=O)n(C)c2cc(Br)c(N)cc21\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"Oc1cccc(OCc2ccccc2)c1\", \"in_stock\": true, \"children\": []}]}]}]}]}]}]}]}}","name":"emit_routes"},"id":"call_4_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"Cn1c(=O)n(C)c2cc(Oc3cccc(OCC4CCN(C(=O)OC(C)(C)C)CC4)c3)c(N)cc21","task_id":"retro_bf71fca3190406442e18","tool_calls":9,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":4}
{"exact_match":true,"id":"retro_c0924fc2e1680464f3d6:reference-expert:a0","kind":"single_route","max_steps":4,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target O=S(=O)(c1ccc(/C=C/c2ccc(O)c(O)c2)cc1)N1CCOCC1 in at most 4 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"O=S(=O)(c1ccc(/C=C/c2ccc(O)c(O)c2)cc1)N1CCOCC1\", \"reactants\": [\"COCOc1ccc(/C=C/c2ccc(S(=O)(=O)N3CCOCC3)cc2)cc1OCOC\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"COCOc1ccc(/C=C/c2ccc(S(=O)(=O)N3CCOCC3)cc2)cc1OCOC\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"JVUAXIBSQOYZIJ-ONEGZZNKSA-N>>CMLINKKZFDNJOE-OWOJBTEDSA-N\", \"model_turns_remaining\": 15, \"product\": \"O=S(=O)(c1ccc(/C=C/c2ccc(O)c(O)c2)cc1)N1CCOCC1\", \"reactants\": [\"COCOc1ccc(/C=C/c2ccc(S(=O)(=O)N3CCOCC3)cc2)cc1OCOC\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"COCOc1ccc(/C=C/c2ccc(S(=O)(=O)N3CCOCC3)cc2)cc1OCOC\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"COCOc1ccc(/C=C/c2ccc(S(=O)(=O)N3CCOCC3)cc2)cc1OCOC was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COCOc1ccc(/C=C/c2ccc(S(=O)(=O)N3CCOCC3)cc2)cc1OCOC\", \"reactants\": [\"C=Cc1ccc(OCOC)c(OCOC)c1\", \"O=S(=O)(c1ccc(Br)cc1)N1CCOCC1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"C=Cc1ccc(OCOC)c(OCOC)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=S(=O)(c1ccc(Br)cc1)N1CCOCC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"AWKQRSNBDFPHKY-UHFFFAOYSA-N.JWJRLABLXQZFAR-UHFFFAOYSA-N>>JVUAXIBSQOYZIJ-ONEGZZNKSA-N\", \"model_turns_remaining\": 14, \"product\": \"COCOc1ccc(/C=C/c2ccc(S(=O)(=O)N3CCOCC3)cc2)cc1OCOC\", \"reactants\": [\"C=Cc1ccc(OCOC)c(OCOC)c1\", \"O=S(=O)(c1ccc(Br)cc1)N1CCOCC1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"C=Cc1ccc(OCOC)c(OCOC)c1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"O=S(=O)(c1ccc(Br)cc1)N1CCOCC1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"C=Cc1ccc(OCOC)c(OCOC)c1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"C=Cc1ccc(OCOC)c(OCOC)c1\", \"reactants\": [\"COCOc1ccc(C=O)cc1OCOC\", \"C[P+](c1ccccc1)(c1ccccc1)c1ccccc1\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"COCOc1ccc(C=O)cc1OCOC\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"C[P+](c1ccccc1)(c1ccccc1)c1ccccc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"AZFQCTBZOPUVOW-UHFFFAOYSA-N.RYTSFSLVJDNOHI-UHFFFAOYSA-N>>AWKQRSNBDFPHKY-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"C=Cc1ccc(OCOC)c(OCOC)c1\", \"reactants\": [\"COCOc1ccc(C=O)cc1OCOC\", \"C[P+](c1ccccc1)(c1ccccc1)c1ccccc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"COCOc1ccc(C=O)cc1OCOC\", \"results\": [{\"inchikey\": \"RYTSFSLVJDNOHI-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"COCOc1ccc(C=O)cc1OCOC\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"C[P+](c1ccccc1)(c1ccccc1)c1ccccc1\", \"results\": [{\"inchikey\": \"AZFQCTBZOPUVOW-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"C[P+](c1ccccc1)(c1ccccc1)c1ccccc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"O=S(=O)(c1ccc(Br)cc1)N1CCOCC1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"O=S(=O)(c1ccc(Br)cc1)N1CCOCC1\", \"reactants\": [\"C1COCCN1\", \"O=S(=O)(Cl)c1ccc(Br)cc1\"]}","name":"validate_disconnection"},"id":"call_4_0","type":"function"},{"function":{"arguments":"{\"query\": \"C1COCCN1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=S(=O)(Cl)c1ccc(Br)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"KMMHZIBWCXYAAH-UHFFFAOYSA-N.YNAVUWVOSKDBBP-UHFFFAOYSA-N>>JWJRLABLXQZFAR-UHFFFAOYSA-N\", \"model_turns_remaining\": 12, \"product\": \"O=S(=O)(c1ccc(Br)cc1)N1CCOCC1\", \"reactants\": [\"C1COCCN1\", \"O=S(=O)(Cl)c1ccc(Br)cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_4_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"C1COCCN1\", \"results\": [{\"inchikey\": \"YNAVUWVOSKDBBP-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"C1COCCN1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"O=S(=O)(Cl)c1ccc(Br)cc1\", \"results\": [{\"inchikey\": \"KMMHZIBWCXYAAH-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=S(=O)(Cl)c1ccc(Br)cc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"O=S(=O)(c1ccc(/C=C/c2ccc(O)c(O)c2)cc1)N1CCOCC1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COCOc1ccc(/C=C/c2ccc(S(=O)(=O)N3CCOCC3)cc2)cc1OCOC\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COCOc1ccc(/C=C/c2ccc(S(=O)(=O)N3CCOCC3)cc2)cc1OCOC\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"C=Cc1ccc(OCOC)c(OCOC)c1\": \"precursor\", \"O=S(=O)(c1ccc(Br)cc1)N1CCOCC1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"C=Cc1ccc(OCOC)c(OCOC)c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COCOc1ccc(C=O)cc1OCOC\": \"precursor\", \"C[P+](c1ccccc1)(c1ccccc1)c1ccccc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COCOc1ccc(C=O)cc1OCOC\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"C[P+](c1ccccc1)(c1ccccc1)c1ccccc1\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"O=S(=O)(c1ccc(Br)cc1)N1CCOCC1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"C1COCCN1\": \"precursor\", \"O=S(=O)(Cl)c1ccc(Br)cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"C1COCCN1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=S(=O)(Cl)c1ccc(Br)cc1\", \"in_stock\": true, \"children\": []}]}]}]}]}]}]}]}}","name":"emit_routes"},"id":"call_5_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"O=S(=O)(c1ccc(/C=C/c2ccc(O)c(O)c2)cc1)N1CCOCC1","task_id":"retro_c0924fc2e1680464f3d6","tool_calls":12,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":5}
{"exact_match":true,"id":"retro_c09480b588a9541ae1cc:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CC(C)(C)c1cc(N)cc(C(C)(C)C)c1O in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(C)(C)c1cc(N)cc(C(C)(C)C)c1O\", \"reactants\": [\"CC(C)(C)c1cc([N+](=O)[O-])cc(C(C)(C)C)c1O\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)c1cc([N+](=O)[O-])cc(C(C)(C)C)c1O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"FCGKUUOTWLWJHE-UHFFFAOYSA-N>>MNDTVJMRXYKBPV-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"CC(C)(C)c1cc(N)cc(C(C)(C)C)c1O\", \"reactants\": [\"CC(C)(C)c1cc([N+](=O)[O-])cc(C(C)(C)C)c1O\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CC(C)(C)c1cc([N+](=O)[O-])cc(C(C)(C)C)c1O\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"CC(C)(C)c1cc([N+](=O)[O-])cc(C(C)(C)C)c1O was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(C)(C)c1cc([N+](=O)[O-])cc(C(C)(C)C)c1O\", \"reactants\": [\"CC(C)(C)c1cccc(C(C)(C)C)c1O\", \"O=[N+]([O-])O\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)c1cccc(C(C)(C)C)c1O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=[N+]([O-])O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"DKCPKDPYUFEZCP-UHFFFAOYSA-N.GRYLNZFGIOXLOG-UHFFFAOYSA-N>>FCGKUUOTWLWJHE-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"CC(C)(C)c1cc([N+](=O)[O-])cc(C(C)(C)C)c1O\", \"reactants\": [\"CC(C)(C)c1cccc(C(C)(C)C)c1O\", \"O=[N+]([O-])O\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CC(C)(C)c1cccc(C(C)(C)C)c1O\", \"results\": [{\"inchikey\": \"DKCPKDPYUFEZCP-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CC(C)(C)c1cccc(C(C)(C)C)c1O\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"O=[N+]([O-])O\", \"results\": [{\"inchikey\": \"GRYLNZFGIOXLOG-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=[N+]([O-])O\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)c1cc(N)cc(C(C)(C)C)c1O\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)(C)c1cc([N+](=O)[O-])cc(C(C)(C)C)c1O\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)c1cc([N+](=O)[O-])cc(C(C)(C)C)c1O\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)(C)c1cccc(C(C)(C)C)c1O\": \"precursor\", \"O=[N+]([O-])O\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)c1cccc(C(C)(C)C)c1O\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=[N+]([O-])O\", \"in_stock\": true, \"children\": []}]}]}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"CC(C)(C)c1cc(N)cc(C(C)(C)C)c1O","task_id":"retro_c09480b588a9541ae1cc","tool_calls":6,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":false,"id":"retro_c1b5fb6b444236accc12:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target COC(=O)c1ccc(OS(=O)(=O)C(F)(F)F)c(Cl)c1 in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COC(=O)c1ccc(OS(=O)(=O)C(F)(F)F)c(Cl)c1\", \"reactants\": [\"COC(=O)c1ccc(O)c(Cl)c1\", \"O=S(=O)(N(c1ccccc1)S(=O)(=O)C(F)(F)F)C(F)(F)F\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"COC(=O)c1ccc(O)c(Cl)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=S(=O)(N(c1ccccc1)S(=O)(=O)C(F)(F)F)C(F)(F)F\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"DIOHEXPTUTVCNX-UHFFFAOYSA-N.ZSBIMTDWIGWJPW-UHFFFAOYSA-N>>JJEJBUNCUNIKPV-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"COC(=O)c1ccc(OS(=O)(=O)C(F)(F)F)c(Cl)c1\", \"reactants\": [\"COC(=O)c1ccc(O)c(Cl)c1\", \"O=S(=O)(N(c1ccccc1)S(=O)(=O)C(F)(F)F)C(F)(F)F\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"COC(=O)c1ccc(O)c(Cl)c1\", \"results\": [{\"inchikey\": \"ZSBIMTDWIGWJPW-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"COC(=O)c1ccc(O)c(Cl)c1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"O=S(=O)(N(c1ccccc1)S(=O)(=O)C(F)(F)F)C(F)(F)F\", \"results\": [{\"inchikey\": \"DIOHEXPTUTVCNX-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=S(=O)(N(c1ccccc1)S(=O)(=O)C(F)(F)F)C(F)(F)F\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"COC(=O)c1ccc(OS(=O)(=O)C(F)(F)F)c(Cl)c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COC(=O)c1ccc(O)c(Cl)c1\": \"precursor\", \"O=S(=O)(N(c1ccccc1)S(=O)(=O)C(F)(F)F)C(F)(F)F\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COC(=O)c1ccc(O)c(Cl)c1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=S(=O)(N(c1ccccc1)S(=O)(=O)C(F)(F)F)C(F)(F)F\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_2_0","type":"function"}]}],"provider":"reference","reward":0.85,"source":"reference-expert","target_smiles":"COC(=O)c1ccc(OS(=O)(=O)C(F)(F)F)c(Cl)c1","task_id":"retro_c1b5fb6b444236accc12","tool_calls":4,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":2}
{"exact_match":true,"id":"retro_c2115312b1fd2954d733:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CS(=O)(=O)OC1CCOC(c2ccc(Cl)cc2Br)C1 in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CS(=O)(=O)OC1CCOC(c2ccc(Cl)cc2Br)C1\", \"reactants\": [\"CS(=O)(=O)Cl\", \"OC1CCOC(c2ccc(Cl)cc2Br)C1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CS(=O)(=O)Cl\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"OC1CCOC(c2ccc(Cl)cc2Br)C1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"HMTKYJYCRZSFJU-UHFFFAOYSA-N.QARBMVPHQWIHKH-UHFFFAOYSA-N>>PRCOWESPVPJBKM-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"CS(=O)(=O)OC1CCOC(c2ccc(Cl)cc2Br)C1\", \"reactants\": [\"CS(=O)(=O)Cl\", \"OC1CCOC(c2ccc(Cl)cc2Br)C1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CS(=O)(=O)Cl\", \"results\": [{\"inchikey\": \"QARBMVPHQWIHKH-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CS(=O)(=O)Cl\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"OC1CCOC(c2ccc(Cl)cc2Br)C1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"OC1CCOC(c2ccc(Cl)cc2Br)C1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"OC1CCOC(c2ccc(Cl)cc2Br)C1\", \"reactants\": [\"C=CCCO\", \"O=Cc1ccc(Cl)cc1Br\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"C=CCCO\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=Cc1ccc(Cl)cc1Br\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_complete\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"AJOAHIKYBSZIEV-UHFFFAOYSA-N.ZSPTYLOMNJNZNG-UHFFFAOYSA-N>>HMTKYJYCRZSFJU-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"OC1CCOC(c2ccc(Cl)cc2Br)C1\", \"reactants\": [\"C=CCCO\", \"O=Cc1ccc(Cl)cc1Br\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"C=CCCO\", \"results\": [{\"inchikey\": \"ZSPTYLOMNJNZNG-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"C=CCCO\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"O=Cc1ccc(Cl)cc1Br\", \"results\": [{\"inchikey\": \"AJOAHIKYBSZIEV-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=Cc1ccc(Cl)cc1Br\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CS(=O)(=O)OC1CCOC(c2ccc(Cl)cc2Br)C1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CS(=O)(=O)Cl\": \"precursor\", \"OC1CCOC(c2ccc(Cl)cc2Br)C1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CS(=O)(=O)Cl\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"OC1CCOC(c2ccc(Cl)cc2Br)C1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"C=CCCO\": \"precursor\", \"O=Cc1ccc(Cl)cc1Br\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"C=CCCO\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=Cc1ccc(Cl)cc1Br\", \"in_stock\": true, \"children\": []}]}]}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"CS(=O)(=O)OC1CCOC(c2ccc(Cl)cc2Br)C1","task_id":"retro_c2115312b1fd2954d733","tool_calls":7,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_c2bc914c39c4c799d1a2:reference-expert:a0","kind":"single_route","max_steps":3,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target Cc1ccc2nc(-c3ccc(C=O)cc3)cn2c1 in at most 3 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Cc1ccc2nc(-c3ccc(C=O)cc3)cn2c1\", \"reactants\": [\"CO\", \"Cc1ccc2nc(-c3ccc(C#N)cc3)cn2c1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CO\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"Cc1ccc2nc(-c3ccc(C#N)cc3)cn2c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"OKKJLVBELUTLKV-UHFFFAOYSA-N.URUGTBXSBNZLKJ-UHFFFAOYSA-N>>RPJOPDMVXDGVQQ-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"Cc1ccc2nc(-c3ccc(C=O)cc3)cn2c1\", \"reactants\": [\"CO\", \"Cc1ccc2nc(-c3ccc(C#N)cc3)cn2c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CO\", \"results\": [{\"inchikey\": \"OKKJLVBELUTLKV-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CO\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"Cc1ccc2nc(-c3ccc(C#N)cc3)cn2c1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"Cc1ccc2nc(-c3ccc(C#N)cc3)cn2c1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Cc1ccc2nc(-c3ccc(C#N)cc3)cn2c1\", \"reactants\": [\"Cc1ccc2nc(-c3ccc(Br)cc3)cn2c1\", \"N#[C][Cu]\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"Cc1ccc2nc(-c3ccc(Br)cc3)cn2c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"N#[C][Cu]\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"DULSAGLWMRMKCQ-UHFFFAOYSA-N.OUTIKDPVXLJCLK-UHFFFAOYSA-N>>URUGTBXSBNZLKJ-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"Cc1ccc2nc(-c3ccc(C#N)cc3)cn2c1\", \"reactants\": [\"Cc1ccc2nc(-c3ccc(Br)cc3)cn2c1\", \"N#[C][Cu]\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"Cc1ccc2nc(-c3ccc(Br)cc3)cn2c1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"N#[C][Cu]\", \"results\": [{\"inchikey\": \"DULSAGLWMRMKCQ-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"N#[C][Cu]\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Cc1ccc2nc(-c3ccc(Br)cc3)cn2c1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Cc1ccc2nc(-c3ccc(Br)cc3)cn2c1\", \"reactants\": [\"Cc1ccc(N)nc1\", \"O=C(CBr)c1ccc(Br)cc1\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"Cc1ccc(N)nc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=C(CBr)c1ccc(Br)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"CMBSSVKZOPZBKW-UHFFFAOYSA-N.FKJSFKCZZIXQIP-UHFFFAOYSA-N>>OUTIKDPVXLJCLK-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"Cc1ccc2nc(-c3ccc(Br)cc3)cn2c1\", \"reactants\": [\"Cc1ccc(N)nc1\", \"O=C(CBr)c1ccc(Br)cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"Cc1ccc(N)nc1\", \"results\": [{\"inchikey\": \"CMBSSVKZOPZBKW-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Cc1ccc(N)nc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"O=C(CBr)c1ccc(Br)cc1\", \"results\": [{\"inchikey\": \"FKJSFKCZZIXQIP-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=C(CBr)c1ccc(Br)cc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"Cc1ccc2nc(-c3ccc(C=O)cc3)cn2c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CO\": \"precursor\", \"Cc1ccc2nc(-c3ccc(C#N)cc3)cn2c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CO\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"Cc1ccc2nc(-c3ccc(C#N)cc3)cn2c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"Cc1ccc2nc(-c3ccc(Br)cc3)cn2c1\": \"precursor\", \"N#[C][Cu]\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"Cc1ccc2nc(-c3ccc(Br)cc3)cn2c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"Cc1ccc(N)nc1\": \"precursor\", \"O=C(CBr)c1ccc(Br)cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"Cc1ccc(N)nc1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=C(CBr)c1ccc(Br)cc1\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"N#[C][Cu]\", \"in_stock\": true, \"children\": []}]}]}]}]}]}}","name":"emit_routes"},"id":"call_4_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"Cc1ccc2nc(-c3ccc(C=O)cc3)cn2c1","task_id":"retro_c2bc914c39c4c799d1a2","tool_calls":10,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":4}
{"exact_match":true,"id":"retro_c2c4cbe1537a76185b1f:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target Fc1cc(SC2CCC2)ccc1Br in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Fc1cc(SC2CCC2)ccc1Br\", \"reactants\": [\"BrC1CCC1\", \"Fc1cc(S)ccc1Br\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"BrC1CCC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"Fc1cc(S)ccc1Br\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"KXVUSQIDCZRUKF-UHFFFAOYSA-N.QWSUMJXRROQYPN-UHFFFAOYSA-N>>FKKQIESWVZUGBW-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"Fc1cc(SC2CCC2)ccc1Br\", \"reactants\": [\"BrC1CCC1\", \"Fc1cc(S)ccc1Br\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"BrC1CCC1\", \"results\": [{\"inchikey\": \"KXVUSQIDCZRUKF-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"BrC1CCC1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"Fc1cc(S)ccc1Br\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"Fc1cc(S)ccc1Br was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Fc1cc(S)ccc1Br\", \"reactants\": [\"O=S(=O)(Cl)c1ccc(Br)c(F)c1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"O=S(=O)(Cl)c1ccc(Br)c(F)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"IZCXVIACMHTZNA-UHFFFAOYSA-N>>QWSUMJXRROQYPN-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"Fc1cc(S)ccc1Br\", \"reactants\": [\"O=S(=O)(Cl)c1ccc(Br)c(F)c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"O=S(=O)(Cl)c1ccc(Br)c(F)c1\", \"results\": [{\"inchikey\": \"IZCXVIACMHTZNA-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=S(=O)(Cl)c1ccc(Br)c(F)c1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"Fc1cc(SC2CCC2)ccc1Br\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"BrC1CCC1\": \"precursor\", \"Fc1cc(S)ccc1Br\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"BrC1CCC1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"Fc1cc(S)ccc1Br\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"O=S(=O)(Cl)c1ccc(Br)c(F)c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"O=S(=O)(Cl)c1ccc(Br)c(F)c1\", \"in_stock\": true, \"children\": []}]}]}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"Fc1cc(SC2CCC2)ccc1Br","task_id":"retro_c2c4cbe1537a76185b1f","tool_calls":6,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_c7801f205928888805b9:reference-expert:a0","kind":"single_route","max_steps":4,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target Cc1cc(Oc2ccc(F)cc2)cc(C)c1-c1csc(N)n1 in at most 4 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Cc1cc(Oc2ccc(F)cc2)cc(C)c1-c1csc(N)n1\", \"reactants\": [\"Cc1cc(Oc2ccc(F)cc2)cc(C)c1C(=O)CBr\", \"NC(N)=S\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"Cc1cc(Oc2ccc(F)cc2)cc(C)c1C(=O)CBr\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"NC(N)=S\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"UMGDCJDMYOKAJW-UHFFFAOYSA-N.ZNRYPXSEYMVXGZ-UHFFFAOYSA-N>>ATLRDTJFWFUUSF-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"Cc1cc(Oc2ccc(F)cc2)cc(C)c1-c1csc(N)n1\", \"reactants\": [\"Cc1cc(Oc2ccc(F)cc2)cc(C)c1C(=O)CBr\", \"NC(N)=S\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"Cc1cc(Oc2ccc(F)cc2)cc(C)c1C(=O)CBr\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"NC(N)=S\", \"results\": [{\"inchikey\": \"UMGDCJDMYOKAJW-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"NC(N)=S\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"Cc1cc(Oc2ccc(F)cc2)cc(C)c1C(=O)CBr was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Cc1cc(Oc2ccc(F)cc2)cc(C)c1C(=O)CBr\", \"reactants\": [\"Br\", \"CC(=O)c1c(C)cc(Oc2ccc(F)cc2)cc1C\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"Br\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"CC(=O)c1c(C)cc(Oc2ccc(F)cc2)cc1C\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_complete\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"CPELXLSAUQHCOX-UHFFFAOYSA-N.MZDDCRHTCBJZRZ-UHFFFAOYSA-N>>ZNRYPXSEYMVXGZ-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"Cc1cc(Oc2ccc(F)cc2)cc(C)c1C(=O)CBr\", \"reactants\": [\"Br\", \"CC(=O)c1c(C)cc(Oc2ccc(F)cc2)cc1C\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"Br\", \"results\": [{\"inchikey\": \"CPELXLSAUQHCOX-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Br\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CC(=O)c1c(C)cc(Oc2ccc(F)cc2)cc1C\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"CC(=O)c1c(C)cc(Oc2ccc(F)cc2)cc1C was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(=O)c1c(C)cc(Oc2ccc(F)cc2)cc1C\", \"reactants\": [\"CC(=O)c1c(C)cc(Cl)cc1C\", \"Oc1ccc(F)cc1\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(=O)c1c(C)cc(Cl)cc1C\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"Oc1ccc(F)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"RHMPLDJJXGPMEX-UHFFFAOYSA-N.YTPYRGOFBLEEBD-UHFFFAOYSA-N>>MZDDCRHTCBJZRZ-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"CC(=O)c1c(C)cc(Oc2ccc(F)cc2)cc1C\", \"reactants\": [\"CC(=O)c1c(C)cc(Cl)cc1C\", \"Oc1ccc(F)cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"CC(=O)c1c(C)cc(Cl)cc1C\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"Oc1ccc(F)cc1\", \"results\": [{\"inchikey\": \"RHMPLDJJXGPMEX-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Oc1ccc(F)cc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"CC(=O)c1c(C)cc(Cl)cc1C was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(=O)c1c(C)cc(Cl)cc1C\", \"reactants\": [\"CC(=O)c1c(C)cc(N)cc1C\", \"Cl\"]}","name":"validate_disconnection"},"id":"call_4_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(=O)c1c(C)cc(N)cc1C\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_1","type":"function"},{"function":{"arguments":"{\"query\": \"Cl\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"GFVYFAYTYSTBOM-UHFFFAOYSA-N.VEXZGXHMUGYJMC-UHFFFAOYSA-N>>YTPYRGOFBLEEBD-UHFFFAOYSA-N\", \"model_turns_remaining\": 12, \"product\": \"CC(=O)c1c(C)cc(Cl)cc1C\", \"reactants\": [\"CC(=O)c1c(C)cc(N)cc1C\", \"Cl\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_4_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"CC(=O)c1c(C)cc(N)cc1C\", \"results\": [{\"inchikey\": \"GFVYFAYTYSTBOM-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CC(=O)c1c(C)cc(N)cc1C\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"Cl\", \"results\": [{\"inchikey\": \"VEXZGXHMUGYJMC-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Cl\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"Cc1cc(Oc2ccc(F)cc2)cc(C)c1-c1csc(N)n1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"Cc1cc(Oc2ccc(F)cc2)cc(C)c1C(=O)CBr\": \"precursor\", \"NC(N)=S\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"Cc1cc(Oc2ccc(F)cc2)cc(C)c1C(=O)CBr\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"Br\": \"precursor\", \"CC(=O)c1c(C)cc(Oc2ccc(F)cc2)cc1C\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"Br\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"CC(=O)c1c(C)cc(Oc2ccc(F)cc2)cc1C\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(=O)c1c(C)cc(Cl)cc1C\": \"precursor\", \"Oc1ccc(F)cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(=O)c1c(C)cc(Cl)cc1C\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(=O)c1c(C)cc(N)cc1C\": \"precursor\", \"Cl\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(=O)c1c(C)cc(N)cc1C\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"Cl\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"Oc1ccc(F)cc1\", \"in_stock\": true, \"children\": []}]}]}]}]}, {\"type\": \"mol\", \"smiles\": \"NC(N)=S\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_5_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"Cc1cc(Oc2ccc(F)cc2)cc(C)c1-c1csc(N)n1","task_id":"retro_c7801f205928888805b9","tool_calls":13,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":5}
{"exact_match":true,"id":"retro_c787b7ac3498735a976a:reference-expert:a0","kind":"single_route","max_steps":5,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CC(C)(C)OC(=O)N1CCc2c(n(CCNS(=O)(=O)c3ccccc3)c3ccccc23)CC1 in at most 5 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(C)(C)OC(=O)N1CCc2c(n(CCNS(=O)(=O)c3ccccc3)c3ccccc23)CC1\", \"reactants\": [\"CC(C)(C)OC(=O)N1CCc2c(n(CCN)c3ccccc23)CC1\", \"O=S(=O)(Cl)c1ccccc1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)OC(=O)N1CCc2c(n(CCN)c3ccccc23)CC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=S(=O)(Cl)c1ccccc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"CSKNSYBAZOQPLR-UHFFFAOYSA-N.XNKYWALMVSQLEB-UHFFFAOYSA-N>>GYMNGMVCPLXFLP-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"CC(C)(C)OC(=O)N1CCc2c(n(CCNS(=O)(=O)c3ccccc3)c3ccccc23)CC1\", \"reactants\": [\"CC(C)(C)OC(=O)N1CCc2c(n(CCN)c3ccccc23)CC1\", \"O=S(=O)(Cl)c1ccccc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CC(C)(C)OC(=O)N1CCc2c(n(CCN)c3ccccc23)CC1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"O=S(=O)(Cl)c1ccccc1\", \"results\": [{\"inchikey\": \"CSKNSYBAZOQPLR-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=S(=O)(Cl)c1ccccc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"CC(C)(C)OC(=O)N1CCc2c(n(CCN)c3ccccc23)CC1 was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(C)(C)OC(=O)N1CCc2c(n(CCN)c3ccccc23)CC1\", \"reactants\": [\"CC(C)(C)OC(=O)N1CCc2c(n(CCN=[N+]=[N-])c3ccccc23)CC1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)OC(=O)N1CCc2c(n(CCN=[N+]=[N-])c3ccccc23)CC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"XQPUQVBQINRPNM-UHFFFAOYSA-N>>XNKYWALMVSQLEB-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"CC(C)(C)OC(=O)N1CCc2c(n(CCN)c3ccccc23)CC1\", \"reactants\": [\"CC(C)(C)OC(=O)N1CCc2c(n(CCN=[N+]=[N-])c3ccccc23)CC1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CC(C)(C)OC(=O)N1CCc2c(n(CCN=[N+]=[N-])c3ccccc23)CC1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"CC(C)(C)OC(=O)N1CCc2c(n(CCN=[N+]=[N-])c3ccccc23)CC1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(C)(C)OC(=O)N1CCc2c(n(CCN=[N+]=[N-])c3ccccc23)CC1\", \"reactants\": [\"CC(C)(C)OC(=O)N1CCc2c(n(CCOS(C)(=O)=O)c3ccccc23)CC1\", \"[N-]=[N+]=[N-]\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)OC(=O)N1CCc2c(n(CCOS(C)(=O)=O)c3ccccc23)CC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"[N-]=[N+]=[N-]\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"IVRMZWNICZWHMI-UHFFFAOYSA-N.YUJDYHZBAVNJKZ-UHFFFAOYSA-N>>XQPUQVBQINRPNM-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"CC(C)(C)OC(=O)N1CCc2c(n(CCN=[N+]=[N-])c3ccccc23)CC1\", \"reactants\": [\"CC(C)(C)OC(=O)N1CCc2c(n(CCOS(C)(=O)=O)c3ccccc23)CC1\", \"[N-]=[N+]=[N-]\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"CC(C)(C)OC(=O)N1CCc2c(n(CCOS(C)(=O)=O)c3ccccc23)CC1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"[N-]=[N+]=[N-]\", \"results\": [{\"inchikey\": \"IVRMZWNICZWHMI-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"[N-]=[N+]=[N-]\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"CC(C)(C)OC(=O)N1CCc2c(n(CCOS(C)(=O)=O)c3ccccc23)CC1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(C)(C)OC(=O)N1CCc2c(n(CCOS(C)(=O)=O)c3ccccc23)CC1\", \"reactants\": [\"CC(C)(C)OC(=O)N1CCc2c(n(CCO)c3ccccc23)CC1\", \"CS(=O)(=O)Cl\"]}","name":"validate_disconnection"},"id":"call_4_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)OC(=O)N1CCc2c(n(CCO)c3ccccc23)CC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_1","type":"function"},{"function":{"arguments":"{\"query\": \"CS(=O)(=O)Cl\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"QARBMVPHQWIHKH-UHFFFAOYSA-N.YLFWNTUPOXOUSX-UHFFFAOYSA-N>>YUJDYHZBAVNJKZ-UHFFFAOYSA-N\", \"model_turns_remaining\": 12, \"product\": \"CC(C)(C)OC(=O)N1CCc2c(n(CCOS(C)(=O)=O)c3ccccc23)CC1\", \"reactants\": [\"CC(C)(C)OC(=O)N1CCc2c(n(CCO)c3ccccc23)CC1\", \"CS(=O)(=O)Cl\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_4_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"CC(C)(C)OC(=O)N1CCc2c(n(CCO)c3ccccc23)CC1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"CS(=O)(=O)Cl\", \"results\": [{\"inchikey\": \"QARBMVPHQWIHKH-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CS(=O)(=O)Cl\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_2"},{"content":"CC(C)(C)OC(=O)N1CCc2c(n(CCO)c3ccccc23)CC1 was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(C)(C)OC(=O)N1CCc2c(n(CCO)c3ccccc23)CC1\", \"reactants\": [\"CCOC(=O)Cn1c2c(c3ccccc31)CCN(C(=O)OC(C)(C)C)CC2\"]}","name":"validate_disconnection"},"id":"call_5_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCOC(=O)Cn1c2c(c3ccccc31)CCN(C(=O)OC(C)(C)C)CC2\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_5_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"FDMRONLLVLVFFI-UHFFFAOYSA-N>>YLFWNTUPOXOUSX-UHFFFAOYSA-N\", \"model_turns_remaining\": 11, \"product\": \"CC(C)(C)OC(=O)N1CCc2c(n(CCO)c3ccccc23)CC1\", \"reactants\": [\"CCOC(=O)Cn1c2c(c3ccccc31)CCN(C(=O)OC(C)(C)C)CC2\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_5_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 11, \"query\": \"CCOC(=O)Cn1c2c(c3ccccc31)CCN(C(=O)OC(C)(C)C)CC2\", \"results\": [{\"inchikey\": \"FDMRONLLVLVFFI-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CCOC(=O)Cn1c2c(c3ccccc31)CCN(C(=O)OC(C)(C)C)CC2\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_5_1"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)OC(=O)N1CCc2c(n(CCNS(=O)(=O)c3ccccc3)c3ccccc23)CC1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)(C)OC(=O)N1CCc2c(n(CCN)c3ccccc23)CC1\": \"precursor\", \"O=S(=O)(Cl)c1ccccc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)OC(=O)N1CCc2c(n(CCN)c3ccccc23)CC1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)(C)OC(=O)N1CCc2c(n(CCN=[N+]=[N-])c3ccccc23)CC1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)OC(=O)N1CCc2c(n(CCN=[N+]=[N-])c3ccccc23)CC1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)(C)OC(=O)N1CCc2c(n(CCOS(C)(=O)=O)c3ccccc23)CC1\": \"precursor\", \"[N-]=[N+]=[N-]\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)OC(=O)N1CCc2c(n(CCOS(C)(=O)=O)c3ccccc23)CC1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)(C)OC(=O)N1CCc2c(n(CCO)c3ccccc23)CC1\": \"precursor\", \"CS(=O)(=O)Cl\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)OC(=O)N1CCc2c(n(CCO)c3ccccc23)CC1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCOC(=O)Cn1c2c(c3ccccc31)CCN(C(=O)OC(C)(C)C)CC2\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCOC(=O)Cn1c2c(c3ccccc31)CCN(C(=O)OC(C)(C)C)CC2\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"CS(=O)(=O)Cl\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"[N-]=[N+]=[N-]\", \"in_stock\": true, \"children\": []}]}]}]}]}, {\"type\": \"mol\", \"smiles\": \"O=S(=O)(Cl)c1ccccc1\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_6_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"CC(C)(C)OC(=O)N1CCc2c(n(CCNS(=O)(=O)c3ccccc3)c3ccccc23)CC1","task_id":"retro_c787b7ac3498735a976a","tool_calls":14,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":6}
{"exact_match":true,"id":"retro_c8e257e6d3d54b9137af:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target Fc1ccccc1-c1ccccc1-c1nnnn1-c1ccccc1F in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Fc1ccccc1-c1ccccc1-c1nnnn1-c1ccccc1F\", \"reactants\": [\"OB(O)c1ccccc1F\", \"Oc1ccccc1-c1ccccc1-c1nnnn1-c1ccccc1F\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"OB(O)c1ccccc1F\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"Oc1ccccc1-c1ccccc1-c1nnnn1-c1ccccc1F\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"QCSLIRFWJPOENV-UHFFFAOYSA-N.ULNKUWIRJYDUKX-UHFFFAOYSA-N>>PCEXPIAKPFJIJI-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"Fc1ccccc1-c1ccccc1-c1nnnn1-c1ccccc1F\", \"reactants\": [\"OB(O)c1ccccc1F\", \"Oc1ccccc1-c1ccccc1-c1nnnn1-c1ccccc1F\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"OB(O)c1ccccc1F\", \"results\": [{\"inchikey\": \"QCSLIRFWJPOENV-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"OB(O)c1ccccc1F\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"Oc1ccccc1-c1ccccc1-c1nnnn1-c1ccccc1F\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"Oc1ccccc1-c1ccccc1-c1nnnn1-c1ccccc1F was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Oc1ccccc1-c1ccccc1-c1nnnn1-c1ccccc1F\", \"reactants\": [\"Fc1ccccc1-n1nnnc1-c1ccccc1I\", \"OB(O)c1ccccc1O\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"Fc1ccccc1-n1nnnc1-c1ccccc1I\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"OB(O)c1ccccc1O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"XJSCELAFDRDPBQ-UHFFFAOYSA-N.YDMRDHQUQIVWBE-UHFFFAOYSA-N>>ULNKUWIRJYDUKX-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"Oc1ccccc1-c1ccccc1-c1nnnn1-c1ccccc1F\", \"reactants\": [\"Fc1ccccc1-n1nnnc1-c1ccccc1I\", \"OB(O)c1ccccc1O\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"Fc1ccccc1-n1nnnc1-c1ccccc1I\", \"results\": [{\"inchikey\": \"XJSCELAFDRDPBQ-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Fc1ccccc1-n1nnnc1-c1ccccc1I\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"OB(O)c1ccccc1O\", \"results\": [{\"inchikey\": \"YDMRDHQUQIVWBE-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"OB(O)c1ccccc1O\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"Fc1ccccc1-c1ccccc1-c1nnnn1-c1ccccc1F\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"OB(O)c1ccccc1F\": \"precursor\", \"Oc1ccccc1-c1ccccc1-c1nnnn1-c1ccccc1F\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"OB(O)c1ccccc1F\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"Oc1ccccc1-c1ccccc1-c1nnnn1-c1ccccc1F\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"Fc1ccccc1-n1nnnc1-c1ccccc1I\": \"precursor\", \"OB(O)c1ccccc1O\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"Fc1ccccc1-n1nnnc1-c1ccccc1I\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"OB(O)c1ccccc1O\", \"in_stock\": true, \"children\": []}]}]}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"Fc1ccccc1-c1ccccc1-c1nnnn1-c1ccccc1F","task_id":"retro_c8e257e6d3d54b9137af","tool_calls":7,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_c96ddaf942e15e1c42c1:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target C=C(C)C(=O)OCCCCCCCCCCCBr in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"C=C(C)C(=O)OCCCCCCCCCCCBr\", \"reactants\": [\"C=C(C)C(=O)OC\", \"OCCCCCCCCCCCBr\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"C=C(C)C(=O)OC\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"OCCCCCCCCCCCBr\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"VVQNEPGJFQJSBK-UHFFFAOYSA-N.XFGANBYCJWQYBI-UHFFFAOYSA-N>>MBGPMDXXPUWUIJ-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"C=C(C)C(=O)OCCCCCCCCCCCBr\", \"reactants\": [\"C=C(C)C(=O)OC\", \"OCCCCCCCCCCCBr\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"C=C(C)C(=O)OC\", \"results\": [{\"inchikey\": \"VVQNEPGJFQJSBK-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"C=C(C)C(=O)OC\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"OCCCCCCCCCCCBr\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"OCCCCCCCCCCCBr was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"OCCCCCCCCCCCBr\", \"reactants\": [\"O=C(O)CCCCCCCCCCBr\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"O=C(O)CCCCCCCCCCBr\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"IUDGNRWYNOEIKF-UHFFFAOYSA-N>>XFGANBYCJWQYBI-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"OCCCCCCCCCCCBr\", \"reactants\": [\"O=C(O)CCCCCCCCCCBr\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"O=C(O)CCCCCCCCCCBr\", \"results\": [{\"inchikey\": \"IUDGNRWYNOEIKF-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=C(O)CCCCCCCCCCBr\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"C=C(C)C(=O)OCCCCCCCCCCCBr\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"C=C(C)C(=O)OC\": \"precursor\", \"OCCCCCCCCCCCBr\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"C=C(C)C(=O)OC\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"OCCCCCCCCCCCBr\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"O=C(O)CCCCCCCCCCBr\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"O=C(O)CCCCCCCCCCBr\", \"in_stock\": true, \"children\": []}]}]}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"C=C(C)C(=O)OCCCCCCCCCCCBr","task_id":"retro_c96ddaf942e15e1c42c1","tool_calls":6,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_c9b3638ed70d457b0d9e:reference-expert:a0","kind":"single_route","max_steps":3,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CC(C)(C)OC(=O)N1C[C@@H]2CN(c3cncc(C(=O)Nc4ccc(Oc5ccccc5)cc4)c3)C[C@@H]2C1 in at most 3 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(C)(C)OC(=O)N1C[C@@H]2CN(c3cncc(C(=O)Nc4ccc(Oc5ccccc5)cc4)c3)C[C@@H]2C1\", \"reactants\": [\"CC(C)(C)OC(=O)N1C[C@@H]2CN(c3cncc(C(=O)O)c3)C[C@@H]2C1\", \"Nc1ccc(Oc2ccccc2)cc1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)OC(=O)N1C[C@@H]2CN(c3cncc(C(=O)O)c3)C[C@@H]2C1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"Nc1ccc(Oc2ccccc2)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"FKPVVCPXELHOEL-BETUJISGSA-N.WOYZXEVUWXQVNV-UHFFFAOYSA-N>>MDJAJFIFLRLOPO-SZPZYZBQSA-N\", \"model_turns_remaining\": 15, \"product\": \"CC(C)(C)OC(=O)N1C[C@@H]2CN(c3cncc(C(=O)Nc4ccc(Oc5ccccc5)cc4)c3)C[C@@H]2C1\", \"reactants\": [\"CC(C)(C)OC(=O)N1C[C@@H]2CN(c3cncc(C(=O)O)c3)C[C@@H]2C1\", \"Nc1ccc(Oc2ccccc2)cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CC(C)(C)OC(=O)N1C[C@@H]2CN(c3cncc(C(=O)O)c3)C[C@@H]2C1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"Nc1ccc(Oc2ccccc2)cc1\", \"results\": [{\"inchikey\": \"WOYZXEVUWXQVNV-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Nc1ccc(Oc2ccccc2)cc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"CC(C)(C)OC(=O)N1C[C@@H]2CN(c3cncc(C(=O)O)c3)C[C@@H]2C1 was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(C)(C)OC(=O)N1C[C@@H]2CN(c3cncc(C(=O)O)c3)C[C@@H]2C1\", \"reactants\": [\"CCOC(=O)c1cncc(N2C[C@H]3CN(C(=O)OC(C)(C)C)C[C@H]3C2)c1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCOC(=O)c1cncc(N2C[C@H]3CN(C(=O)OC(C)(C)C)C[C@H]3C2)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"RCRFFLKTNQJWET-GASCZTMLSA-N>>FKPVVCPXELHOEL-BETUJISGSA-N\", \"model_turns_remaining\": 14, \"product\": \"CC(C)(C)OC(=O)N1C[C@@H]2CN(c3cncc(C(=O)O)c3)C[C@@H]2C1\", \"reactants\": [\"CCOC(=O)c1cncc(N2C[C@H]3CN(C(=O)OC(C)(C)C)C[C@H]3C2)c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CCOC(=O)c1cncc(N2C[C@H]3CN(C(=O)OC(C)(C)C)C[C@H]3C2)c1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"CCOC(=O)c1cncc(N2C[C@H]3CN(C(=O)OC(C)(C)C)C[C@H]3C2)c1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCOC(=O)c1cncc(N2C[C@H]3CN(C(=O)OC(C)(C)C)C[C@H]3C2)c1\", \"reactants\": [\"CC(C)(C)OC(=O)N1C[C@H]2CNC[C@H]2C1\", \"CCOC(=O)c1cncc(Br)c1\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)OC(=O)N1C[C@H]2CNC[C@H]2C1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"CCOC(=O)c1cncc(Br)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"FYUVLZRRIRGSTE-DTORHVGOSA-N.PCPIANOJERKFJI-UHFFFAOYSA-N>>RCRFFLKTNQJWET-GASCZTMLSA-N\", \"model_turns_remaining\": 13, \"product\": \"CCOC(=O)c1cncc(N2C[C@H]3CN(C(=O)OC(C)(C)C)C[C@H]3C2)c1\", \"reactants\": [\"CC(C)(C)OC(=O)N1C[C@H]2CNC[C@H]2C1\", \"CCOC(=O)c1cncc(Br)c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"CC(C)(C)OC(=O)N1C[C@H]2CNC[C@H]2C1\", \"results\": [{\"inchikey\": \"FYUVLZRRIRGSTE-DTORHVGOSA-N\", \"similarity\": 1.0, \"smiles\": \"CC(C)(C)OC(=O)N1C[C@H]2CNC[C@H]2C1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"CCOC(=O)c1cncc(Br)c1\", \"results\": [{\"inchikey\": \"PCPIANOJERKFJI-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CCOC(=O)c1cncc(Br)c1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)OC(=O)N1C[C@@H]2CN(c3cncc(C(=O)Nc4ccc(Oc5ccccc5)cc4)c3)C[C@@H]2C1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)(C)OC(=O)N1C[C@@H]2CN(c3cncc(C(=O)O)c3)C[C@@H]2C1\": \"precursor\", \"Nc1ccc(Oc2ccccc2)cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)OC(=O)N1C[C@@H]2CN(c3cncc(C(=O)O)c3)C[C@@H]2C1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCOC(=O)c1cncc(N2C[C@H]3CN(C(=O)OC(C)(C)C)C[C@H]3C2)c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCOC(=O)c1cncc(N2C[C@H]3CN(C(=O)OC(C)(C)C)C[C@H]3C2)c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)(C)OC(=O)N1C[C@H]2CNC[C@H]2C1\": \"precursor\", \"CCOC(=O)c1cncc(Br)c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)OC(=O)N1C[C@H]2CNC[C@H]2C1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"CCOC(=O)c1cncc(Br)c1\", \"in_stock\": true, \"children\": []}]}]}]}]}, {\"type\": \"mol\", \"smiles\": \"Nc1ccc(Oc2ccccc2)cc1\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_4_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"CC(C)(C)OC(=O)N1C[C@@H]2CN(c3cncc(C(=O)Nc4ccc(Oc5ccccc5)cc4)c3)C[C@@H]2C1","task_id":"retro_c9b3638ed70d457b0d9e","tool_calls":9,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":4}
{"exact_match":true,"id":"retro_c9b987b0d09678ab5ffc:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CC1(C)C(C(=O)c2c[nH]c3ccc(OCc4ccccc4)cc23)C1(C)C in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC1(C)C(C(=O)c2c[nH]c3ccc(OCc4ccccc4)cc23)C1(C)C\", \"reactants\": [\"CC1(C)C(C(=O)Cl)C1(C)C\", \"c1ccc(COc2ccc3[nH]ccc3c2)cc1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC1(C)C(C(=O)Cl)C1(C)C\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"c1ccc(COc2ccc3[nH]ccc3c2)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"JCQLPDZCNSVBMS-UHFFFAOYSA-N.PAPVPNRFJQMQLS-UHFFFAOYSA-N>>WSPXLGBGFFZGJV-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"CC1(C)C(C(=O)c2c[nH]c3ccc(OCc4ccccc4)cc23)C1(C)C\", \"reactants\": [\"CC1(C)C(C(=O)Cl)C1(C)C\", \"c1ccc(COc2ccc3[nH]ccc3c2)cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CC1(C)C(C(=O)Cl)C1(C)C\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"c1ccc(COc2ccc3[nH]ccc3c2)cc1\", \"results\": [{\"inchikey\": \"JCQLPDZCNSVBMS-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"c1ccc(COc2ccc3[nH]ccc3c2)cc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"CC1(C)C(C(=O)Cl)C1(C)C was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC1(C)C(C(=O)Cl)C1(C)C\", \"reactants\": [\"CC1(C)C(C(=O)O)C1(C)C\", \"O=S(Cl)Cl\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC1(C)C(C(=O)O)C1(C)C\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=S(Cl)Cl\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"FYSNRJHAOHDILO-UHFFFAOYSA-N.SFHVXKNMCGSLAR-UHFFFAOYSA-N>>PAPVPNRFJQMQLS-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"CC1(C)C(C(=O)Cl)C1(C)C\", \"reactants\": [\"CC1(C)C(C(=O)O)C1(C)C\", \"O=S(Cl)Cl\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CC1(C)C(C(=O)O)C1(C)C\", \"results\": [{\"inchikey\": \"SFHVXKNMCGSLAR-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CC1(C)C(C(=O)O)C1(C)C\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"O=S(Cl)Cl\", \"results\": [{\"inchikey\": \"FYSNRJHAOHDILO-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=S(Cl)Cl\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CC1(C)C(C(=O)c2c[nH]c3ccc(OCc4ccccc4)cc23)C1(C)C\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC1(C)C(C(=O)Cl)C1(C)C\": \"precursor\", \"c1ccc(COc2ccc3[nH]ccc3c2)cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC1(C)C(C(=O)Cl)C1(C)C\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC1(C)C(C(=O)O)C1(C)C\": \"precursor\", \"O=S(Cl)Cl\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC1(C)C(C(=O)O)C1(C)C\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=S(Cl)Cl\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"c1ccc(COc2ccc3[nH]ccc3c2)cc1\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"CC1(C)C(C(=O)c2c[nH]c3ccc(OCc4ccccc4)cc23)C1(C)C","task_id":"retro_c9b987b0d09678ab5ffc","tool_calls":7,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_c9c514b0fc0e53970d38:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CNc1cc(CN)ccn1 in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CNc1cc(CN)ccn1\", \"reactants\": [\"CNc1cc(C#N)ccn1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CNc1cc(C#N)ccn1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_complete\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"WWADDKFIMVEGBH-UHFFFAOYSA-N>>YXVFOUXEPOSPTE-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"CNc1cc(CN)ccn1\", \"reactants\": [\"CNc1cc(C#N)ccn1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CNc1cc(C#N)ccn1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"CNc1cc(C#N)ccn1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CNc1cc(C#N)ccn1\", \"reactants\": [\"CN\", \"N#Cc1ccnc(Cl)c1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CN\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"N#Cc1ccnc(Cl)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"BAVYZALUXZFZLV-UHFFFAOYSA-N.QRXBTPFMCTXCRD-UHFFFAOYSA-N>>WWADDKFIMVEGBH-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"CNc1cc(C#N)ccn1\", \"reactants\": [\"CN\", \"N#Cc1ccnc(Cl)c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CN\", \"results\": [{\"inchikey\": \"BAVYZALUXZFZLV-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CN\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"N#Cc1ccnc(Cl)c1\", \"results\": [{\"inchikey\": \"QRXBTPFMCTXCRD-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"N#Cc1ccnc(Cl)c1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CNc1cc(CN)ccn1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CNc1cc(C#N)ccn1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CNc1cc(C#N)ccn1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CN\": \"precursor\", \"N#Cc1ccnc(Cl)c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CN\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"N#Cc1ccnc(Cl)c1\", \"in_stock\": true, \"children\": []}]}]}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"CNc1cc(CN)ccn1","task_id":"retro_c9c514b0fc0e53970d38","tool_calls":6,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_ca6286b76e83dda19f3c:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CSc1cc2ccccc2cc1O in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CSc1cc2ccccc2cc1O\", \"reactants\": [\"COc1cc2ccccc2cc1SC\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"COc1cc2ccccc2cc1SC\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"DENVFRPAVPSEDJ-UHFFFAOYSA-N>>JJGVWXJYHLLWTA-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"CSc1cc2ccccc2cc1O\", \"reactants\": [\"COc1cc2ccccc2cc1SC\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"COc1cc2ccccc2cc1SC\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"COc1cc2ccccc2cc1SC was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COc1cc2ccccc2cc1SC\", \"reactants\": [\"COc1ccc2ccccc2c1\", \"CSSC\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"COc1ccc2ccccc2c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"CSSC\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"LUZDYPLAQQGJEA-UHFFFAOYSA-N.WQOXQRCZOLPYPM-UHFFFAOYSA-N>>DENVFRPAVPSEDJ-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"COc1cc2ccccc2cc1SC\", \"reactants\": [\"COc1ccc2ccccc2c1\", \"CSSC\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"COc1ccc2ccccc2c1\", \"results\": [{\"inchikey\": \"LUZDYPLAQQGJEA-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"COc1ccc2ccccc2c1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CSSC\", \"results\": [{\"inchikey\": \"WQOXQRCZOLPYPM-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CSSC\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CSc1cc2ccccc2cc1O\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COc1cc2ccccc2cc1SC\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COc1cc2ccccc2cc1SC\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COc1ccc2ccccc2c1\": \"precursor\", \"CSSC\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COc1ccc2ccccc2c1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"CSSC\", \"in_stock\": true, \"children\": []}]}]}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"CSc1cc2ccccc2cc1O","task_id":"retro_ca6286b76e83dda19f3c","tool_calls":6,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_ca8abed5c52fcb639b21:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CCOC(=O)COc1cccc(NC(=O)c2cccc(-c3cccc(F)c3)n2)c1 in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCOC(=O)COc1cccc(NC(=O)c2cccc(-c3cccc(F)c3)n2)c1\", \"reactants\": [\"CCOC(=O)COc1cccc(NC(=O)c2cccc(Br)n2)c1\", \"OB(O)c1cccc(F)c1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCOC(=O)COc1cccc(NC(=O)c2cccc(Br)n2)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"OB(O)c1cccc(F)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"FDNMDOATYACFIU-UHFFFAOYSA-N.KNXQDJCZSVHEIW-UHFFFAOYSA-N>>ZALNNYNFURABMF-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"CCOC(=O)COc1cccc(NC(=O)c2cccc(-c3cccc(F)c3)n2)c1\", \"reactants\": [\"CCOC(=O)COc1cccc(NC(=O)c2cccc(Br)n2)c1\", \"OB(O)c1cccc(F)c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CCOC(=O)COc1cccc(NC(=O)c2cccc(Br)n2)c1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"OB(O)c1cccc(F)c1\", \"results\": [{\"inchikey\": \"KNXQDJCZSVHEIW-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"OB(O)c1cccc(F)c1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"CCOC(=O)COc1cccc(NC(=O)c2cccc(Br)n2)c1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCOC(=O)COc1cccc(NC(=O)c2cccc(Br)n2)c1\", \"reactants\": [\"CCOC(=O)COc1cccc(N)c1\", \"O=C(O)c1cccc(Br)n1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCOC(=O)COc1cccc(N)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=C(O)c1cccc(Br)n1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"IVWPPUWTINZQIK-UHFFFAOYSA-N.XURXQNUIGWHWHU-UHFFFAOYSA-N>>FDNMDOATYACFIU-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"CCOC(=O)COc1cccc(NC(=O)c2cccc(Br)n2)c1\", \"reactants\": [\"CCOC(=O)COc1cccc(N)c1\", \"O=C(O)c1cccc(Br)n1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CCOC(=O)COc1cccc(N)c1\", \"results\": [{\"inchikey\": \"IVWPPUWTINZQIK-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CCOC(=O)COc1cccc(N)c1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"O=C(O)c1cccc(Br)n1\", \"results\": [{\"inchikey\": \"XURXQNUIGWHWHU-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=C(O)c1cccc(Br)n1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CCOC(=O)COc1cccc(NC(=O)c2cccc(-c3cccc(F)c3)n2)c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCOC(=O)COc1cccc(NC(=O)c2cccc(Br)n2)c1\": \"precursor\", \"OB(O)c1cccc(F)c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCOC(=O)COc1cccc(NC(=O)c2cccc(Br)n2)c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCOC(=O)COc1cccc(N)c1\": \"precursor\", \"O=C(O)c1cccc(Br)n1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCOC(=O)COc1cccc(N)c1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=C(O)c1cccc(Br)n1\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"OB(O)c1cccc(F)c1\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"CCOC(=O)COc1cccc(NC(=O)c2cccc(-c3cccc(F)c3)n2)c1","task_id":"retro_ca8abed5c52fcb639b21","tool_calls":7,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_cb9fff601023dae8be13:reference-expert:a0","kind":"single_route","max_steps":4,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target COC(=O)c1cc(B2OC(C)(C)C(C)(C)O2)c(C2CC2)cc1C in at most 4 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COC(=O)c1cc(B2OC(C)(C)C(C)(C)O2)c(C2CC2)cc1C\", \"reactants\": [\"CC1(C)OB(B2OC(C)(C)C(C)(C)O2)OC1(C)C\", \"COC(=O)c1cc(I)c(C2CC2)cc1C\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC1(C)OB(B2OC(C)(C)C(C)(C)O2)OC1(C)C\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"COC(=O)c1cc(I)c(C2CC2)cc1C\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"AJEOSUOFXOCLAF-UHFFFAOYSA-N.IPWKHHSGDUIRAH-UHFFFAOYSA-N>>NWRBJBLRNXDYJA-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"COC(=O)c1cc(B2OC(C)(C)C(C)(C)O2)c(C2CC2)cc1C\", \"reactants\": [\"CC1(C)OB(B2OC(C)(C)C(C)(C)O2)OC1(C)C\", \"COC(=O)c1cc(I)c(C2CC2)cc1C\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CC1(C)OB(B2OC(C)(C)C(C)(C)O2)OC1(C)C\", \"results\": [{\"inchikey\": \"IPWKHHSGDUIRAH-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CC1(C)OB(B2OC(C)(C)C(C)(C)O2)OC1(C)C\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"COC(=O)c1cc(I)c(C2CC2)cc1C\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"COC(=O)c1cc(I)c(C2CC2)cc1C was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COC(=O)c1cc(I)c(C2CC2)cc1C\", \"reactants\": [\"COC(=O)c1ccc(C2CC2)cc1C\", \"II\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"COC(=O)c1ccc(C2CC2)cc1C\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"II\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"PNDPGZBMCMUPRI-UHFFFAOYSA-N.ULOSWMDGEIECAT-UHFFFAOYSA-N>>AJEOSUOFXOCLAF-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"COC(=O)c1cc(I)c(C2CC2)cc1C\", \"reactants\": [\"COC(=O)c1ccc(C2CC2)cc1C\", \"II\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"COC(=O)c1ccc(C2CC2)cc1C\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"II\", \"results\": [{\"inchikey\": \"PNDPGZBMCMUPRI-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"II\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"COC(=O)c1ccc(C2CC2)cc1C was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COC(=O)c1ccc(C2CC2)cc1C\", \"reactants\": [\"COC(=O)c1ccc(Br)cc1C\", \"OB(O)C1CC1\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"COC(=O)c1ccc(Br)cc1C\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"OB(O)C1CC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"CYEXEOXALMJXDI-UHFFFAOYSA-N.WLVKDFJTYKELLQ-UHFFFAOYSA-N>>ULOSWMDGEIECAT-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"COC(=O)c1ccc(C2CC2)cc1C\", \"reactants\": [\"COC(=O)c1ccc(Br)cc1C\", \"OB(O)C1CC1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"COC(=O)c1ccc(Br)cc1C\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"OB(O)C1CC1\", \"results\": [{\"inchikey\": \"WLVKDFJTYKELLQ-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"OB(O)C1CC1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"COC(=O)c1ccc(Br)cc1C was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COC(=O)c1ccc(Br)cc1C\", \"reactants\": [\"CO\", \"Cc1cc(Br)ccc1C(=O)O\"]}","name":"validate_disconnection"},"id":"call_4_0","type":"function"},{"function":{"arguments":"{\"query\": \"CO\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_1","type":"function"},{"function":{"arguments":"{\"query\": \"Cc1cc(Br)ccc1C(=O)O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"OKKJLVBELUTLKV-UHFFFAOYSA-N.RVCJOGNLYVNRDN-UHFFFAOYSA-N>>CYEXEOXALMJXDI-UHFFFAOYSA-N\", \"model_turns_remaining\": 12, \"product\": \"COC(=O)c1ccc(Br)cc1C\", \"reactants\": [\"CO\", \"Cc1cc(Br)ccc1C(=O)O\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_4_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"CO\", \"results\": [{\"inchikey\": \"OKKJLVBELUTLKV-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CO\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"Cc1cc(Br)ccc1C(=O)O\", \"results\": [{\"inchikey\": \"RVCJOGNLYVNRDN-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Cc1cc(Br)ccc1C(=O)O\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"COC(=O)c1cc(B2OC(C)(C)C(C)(C)O2)c(C2CC2)cc1C\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC1(C)OB(B2OC(C)(C)C(C)(C)O2)OC1(C)C\": \"precursor\", \"COC(=O)c1cc(I)c(C2CC2)cc1C\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC1(C)OB(B2OC(C)(C)C(C)(C)O2)OC1(C)C\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"COC(=O)c1cc(I)c(C2CC2)cc1C\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COC(=O)c1ccc(C2CC2)cc1C\": \"precursor\", \"II\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COC(=O)c1ccc(C2CC2)cc1C\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COC(=O)c1ccc(Br)cc1C\": \"precursor\", \"OB(O)C1CC1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COC(=O)c1ccc(Br)cc1C\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CO\": \"precursor\", \"Cc1cc(Br)ccc1C(=O)O\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CO\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"Cc1cc(Br)ccc1C(=O)O\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"OB(O)C1CC1\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"II\", \"in_stock\": true, \"children\": []}]}]}]}]}]}}","name":"emit_routes"},"id":"call_5_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"COC(=O)c1cc(B2OC(C)(C)C(C)(C)O2)c(C2CC2)cc1C","task_id":"retro_cb9fff601023dae8be13","tool_calls":13,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":5}
{"exact_match":true,"id":"retro_cd068b9093b645f1f20f:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target COc1cccc(CNC(=O)c2cccc(N)c2)c1 in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COc1cccc(CNC(=O)c2cccc(N)c2)c1\", \"reactants\": [\"COc1cccc(CNC(=O)c2cccc([N+](=O)[O-])c2)c1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"COc1cccc(CNC(=O)c2cccc([N+](=O)[O-])c2)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"HPTGZRMYKNDACI-UHFFFAOYSA-N>>ZTSANNRXCBSHPM-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"COc1cccc(CNC(=O)c2cccc(N)c2)c1\", \"reactants\": [\"COc1cccc(CNC(=O)c2cccc([N+](=O)[O-])c2)c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"COc1cccc(CNC(=O)c2cccc([N+](=O)[O-])c2)c1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"COc1cccc(CNC(=O)c2cccc([N+](=O)[O-])c2)c1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COc1cccc(CNC(=O)c2cccc([N+](=O)[O-])c2)c1\", \"reactants\": [\"COc1cccc(CN)c1\", \"O=C(Cl)c1cccc([N+](=O)[O-])c1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"COc1cccc(CN)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=C(Cl)c1cccc([N+](=O)[O-])c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"GRRIMVWABNHKBX-UHFFFAOYSA-N.NXTNASSYJUXJDV-UHFFFAOYSA-N>>HPTGZRMYKNDACI-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"COc1cccc(CNC(=O)c2cccc([N+](=O)[O-])c2)c1\", \"reactants\": [\"COc1cccc(CN)c1\", \"O=C(Cl)c1cccc([N+](=O)[O-])c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"COc1cccc(CN)c1\", \"results\": [{\"inchikey\": \"GRRIMVWABNHKBX-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"COc1cccc(CN)c1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"O=C(Cl)c1cccc([N+](=O)[O-])c1\", \"results\": [{\"inchikey\": \"NXTNASSYJUXJDV-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=C(Cl)c1cccc([N+](=O)[O-])c1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"COc1cccc(CNC(=O)c2cccc(N)c2)c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COc1cccc(CNC(=O)c2cccc([N+](=O)[O-])c2)c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COc1cccc(CNC(=O)c2cccc([N+](=O)[O-])c2)c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COc1cccc(CN)c1\": \"precursor\", \"O=C(Cl)c1cccc([N+](=O)[O-])c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COc1cccc(CN)c1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=C(Cl)c1cccc([N+](=O)[O-])c1\", \"in_stock\": true, \"children\": []}]}]}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"COc1cccc(CNC(=O)c2cccc(N)c2)c1","task_id":"retro_cd068b9093b645f1f20f","tool_calls":6,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_cd083da7064c4569c215:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target COc1ccccc1N1CCC(CNC[C@H]2COc3ccccc3O2)CC1 in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COc1ccccc1N1CCC(CNC[C@H]2COc3ccccc3O2)CC1\", \"reactants\": [\"COc1ccccc1N1CCC(CN)CC1\", \"Cc1ccc(S(=O)(=O)OC[C@H]2COc3ccccc3O2)cc1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"COc1ccccc1N1CCC(CN)CC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"Cc1ccc(S(=O)(=O)OC[C@H]2COc3ccccc3O2)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"OTGAYUCEDFKLHW-CYBMUJFWSA-N.PBOYJAITSSDOFN-UHFFFAOYSA-N>>XYBADQIMVGSILK-SFHVURJKSA-N\", \"model_turns_remaining\": 15, \"product\": \"COc1ccccc1N1CCC(CNC[C@H]2COc3ccccc3O2)CC1\", \"reactants\": [\"COc1ccccc1N1CCC(CN)CC1\", \"Cc1ccc(S(=O)(=O)OC[C@H]2COc3ccccc3O2)cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"COc1ccccc1N1CCC(CN)CC1\", \"results\": [{\"inchikey\": \"PBOYJAITSSDOFN-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"COc1ccccc1N1CCC(CN)CC1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"Cc1ccc(S(=O)(=O)OC[C@H]2COc3ccccc3O2)cc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"Cc1ccc(S(=O)(=O)OC[C@H]2COc3ccccc3O2)cc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Cc1ccc(S(=O)(=O)OC[C@H]2COc3ccccc3O2)cc1\", \"reactants\": [\"Cc1ccc(S(=O)(=O)Cl)cc1\", \"OC[C@H]1COc2ccccc2O1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"Cc1ccc(S(=O)(=O)Cl)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"OC[C@H]1COc2ccccc2O1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"GWQOQQVKVOOHTI-ZETCQYMHSA-N.YYROPELSRYBVMQ-UHFFFAOYSA-N>>OTGAYUCEDFKLHW-CYBMUJFWSA-N\", \"model_turns_remaining\": 14, \"product\": \"Cc1ccc(S(=O)(=O)OC[C@H]2COc3ccccc3O2)cc1\", \"reactants\": [\"Cc1ccc(S(=O)(=O)Cl)cc1\", \"OC[C@H]1COc2ccccc2O1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"Cc1ccc(S(=O)(=O)Cl)cc1\", \"results\": [{\"inchikey\": \"YYROPELSRYBVMQ-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Cc1ccc(S(=O)(=O)Cl)cc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"OC[C@H]1COc2ccccc2O1\", \"results\": [{\"inchikey\": \"GWQOQQVKVOOHTI-ZETCQYMHSA-N\", \"similarity\": 1.0, \"smiles\": \"OC[C@H]1COc2ccccc2O1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"COc1ccccc1N1CCC(CNC[C@H]2COc3ccccc3O2)CC1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COc1ccccc1N1CCC(CN)CC1\": \"precursor\", \"Cc1ccc(S(=O)(=O)OC[C@H]2COc3ccccc3O2)cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COc1ccccc1N1CCC(CN)CC1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"Cc1ccc(S(=O)(=O)OC[C@H]2COc3ccccc3O2)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"Cc1ccc(S(=O)(=O)Cl)cc1\": \"precursor\", \"OC[C@H]1COc2ccccc2O1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"Cc1ccc(S(=O)(=O)Cl)cc1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"OC[C@H]1COc2ccccc2O1\", \"in_stock\": true, \"children\": []}]}]}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"COc1ccccc1N1CCC(CNC[C@H]2COc3ccccc3O2)CC1","task_id":"retro_cd083da7064c4569c215","tool_calls":7,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_d00798122fe1564c3e4b:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target C#CC(C)(C)NC(=O)c1ccc(Cl)nc1NC(C)C in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"C#CC(C)(C)NC(=O)c1ccc(Cl)nc1NC(C)C\", \"reactants\": [\"C#CC(C)(C)N\", \"CC(C)Nc1nc(Cl)ccc1C(=O)O\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"C#CC(C)(C)N\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)Nc1nc(Cl)ccc1C(=O)O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"GYRKLKAIUVXRPR-UHFFFAOYSA-N.VUGCBIWQHSRQBZ-UHFFFAOYSA-N>>KSSOPUSXQCMBTG-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"C#CC(C)(C)NC(=O)c1ccc(Cl)nc1NC(C)C\", \"reactants\": [\"C#CC(C)(C)N\", \"CC(C)Nc1nc(Cl)ccc1C(=O)O\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"C#CC(C)(C)N\", \"results\": [{\"inchikey\": \"VUGCBIWQHSRQBZ-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"C#CC(C)(C)N\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CC(C)Nc1nc(Cl)ccc1C(=O)O\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"CC(C)Nc1nc(Cl)ccc1C(=O)O was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(C)Nc1nc(Cl)ccc1C(=O)O\", \"reactants\": [\"CC(C)N\", \"O=C(O)c1ccc(Cl)nc1Cl\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)N\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=C(O)c1ccc(Cl)nc1Cl\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"AJPKQSSFYHPYMH-UHFFFAOYSA-N.JJWLVOIRVHMVIS-UHFFFAOYSA-N>>GYRKLKAIUVXRPR-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"CC(C)Nc1nc(Cl)ccc1C(=O)O\", \"reactants\": [\"CC(C)N\", \"O=C(O)c1ccc(Cl)nc1Cl\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CC(C)N\", \"results\": [{\"inchikey\": \"JJWLVOIRVHMVIS-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CC(C)N\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"O=C(O)c1ccc(Cl)nc1Cl\", \"results\": [{\"inchikey\": \"AJPKQSSFYHPYMH-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=C(O)c1ccc(Cl)nc1Cl\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"C#CC(C)(C)NC(=O)c1ccc(Cl)nc1NC(C)C\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"C#CC(C)(C)N\": \"precursor\", \"CC(C)Nc1nc(Cl)ccc1C(=O)O\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"C#CC(C)(C)N\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"CC(C)Nc1nc(Cl)ccc1C(=O)O\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)N\": \"precursor\", \"O=C(O)c1ccc(Cl)nc1Cl\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)N\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=C(O)c1ccc(Cl)nc1Cl\", \"in_stock\": true, \"children\": []}]}]}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"C#CC(C)(C)NC(=O)c1ccc(Cl)nc1NC(C)C","task_id":"retro_d00798122fe1564c3e4b","tool_calls":7,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":false,"id":"retro_d0147fcf3652aeab8b82:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target Fc1ccc(Br)cc1CBr in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Fc1ccc(Br)cc1CBr\", \"reactants\": [\"O=C1CCC(=O)N1Br\", \"OCc1cc(Br)ccc1F\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"O=C1CCC(=O)N1Br\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"OCc1cc(Br)ccc1F\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"PCLIMKBDDGJMGD-UHFFFAOYSA-N.UOSBHJFKMGLWGX-UHFFFAOYSA-N>>ZLXSSLJXCUISKG-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"Fc1ccc(Br)cc1CBr\", \"reactants\": [\"O=C1CCC(=O)N1Br\", \"OCc1cc(Br)ccc1F\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"O=C1CCC(=O)N1Br\", \"results\": [{\"inchikey\": \"PCLIMKBDDGJMGD-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=C1CCC(=O)N1Br\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"OCc1cc(Br)ccc1F\", \"results\": [{\"inchikey\": \"UOSBHJFKMGLWGX-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"OCc1cc(Br)ccc1F\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"Fc1ccc(Br)cc1CBr\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"O=C1CCC(=O)N1Br\": \"precursor\", \"OCc1cc(Br)ccc1F\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"O=C1CCC(=O)N1Br\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"OCc1cc(Br)ccc1F\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_2_0","type":"function"}]}],"provider":"reference","reward":0.85,"source":"reference-expert","target_smiles":"Fc1ccc(Br)cc1CBr","task_id":"retro_d0147fcf3652aeab8b82","tool_calls":4,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":2}
{"exact_match":true,"id":"retro_d0bb77534f3bdc219031:reference-expert:a0","kind":"single_route","max_steps":3,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target Cn1cc(C(=O)Nc2nnn[nH]2)c(=O)c2c3ccccc3oc(=O)c21 in at most 3 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Cn1cc(C(=O)Nc2nnn[nH]2)c(=O)c2c3ccccc3oc(=O)c21\", \"reactants\": [\"Cn1cc(C(=O)O)c(=O)c2c3ccccc3oc(=O)c21\", \"Nc1nnn[nH]1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"Cn1cc(C(=O)O)c(=O)c2c3ccccc3oc(=O)c21\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"Nc1nnn[nH]1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"NJRAZZPZWDAJMM-UHFFFAOYSA-N.ULRPISSMEBPJLN-UHFFFAOYSA-N>>FDUUVFIHJBYPRB-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"Cn1cc(C(=O)Nc2nnn[nH]2)c(=O)c2c3ccccc3oc(=O)c21\", \"reactants\": [\"Cn1cc(C(=O)O)c(=O)c2c3ccccc3oc(=O)c21\", \"Nc1nnn[nH]1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"Cn1cc(C(=O)O)c(=O)c2c3ccccc3oc(=O)c21\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"Nc1nnn[nH]1\", \"results\": [{\"inchikey\": \"ULRPISSMEBPJLN-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Nc1nnn[nH]1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"Cn1cc(C(=O)O)c(=O)c2c3ccccc3oc(=O)c21 was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Cn1cc(C(=O)O)c(=O)c2c3ccccc3oc(=O)c21\", \"reactants\": [\"CCOC(=O)c1cn(C)c2c(=O)oc3ccccc3c2c1=O\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCOC(=O)c1cn(C)c2c(=O)oc3ccccc3c2c1=O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"XREJKQLPKRRNAK-UHFFFAOYSA-N>>NJRAZZPZWDAJMM-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"Cn1cc(C(=O)O)c(=O)c2c3ccccc3oc(=O)c21\", \"reactants\": [\"CCOC(=O)c1cn(C)c2c(=O)oc3ccccc3c2c1=O\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CCOC(=O)c1cn(C)c2c(=O)oc3ccccc3c2c1=O\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"CCOC(=O)c1cn(C)c2c(=O)oc3ccccc3c2c1=O was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCOC(=O)c1cn(C)c2c(=O)oc3ccccc3c2c1=O\", \"reactants\": [\"CCOC(=O)c1c[nH]c2c(=O)oc3ccccc3c2c1=O\", \"CI\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCOC(=O)c1c[nH]c2c(=O)oc3ccccc3c2c1=O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"CI\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"INQOMBQAUSQDDS-UHFFFAOYSA-N.ZQVMCLBNBIBRGM-UHFFFAOYSA-N>>XREJKQLPKRRNAK-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"CCOC(=O)c1cn(C)c2c(=O)oc3ccccc3c2c1=O\", \"reactants\": [\"CCOC(=O)c1c[nH]c2c(=O)oc3ccccc3c2c1=O\", \"CI\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"CCOC(=O)c1c[nH]c2c(=O)oc3ccccc3c2c1=O\", \"results\": [{\"inchikey\": \"ZQVMCLBNBIBRGM-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CCOC(=O)c1c[nH]c2c(=O)oc3ccccc3c2c1=O\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"CI\", \"results\": [{\"inchikey\": \"INQOMBQAUSQDDS-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CI\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"Cn1cc(C(=O)Nc2nnn[nH]2)c(=O)c2c3ccccc3oc(=O)c21\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"Cn1cc(C(=O)O)c(=O)c2c3ccccc3oc(=O)c21\": \"precursor\", \"Nc1nnn[nH]1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"Cn1cc(C(=O)O)c(=O)c2c3ccccc3oc(=O)c21\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCOC(=O)c1cn(C)c2c(=O)oc3ccccc3c2c1=O\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCOC(=O)c1cn(C)c2c(=O)oc3ccccc3c2c1=O\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCOC(=O)c1c[nH]c2c(=O)oc3ccccc3c2c1=O\": \"precursor\", \"CI\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCOC(=O)c1c[nH]c2c(=O)oc3ccccc3c2c1=O\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"CI\", \"in_stock\": true, \"children\": []}]}]}]}]}, {\"type\": \"mol\", \"smiles\": \"Nc1nnn[nH]1\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_4_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"Cn1cc(C(=O)Nc2nnn[nH]2)c(=O)c2c3ccccc3oc(=O)c21","task_id":"retro_d0bb77534f3bdc219031","tool_calls":9,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":4}
{"exact_match":true,"id":"retro_d2186e13aff8ad348929:reference-expert:a0","kind":"single_route","max_steps":4,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CN(C)c1cc(-c2c(CN(C)[C@H]3CCCc4cccnc43)nc3ccccn23)ccn1 in at most 4 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CN(C)c1cc(-c2c(CN(C)[C@H]3CCCc4cccnc43)nc3ccccn23)ccn1\", \"reactants\": [\"CN(C)c1cc(-c2c(C=O)nc3ccccn23)ccn1\", \"CN[C@H]1CCCc2cccnc21\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CN(C)c1cc(-c2c(C=O)nc3ccccn23)ccn1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"CN[C@H]1CCCc2cccnc21\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"ZDTITKSWJQILCR-UHFFFAOYSA-N.ZXTRMHOUGKPHHM-VIFPVBQESA-N>>DXJRZWPPPKXTDC-NRFANRHFSA-N\", \"model_turns_remaining\": 15, \"product\": \"CN(C)c1cc(-c2c(CN(C)[C@H]3CCCc4cccnc43)nc3ccccn23)ccn1\", \"reactants\": [\"CN(C)c1cc(-c2c(C=O)nc3ccccn23)ccn1\", \"CN[C@H]1CCCc2cccnc21\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CN(C)c1cc(-c2c(C=O)nc3ccccn23)ccn1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CN[C@H]1CCCc2cccnc21\", \"results\": [{\"inchikey\": \"ZXTRMHOUGKPHHM-VIFPVBQESA-N\", \"similarity\": 1.0, \"smiles\": \"CN[C@H]1CCCc2cccnc21\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"CN(C)c1cc(-c2c(C=O)nc3ccccn23)ccn1 was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CN(C)c1cc(-c2c(C=O)nc3ccccn23)ccn1\", \"reactants\": [\"CN(C)c1cc(-c2c(CO)nc3ccccn23)ccn1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CN(C)c1cc(-c2c(CO)nc3ccccn23)ccn1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_complete\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"VHWKBTILUKQDPL-UHFFFAOYSA-N>>ZDTITKSWJQILCR-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"CN(C)c1cc(-c2c(C=O)nc3ccccn23)ccn1\", \"reactants\": [\"CN(C)c1cc(-c2c(CO)nc3ccccn23)ccn1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CN(C)c1cc(-c2c(CO)nc3ccccn23)ccn1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"CN(C)c1cc(-c2c(CO)nc3ccccn23)ccn1 was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CN(C)c1cc(-c2c(CO)nc3ccccn23)ccn1\", \"reactants\": [\"CCOC(=O)c1nc2ccccn2c1-c1ccnc(N(C)C)c1\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCOC(=O)c1nc2ccccn2c1-c1ccnc(N(C)C)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"KFQRMNUACSVCMT-UHFFFAOYSA-N>>VHWKBTILUKQDPL-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"CN(C)c1cc(-c2c(CO)nc3ccccn23)ccn1\", \"reactants\": [\"CCOC(=O)c1nc2ccccn2c1-c1ccnc(N(C)C)c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"CCOC(=O)c1nc2ccccn2c1-c1ccnc(N(C)C)c1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"CCOC(=O)c1nc2ccccn2c1-c1ccnc(N(C)C)c1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCOC(=O)c1nc2ccccn2c1-c1ccnc(N(C)C)c1\", \"reactants\": [\"CCOC(=O)c1nc2ccccn2c1-c1ccnc(F)c1\", \"CNC\"]}","name":"validate_disconnection"},"id":"call_4_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCOC(=O)c1nc2ccccn2c1-c1ccnc(F)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_1","type":"function"},{"function":{"arguments":"{\"query\": \"CNC\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"JEIOHNJTYVIPDZ-UHFFFAOYSA-N.ROSDSFDQCJNGOL-UHFFFAOYSA-N>>KFQRMNUACSVCMT-UHFFFAOYSA-N\", \"model_turns_remaining\": 12, \"product\": \"CCOC(=O)c1nc2ccccn2c1-c1ccnc(N(C)C)c1\", \"reactants\": [\"CCOC(=O)c1nc2ccccn2c1-c1ccnc(F)c1\", \"CNC\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_4_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"CCOC(=O)c1nc2ccccn2c1-c1ccnc(F)c1\", \"results\": [{\"inchikey\": \"JEIOHNJTYVIPDZ-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CCOC(=O)c1nc2ccccn2c1-c1ccnc(F)c1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"CNC\", \"results\": [{\"inchikey\": \"ROSDSFDQCJNGOL-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CNC\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CN(C)c1cc(-c2c(CN(C)[C@H]3CCCc4cccnc43)nc3ccccn23)ccn1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CN(C)c1cc(-c2c(C=O)nc3ccccn23)ccn1\": \"precursor\", \"CN[C@H]1CCCc2cccnc21\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CN(C)c1cc(-c2c(C=O)nc3ccccn23)ccn1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CN(C)c1cc(-c2c(CO)nc3ccccn23)ccn1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CN(C)c1cc(-c2c(CO)nc3ccccn23)ccn1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCOC(=O)c1nc2ccccn2c1-c1ccnc(N(C)C)c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCOC(=O)c1nc2ccccn2c1-c1ccnc(N(C)C)c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCOC(=O)c1nc2ccccn2c1-c1ccnc(F)c1\": \"precursor\", \"CNC\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCOC(=O)c1nc2ccccn2c1-c1ccnc(F)c1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"CNC\", \"in_stock\": true, \"children\": []}]}]}]}]}]}]}, {\"type\": \"mol\", \"smiles\": \"CN[C@H]1CCCc2cccnc21\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_5_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"CN(C)c1cc(-c2c(CN(C)[C@H]3CCCc4cccnc43)nc3ccccn23)ccn1","task_id":"retro_d2186e13aff8ad348929","tool_calls":11,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":5}
{"exact_match":true,"id":"retro_d2bf0228ca892365b99c:reference-expert:a0","kind":"single_route","max_steps":3,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CN(C)C=Nc1ccc(-c2ncnn2-c2ccc(F)cc2)cc1 in at most 3 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CN(C)C=Nc1ccc(-c2ncnn2-c2ccc(F)cc2)cc1\", \"reactants\": [\"COC(OC)N(C)C\", \"Nc1ccc(-c2ncnn2-c2ccc(F)cc2)cc1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"COC(OC)N(C)C\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"Nc1ccc(-c2ncnn2-c2ccc(F)cc2)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"YGUXZMVCJOUNNB-UHFFFAOYSA-N.ZSXGLVDWWRXATF-UHFFFAOYSA-N>>UVFGQIPXSAGCIY-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"CN(C)C=Nc1ccc(-c2ncnn2-c2ccc(F)cc2)cc1\", \"reactants\": [\"COC(OC)N(C)C\", \"Nc1ccc(-c2ncnn2-c2ccc(F)cc2)cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"COC(OC)N(C)C\", \"results\": [{\"inchikey\": \"ZSXGLVDWWRXATF-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"COC(OC)N(C)C\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"Nc1ccc(-c2ncnn2-c2ccc(F)cc2)cc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"Nc1ccc(-c2ncnn2-c2ccc(F)cc2)cc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Nc1ccc(-c2ncnn2-c2ccc(F)cc2)cc1\", \"reactants\": [\"O=[N+]([O-])c1ccc(-c2ncnn2-c2ccc(F)cc2)cc1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"O=[N+]([O-])c1ccc(-c2ncnn2-c2ccc(F)cc2)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"KEDBMNVLYWBXLU-UHFFFAOYSA-N>>YGUXZMVCJOUNNB-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"Nc1ccc(-c2ncnn2-c2ccc(F)cc2)cc1\", \"reactants\": [\"O=[N+]([O-])c1ccc(-c2ncnn2-c2ccc(F)cc2)cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"O=[N+]([O-])c1ccc(-c2ncnn2-c2ccc(F)cc2)cc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"O=[N+]([O-])c1ccc(-c2ncnn2-c2ccc(F)cc2)cc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"O=[N+]([O-])c1ccc(-c2ncnn2-c2ccc(F)cc2)cc1\", \"reactants\": [\"CN(C)C=NC(=O)c1ccc([N+](=O)[O-])cc1\", \"NNc1ccc(F)cc1\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"CN(C)C=NC(=O)c1ccc([N+](=O)[O-])cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"NNc1ccc(F)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"XZBZFGOUJNAAHS-UHFFFAOYSA-N.ZXBMIRYQUFQQNX-UHFFFAOYSA-N>>KEDBMNVLYWBXLU-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"O=[N+]([O-])c1ccc(-c2ncnn2-c2ccc(F)cc2)cc1\", \"reactants\": [\"CN(C)C=NC(=O)c1ccc([N+](=O)[O-])cc1\", \"NNc1ccc(F)cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"CN(C)C=NC(=O)c1ccc([N+](=O)[O-])cc1\", \"results\": [{\"inchikey\": \"XZBZFGOUJNAAHS-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CN(C)C=NC(=O)c1ccc([N+](=O)[O-])cc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"NNc1ccc(F)cc1\", \"results\": [{\"inchikey\": \"ZXBMIRYQUFQQNX-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"NNc1ccc(F)cc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CN(C)C=Nc1ccc(-c2ncnn2-c2ccc(F)cc2)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COC(OC)N(C)C\": \"precursor\", \"Nc1ccc(-c2ncnn2-c2ccc(F)cc2)cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COC(OC)N(C)C\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"Nc1ccc(-c2ncnn2-c2ccc(F)cc2)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"O=[N+]([O-])c1ccc(-c2ncnn2-c2ccc(F)cc2)cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"O=[N+]([O-])c1ccc(-c2ncnn2-c2ccc(F)cc2)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CN(C)C=NC(=O)c1ccc([N+](=O)[O-])cc1\": \"precursor\", \"NNc1ccc(F)cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CN(C)C=NC(=O)c1ccc([N+](=O)[O-])cc1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"NNc1ccc(F)cc1\", \"in_stock\": true, \"children\": []}]}]}]}]}]}]}]}}","name":"emit_routes"},"id":"call_4_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"CN(C)C=Nc1ccc(-c2ncnn2-c2ccc(F)cc2)cc1","task_id":"retro_d2bf0228ca892365b99c","tool_calls":9,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":4}
{"exact_match":true,"id":"retro_d2c94ee32c653a6a0796:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target Cc1ccc(C(=O)C=Cc2cc(O)c(O)c([N+](=O)[O-])c2)cc1 in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Cc1ccc(C(=O)C=Cc2cc(O)c(O)c([N+](=O)[O-])c2)cc1\", \"reactants\": [\"CC(=O)c1ccc(C)cc1\", \"O=Cc1cc(O)c(O)c([N+](=O)[O-])c1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(=O)c1ccc(C)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=Cc1cc(O)c(O)c([N+](=O)[O-])c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"BBFJODMCHICIAA-UHFFFAOYSA-N.GNKZMNRKLCTJAY-UHFFFAOYSA-N>>KEEJYRVPFGKFOM-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"Cc1ccc(C(=O)C=Cc2cc(O)c(O)c([N+](=O)[O-])c2)cc1\", \"reactants\": [\"CC(=O)c1ccc(C)cc1\", \"O=Cc1cc(O)c(O)c([N+](=O)[O-])c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CC(=O)c1ccc(C)cc1\", \"results\": [{\"inchikey\": \"GNKZMNRKLCTJAY-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CC(=O)c1ccc(C)cc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"O=Cc1cc(O)c(O)c([N+](=O)[O-])c1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"O=Cc1cc(O)c(O)c([N+](=O)[O-])c1 was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"O=Cc1cc(O)c(O)c([N+](=O)[O-])c1\", \"reactants\": [\"COc1cc(C=O)cc([N+](=O)[O-])c1O\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"COc1cc(C=O)cc([N+](=O)[O-])c1O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"ZEHYRTJBFMZHCY-UHFFFAOYSA-N>>BBFJODMCHICIAA-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"O=Cc1cc(O)c(O)c([N+](=O)[O-])c1\", \"reactants\": [\"COc1cc(C=O)cc([N+](=O)[O-])c1O\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"COc1cc(C=O)cc([N+](=O)[O-])c1O\", \"results\": [{\"inchikey\": \"ZEHYRTJBFMZHCY-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"COc1cc(C=O)cc([N+](=O)[O-])c1O\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"Cc1ccc(C(=O)C=Cc2cc(O)c(O)c([N+](=O)[O-])c2)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(=O)c1ccc(C)cc1\": \"precursor\", \"O=Cc1cc(O)c(O)c([N+](=O)[O-])c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(=O)c1ccc(C)cc1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=Cc1cc(O)c(O)c([N+](=O)[O-])c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COc1cc(C=O)cc([N+](=O)[O-])c1O\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COc1cc(C=O)cc([N+](=O)[O-])c1O\", \"in_stock\": true, \"children\": []}]}]}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"Cc1ccc(C(=O)C=Cc2cc(O)c(O)c([N+](=O)[O-])c2)cc1","task_id":"retro_d2c94ee32c653a6a0796","tool_calls":6,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_d2fb68feebc6b8d92e05:reference-expert:a0","kind":"single_route","max_steps":3,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CC(=O)Nc1ccc(C(=O)NS(=O)(=O)c2ccccc2)cc1NCc1ccc(F)cc1F in at most 3 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(=O)Nc1ccc(C(=O)NS(=O)(=O)c2ccccc2)cc1NCc1ccc(F)cc1F\", \"reactants\": [\"CC(=O)Nc1ccc(C(=O)NS(=O)(=O)c2ccccc2)cc1N\", \"Fc1ccc(CBr)c(F)c1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(=O)Nc1ccc(C(=O)NS(=O)(=O)c2ccccc2)cc1N\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"Fc1ccc(CBr)c(F)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"IBLMYGXJKQIGSN-UHFFFAOYSA-N.SMUPCXIVIMRZES-UHFFFAOYSA-N>>JYLFNCWWNGUQGS-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"CC(=O)Nc1ccc(C(=O)NS(=O)(=O)c2ccccc2)cc1NCc1ccc(F)cc1F\", \"reactants\": [\"CC(=O)Nc1ccc(C(=O)NS(=O)(=O)c2ccccc2)cc1N\", \"Fc1ccc(CBr)c(F)c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CC(=O)Nc1ccc(C(=O)NS(=O)(=O)c2ccccc2)cc1N\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"Fc1ccc(CBr)c(F)c1\", \"results\": [{\"inchikey\": \"IBLMYGXJKQIGSN-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Fc1ccc(CBr)c(F)c1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"CC(=O)Nc1ccc(C(=O)NS(=O)(=O)c2ccccc2)cc1N was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(=O)Nc1ccc(C(=O)NS(=O)(=O)c2ccccc2)cc1N\", \"reactants\": [\"CC(=O)Nc1ccc(C(=O)NS(=O)(=O)c2ccccc2)cc1[N+](=O)[O-]\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(=O)Nc1ccc(C(=O)NS(=O)(=O)c2ccccc2)cc1[N+](=O)[O-]\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"KDEKVTFBMUIKBP-UHFFFAOYSA-N>>SMUPCXIVIMRZES-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"CC(=O)Nc1ccc(C(=O)NS(=O)(=O)c2ccccc2)cc1N\", \"reactants\": [\"CC(=O)Nc1ccc(C(=O)NS(=O)(=O)c2ccccc2)cc1[N+](=O)[O-]\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CC(=O)Nc1ccc(C(=O)NS(=O)(=O)c2ccccc2)cc1[N+](=O)[O-]\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"CC(=O)Nc1ccc(C(=O)NS(=O)(=O)c2ccccc2)cc1[N+](=O)[O-] was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(=O)Nc1ccc(C(=O)NS(=O)(=O)c2ccccc2)cc1[N+](=O)[O-]\", \"reactants\": [\"CC(=O)Nc1ccc(C(=O)O)cc1[N+](=O)[O-]\", \"NS(=O)(=O)c1ccccc1\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(=O)Nc1ccc(C(=O)O)cc1[N+](=O)[O-]\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"NS(=O)(=O)c1ccccc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"BRQIMWBIZLRLSV-UHFFFAOYSA-N.KHBQMWCZKVMBLN-UHFFFAOYSA-N>>KDEKVTFBMUIKBP-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"CC(=O)Nc1ccc(C(=O)NS(=O)(=O)c2ccccc2)cc1[N+](=O)[O-]\", \"reactants\": [\"CC(=O)Nc1ccc(C(=O)O)cc1[N+](=O)[O-]\", \"NS(=O)(=O)c1ccccc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"CC(=O)Nc1ccc(C(=O)O)cc1[N+](=O)[O-]\", \"results\": [{\"inchikey\": \"BRQIMWBIZLRLSV-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CC(=O)Nc1ccc(C(=O)O)cc1[N+](=O)[O-]\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"NS(=O)(=O)c1ccccc1\", \"results\": [{\"inchikey\": \"KHBQMWCZKVMBLN-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"NS(=O)(=O)c1ccccc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CC(=O)Nc1ccc(C(=O)NS(=O)(=O)c2ccccc2)cc1NCc1ccc(F)cc1F\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(=O)Nc1ccc(C(=O)NS(=O)(=O)c2ccccc2)cc1N\": \"precursor\", \"Fc1ccc(CBr)c(F)c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(=O)Nc1ccc(C(=O)NS(=O)(=O)c2ccccc2)cc1N\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(=O)Nc1ccc(C(=O)NS(=O)(=O)c2ccccc2)cc1[N+](=O)[O-]\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(=O)Nc1ccc(C(=O)NS(=O)(=O)c2ccccc2)cc1[N+](=O)[O-]\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(=O)Nc1ccc(C(=O)O)cc1[N+](=O)[O-]\": \"precursor\", \"NS(=O)(=O)c1ccccc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(=O)Nc1ccc(C(=O)O)cc1[N+](=O)[O-]\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"NS(=O)(=O)c1ccccc1\", \"in_stock\": true, \"children\": []}]}]}]}]}, {\"type\": \"mol\", \"smiles\": \"Fc1ccc(CBr)c(F)c1\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_4_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"CC(=O)Nc1ccc(C(=O)NS(=O)(=O)c2ccccc2)cc1NCc1ccc(F)cc1F","task_id":"retro_d2fb68feebc6b8d92e05","tool_calls":9,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":4}
{"exact_match":true,"id":"retro_d3fd7b015da108986d56:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CC(C)(O)Cn1cc(B2OC(C)(C)C(C)(C)O2)ccc1=O in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(C)(O)Cn1cc(B2OC(C)(C)C(C)(C)O2)ccc1=O\", \"reactants\": [\"CC(C)(O)Cn1cc(Br)ccc1=O\", \"CC1(C)OB(B2OC(C)(C)C(C)(C)O2)OC1(C)C\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(O)Cn1cc(Br)ccc1=O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"CC1(C)OB(B2OC(C)(C)C(C)(C)O2)OC1(C)C\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"IDMZCFVZYIPOJF-UHFFFAOYSA-N.IPWKHHSGDUIRAH-UHFFFAOYSA-N>>XYOQGYFKDAYVJJ-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"CC(C)(O)Cn1cc(B2OC(C)(C)C(C)(C)O2)ccc1=O\", \"reactants\": [\"CC(C)(O)Cn1cc(Br)ccc1=O\", \"CC1(C)OB(B2OC(C)(C)C(C)(C)O2)OC1(C)C\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CC(C)(O)Cn1cc(Br)ccc1=O\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CC1(C)OB(B2OC(C)(C)C(C)(C)O2)OC1(C)C\", \"results\": [{\"inchikey\": \"IPWKHHSGDUIRAH-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CC1(C)OB(B2OC(C)(C)C(C)(C)O2)OC1(C)C\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"CC(C)(O)Cn1cc(Br)ccc1=O was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(C)(O)Cn1cc(Br)ccc1=O\", \"reactants\": [\"CC1(C)CO1\", \"O=c1ccc(Br)c[nH]1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC1(C)CO1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=c1ccc(Br)c[nH]1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_complete\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"GELKGHVAFRCJNA-UHFFFAOYSA-N.NDMZZQRNZFWMEZ-UHFFFAOYSA-N>>IDMZCFVZYIPOJF-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"CC(C)(O)Cn1cc(Br)ccc1=O\", \"reactants\": [\"CC1(C)CO1\", \"O=c1ccc(Br)c[nH]1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CC1(C)CO1\", \"results\": [{\"inchikey\": \"GELKGHVAFRCJNA-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CC1(C)CO1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"O=c1ccc(Br)c[nH]1\", \"results\": [{\"inchikey\": \"NDMZZQRNZFWMEZ-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=c1ccc(Br)c[nH]1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(O)Cn1cc(B2OC(C)(C)C(C)(C)O2)ccc1=O\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)(O)Cn1cc(Br)ccc1=O\": \"precursor\", \"CC1(C)OB(B2OC(C)(C)C(C)(C)O2)OC1(C)C\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(O)Cn1cc(Br)ccc1=O\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC1(C)CO1\": \"precursor\", \"O=c1ccc(Br)c[nH]1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC1(C)CO1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=c1ccc(Br)c[nH]1\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"CC1(C)OB(B2OC(C)(C)C(C)(C)O2)OC1(C)C\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"CC(C)(O)Cn1cc(B2OC(C)(C)C(C)(C)O2)ccc1=O","task_id":"retro_d3fd7b015da108986d56","tool_calls":7,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_d49b393e1d430da1ebb1:reference-expert:a0","kind":"single_route","max_steps":5,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target Cn1cc(-c2ccc(-c3cnc(N)c4ccc(C(=O)N5CCCC5)nc34)cc2)cn1 in at most 5 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Cn1cc(-c2ccc(-c3cnc(N)c4ccc(C(=O)N5CCCC5)nc34)cc2)cn1\", \"reactants\": [\"Cn1cc(-c2ccc(-c3cncc4ccc(C(=O)N5CCCC5)nc34)cc2)cn1\", \"NCCO\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"Cn1cc(-c2ccc(-c3cncc4ccc(C(=O)N5CCCC5)nc34)cc2)cn1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"NCCO\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"HZAXFHJVJLSVMW-UHFFFAOYSA-N.KPJPEYWXGRKBQF-UHFFFAOYSA-N>>FBBJFNNZHXLBCQ-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"Cn1cc(-c2ccc(-c3cnc(N)c4ccc(C(=O)N5CCCC5)nc34)cc2)cn1\", \"reactants\": [\"Cn1cc(-c2ccc(-c3cncc4ccc(C(=O)N5CCCC5)nc34)cc2)cn1\", \"NCCO\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"Cn1cc(-c2ccc(-c3cncc4ccc(C(=O)N5CCCC5)nc34)cc2)cn1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"NCCO\", \"results\": [{\"inchikey\": \"HZAXFHJVJLSVMW-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"NCCO\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"Cn1cc(-c2ccc(-c3cncc4ccc(C(=O)N5CCCC5)nc34)cc2)cn1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Cn1cc(-c2ccc(-c3cncc4ccc(C(=O)N5CCCC5)nc34)cc2)cn1\", \"reactants\": [\"Cn1cc(-c2ccc(B3OC(C)(C)C(C)(C)O3)cc2)cn1\", \"O=C(c1ccc2cncc(Br)c2n1)N1CCCC1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"Cn1cc(-c2ccc(B3OC(C)(C)C(C)(C)O3)cc2)cn1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=C(c1ccc2cncc(Br)c2n1)N1CCCC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"GTKBWEUPESFUGI-UHFFFAOYSA-N.ZEPBSTUVYZIDKP-UHFFFAOYSA-N>>KPJPEYWXGRKBQF-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"Cn1cc(-c2ccc(-c3cncc4ccc(C(=O)N5CCCC5)nc34)cc2)cn1\", \"reactants\": [\"Cn1cc(-c2ccc(B3OC(C)(C)C(C)(C)O3)cc2)cn1\", \"O=C(c1ccc2cncc(Br)c2n1)N1CCCC1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"Cn1cc(-c2ccc(B3OC(C)(C)C(C)(C)O3)cc2)cn1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"O=C(c1ccc2cncc(Br)c2n1)N1CCCC1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Cn1cc(-c2ccc(B3OC(C)(C)C(C)(C)O3)cc2)cn1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Cn1cc(-c2ccc(B3OC(C)(C)C(C)(C)O3)cc2)cn1\", \"reactants\": [\"CC1(C)OB(B2OC(C)(C)C(C)(C)O2)OC1(C)C\", \"Cn1cc(-c2ccc(Cl)cc2)cn1\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC1(C)OB(B2OC(C)(C)C(C)(C)O2)OC1(C)C\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"Cn1cc(-c2ccc(Cl)cc2)cn1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"IPWKHHSGDUIRAH-UHFFFAOYSA-N.OYNISOBYGVIGGH-UHFFFAOYSA-N>>GTKBWEUPESFUGI-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"Cn1cc(-c2ccc(B3OC(C)(C)C(C)(C)O3)cc2)cn1\", \"reactants\": [\"CC1(C)OB(B2OC(C)(C)C(C)(C)O2)OC1(C)C\", \"Cn1cc(-c2ccc(Cl)cc2)cn1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"CC1(C)OB(B2OC(C)(C)C(C)(C)O2)OC1(C)C\", \"results\": [{\"inchikey\": \"IPWKHHSGDUIRAH-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CC1(C)OB(B2OC(C)(C)C(C)(C)O2)OC1(C)C\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"Cn1cc(-c2ccc(Cl)cc2)cn1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"O=C(c1ccc2cncc(Br)c2n1)N1CCCC1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"O=C(c1ccc2cncc(Br)c2n1)N1CCCC1\", \"reactants\": [\"C1CCNC1\", \"O=C(O)c1ccc2cncc(Br)c2n1\"]}","name":"validate_disconnection"},"id":"call_4_0","type":"function"},{"function":{"arguments":"{\"query\": \"C1CCNC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=C(O)c1ccc2cncc(Br)c2n1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"ISJKXVUODLFGIU-UHFFFAOYSA-N.RWRDLPDLKQPQOW-UHFFFAOYSA-N>>ZEPBSTUVYZIDKP-UHFFFAOYSA-N\", \"model_turns_remaining\": 12, \"product\": \"O=C(c1ccc2cncc(Br)c2n1)N1CCCC1\", \"reactants\": [\"C1CCNC1\", \"O=C(O)c1ccc2cncc(Br)c2n1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_4_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"C1CCNC1\", \"results\": [{\"inchikey\": \"RWRDLPDLKQPQOW-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"C1CCNC1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"O=C(O)c1ccc2cncc(Br)c2n1\", \"results\": [{\"inchikey\": \"ISJKXVUODLFGIU-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=C(O)c1ccc2cncc(Br)c2n1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_2"},{"content":"Cn1cc(-c2ccc(Cl)cc2)cn1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Cn1cc(-c2ccc(Cl)cc2)cn1\", \"reactants\": [\"Clc1ccc(I)cc1\", \"Cn1cc(B2OC(C)(C)C(C)(C)O2)cn1\"]}","name":"validate_disconnection"},"id":"call_5_0","type":"function"},{"function":{"arguments":"{\"query\": \"Clc1ccc(I)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_5_1","type":"function"},{"function":{"arguments":"{\"query\": \"Cn1cc(B2OC(C)(C)C(C)(C)O2)cn1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_5_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"GWQSENYKCGJTRI-UHFFFAOYSA-N.UCNGGGYMLHAMJG-UHFFFAOYSA-N>>OYNISOBYGVIGGH-UHFFFAOYSA-N\", \"model_turns_remaining\": 11, \"product\": \"Cn1cc(-c2ccc(Cl)cc2)cn1\", \"reactants\": [\"Clc1ccc(I)cc1\", \"Cn1cc(B2OC(C)(C)C(C)(C)O2)cn1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_5_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 11, \"query\": \"Clc1ccc(I)cc1\", \"results\": [{\"inchikey\": \"GWQSENYKCGJTRI-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Clc1ccc(I)cc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_5_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 11, \"query\": \"Cn1cc(B2OC(C)(C)C(C)(C)O2)cn1\", \"results\": [{\"inchikey\": \"UCNGGGYMLHAMJG-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Cn1cc(B2OC(C)(C)C(C)(C)O2)cn1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_5_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"Cn1cc(-c2ccc(-c3cnc(N)c4ccc(C(=O)N5CCCC5)nc34)cc2)cn1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"Cn1cc(-c2ccc(-c3cncc4ccc(C(=O)N5CCCC5)nc34)cc2)cn1\": \"precursor\", \"NCCO\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"Cn1cc(-c2ccc(-c3cncc4ccc(C(=O)N5CCCC5)nc34)cc2)cn1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"Cn1cc(-c2ccc(B3OC(C)(C)C(C)(C)O3)cc2)cn1\": \"precursor\", \"O=C(c1ccc2cncc(Br)c2n1)N1CCCC1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"Cn1cc(-c2ccc(B3OC(C)(C)C(C)(C)O3)cc2)cn1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC1(C)OB(B2OC(C)(C)C(C)(C)O2)OC1(C)C\": \"precursor\", \"Cn1cc(-c2ccc(Cl)cc2)cn1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC1(C)OB(B2OC(C)(C)C(C)(C)O2)OC1(C)C\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"Cn1cc(-c2ccc(Cl)cc2)cn1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"Clc1ccc(I)cc1\": \"precursor\", \"Cn1cc(B2OC(C)(C)C(C)(C)O2)cn1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"Clc1ccc(I)cc1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"Cn1cc(B2OC(C)(C)C(C)(C)O2)cn1\", \"in_stock\": true, \"children\": []}]}]}]}]}, {\"type\": \"mol\", \"smiles\": \"O=C(c1ccc2cncc(Br)c2n1)N1CCCC1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"C1CCNC1\": \"precursor\", \"O=C(O)c1ccc2cncc(Br)c2n1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"C1CCNC1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=C(O)c1ccc2cncc(Br)c2n1\", \"in_stock\": true, \"children\": []}]}]}]}]}, {\"type\": \"mol\", \"smiles\": \"NCCO\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_6_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"Cn1cc(-c2ccc(-c3cnc(N)c4ccc(C(=O)N5CCCC5)nc34)cc2)cn1","task_id":"retro_d49b393e1d430da1ebb1","tool_calls":16,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":6}
{"exact_match":true,"id":"retro_d55009b68ffc4c074cf9:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CC1(C)Cc2cccc(Oc3ncccc3N)c2O1 in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC1(C)Cc2cccc(Oc3ncccc3N)c2O1\", \"reactants\": [\"CC1(C)Cc2cccc(Oc3ncccc3[N+](=O)[O-])c2O1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC1(C)Cc2cccc(Oc3ncccc3[N+](=O)[O-])c2O1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"ZDEYFOTZNNRHPD-UHFFFAOYSA-N>>FZQYZCSXWQTBFA-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"CC1(C)Cc2cccc(Oc3ncccc3N)c2O1\", \"reactants\": [\"CC1(C)Cc2cccc(Oc3ncccc3[N+](=O)[O-])c2O1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CC1(C)Cc2cccc(Oc3ncccc3[N+](=O)[O-])c2O1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"CC1(C)Cc2cccc(Oc3ncccc3[N+](=O)[O-])c2O1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC1(C)Cc2cccc(Oc3ncccc3[N+](=O)[O-])c2O1\", \"reactants\": [\"CC1(C)Cc2cccc(O)c2O1\", \"O=[N+]([O-])c1cccnc1Cl\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC1(C)Cc2cccc(O)c2O1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=[N+]([O-])c1cccnc1Cl\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"UUOLETYDNTVQDY-UHFFFAOYSA-N.WJGPNUBJBMCRQH-UHFFFAOYSA-N>>ZDEYFOTZNNRHPD-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"CC1(C)Cc2cccc(Oc3ncccc3[N+](=O)[O-])c2O1\", \"reactants\": [\"CC1(C)Cc2cccc(O)c2O1\", \"O=[N+]([O-])c1cccnc1Cl\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CC1(C)Cc2cccc(O)c2O1\", \"results\": [{\"inchikey\": \"WJGPNUBJBMCRQH-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CC1(C)Cc2cccc(O)c2O1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"O=[N+]([O-])c1cccnc1Cl\", \"results\": [{\"inchikey\": \"UUOLETYDNTVQDY-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=[N+]([O-])c1cccnc1Cl\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CC1(C)Cc2cccc(Oc3ncccc3N)c2O1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC1(C)Cc2cccc(Oc3ncccc3[N+](=O)[O-])c2O1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC1(C)Cc2cccc(Oc3ncccc3[N+](=O)[O-])c2O1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC1(C)Cc2cccc(O)c2O1\": \"precursor\", \"O=[N+]([O-])c1cccnc1Cl\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC1(C)Cc2cccc(O)c2O1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=[N+]([O-])c1cccnc1Cl\", \"in_stock\": true, \"children\": []}]}]}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"CC1(C)Cc2cccc(Oc3ncccc3N)c2O1","task_id":"retro_d55009b68ffc4c074cf9","tool_calls":6,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_d76bfb7a43180844e44f:reference-expert:a0","kind":"single_route","max_steps":4,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target COc1c(C=O)cc(Br)cc1C(F)(F)F in at most 4 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COc1c(C=O)cc(Br)cc1C(F)(F)F\", \"reactants\": [\"COS(=O)(=O)OC\", \"O=Cc1cc(Br)cc(C(F)(F)F)c1O\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"COS(=O)(=O)OC\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=Cc1cc(Br)cc(C(F)(F)F)c1O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"NCOPDQCEVBJGNB-UHFFFAOYSA-N.VAYGXNSJCAHWJZ-UHFFFAOYSA-N>>GLIBUUMOKPPOAL-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"COc1c(C=O)cc(Br)cc1C(F)(F)F\", \"reactants\": [\"COS(=O)(=O)OC\", \"O=Cc1cc(Br)cc(C(F)(F)F)c1O\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"COS(=O)(=O)OC\", \"results\": [{\"inchikey\": \"VAYGXNSJCAHWJZ-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"COS(=O)(=O)OC\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"O=Cc1cc(Br)cc(C(F)(F)F)c1O\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"O=Cc1cc(Br)cc(C(F)(F)F)c1O was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"O=Cc1cc(Br)cc(C(F)(F)F)c1O\", \"reactants\": [\"O=C1CCC(=O)N1Br\", \"O=Cc1cccc(C(F)(F)F)c1O\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"O=C1CCC(=O)N1Br\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=Cc1cccc(C(F)(F)F)c1O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"PCLIMKBDDGJMGD-UHFFFAOYSA-N.ZUNOXMJBNMKYOM-UHFFFAOYSA-N>>NCOPDQCEVBJGNB-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"O=Cc1cc(Br)cc(C(F)(F)F)c1O\", \"reactants\": [\"O=C1CCC(=O)N1Br\", \"O=Cc1cccc(C(F)(F)F)c1O\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"O=C1CCC(=O)N1Br\", \"results\": [{\"inchikey\": \"PCLIMKBDDGJMGD-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=C1CCC(=O)N1Br\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"O=Cc1cccc(C(F)(F)F)c1O\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"O=Cc1cccc(C(F)(F)F)c1O was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"O=Cc1cccc(C(F)(F)F)c1O\", \"reactants\": [\"CN(C)C=O\", \"COCOc1ccccc1C(F)(F)F\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"CN(C)C=O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"COCOc1ccccc1C(F)(F)F\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"KDGCARXCCUSENF-UHFFFAOYSA-N.ZMXDDKWLCZADIW-UHFFFAOYSA-N>>ZUNOXMJBNMKYOM-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"O=Cc1cccc(C(F)(F)F)c1O\", \"reactants\": [\"CN(C)C=O\", \"COCOc1ccccc1C(F)(F)F\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"CN(C)C=O\", \"results\": [{\"inchikey\": \"ZMXDDKWLCZADIW-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CN(C)C=O\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"COCOc1ccccc1C(F)(F)F\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"COCOc1ccccc1C(F)(F)F was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COCOc1ccccc1C(F)(F)F\", \"reactants\": [\"COCCl\", \"Oc1ccccc1C(F)(F)F\"]}","name":"validate_disconnection"},"id":"call_4_0","type":"function"},{"function":{"arguments":"{\"query\": \"COCCl\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_1","type":"function"},{"function":{"arguments":"{\"query\": \"Oc1ccccc1C(F)(F)F\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"XJUZRXYOEPSWMB-UHFFFAOYSA-N.ZOQOPXVJANRGJZ-UHFFFAOYSA-N>>KDGCARXCCUSENF-UHFFFAOYSA-N\", \"model_turns_remaining\": 12, \"product\": \"COCOc1ccccc1C(F)(F)F\", \"reactants\": [\"COCCl\", \"Oc1ccccc1C(F)(F)F\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_4_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"COCCl\", \"results\": [{\"inchikey\": \"XJUZRXYOEPSWMB-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"COCCl\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"Oc1ccccc1C(F)(F)F\", \"results\": [{\"inchikey\": \"ZOQOPXVJANRGJZ-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Oc1ccccc1C(F)(F)F\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"COc1c(C=O)cc(Br)cc1C(F)(F)F\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COS(=O)(=O)OC\": \"precursor\", \"O=Cc1cc(Br)cc(C(F)(F)F)c1O\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COS(=O)(=O)OC\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=Cc1cc(Br)cc(C(F)(F)F)c1O\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"O=C1CCC(=O)N1Br\": \"precursor\", \"O=Cc1cccc(C(F)(F)F)c1O\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"O=C1CCC(=O)N1Br\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=Cc1cccc(C(F)(F)F)c1O\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CN(C)C=O\": \"precursor\", \"COCOc1ccccc1C(F)(F)F\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CN(C)C=O\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"COCOc1ccccc1C(F)(F)F\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COCCl\": \"precursor\", \"Oc1ccccc1C(F)(F)F\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COCCl\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"Oc1ccccc1C(F)(F)F\", \"in_stock\": true, \"children\": []}]}]}]}]}]}]}]}]}]}}","name":"emit_routes"},"id":"call_5_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"COc1c(C=O)cc(Br)cc1C(F)(F)F","task_id":"retro_d76bfb7a43180844e44f","tool_calls":13,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":5}
{"exact_match":true,"id":"retro_d7a35afdbf3e510c0d4b:reference-expert:a0","kind":"single_route","max_steps":3,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target NC(=O)c1[nH]nc2c1CCN(c1ccc(NC(=O)Nc3cc(C(F)(F)F)ccc3F)cn1)C2 in at most 3 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"NC(=O)c1[nH]nc2c1CCN(c1ccc(NC(=O)Nc3cc(C(F)(F)F)ccc3F)cn1)C2\", \"reactants\": [\"NC(=O)c1[nH]nc2c1CCN(c1ccc(N)cn1)C2\", \"O=C=Nc1cc(C(F)(F)F)ccc1F\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"NC(=O)c1[nH]nc2c1CCN(c1ccc(N)cn1)C2\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=C=Nc1cc(C(F)(F)F)ccc1F\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_complete\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"NAIKHCBDZGSGHH-UHFFFAOYSA-N.VKWQIFYXHNLNAJ-UHFFFAOYSA-N>>XTFJPVYZDFZQLQ-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"NC(=O)c1[nH]nc2c1CCN(c1ccc(NC(=O)Nc3cc(C(F)(F)F)ccc3F)cn1)C2\", \"reactants\": [\"NC(=O)c1[nH]nc2c1CCN(c1ccc(N)cn1)C2\", \"O=C=Nc1cc(C(F)(F)F)ccc1F\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"NC(=O)c1[nH]nc2c1CCN(c1ccc(N)cn1)C2\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"O=C=Nc1cc(C(F)(F)F)ccc1F\", \"results\": [{\"inchikey\": \"NAIKHCBDZGSGHH-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=C=Nc1cc(C(F)(F)F)ccc1F\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"NC(=O)c1[nH]nc2c1CCN(c1ccc(N)cn1)C2 was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"NC(=O)c1[nH]nc2c1CCN(c1ccc(N)cn1)C2\", \"reactants\": [\"CC(C)(C)OC(=O)Nc1ccc(N2CCc3c(n[nH]c3C(N)=O)C2)nc1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)OC(=O)Nc1ccc(N2CCc3c(n[nH]c3C(N)=O)C2)nc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"YGOQQHPCPPLLSB-UHFFFAOYSA-N>>VKWQIFYXHNLNAJ-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"NC(=O)c1[nH]nc2c1CCN(c1ccc(N)cn1)C2\", \"reactants\": [\"CC(C)(C)OC(=O)Nc1ccc(N2CCc3c(n[nH]c3C(N)=O)C2)nc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CC(C)(C)OC(=O)Nc1ccc(N2CCc3c(n[nH]c3C(N)=O)C2)nc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"CC(C)(C)OC(=O)Nc1ccc(N2CCc3c(n[nH]c3C(N)=O)C2)nc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(C)(C)OC(=O)Nc1ccc(N2CCc3c(n[nH]c3C(N)=O)C2)nc1\", \"reactants\": [\"CCOC(=O)c1[nH]nc2c1CCN(c1ccc(NC(=O)OC(C)(C)C)cn1)C2\", \"N\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCOC(=O)c1[nH]nc2c1CCN(c1ccc(NC(=O)OC(C)(C)C)cn1)C2\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"N\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"MGQQUAFUTUHRRG-UHFFFAOYSA-N.QGZKDVFQNNGYKY-UHFFFAOYSA-N>>YGOQQHPCPPLLSB-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"CC(C)(C)OC(=O)Nc1ccc(N2CCc3c(n[nH]c3C(N)=O)C2)nc1\", \"reactants\": [\"CCOC(=O)c1[nH]nc2c1CCN(c1ccc(NC(=O)OC(C)(C)C)cn1)C2\", \"N\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"CCOC(=O)c1[nH]nc2c1CCN(c1ccc(NC(=O)OC(C)(C)C)cn1)C2\", \"results\": [{\"inchikey\": \"MGQQUAFUTUHRRG-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CCOC(=O)c1[nH]nc2c1CCN(c1ccc(NC(=O)OC(C)(C)C)cn1)C2\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"N\", \"results\": [{\"inchikey\": \"QGZKDVFQNNGYKY-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"N\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"NC(=O)c1[nH]nc2c1CCN(c1ccc(NC(=O)Nc3cc(C(F)(F)F)ccc3F)cn1)C2\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"NC(=O)c1[nH]nc2c1CCN(c1ccc(N)cn1)C2\": \"precursor\", \"O=C=Nc1cc(C(F)(F)F)ccc1F\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"NC(=O)c1[nH]nc2c1CCN(c1ccc(N)cn1)C2\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)(C)OC(=O)Nc1ccc(N2CCc3c(n[nH]c3C(N)=O)C2)nc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)OC(=O)Nc1ccc(N2CCc3c(n[nH]c3C(N)=O)C2)nc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCOC(=O)c1[nH]nc2c1CCN(c1ccc(NC(=O)OC(C)(C)C)cn1)C2\": \"precursor\", \"N\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCOC(=O)c1[nH]nc2c1CCN(c1ccc(NC(=O)OC(C)(C)C)cn1)C2\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"N\", \"in_stock\": true, \"children\": []}]}]}]}]}, {\"type\": \"mol\", \"smiles\": \"O=C=Nc1cc(C(F)(F)F)ccc1F\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_4_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"NC(=O)c1[nH]nc2c1CCN(c1ccc(NC(=O)Nc3cc(C(F)(F)F)ccc3F)cn1)C2","task_id":"retro_d7a35afdbf3e510c0d4b","tool_calls":9,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":4}
{"exact_match":true,"id":"retro_db0e5fae17d9af54e4c8:reference-expert:a0","kind":"single_route","max_steps":4,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target S=C=Nc1ccc(C2CC2)c2ccccc12 in at most 4 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"S=C=Nc1ccc(C2CC2)c2ccccc12\", \"reactants\": [\"Nc1ccc(C2CC2)c2ccccc12\", \"S=C(Cl)Cl\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"Nc1ccc(C2CC2)c2ccccc12\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"S=C(Cl)Cl\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"NYKSBMRQNSCVMO-UHFFFAOYSA-N.ZWZVWGITAAIFPS-UHFFFAOYSA-N>>CCPTWMNSFHCZPB-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"S=C=Nc1ccc(C2CC2)c2ccccc12\", \"reactants\": [\"Nc1ccc(C2CC2)c2ccccc12\", \"S=C(Cl)Cl\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"Nc1ccc(C2CC2)c2ccccc12\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"S=C(Cl)Cl\", \"results\": [{\"inchikey\": \"ZWZVWGITAAIFPS-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"S=C(Cl)Cl\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"Nc1ccc(C2CC2)c2ccccc12 was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Nc1ccc(C2CC2)c2ccccc12\", \"reactants\": [\"O=[N+]([O-])c1ccc(C2CC2)c2ccccc12\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"O=[N+]([O-])c1ccc(C2CC2)c2ccccc12\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"CHOXFKFUEGIWTO-UHFFFAOYSA-N>>NYKSBMRQNSCVMO-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"Nc1ccc(C2CC2)c2ccccc12\", \"reactants\": [\"O=[N+]([O-])c1ccc(C2CC2)c2ccccc12\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"O=[N+]([O-])c1ccc(C2CC2)c2ccccc12\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"O=[N+]([O-])c1ccc(C2CC2)c2ccccc12 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"O=[N+]([O-])c1ccc(C2CC2)c2ccccc12\", \"reactants\": [\"O=NO\", \"c1ccc2c(C3CC3)cccc2c1\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"O=NO\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"c1ccc2c(C3CC3)cccc2c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_complete\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"IOVCWXUNBOPUCH-UHFFFAOYSA-N.VZZBXOLWBXJHEK-UHFFFAOYSA-N>>CHOXFKFUEGIWTO-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"O=[N+]([O-])c1ccc(C2CC2)c2ccccc12\", \"reactants\": [\"O=NO\", \"c1ccc2c(C3CC3)cccc2c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"O=NO\", \"results\": [{\"inchikey\": \"IOVCWXUNBOPUCH-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=NO\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"c1ccc2c(C3CC3)cccc2c1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"c1ccc2c(C3CC3)cccc2c1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"c1ccc2c(C3CC3)cccc2c1\", \"reactants\": [\"Brc1cccc2ccccc12\", \"[Br][Mg][CH]1CC1\"]}","name":"validate_disconnection"},"id":"call_4_0","type":"function"},{"function":{"arguments":"{\"query\": \"Brc1cccc2ccccc12\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_1","type":"function"},{"function":{"arguments":"{\"query\": \"[Br][Mg][CH]1CC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"DLKQHBOKULLWDQ-UHFFFAOYSA-N.QUPLLJGAJVXXBW-UHFFFAOYSA-M>>VZZBXOLWBXJHEK-UHFFFAOYSA-N\", \"model_turns_remaining\": 12, \"product\": \"c1ccc2c(C3CC3)cccc2c1\", \"reactants\": [\"Brc1cccc2ccccc12\", \"[Br][Mg][CH]1CC1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_4_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"Brc1cccc2ccccc12\", \"results\": [{\"inchikey\": \"DLKQHBOKULLWDQ-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Brc1cccc2ccccc12\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"[Br][Mg][CH]1CC1\", \"results\": [{\"inchikey\": \"QUPLLJGAJVXXBW-UHFFFAOYSA-M\", \"similarity\": 1.0, \"smiles\": \"[Br][Mg][CH]1CC1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"S=C=Nc1ccc(C2CC2)c2ccccc12\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"Nc1ccc(C2CC2)c2ccccc12\": \"precursor\", \"S=C(Cl)Cl\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"Nc1ccc(C2CC2)c2ccccc12\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"O=[N+]([O-])c1ccc(C2CC2)c2ccccc12\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"O=[N+]([O-])c1ccc(C2CC2)c2ccccc12\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"O=NO\": \"precursor\", \"c1ccc2c(C3CC3)cccc2c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"O=NO\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"c1ccc2c(C3CC3)cccc2c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"Brc1cccc2ccccc12\": \"precursor\", \"[Br][Mg][CH]1CC1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"Brc1cccc2ccccc12\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"[Br][Mg][CH]1CC1\", \"in_stock\": true, \"children\": []}]}]}]}]}]}]}, {\"type\": \"mol\", \"smiles\": \"S=C(Cl)Cl\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_5_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"S=C=Nc1ccc(C2CC2)c2ccccc12","task_id":"retro_db0e5fae17d9af54e4c8","tool_calls":12,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":5}
{"exact_match":true,"id":"retro_db172814a659d2229147:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target BrCc1ccc(-c2nc3ccccc3s2)cc1 in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"BrCc1ccc(-c2nc3ccccc3s2)cc1\", \"reactants\": [\"Cc1ccc(-c2nc3ccccc3s2)cc1\", \"O=C1CCC(=O)N1Br\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"Cc1ccc(-c2nc3ccccc3s2)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=C1CCC(=O)N1Br\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"JVPGYYNQTPWXGE-UHFFFAOYSA-N.PCLIMKBDDGJMGD-UHFFFAOYSA-N>>XXGFUKAVDJZZAM-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"BrCc1ccc(-c2nc3ccccc3s2)cc1\", \"reactants\": [\"Cc1ccc(-c2nc3ccccc3s2)cc1\", \"O=C1CCC(=O)N1Br\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"Cc1ccc(-c2nc3ccccc3s2)cc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"O=C1CCC(=O)N1Br\", \"results\": [{\"inchikey\": \"PCLIMKBDDGJMGD-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=C1CCC(=O)N1Br\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"Cc1ccc(-c2nc3ccccc3s2)cc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Cc1ccc(-c2nc3ccccc3s2)cc1\", \"reactants\": [\"Cc1ccc(C(=O)O)cc1\", \"Nc1ccccc1S\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"Cc1ccc(C(=O)O)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"Nc1ccccc1S\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"LPNBBFKOUUSUDB-UHFFFAOYSA-N.VRVRGVPWCUEOGV-UHFFFAOYSA-N>>JVPGYYNQTPWXGE-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"Cc1ccc(-c2nc3ccccc3s2)cc1\", \"reactants\": [\"Cc1ccc(C(=O)O)cc1\", \"Nc1ccccc1S\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"Cc1ccc(C(=O)O)cc1\", \"results\": [{\"inchikey\": \"LPNBBFKOUUSUDB-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Cc1ccc(C(=O)O)cc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"Nc1ccccc1S\", \"results\": [{\"inchikey\": \"VRVRGVPWCUEOGV-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Nc1ccccc1S\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"BrCc1ccc(-c2nc3ccccc3s2)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"Cc1ccc(-c2nc3ccccc3s2)cc1\": \"precursor\", \"O=C1CCC(=O)N1Br\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"Cc1ccc(-c2nc3ccccc3s2)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"Cc1ccc(C(=O)O)cc1\": \"precursor\", \"Nc1ccccc1S\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"Cc1ccc(C(=O)O)cc1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"Nc1ccccc1S\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"O=C1CCC(=O)N1Br\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"BrCc1ccc(-c2nc3ccccc3s2)cc1","task_id":"retro_db172814a659d2229147","tool_calls":7,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_ddc5575425e91660903b:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target O=C1NCCN1c1cccc(F)c1 in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"O=C1NCCN1c1cccc(F)c1\", \"reactants\": [\"O=C(NCCCl)Nc1cccc(F)c1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"O=C(NCCCl)Nc1cccc(F)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"OMTBVYGKVUTWNV-UHFFFAOYSA-N>>JYIXWDAEDKBYEE-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"O=C1NCCN1c1cccc(F)c1\", \"reactants\": [\"O=C(NCCCl)Nc1cccc(F)c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"O=C(NCCCl)Nc1cccc(F)c1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"O=C(NCCCl)Nc1cccc(F)c1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"O=C(NCCCl)Nc1cccc(F)c1\", \"reactants\": [\"Nc1cccc(F)c1\", \"O=C=NCCCl\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"Nc1cccc(F)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=C=NCCCl\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_complete\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"BCMYXYHEMGPZJN-UHFFFAOYSA-N.QZVQQUVWFIZUBQ-UHFFFAOYSA-N>>OMTBVYGKVUTWNV-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"O=C(NCCCl)Nc1cccc(F)c1\", \"reactants\": [\"Nc1cccc(F)c1\", \"O=C=NCCCl\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"Nc1cccc(F)c1\", \"results\": [{\"inchikey\": \"QZVQQUVWFIZUBQ-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Nc1cccc(F)c1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"O=C=NCCCl\", \"results\": [{\"inchikey\": \"BCMYXYHEMGPZJN-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=C=NCCCl\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"O=C1NCCN1c1cccc(F)c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"O=C(NCCCl)Nc1cccc(F)c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"O=C(NCCCl)Nc1cccc(F)c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"Nc1cccc(F)c1\": \"precursor\", \"O=C=NCCCl\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"Nc1cccc(F)c1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=C=NCCCl\", \"in_stock\": true, \"children\": []}]}]}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"O=C1NCCN1c1cccc(F)c1","task_id":"retro_ddc5575425e91660903b","tool_calls":6,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_e271a30615f1ea6425b0:reference-expert:a0","kind":"single_route","max_steps":3,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CCCCCCCCCCCCc1ccsc1C=O in at most 3 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCCCCCCCCCCCc1ccsc1C=O\", \"reactants\": [\"CCCCCCCCCCCCc1ccsc1Br\", \"CN(C)C=O\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCCCCCCCCCCCc1ccsc1Br\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"CN(C)C=O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"IMILVTHOOISGRW-UHFFFAOYSA-N.ZMXDDKWLCZADIW-UHFFFAOYSA-N>>HKFGSESJCHINGM-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"CCCCCCCCCCCCc1ccsc1C=O\", \"reactants\": [\"CCCCCCCCCCCCc1ccsc1Br\", \"CN(C)C=O\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CCCCCCCCCCCCc1ccsc1Br\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CN(C)C=O\", \"results\": [{\"inchikey\": \"ZMXDDKWLCZADIW-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CN(C)C=O\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"CCCCCCCCCCCCc1ccsc1Br was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCCCCCCCCCCCc1ccsc1Br\", \"reactants\": [\"CCCCCCCCCCCCc1ccsc1\", \"O=C1CCC(=O)N1Br\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCCCCCCCCCCCc1ccsc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=C1CCC(=O)N1Br\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"PCLIMKBDDGJMGD-UHFFFAOYSA-N.RFKWIEFTBMACPZ-UHFFFAOYSA-N>>IMILVTHOOISGRW-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"CCCCCCCCCCCCc1ccsc1Br\", \"reactants\": [\"CCCCCCCCCCCCc1ccsc1\", \"O=C1CCC(=O)N1Br\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CCCCCCCCCCCCc1ccsc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"O=C1CCC(=O)N1Br\", \"results\": [{\"inchikey\": \"PCLIMKBDDGJMGD-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=C1CCC(=O)N1Br\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"CCCCCCCCCCCCc1ccsc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCCCCCCCCCCCc1ccsc1\", \"reactants\": [\"Brc1ccsc1\", \"CCCCCCCCCCCCBr\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"Brc1ccsc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"CCCCCCCCCCCCBr\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"PBLNBZIONSLZBU-UHFFFAOYSA-N.XCMISAPCWHTVNG-UHFFFAOYSA-N>>RFKWIEFTBMACPZ-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"CCCCCCCCCCCCc1ccsc1\", \"reactants\": [\"Brc1ccsc1\", \"CCCCCCCCCCCCBr\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"Brc1ccsc1\", \"results\": [{\"inchikey\": \"XCMISAPCWHTVNG-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Brc1ccsc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"CCCCCCCCCCCCBr\", \"results\": [{\"inchikey\": \"PBLNBZIONSLZBU-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CCCCCCCCCCCCBr\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CCCCCCCCCCCCc1ccsc1C=O\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCCCCCCCCCCCc1ccsc1Br\": \"precursor\", \"CN(C)C=O\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCCCCCCCCCCCc1ccsc1Br\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCCCCCCCCCCCc1ccsc1\": \"precursor\", \"O=C1CCC(=O)N1Br\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCCCCCCCCCCCc1ccsc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"Brc1ccsc1\": \"precursor\", \"CCCCCCCCCCCCBr\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"Brc1ccsc1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"CCCCCCCCCCCCBr\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"O=C1CCC(=O)N1Br\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"CN(C)C=O\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_4_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"CCCCCCCCCCCCc1ccsc1C=O","task_id":"retro_e271a30615f1ea6425b0","tool_calls":10,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":4}
{"exact_match":true,"id":"retro_e2c0a70cc7baf48eac30:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CC1(C)OB(c2ccc(OCCCC(=O)O)cc2)OC1(C)C in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC1(C)OB(c2ccc(OCCCC(=O)O)cc2)OC1(C)C\", \"reactants\": [\"CCOC(=O)CCCOc1ccc(B2OC(C)(C)C(C)(C)O2)cc1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCOC(=O)CCCOc1ccc(B2OC(C)(C)C(C)(C)O2)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"ULQLSUMGMISQGT-UHFFFAOYSA-N>>CRRCQQLEPDZRAA-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"CC1(C)OB(c2ccc(OCCCC(=O)O)cc2)OC1(C)C\", \"reactants\": [\"CCOC(=O)CCCOc1ccc(B2OC(C)(C)C(C)(C)O2)cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CCOC(=O)CCCOc1ccc(B2OC(C)(C)C(C)(C)O2)cc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"CCOC(=O)CCCOc1ccc(B2OC(C)(C)C(C)(C)O2)cc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCOC(=O)CCCOc1ccc(B2OC(C)(C)C(C)(C)O2)cc1\", \"reactants\": [\"CC1(C)OB(c2ccc(O)cc2)OC1(C)C\", \"CCOC(=O)CCCBr\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC1(C)OB(c2ccc(O)cc2)OC1(C)C\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"CCOC(=O)CCCBr\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"BICZJRAGTCRORZ-UHFFFAOYSA-N.XBPOBCXHALHJFP-UHFFFAOYSA-N>>ULQLSUMGMISQGT-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"CCOC(=O)CCCOc1ccc(B2OC(C)(C)C(C)(C)O2)cc1\", \"reactants\": [\"CC1(C)OB(c2ccc(O)cc2)OC1(C)C\", \"CCOC(=O)CCCBr\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CC1(C)OB(c2ccc(O)cc2)OC1(C)C\", \"results\": [{\"inchikey\": \"BICZJRAGTCRORZ-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CC1(C)OB(c2ccc(O)cc2)OC1(C)C\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CCOC(=O)CCCBr\", \"results\": [{\"inchikey\": \"XBPOBCXHALHJFP-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CCOC(=O)CCCBr\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CC1(C)OB(c2ccc(OCCCC(=O)O)cc2)OC1(C)C\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCOC(=O)CCCOc1ccc(B2OC(C)(C)C(C)(C)O2)cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCOC(=O)CCCOc1ccc(B2OC(C)(C)C(C)(C)O2)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC1(C)OB(c2ccc(O)cc2)OC1(C)C\": \"precursor\", \"CCOC(=O)CCCBr\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC1(C)OB(c2ccc(O)cc2)OC1(C)C\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"CCOC(=O)CCCBr\", \"in_stock\": true, \"children\": []}]}]}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"CC1(C)OB(c2ccc(OCCCC(=O)O)cc2)OC1(C)C","task_id":"retro_e2c0a70cc7baf48eac30","tool_calls":6,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_e5262ad88438bbb6f4ec:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target C=CC(=O)OCCCCCCN(CC)c1ccc(/N=N/c2ccc([N+](=O)[O-])cc2C#N)cc1 in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"C=CC(=O)OCCCCCCN(CC)c1ccc(/N=N/c2ccc([N+](=O)[O-])cc2C#N)cc1\", \"reactants\": [\"C=CC(=O)Cl\", \"CCN(CCCCCCO)c1ccc(/N=N/c2ccc([N+](=O)[O-])cc2C#N)cc1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"C=CC(=O)Cl\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"CCN(CCCCCCO)c1ccc(/N=N/c2ccc([N+](=O)[O-])cc2C#N)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"HFBMWMNUJJDEQZ-UHFFFAOYSA-N.NDLWRAXBZSHMFU-WCWDXBQESA-N>>NGFRIHNSICCVQL-CYYJNZCTSA-N\", \"model_turns_remaining\": 15, \"product\": \"C=CC(=O)OCCCCCCN(CC)c1ccc(/N=N/c2ccc([N+](=O)[O-])cc2C#N)cc1\", \"reactants\": [\"C=CC(=O)Cl\", \"CCN(CCCCCCO)c1ccc(/N=N/c2ccc([N+](=O)[O-])cc2C#N)cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"C=CC(=O)Cl\", \"results\": [{\"inchikey\": \"HFBMWMNUJJDEQZ-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"C=CC(=O)Cl\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CCN(CCCCCCO)c1ccc(/N=N/c2ccc([N+](=O)[O-])cc2C#N)cc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"CCN(CCCCCCO)c1ccc(/N=N/c2ccc([N+](=O)[O-])cc2C#N)cc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCN(CCCCCCO)c1ccc(/N=N/c2ccc([N+](=O)[O-])cc2C#N)cc1\", \"reactants\": [\"CCN(CCCCCCO)c1ccccc1\", \"N#Cc1cc([N+](=O)[O-])ccc1N\", \"O=NO\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCN(CCCCCCO)c1ccccc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"N#Cc1cc([N+](=O)[O-])ccc1N\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"},{"function":{"arguments":"{\"query\": \"O=NO\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_3","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"IOVCWXUNBOPUCH-UHFFFAOYSA-N.LIDHWGMXXKSFNT-UHFFFAOYSA-N.MGCGMYPNXAFGFA-UHFFFAOYSA-N>>NDLWRAXBZSHMFU-WCWDXBQESA-N\", \"model_turns_remaining\": 14, \"product\": \"CCN(CCCCCCO)c1ccc(/N=N/c2ccc([N+](=O)[O-])cc2C#N)cc1\", \"reactants\": [\"CCN(CCCCCCO)c1ccccc1\", \"N#Cc1cc([N+](=O)[O-])ccc1N\", \"O=NO\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CCN(CCCCCCO)c1ccccc1\", \"results\": [{\"inchikey\": \"LIDHWGMXXKSFNT-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CCN(CCCCCCO)c1ccccc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"N#Cc1cc([N+](=O)[O-])ccc1N\", \"results\": [{\"inchikey\": \"MGCGMYPNXAFGFA-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"N#Cc1cc([N+](=O)[O-])ccc1N\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"O=NO\", \"results\": [{\"inchikey\": \"IOVCWXUNBOPUCH-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=NO\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_3"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"C=CC(=O)OCCCCCCN(CC)c1ccc(/N=N/c2ccc([N+](=O)[O-])cc2C#N)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"C=CC(=O)Cl\": \"precursor\", \"CCN(CCCCCCO)c1ccc(/N=N/c2ccc([N+](=O)[O-])cc2C#N)cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"C=CC(=O)Cl\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"CCN(CCCCCCO)c1ccc(/N=N/c2ccc([N+](=O)[O-])cc2C#N)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCN(CCCCCCO)c1ccccc1\": \"precursor\", \"N#Cc1cc([N+](=O)[O-])ccc1N\": \"precursor\", \"O=NO\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCN(CCCCCCO)c1ccccc1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"N#Cc1cc([N+](=O)[O-])ccc1N\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=NO\", \"in_stock\": true, \"children\": []}]}]}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"C=CC(=O)OCCCCCCN(CC)c1ccc(/N=N/c2ccc([N+](=O)[O-])cc2C#N)cc1","task_id":"retro_e5262ad88438bbb6f4ec","tool_calls":8,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_e57f377765ca27b6a9d8:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target O=C(CCN1CCN(c2ccc(F)cc2)CC1)Nc1ccc(F)cc1[N+](=O)[O-] in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"O=C(CCN1CCN(c2ccc(F)cc2)CC1)Nc1ccc(F)cc1[N+](=O)[O-]\", \"reactants\": [\"Fc1ccc(N2CCNCC2)cc1\", \"O=C(CCBr)Nc1ccc(F)cc1[N+](=O)[O-]\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"Fc1ccc(N2CCNCC2)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=C(CCBr)Nc1ccc(F)cc1[N+](=O)[O-]\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"AVJKDKWRVSSJPK-UHFFFAOYSA-N.NKCNHZSFTYPJOH-UHFFFAOYSA-N>>AMOYCXAVTCEJBS-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"O=C(CCN1CCN(c2ccc(F)cc2)CC1)Nc1ccc(F)cc1[N+](=O)[O-]\", \"reactants\": [\"Fc1ccc(N2CCNCC2)cc1\", \"O=C(CCBr)Nc1ccc(F)cc1[N+](=O)[O-]\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"Fc1ccc(N2CCNCC2)cc1\", \"results\": [{\"inchikey\": \"AVJKDKWRVSSJPK-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Fc1ccc(N2CCNCC2)cc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"O=C(CCBr)Nc1ccc(F)cc1[N+](=O)[O-]\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"O=C(CCBr)Nc1ccc(F)cc1[N+](=O)[O-] was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"O=C(CCBr)Nc1ccc(F)cc1[N+](=O)[O-]\", \"reactants\": [\"Nc1ccc(F)cc1[N+](=O)[O-]\", \"O=C(Cl)CCBr\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"Nc1ccc(F)cc1[N+](=O)[O-]\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=C(Cl)CCBr\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"IHBVNSPHKMCPST-UHFFFAOYSA-N.PUGDHSSOXPHLPT-UHFFFAOYSA-N>>NKCNHZSFTYPJOH-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"O=C(CCBr)Nc1ccc(F)cc1[N+](=O)[O-]\", \"reactants\": [\"Nc1ccc(F)cc1[N+](=O)[O-]\", \"O=C(Cl)CCBr\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"Nc1ccc(F)cc1[N+](=O)[O-]\", \"results\": [{\"inchikey\": \"PUGDHSSOXPHLPT-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Nc1ccc(F)cc1[N+](=O)[O-]\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"O=C(Cl)CCBr\", \"results\": [{\"inchikey\": \"IHBVNSPHKMCPST-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=C(Cl)CCBr\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"O=C(CCN1CCN(c2ccc(F)cc2)CC1)Nc1ccc(F)cc1[N+](=O)[O-]\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"Fc1ccc(N2CCNCC2)cc1\": \"precursor\", \"O=C(CCBr)Nc1ccc(F)cc1[N+](=O)[O-]\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"Fc1ccc(N2CCNCC2)cc1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=C(CCBr)Nc1ccc(F)cc1[N+](=O)[O-]\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"Nc1ccc(F)cc1[N+](=O)[O-]\": \"precursor\", \"O=C(Cl)CCBr\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"Nc1ccc(F)cc1[N+](=O)[O-]\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=C(Cl)CCBr\", \"in_stock\": true, \"children\": []}]}]}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"O=C(CCN1CCN(c2ccc(F)cc2)CC1)Nc1ccc(F)cc1[N+](=O)[O-]","task_id":"retro_e57f377765ca27b6a9d8","tool_calls":7,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_e5c53dfeaaa4fe8bf5a5:reference-expert:a0","kind":"single_route","max_steps":5,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target N#Cc1ccc(N2N=C3c4ccc(C(=O)OCc5ccccc5)cc4CCC3C2C2CCCC2)cc1Cl in at most 5 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"N#Cc1ccc(N2N=C3c4ccc(C(=O)OCc5ccccc5)cc4CCC3C2C2CCCC2)cc1Cl\", \"reactants\": [\"N#Cc1ccc(N2N=C3c4ccc(C(=O)O)cc4CCC3C2C2CCCC2)cc1Cl\", \"OCc1ccccc1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"N#Cc1ccc(N2N=C3c4ccc(C(=O)O)cc4CCC3C2C2CCCC2)cc1Cl\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"OCc1ccccc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"WVDDGKGOMKODPV-UHFFFAOYSA-N.XNULRSOGWPFPBL-UHFFFAOYSA-N>>ASWLSZLORUOBPD-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"N#Cc1ccc(N2N=C3c4ccc(C(=O)OCc5ccccc5)cc4CCC3C2C2CCCC2)cc1Cl\", \"reactants\": [\"N#Cc1ccc(N2N=C3c4ccc(C(=O)O)cc4CCC3C2C2CCCC2)cc1Cl\", \"OCc1ccccc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"N#Cc1ccc(N2N=C3c4ccc(C(=O)O)cc4CCC3C2C2CCCC2)cc1Cl\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"OCc1ccccc1\", \"results\": [{\"inchikey\": \"WVDDGKGOMKODPV-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"OCc1ccccc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"N#Cc1ccc(N2N=C3c4ccc(C(=O)O)cc4CCC3C2C2CCCC2)cc1Cl was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"N#Cc1ccc(N2N=C3c4ccc(C(=O)O)cc4CCC3C2C2CCCC2)cc1Cl\", \"reactants\": [\"COC(=O)c1ccc2c(c1)CCC1C2=NN(c2ccc(C#N)c(Cl)c2)C1C1CCCC1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"COC(=O)c1ccc2c(c1)CCC1C2=NN(c2ccc(C#N)c(Cl)c2)C1C1CCCC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"MZBNNMPUCTYVEZ-UHFFFAOYSA-N>>XNULRSOGWPFPBL-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"N#Cc1ccc(N2N=C3c4ccc(C(=O)O)cc4CCC3C2C2CCCC2)cc1Cl\", \"reactants\": [\"COC(=O)c1ccc2c(c1)CCC1C2=NN(c2ccc(C#N)c(Cl)c2)C1C1CCCC1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"COC(=O)c1ccc2c(c1)CCC1C2=NN(c2ccc(C#N)c(Cl)c2)C1C1CCCC1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"COC(=O)c1ccc2c(c1)CCC1C2=NN(c2ccc(C#N)c(Cl)c2)C1C1CCCC1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COC(=O)c1ccc2c(c1)CCC1C2=NN(c2ccc(C#N)c(Cl)c2)C1C1CCCC1\", \"reactants\": [\"COC(=O)c1ccc2c(c1)CCC(=CC1CCCC1)C2=O\", \"N#Cc1ccc(NN)cc1Cl\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"COC(=O)c1ccc2c(c1)CCC(=CC1CCCC1)C2=O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"N#Cc1ccc(NN)cc1Cl\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"NRWOMMXRCHVLFK-UHFFFAOYSA-N.OWUBFRQSDPZYQG-UHFFFAOYSA-N>>MZBNNMPUCTYVEZ-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"COC(=O)c1ccc2c(c1)CCC1C2=NN(c2ccc(C#N)c(Cl)c2)C1C1CCCC1\", \"reactants\": [\"COC(=O)c1ccc2c(c1)CCC(=CC1CCCC1)C2=O\", \"N#Cc1ccc(NN)cc1Cl\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"COC(=O)c1ccc2c(c1)CCC(=CC1CCCC1)C2=O\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"N#Cc1ccc(NN)cc1Cl\", \"results\": [{\"inchikey\": \"NRWOMMXRCHVLFK-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"N#Cc1ccc(NN)cc1Cl\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"COC(=O)c1ccc2c(c1)CCC(=CC1CCCC1)C2=O was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COC(=O)c1ccc2c(c1)CCC(=CC1CCCC1)C2=O\", \"reactants\": [\"COC(=O)c1ccc2c(c1)CCCC2=O\", \"O=CC1CCCC1\"]}","name":"validate_disconnection"},"id":"call_4_0","type":"function"},{"function":{"arguments":"{\"query\": \"COC(=O)c1ccc2c(c1)CCCC2=O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=CC1CCCC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"QMICDTYERUBTNO-UHFFFAOYSA-N.VELDYOPRLMJFIK-UHFFFAOYSA-N>>OWUBFRQSDPZYQG-UHFFFAOYSA-N\", \"model_turns_remaining\": 12, \"product\": \"COC(=O)c1ccc2c(c1)CCC(=CC1CCCC1)C2=O\", \"reactants\": [\"COC(=O)c1ccc2c(c1)CCCC2=O\", \"O=CC1CCCC1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_4_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"COC(=O)c1ccc2c(c1)CCCC2=O\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"O=CC1CCCC1\", \"results\": [{\"inchikey\": \"VELDYOPRLMJFIK-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=CC1CCCC1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_2"},{"content":"COC(=O)c1ccc2c(c1)CCCC2=O was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COC(=O)c1ccc2c(c1)CCCC2=O\", \"reactants\": [\"CO\", \"O=C(O)c1ccc2c(c1)CCCC2=O\"]}","name":"validate_disconnection"},"id":"call_5_0","type":"function"},{"function":{"arguments":"{\"query\": \"CO\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_5_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=C(O)c1ccc2c(c1)CCCC2=O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_5_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"OKKJLVBELUTLKV-UHFFFAOYSA-N.QSQVJZPPZDEILK-UHFFFAOYSA-N>>QMICDTYERUBTNO-UHFFFAOYSA-N\", \"model_turns_remaining\": 11, \"product\": \"COC(=O)c1ccc2c(c1)CCCC2=O\", \"reactants\": [\"CO\", \"O=C(O)c1ccc2c(c1)CCCC2=O\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_5_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 11, \"query\": \"CO\", \"results\": [{\"inchikey\": \"OKKJLVBELUTLKV-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CO\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_5_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 11, \"query\": \"O=C(O)c1ccc2c(c1)CCCC2=O\", \"results\": [{\"inchikey\": \"QSQVJZPPZDEILK-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=C(O)c1ccc2c(c1)CCCC2=O\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_5_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"N#Cc1ccc(N2N=C3c4ccc(C(=O)OCc5ccccc5)cc4CCC3C2C2CCCC2)cc1Cl\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"N#Cc1ccc(N2N=C3c4ccc(C(=O)O)cc4CCC3C2C2CCCC2)cc1Cl\": \"precursor\", \"OCc1ccccc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"N#Cc1ccc(N2N=C3c4ccc(C(=O)O)cc4CCC3C2C2CCCC2)cc1Cl\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COC(=O)c1ccc2c(c1)CCC1C2=NN(c2ccc(C#N)c(Cl)c2)C1C1CCCC1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COC(=O)c1ccc2c(c1)CCC1C2=NN(c2ccc(C#N)c(Cl)c2)C1C1CCCC1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COC(=O)c1ccc2c(c1)CCC(=CC1CCCC1)C2=O\": \"precursor\", \"N#Cc1ccc(NN)cc1Cl\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COC(=O)c1ccc2c(c1)CCC(=CC1CCCC1)C2=O\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COC(=O)c1ccc2c(c1)CCCC2=O\": \"precursor\", \"O=CC1CCCC1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COC(=O)c1ccc2c(c1)CCCC2=O\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CO\": \"precursor\", \"O=C(O)c1ccc2c(c1)CCCC2=O\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CO\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=C(O)c1ccc2c(c1)CCCC2=O\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"O=CC1CCCC1\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"N#Cc1ccc(NN)cc1Cl\", \"in_stock\": true, \"children\": []}]}]}]}]}, {\"type\": \"mol\", \"smiles\": \"OCc1ccccc1\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_6_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"N#Cc1ccc(N2N=C3c4ccc(C(=O)OCc5ccccc5)cc4CCC3C2C2CCCC2)cc1Cl","task_id":"retro_e5c53dfeaaa4fe8bf5a5","tool_calls":15,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":6}
{"exact_match":true,"id":"retro_e7c9effc3d9ab47ddf50:reference-expert:a0","kind":"single_route","max_steps":4,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CC(C)(C)OC(=O)Nc1ccc(Sc2ccc(OCc3ccccc3)cc2N)cc1 in at most 4 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(C)(C)OC(=O)Nc1ccc(Sc2ccc(OCc3ccccc3)cc2N)cc1\", \"reactants\": [\"CC(C)(C)OC(=O)Nc1ccc(Sc2ccc(OCc3ccccc3)cc2[N+](=O)[O-])cc1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)OC(=O)Nc1ccc(Sc2ccc(OCc3ccccc3)cc2[N+](=O)[O-])cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"ZHYNWUHNZKPYSG-UHFFFAOYSA-N>>JZTHMTQGOZOTJJ-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"CC(C)(C)OC(=O)Nc1ccc(Sc2ccc(OCc3ccccc3)cc2N)cc1\", \"reactants\": [\"CC(C)(C)OC(=O)Nc1ccc(Sc2ccc(OCc3ccccc3)cc2[N+](=O)[O-])cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CC(C)(C)OC(=O)Nc1ccc(Sc2ccc(OCc3ccccc3)cc2[N+](=O)[O-])cc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"CC(C)(C)OC(=O)Nc1ccc(Sc2ccc(OCc3ccccc3)cc2[N+](=O)[O-])cc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(C)(C)OC(=O)Nc1ccc(Sc2ccc(OCc3ccccc3)cc2[N+](=O)[O-])cc1\", \"reactants\": [\"CC(C)(C)OC(=O)OC(=O)OC(C)(C)C\", \"Nc1ccc(Sc2ccc(OCc3ccccc3)cc2[N+](=O)[O-])cc1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)OC(=O)OC(=O)OC(C)(C)C\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"Nc1ccc(Sc2ccc(OCc3ccccc3)cc2[N+](=O)[O-])cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"DYHSDKLCOJIUFX-UHFFFAOYSA-N.UEWLBMPRXFUGJX-UHFFFAOYSA-N>>ZHYNWUHNZKPYSG-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"CC(C)(C)OC(=O)Nc1ccc(Sc2ccc(OCc3ccccc3)cc2[N+](=O)[O-])cc1\", \"reactants\": [\"CC(C)(C)OC(=O)OC(=O)OC(C)(C)C\", \"Nc1ccc(Sc2ccc(OCc3ccccc3)cc2[N+](=O)[O-])cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CC(C)(C)OC(=O)OC(=O)OC(C)(C)C\", \"results\": [{\"inchikey\": \"DYHSDKLCOJIUFX-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CC(C)(C)OC(=O)OC(=O)OC(C)(C)C\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"Nc1ccc(Sc2ccc(OCc3ccccc3)cc2[N+](=O)[O-])cc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Nc1ccc(Sc2ccc(OCc3ccccc3)cc2[N+](=O)[O-])cc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Nc1ccc(Sc2ccc(OCc3ccccc3)cc2[N+](=O)[O-])cc1\", \"reactants\": [\"Nc1ccc(S)cc1\", \"O=[N+]([O-])c1cc(OCc2ccccc2)ccc1Cl\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"Nc1ccc(S)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=[N+]([O-])c1cc(OCc2ccccc2)ccc1Cl\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"KVBJIVDDLMDAPB-UHFFFAOYSA-N.WCDSVWRUXWCYFN-UHFFFAOYSA-N>>UEWLBMPRXFUGJX-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"Nc1ccc(Sc2ccc(OCc3ccccc3)cc2[N+](=O)[O-])cc1\", \"reactants\": [\"Nc1ccc(S)cc1\", \"O=[N+]([O-])c1cc(OCc2ccccc2)ccc1Cl\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"Nc1ccc(S)cc1\", \"results\": [{\"inchikey\": \"WCDSVWRUXWCYFN-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Nc1ccc(S)cc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"O=[N+]([O-])c1cc(OCc2ccccc2)ccc1Cl\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"O=[N+]([O-])c1cc(OCc2ccccc2)ccc1Cl was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"O=[N+]([O-])c1cc(OCc2ccccc2)ccc1Cl\", \"reactants\": [\"BrCc1ccccc1\", \"O=[N+]([O-])c1cc(O)ccc1Cl\"]}","name":"validate_disconnection"},"id":"call_4_0","type":"function"},{"function":{"arguments":"{\"query\": \"BrCc1ccccc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=[N+]([O-])c1cc(O)ccc1Cl\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"AGEZXYOZHKGVCM-UHFFFAOYSA-N.JUIKCULGDIZNDI-UHFFFAOYSA-N>>KVBJIVDDLMDAPB-UHFFFAOYSA-N\", \"model_turns_remaining\": 12, \"product\": \"O=[N+]([O-])c1cc(OCc2ccccc2)ccc1Cl\", \"reactants\": [\"BrCc1ccccc1\", \"O=[N+]([O-])c1cc(O)ccc1Cl\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_4_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"BrCc1ccccc1\", \"results\": [{\"inchikey\": \"AGEZXYOZHKGVCM-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"BrCc1ccccc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"O=[N+]([O-])c1cc(O)ccc1Cl\", \"results\": [{\"inchikey\": \"JUIKCULGDIZNDI-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=[N+]([O-])c1cc(O)ccc1Cl\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)OC(=O)Nc1ccc(Sc2ccc(OCc3ccccc3)cc2N)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)(C)OC(=O)Nc1ccc(Sc2ccc(OCc3ccccc3)cc2[N+](=O)[O-])cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)OC(=O)Nc1ccc(Sc2ccc(OCc3ccccc3)cc2[N+](=O)[O-])cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)(C)OC(=O)OC(=O)OC(C)(C)C\": \"precursor\", \"Nc1ccc(Sc2ccc(OCc3ccccc3)cc2[N+](=O)[O-])cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)OC(=O)OC(=O)OC(C)(C)C\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"Nc1ccc(Sc2ccc(OCc3ccccc3)cc2[N+](=O)[O-])cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"Nc1ccc(S)cc1\": \"precursor\", \"O=[N+]([O-])c1cc(OCc2ccccc2)ccc1Cl\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"Nc1ccc(S)cc1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=[N+]([O-])c1cc(OCc2ccccc2)ccc1Cl\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"BrCc1ccccc1\": \"precursor\", \"O=[N+]([O-])c1cc(O)ccc1Cl\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"BrCc1ccccc1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=[N+]([O-])c1cc(O)ccc1Cl\", \"in_stock\": true, \"children\": []}]}]}]}]}]}]}]}]}]}}","name":"emit_routes"},"id":"call_5_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"CC(C)(C)OC(=O)Nc1ccc(Sc2ccc(OCc3ccccc3)cc2N)cc1","task_id":"retro_e7c9effc3d9ab47ddf50","tool_calls":12,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":5}
{"exact_match":true,"id":"retro_e873b349f5e47dae69ac:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CCOC(=O)c1nc(Cl)cc2ccccc12 in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCOC(=O)c1nc(Cl)cc2ccccc12\", \"reactants\": [\"C=C(OCC)c1nc(Cl)cc2ccccc12\", \"[O]=[Mn](=[O])(=[O])[OH]\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"C=C(OCC)c1nc(Cl)cc2ccccc12\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"[O]=[Mn](=[O])(=[O])[OH]\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"YGIVZADMWSRFID-UHFFFAOYSA-N.ZJBYBXHCMWGGRR-UHFFFAOYSA-M>>ZJIGSOOQUFUKPD-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"CCOC(=O)c1nc(Cl)cc2ccccc12\", \"reactants\": [\"C=C(OCC)c1nc(Cl)cc2ccccc12\", \"[O]=[Mn](=[O])(=[O])[OH]\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"C=C(OCC)c1nc(Cl)cc2ccccc12\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"[O]=[Mn](=[O])(=[O])[OH]\", \"results\": [{\"inchikey\": \"ZJBYBXHCMWGGRR-UHFFFAOYSA-M\", \"similarity\": 1.0, \"smiles\": \"[O]=[Mn](=[O])(=[O])[OH]\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"C=C(OCC)c1nc(Cl)cc2ccccc12 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"C=C(OCC)c1nc(Cl)cc2ccccc12\", \"reactants\": [\"C=[C](OCC)[Sn]([CH2]CCC)([CH2]CCC)[CH2]CCC\", \"Clc1cc2ccccc2c(Cl)n1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"C=[C](OCC)[Sn]([CH2]CCC)([CH2]CCC)[CH2]CCC\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"Clc1cc2ccccc2c(Cl)n1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"BRGZEQXWZWBPJH-UHFFFAOYSA-N.HGXJOXHYPGNVNK-UHFFFAOYSA-N>>YGIVZADMWSRFID-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"C=C(OCC)c1nc(Cl)cc2ccccc12\", \"reactants\": [\"C=[C](OCC)[Sn]([CH2]CCC)([CH2]CCC)[CH2]CCC\", \"Clc1cc2ccccc2c(Cl)n1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"C=[C](OCC)[Sn]([CH2]CCC)([CH2]CCC)[CH2]CCC\", \"results\": [{\"inchikey\": \"HGXJOXHYPGNVNK-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"C=[C](OCC)[Sn]([CH2]CCC)([CH2]CCC)[CH2]CCC\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"Clc1cc2ccccc2c(Cl)n1\", \"results\": [{\"inchikey\": \"BRGZEQXWZWBPJH-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Clc1cc2ccccc2c(Cl)n1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CCOC(=O)c1nc(Cl)cc2ccccc12\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"C=C(OCC)c1nc(Cl)cc2ccccc12\": \"precursor\", \"[O]=[Mn](=[O])(=[O])[OH]\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"C=C(OCC)c1nc(Cl)cc2ccccc12\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"C=[C](OCC)[Sn]([CH2]CCC)([CH2]CCC)[CH2]CCC\": \"precursor\", \"Clc1cc2ccccc2c(Cl)n1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"C=[C](OCC)[Sn]([CH2]CCC)([CH2]CCC)[CH2]CCC\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"Clc1cc2ccccc2c(Cl)n1\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"[O]=[Mn](=[O])(=[O])[OH]\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"CCOC(=O)c1nc(Cl)cc2ccccc12","task_id":"retro_e873b349f5e47dae69ac","tool_calls":7,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_e875dc55b885ca3556ed:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target COc1c(C)cc(C(=O)c2ccc([N+](=O)[O-])cc2)cc1C in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COc1c(C)cc(C(=O)c2ccc([N+](=O)[O-])cc2)cc1C\", \"reactants\": [\"CI\", \"Cc1cc(C(=O)c2ccc([N+](=O)[O-])cc2)cc(C)c1O\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CI\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"Cc1cc(C(=O)c2ccc([N+](=O)[O-])cc2)cc(C)c1O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"INQOMBQAUSQDDS-UHFFFAOYSA-N.PRXNFCOJKASGOL-UHFFFAOYSA-N>>CBVVXJREHIJLGN-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"COc1c(C)cc(C(=O)c2ccc([N+](=O)[O-])cc2)cc1C\", \"reactants\": [\"CI\", \"Cc1cc(C(=O)c2ccc([N+](=O)[O-])cc2)cc(C)c1O\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CI\", \"results\": [{\"inchikey\": \"INQOMBQAUSQDDS-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CI\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"Cc1cc(C(=O)c2ccc([N+](=O)[O-])cc2)cc(C)c1O\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"Cc1cc(C(=O)c2ccc([N+](=O)[O-])cc2)cc(C)c1O was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Cc1cc(C(=O)c2ccc([N+](=O)[O-])cc2)cc(C)c1O\", \"reactants\": [\"Cc1cccc(C)c1O\", \"O=C(Cl)c1ccc([N+](=O)[O-])cc1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"Cc1cccc(C)c1O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=C(Cl)c1ccc([N+](=O)[O-])cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"NXXYKOUNUYWIHA-UHFFFAOYSA-N.SKDHHIUENRGTHK-UHFFFAOYSA-N>>PRXNFCOJKASGOL-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"Cc1cc(C(=O)c2ccc([N+](=O)[O-])cc2)cc(C)c1O\", \"reactants\": [\"Cc1cccc(C)c1O\", \"O=C(Cl)c1ccc([N+](=O)[O-])cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"Cc1cccc(C)c1O\", \"results\": [{\"inchikey\": \"NXXYKOUNUYWIHA-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Cc1cccc(C)c1O\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"O=C(Cl)c1ccc([N+](=O)[O-])cc1\", \"results\": [{\"inchikey\": \"SKDHHIUENRGTHK-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=C(Cl)c1ccc([N+](=O)[O-])cc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"COc1c(C)cc(C(=O)c2ccc([N+](=O)[O-])cc2)cc1C\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CI\": \"precursor\", \"Cc1cc(C(=O)c2ccc([N+](=O)[O-])cc2)cc(C)c1O\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CI\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"Cc1cc(C(=O)c2ccc([N+](=O)[O-])cc2)cc(C)c1O\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"Cc1cccc(C)c1O\": \"precursor\", \"O=C(Cl)c1ccc([N+](=O)[O-])cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"Cc1cccc(C)c1O\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=C(Cl)c1ccc([N+](=O)[O-])cc1\", \"in_stock\": true, \"children\": []}]}]}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"COc1c(C)cc(C(=O)c2ccc([N+](=O)[O-])cc2)cc1C","task_id":"retro_e875dc55b885ca3556ed","tool_calls":7,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_e8b5db3e88b3a1a0ce95:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target c1cc(-c2cnn(C3CCCCO3)c2)ccn1 in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"c1cc(-c2cnn(C3CCCCO3)c2)ccn1\", \"reactants\": [\"Brc1cnn(C2CCCCO2)c1\", \"OB(O)c1ccncc1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"Brc1cnn(C2CCCCO2)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"OB(O)c1ccncc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"HDNCEUNJWJHWMO-UHFFFAOYSA-N.QLULGIRFKAWHOJ-UHFFFAOYSA-N>>SNDQTQDSDRDSAF-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"c1cc(-c2cnn(C3CCCCO3)c2)ccn1\", \"reactants\": [\"Brc1cnn(C2CCCCO2)c1\", \"OB(O)c1ccncc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"Brc1cnn(C2CCCCO2)c1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"OB(O)c1ccncc1\", \"results\": [{\"inchikey\": \"QLULGIRFKAWHOJ-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"OB(O)c1ccncc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"Brc1cnn(C2CCCCO2)c1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Brc1cnn(C2CCCCO2)c1\", \"reactants\": [\"Brc1cn[nH]c1\", \"C1=COCCC1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"Brc1cn[nH]c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"C1=COCCC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_complete\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"BUDQDWGNQVEFAC-UHFFFAOYSA-N.WVGCPEDBFHEHEZ-UHFFFAOYSA-N>>HDNCEUNJWJHWMO-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"Brc1cnn(C2CCCCO2)c1\", \"reactants\": [\"Brc1cn[nH]c1\", \"C1=COCCC1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"Brc1cn[nH]c1\", \"results\": [{\"inchikey\": \"WVGCPEDBFHEHEZ-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Brc1cn[nH]c1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"C1=COCCC1\", \"results\": [{\"inchikey\": \"BUDQDWGNQVEFAC-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"C1=COCCC1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"c1cc(-c2cnn(C3CCCCO3)c2)ccn1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"Brc1cnn(C2CCCCO2)c1\": \"precursor\", \"OB(O)c1ccncc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"Brc1cnn(C2CCCCO2)c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"Brc1cn[nH]c1\": \"precursor\", \"C1=COCCC1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"Brc1cn[nH]c1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"C1=COCCC1\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"OB(O)c1ccncc1\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"c1cc(-c2cnn(C3CCCCO3)c2)ccn1","task_id":"retro_e8b5db3e88b3a1a0ce95","tool_calls":7,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_e9782910f8e853822ec9:reference-expert:a0","kind":"single_route","max_steps":4,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target NC(=O)Nc1cccc(CCCCOCCCCCCBr)c1 in at most 4 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"NC(=O)Nc1cccc(CCCCOCCCCCCBr)c1\", \"reactants\": [\"NC(=O)Nc1cccc(C#CCCOCCCCCCBr)c1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"NC(=O)Nc1cccc(C#CCCOCCCCCCBr)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_complete\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"XYCLPZLZPWDCMI-UHFFFAOYSA-N>>ZEIWOSINHMWGRS-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"NC(=O)Nc1cccc(CCCCOCCCCCCBr)c1\", \"reactants\": [\"NC(=O)Nc1cccc(C#CCCOCCCCCCBr)c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"NC(=O)Nc1cccc(C#CCCOCCCCCCBr)c1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"NC(=O)Nc1cccc(C#CCCOCCCCCCBr)c1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"NC(=O)Nc1cccc(C#CCCOCCCCCCBr)c1\", \"reactants\": [\"C#CCCOCCCCCCBr\", \"NC(=O)Nc1cccc(I)c1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"C#CCCOCCCCCCBr\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"NC(=O)Nc1cccc(I)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"KZIWFMXWSZGCQH-UHFFFAOYSA-N.OSCNSMUGOQHBLN-UHFFFAOYSA-N>>XYCLPZLZPWDCMI-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"NC(=O)Nc1cccc(C#CCCOCCCCCCBr)c1\", \"reactants\": [\"C#CCCOCCCCCCBr\", \"NC(=O)Nc1cccc(I)c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"C#CCCOCCCCCCBr\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"NC(=O)Nc1cccc(I)c1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"C#CCCOCCCCCCBr was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"C#CCCOCCCCCCBr\", \"reactants\": [\"BrCCCCCCBr\", \"C#CCCO\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"BrCCCCCCBr\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"C#CCCO\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"OTJZCIYGRUNXTP-UHFFFAOYSA-N.SGRHVVLXEBNBDV-UHFFFAOYSA-N>>KZIWFMXWSZGCQH-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"C#CCCOCCCCCCBr\", \"reactants\": [\"BrCCCCCCBr\", \"C#CCCO\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"BrCCCCCCBr\", \"results\": [{\"inchikey\": \"SGRHVVLXEBNBDV-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"BrCCCCCCBr\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"C#CCCO\", \"results\": [{\"inchikey\": \"OTJZCIYGRUNXTP-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"C#CCCO\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"NC(=O)Nc1cccc(I)c1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"NC(=O)Nc1cccc(I)c1\", \"reactants\": [\"N#CO\", \"Nc1cccc(I)c1\"]}","name":"validate_disconnection"},"id":"call_4_0","type":"function"},{"function":{"arguments":"{\"query\": \"N#CO\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_1","type":"function"},{"function":{"arguments":"{\"query\": \"Nc1cccc(I)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_complete\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"FFCSRWGYGMRBGD-UHFFFAOYSA-N.XLJMAIOERFSOGZ-UHFFFAOYSA-N>>OSCNSMUGOQHBLN-UHFFFAOYSA-N\", \"model_turns_remaining\": 12, \"product\": \"NC(=O)Nc1cccc(I)c1\", \"reactants\": [\"N#CO\", \"Nc1cccc(I)c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_4_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"N#CO\", \"results\": [{\"inchikey\": \"XLJMAIOERFSOGZ-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"N#CO\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"Nc1cccc(I)c1\", \"results\": [{\"inchikey\": \"FFCSRWGYGMRBGD-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Nc1cccc(I)c1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"NC(=O)Nc1cccc(CCCCOCCCCCCBr)c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"NC(=O)Nc1cccc(C#CCCOCCCCCCBr)c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"NC(=O)Nc1cccc(C#CCCOCCCCCCBr)c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"C#CCCOCCCCCCBr\": \"precursor\", \"NC(=O)Nc1cccc(I)c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"C#CCCOCCCCCCBr\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"BrCCCCCCBr\": \"precursor\", \"C#CCCO\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"BrCCCCCCBr\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"C#CCCO\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"NC(=O)Nc1cccc(I)c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"N#CO\": \"precursor\", \"Nc1cccc(I)c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"N#CO\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"Nc1cccc(I)c1\", \"in_stock\": true, \"children\": []}]}]}]}]}]}]}]}}","name":"emit_routes"},"id":"call_5_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"NC(=O)Nc1cccc(CCCCOCCCCCCBr)c1","task_id":"retro_e9782910f8e853822ec9","tool_calls":12,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":5}
{"exact_match":true,"id":"retro_ea78b4403ad4015452f4:reference-expert:a0","kind":"single_route","max_steps":3,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CSc1ncc2c(n1)CCN(c1cccc(C(=O)Nc3ccccc3)n1)C2 in at most 3 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CSc1ncc2c(n1)CCN(c1cccc(C(=O)Nc3ccccc3)n1)C2\", \"reactants\": [\"CSc1ncc2c(n1)CCN(c1cccc(C(=O)O)n1)C2\", \"Nc1ccccc1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CSc1ncc2c(n1)CCN(c1cccc(C(=O)O)n1)C2\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"Nc1ccccc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"NTCVMCIXQIADCK-UHFFFAOYSA-N.PAYRUJLWNCNPSJ-UHFFFAOYSA-N>>PVDXQMQSRQZVAO-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"CSc1ncc2c(n1)CCN(c1cccc(C(=O)Nc3ccccc3)n1)C2\", \"reactants\": [\"CSc1ncc2c(n1)CCN(c1cccc(C(=O)O)n1)C2\", \"Nc1ccccc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CSc1ncc2c(n1)CCN(c1cccc(C(=O)O)n1)C2\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"Nc1ccccc1\", \"results\": [{\"inchikey\": \"PAYRUJLWNCNPSJ-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Nc1ccccc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"CSc1ncc2c(n1)CCN(c1cccc(C(=O)O)n1)C2 was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CSc1ncc2c(n1)CCN(c1cccc(C(=O)O)n1)C2\", \"reactants\": [\"COC(=O)c1cccc(N2CCc3nc(SC)ncc3C2)n1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"COC(=O)c1cccc(N2CCc3nc(SC)ncc3C2)n1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"SPNALFJVCKBWGF-UHFFFAOYSA-N>>NTCVMCIXQIADCK-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"CSc1ncc2c(n1)CCN(c1cccc(C(=O)O)n1)C2\", \"reactants\": [\"COC(=O)c1cccc(N2CCc3nc(SC)ncc3C2)n1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"COC(=O)c1cccc(N2CCc3nc(SC)ncc3C2)n1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"COC(=O)c1cccc(N2CCc3nc(SC)ncc3C2)n1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COC(=O)c1cccc(N2CCc3nc(SC)ncc3C2)n1\", \"reactants\": [\"COC(=O)c1cccc(Br)n1\", \"CSc1ncc2c(n1)CCNC2\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"COC(=O)c1cccc(Br)n1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"CSc1ncc2c(n1)CCNC2\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"KRNFMHYGPVOQDF-UHFFFAOYSA-N.SGNCOKUHMXLGAH-UHFFFAOYSA-N>>SPNALFJVCKBWGF-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"COC(=O)c1cccc(N2CCc3nc(SC)ncc3C2)n1\", \"reactants\": [\"COC(=O)c1cccc(Br)n1\", \"CSc1ncc2c(n1)CCNC2\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"COC(=O)c1cccc(Br)n1\", \"results\": [{\"inchikey\": \"SGNCOKUHMXLGAH-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"COC(=O)c1cccc(Br)n1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"CSc1ncc2c(n1)CCNC2\", \"results\": [{\"inchikey\": \"KRNFMHYGPVOQDF-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CSc1ncc2c(n1)CCNC2\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CSc1ncc2c(n1)CCN(c1cccc(C(=O)Nc3ccccc3)n1)C2\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CSc1ncc2c(n1)CCN(c1cccc(C(=O)O)n1)C2\": \"precursor\", \"Nc1ccccc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CSc1ncc2c(n1)CCN(c1cccc(C(=O)O)n1)C2\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COC(=O)c1cccc(N2CCc3nc(SC)ncc3C2)n1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COC(=O)c1cccc(N2CCc3nc(SC)ncc3C2)n1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COC(=O)c1cccc(Br)n1\": \"precursor\", \"CSc1ncc2c(n1)CCNC2\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COC(=O)c1cccc(Br)n1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"CSc1ncc2c(n1)CCNC2\", \"in_stock\": true, \"children\": []}]}]}]}]}, {\"type\": \"mol\", \"smiles\": \"Nc1ccccc1\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_4_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"CSc1ncc2c(n1)CCN(c1cccc(C(=O)Nc3ccccc3)n1)C2","task_id":"retro_ea78b4403ad4015452f4","tool_calls":9,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":4}
{"exact_match":true,"id":"retro_ec34b75794f36d90b963:reference-expert:a0","kind":"single_route","max_steps":3,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CNC(=O)c1c2cccc(-c3ccc(Cl)cc3Cl)c2nn1C in at most 3 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CNC(=O)c1c2cccc(-c3ccc(Cl)cc3Cl)c2nn1C\", \"reactants\": [\"CN\", \"COC(=O)c1c2cccc(-c3ccc(Cl)cc3Cl)c2nn1C\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CN\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"COC(=O)c1c2cccc(-c3ccc(Cl)cc3Cl)c2nn1C\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"BAVYZALUXZFZLV-UHFFFAOYSA-N.KLRJUPQSJZUZKN-UHFFFAOYSA-N>>GBKIVXAAZWKWMZ-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"CNC(=O)c1c2cccc(-c3ccc(Cl)cc3Cl)c2nn1C\", \"reactants\": [\"CN\", \"COC(=O)c1c2cccc(-c3ccc(Cl)cc3Cl)c2nn1C\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CN\", \"results\": [{\"inchikey\": \"BAVYZALUXZFZLV-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CN\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"COC(=O)c1c2cccc(-c3ccc(Cl)cc3Cl)c2nn1C\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"COC(=O)c1c2cccc(-c3ccc(Cl)cc3Cl)c2nn1C was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COC(=O)c1c2cccc(-c3ccc(Cl)cc3Cl)c2nn1C\", \"reactants\": [\"COC(=O)c1c2cccc(Br)c2nn1C\", \"OB(O)c1ccc(Cl)cc1Cl\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"COC(=O)c1c2cccc(Br)c2nn1C\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"OB(O)c1ccc(Cl)cc1Cl\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"QNEGDGPAXKYZHZ-UHFFFAOYSA-N.YTSIVUDSPSRYST-UHFFFAOYSA-N>>KLRJUPQSJZUZKN-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"COC(=O)c1c2cccc(-c3ccc(Cl)cc3Cl)c2nn1C\", \"reactants\": [\"COC(=O)c1c2cccc(Br)c2nn1C\", \"OB(O)c1ccc(Cl)cc1Cl\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"COC(=O)c1c2cccc(Br)c2nn1C\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"OB(O)c1ccc(Cl)cc1Cl\", \"results\": [{\"inchikey\": \"QNEGDGPAXKYZHZ-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"OB(O)c1ccc(Cl)cc1Cl\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"COC(=O)c1c2cccc(Br)c2nn1C was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COC(=O)c1c2cccc(Br)c2nn1C\", \"reactants\": [\"COC(=O)Cl\", \"Cn1cc2cccc(Br)c2n1\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"COC(=O)Cl\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"Cn1cc2cccc(Br)c2n1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"KPAYIFGPJOYWMM-UHFFFAOYSA-N.XMJHPCRAQCTCFT-UHFFFAOYSA-N>>YTSIVUDSPSRYST-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"COC(=O)c1c2cccc(Br)c2nn1C\", \"reactants\": [\"COC(=O)Cl\", \"Cn1cc2cccc(Br)c2n1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"COC(=O)Cl\", \"results\": [{\"inchikey\": \"XMJHPCRAQCTCFT-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"COC(=O)Cl\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"Cn1cc2cccc(Br)c2n1\", \"results\": [{\"inchikey\": \"KPAYIFGPJOYWMM-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Cn1cc2cccc(Br)c2n1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CNC(=O)c1c2cccc(-c3ccc(Cl)cc3Cl)c2nn1C\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CN\": \"precursor\", \"COC(=O)c1c2cccc(-c3ccc(Cl)cc3Cl)c2nn1C\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CN\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"COC(=O)c1c2cccc(-c3ccc(Cl)cc3Cl)c2nn1C\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COC(=O)c1c2cccc(Br)c2nn1C\": \"precursor\", \"OB(O)c1ccc(Cl)cc1Cl\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COC(=O)c1c2cccc(Br)c2nn1C\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COC(=O)Cl\": \"precursor\", \"Cn1cc2cccc(Br)c2n1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COC(=O)Cl\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"Cn1cc2cccc(Br)c2n1\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"OB(O)c1ccc(Cl)cc1Cl\", \"in_stock\": true, \"children\": []}]}]}]}]}]}}","name":"emit_routes"},"id":"call_4_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"CNC(=O)c1c2cccc(-c3ccc(Cl)cc3Cl)c2nn1C","task_id":"retro_ec34b75794f36d90b963","tool_calls":10,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":4}
{"exact_match":true,"id":"retro_ece576605fb7843c52c0:reference-expert:a0","kind":"single_route","max_steps":3,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CC[C@H](C)[C@@H](CN1CC(O)C1)N(C)C(=O)c1ccc(F)c(F)c1 in at most 3 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC[C@H](C)[C@@H](CN1CC(O)C1)N(C)C(=O)c1ccc(F)c(F)c1\", \"reactants\": [\"CC[C@H](C)[C@@H](CN1CC(O)C1)NC\", \"O=C(O)c1ccc(F)c(F)c1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC[C@H](C)[C@@H](CN1CC(O)C1)NC\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=C(O)c1ccc(F)c(F)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"FPENCTDAQQQKNY-UHFFFAOYSA-N.QBJOSBOYAJPJJA-WCBMZHEXSA-N>>BACAAUUDVOTVDK-MEDUHNTESA-N\", \"model_turns_remaining\": 15, \"product\": \"CC[C@H](C)[C@@H](CN1CC(O)C1)N(C)C(=O)c1ccc(F)c(F)c1\", \"reactants\": [\"CC[C@H](C)[C@@H](CN1CC(O)C1)NC\", \"O=C(O)c1ccc(F)c(F)c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CC[C@H](C)[C@@H](CN1CC(O)C1)NC\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"O=C(O)c1ccc(F)c(F)c1\", \"results\": [{\"inchikey\": \"FPENCTDAQQQKNY-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=C(O)c1ccc(F)c(F)c1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"CC[C@H](C)[C@@H](CN1CC(O)C1)NC was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC[C@H](C)[C@@H](CN1CC(O)C1)NC\", \"reactants\": [\"CC[C@H](C)[C@H](NC(=O)OC(C)(C)C)C(=O)N1CC(O)C1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC[C@H](C)[C@H](NC(=O)OC(C)(C)C)C(=O)N1CC(O)C1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"TXFLAVNNHRGOCJ-ONGXEEELSA-N>>QBJOSBOYAJPJJA-WCBMZHEXSA-N\", \"model_turns_remaining\": 14, \"product\": \"CC[C@H](C)[C@@H](CN1CC(O)C1)NC\", \"reactants\": [\"CC[C@H](C)[C@H](NC(=O)OC(C)(C)C)C(=O)N1CC(O)C1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CC[C@H](C)[C@H](NC(=O)OC(C)(C)C)C(=O)N1CC(O)C1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"CC[C@H](C)[C@H](NC(=O)OC(C)(C)C)C(=O)N1CC(O)C1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC[C@H](C)[C@H](NC(=O)OC(C)(C)C)C(=O)N1CC(O)C1\", \"reactants\": [\"CC[C@H](C)[C@H](NC(=O)OC(C)(C)C)C(=O)O\", \"OC1CNC1\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC[C@H](C)[C@H](NC(=O)OC(C)(C)C)C(=O)O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"OC1CNC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"GMWFCJXSQQHBPI-UHFFFAOYSA-N.QJCNLJWUIOIMMF-YUMQZZPRSA-N>>TXFLAVNNHRGOCJ-ONGXEEELSA-N\", \"model_turns_remaining\": 13, \"product\": \"CC[C@H](C)[C@H](NC(=O)OC(C)(C)C)C(=O)N1CC(O)C1\", \"reactants\": [\"CC[C@H](C)[C@H](NC(=O)OC(C)(C)C)C(=O)O\", \"OC1CNC1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"CC[C@H](C)[C@H](NC(=O)OC(C)(C)C)C(=O)O\", \"results\": [{\"inchikey\": \"QJCNLJWUIOIMMF-YUMQZZPRSA-N\", \"similarity\": 1.0, \"smiles\": \"CC[C@H](C)[C@H](NC(=O)OC(C)(C)C)C(=O)O\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"OC1CNC1\", \"results\": [{\"inchikey\": \"GMWFCJXSQQHBPI-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"OC1CNC1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CC[C@H](C)[C@@H](CN1CC(O)C1)N(C)C(=O)c1ccc(F)c(F)c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC[C@H](C)[C@@H](CN1CC(O)C1)NC\": \"precursor\", \"O=C(O)c1ccc(F)c(F)c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC[C@H](C)[C@@H](CN1CC(O)C1)NC\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC[C@H](C)[C@H](NC(=O)OC(C)(C)C)C(=O)N1CC(O)C1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC[C@H](C)[C@H](NC(=O)OC(C)(C)C)C(=O)N1CC(O)C1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC[C@H](C)[C@H](NC(=O)OC(C)(C)C)C(=O)O\": \"precursor\", \"OC1CNC1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC[C@H](C)[C@H](NC(=O)OC(C)(C)C)C(=O)O\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"OC1CNC1\", \"in_stock\": true, \"children\": []}]}]}]}]}, {\"type\": \"mol\", \"smiles\": \"O=C(O)c1ccc(F)c(F)c1\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_4_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"CC[C@H](C)[C@@H](CN1CC(O)C1)N(C)C(=O)c1ccc(F)c(F)c1","task_id":"retro_ece576605fb7843c52c0","tool_calls":9,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":4}
{"exact_match":true,"id":"retro_eea542e67b633f513a26:reference-expert:a0","kind":"single_route","max_steps":3,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target COc1cc2c(cc1C)oc(=O)n2CC(=O)N(C)C(CN1CCOCC1)c1ccc(-c2ccccc2)cc1 in at most 3 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COc1cc2c(cc1C)oc(=O)n2CC(=O)N(C)C(CN1CCOCC1)c1ccc(-c2ccccc2)cc1\", \"reactants\": [\"CNC(CN1CCOCC1)c1ccc(-c2ccccc2)cc1\", \"COc1cc2c(cc1C)oc(=O)n2CC(=O)O\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CNC(CN1CCOCC1)c1ccc(-c2ccccc2)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"COc1cc2c(cc1C)oc(=O)n2CC(=O)O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"AMLOGFTYNKQZNP-UHFFFAOYSA-N.GHAKSVXBJSKBJA-UHFFFAOYSA-N>>JYPLFGYSHYSLBS-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"COc1cc2c(cc1C)oc(=O)n2CC(=O)N(C)C(CN1CCOCC1)c1ccc(-c2ccccc2)cc1\", \"reactants\": [\"CNC(CN1CCOCC1)c1ccc(-c2ccccc2)cc1\", \"COc1cc2c(cc1C)oc(=O)n2CC(=O)O\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CNC(CN1CCOCC1)c1ccc(-c2ccccc2)cc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"COc1cc2c(cc1C)oc(=O)n2CC(=O)O\", \"results\": [{\"inchikey\": \"AMLOGFTYNKQZNP-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"COc1cc2c(cc1C)oc(=O)n2CC(=O)O\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"CNC(CN1CCOCC1)c1ccc(-c2ccccc2)cc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CNC(CN1CCOCC1)c1ccc(-c2ccccc2)cc1\", \"reactants\": [\"CN\", \"O=C(CN1CCOCC1)c1ccc(-c2ccccc2)cc1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CN\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=C(CN1CCOCC1)c1ccc(-c2ccccc2)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"BAVYZALUXZFZLV-UHFFFAOYSA-N.ODGCGDCJPHAFII-UHFFFAOYSA-N>>GHAKSVXBJSKBJA-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"CNC(CN1CCOCC1)c1ccc(-c2ccccc2)cc1\", \"reactants\": [\"CN\", \"O=C(CN1CCOCC1)c1ccc(-c2ccccc2)cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CN\", \"results\": [{\"inchikey\": \"BAVYZALUXZFZLV-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CN\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"O=C(CN1CCOCC1)c1ccc(-c2ccccc2)cc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"O=C(CN1CCOCC1)c1ccc(-c2ccccc2)cc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"O=C(CN1CCOCC1)c1ccc(-c2ccccc2)cc1\", \"reactants\": [\"C1COCCN1\", \"O=C(CBr)c1ccc(-c2ccccc2)cc1\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"C1COCCN1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=C(CBr)c1ccc(-c2ccccc2)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"KGHGZRVXCKCJGX-UHFFFAOYSA-N.YNAVUWVOSKDBBP-UHFFFAOYSA-N>>ODGCGDCJPHAFII-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"O=C(CN1CCOCC1)c1ccc(-c2ccccc2)cc1\", \"reactants\": [\"C1COCCN1\", \"O=C(CBr)c1ccc(-c2ccccc2)cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"C1COCCN1\", \"results\": [{\"inchikey\": \"YNAVUWVOSKDBBP-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"C1COCCN1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"O=C(CBr)c1ccc(-c2ccccc2)cc1\", \"results\": [{\"inchikey\": \"KGHGZRVXCKCJGX-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=C(CBr)c1ccc(-c2ccccc2)cc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"COc1cc2c(cc1C)oc(=O)n2CC(=O)N(C)C(CN1CCOCC1)c1ccc(-c2ccccc2)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CNC(CN1CCOCC1)c1ccc(-c2ccccc2)cc1\": \"precursor\", \"COc1cc2c(cc1C)oc(=O)n2CC(=O)O\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CNC(CN1CCOCC1)c1ccc(-c2ccccc2)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CN\": \"precursor\", \"O=C(CN1CCOCC1)c1ccc(-c2ccccc2)cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CN\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=C(CN1CCOCC1)c1ccc(-c2ccccc2)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"C1COCCN1\": \"precursor\", \"O=C(CBr)c1ccc(-c2ccccc2)cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"C1COCCN1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=C(CBr)c1ccc(-c2ccccc2)cc1\", \"in_stock\": true, \"children\": []}]}]}]}]}, {\"type\": \"mol\", \"smiles\": \"COc1cc2c(cc1C)oc(=O)n2CC(=O)O\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_4_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"COc1cc2c(cc1C)oc(=O)n2CC(=O)N(C)C(CN1CCOCC1)c1ccc(-c2ccccc2)cc1","task_id":"retro_eea542e67b633f513a26","tool_calls":10,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":4}
{"exact_match":true,"id":"retro_ef14f1f01149e1d4fcc5:reference-expert:a0","kind":"single_route","max_steps":3,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target Cn1nc(C#N)c2cc([N+](=O)[O-])ccc21 in at most 3 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Cn1nc(C#N)c2cc([N+](=O)[O-])ccc21\", \"reactants\": [\"CI\", \"N#Cc1n[nH]c2ccc([N+](=O)[O-])cc12\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CI\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"N#Cc1n[nH]c2ccc([N+](=O)[O-])cc12\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"INQOMBQAUSQDDS-UHFFFAOYSA-N.WXTZAAHDBOKXDI-UHFFFAOYSA-N>>SNUBGALOBDAJKM-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"Cn1nc(C#N)c2cc([N+](=O)[O-])ccc21\", \"reactants\": [\"CI\", \"N#Cc1n[nH]c2ccc([N+](=O)[O-])cc12\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CI\", \"results\": [{\"inchikey\": \"INQOMBQAUSQDDS-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CI\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"N#Cc1n[nH]c2ccc([N+](=O)[O-])cc12\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"N#Cc1n[nH]c2ccc([N+](=O)[O-])cc12 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"N#Cc1n[nH]c2ccc([N+](=O)[O-])cc12\", \"reactants\": [\"N#[C][Cu]\", \"O=[N+]([O-])c1ccc2[nH]nc(I)c2c1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"N#[C][Cu]\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=[N+]([O-])c1ccc2[nH]nc(I)c2c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"DULSAGLWMRMKCQ-UHFFFAOYSA-N.UCTRCMYXPOXOSN-UHFFFAOYSA-N>>WXTZAAHDBOKXDI-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"N#Cc1n[nH]c2ccc([N+](=O)[O-])cc12\", \"reactants\": [\"N#[C][Cu]\", \"O=[N+]([O-])c1ccc2[nH]nc(I)c2c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"N#[C][Cu]\", \"results\": [{\"inchikey\": \"DULSAGLWMRMKCQ-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"N#[C][Cu]\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"O=[N+]([O-])c1ccc2[nH]nc(I)c2c1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"O=[N+]([O-])c1ccc2[nH]nc(I)c2c1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"O=[N+]([O-])c1ccc2[nH]nc(I)c2c1\", \"reactants\": [\"O=C1CCC(=O)N1I\", \"O=[N+]([O-])c1ccc2[nH]ncc2c1\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"O=C1CCC(=O)N1I\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=[N+]([O-])c1ccc2[nH]ncc2c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"LQZMLBORDGWNPD-UHFFFAOYSA-N.WSGURAYTCUVDQL-UHFFFAOYSA-N>>UCTRCMYXPOXOSN-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"O=[N+]([O-])c1ccc2[nH]nc(I)c2c1\", \"reactants\": [\"O=C1CCC(=O)N1I\", \"O=[N+]([O-])c1ccc2[nH]ncc2c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"O=C1CCC(=O)N1I\", \"results\": [{\"inchikey\": \"LQZMLBORDGWNPD-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=C1CCC(=O)N1I\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"O=[N+]([O-])c1ccc2[nH]ncc2c1\", \"results\": [{\"inchikey\": \"WSGURAYTCUVDQL-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=[N+]([O-])c1ccc2[nH]ncc2c1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"Cn1nc(C#N)c2cc([N+](=O)[O-])ccc21\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CI\": \"precursor\", \"N#Cc1n[nH]c2ccc([N+](=O)[O-])cc12\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CI\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"N#Cc1n[nH]c2ccc([N+](=O)[O-])cc12\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"N#[C][Cu]\": \"precursor\", \"O=[N+]([O-])c1ccc2[nH]nc(I)c2c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"N#[C][Cu]\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=[N+]([O-])c1ccc2[nH]nc(I)c2c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"O=C1CCC(=O)N1I\": \"precursor\", \"O=[N+]([O-])c1ccc2[nH]ncc2c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"O=C1CCC(=O)N1I\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=[N+]([O-])c1ccc2[nH]ncc2c1\", \"in_stock\": true, \"children\": []}]}]}]}]}]}]}]}}","name":"emit_routes"},"id":"call_4_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"Cn1nc(C#N)c2cc([N+](=O)[O-])ccc21","task_id":"retro_ef14f1f01149e1d4fcc5","tool_calls":10,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":4}
{"exact_match":true,"id":"retro_f0a7a9822ce0aa0f7e0f:reference-expert:a0","kind":"single_route","max_steps":5,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CS(=O)(=O)Cc1cc(N2CCOCC2)nc(-c2ccc3[nH]ncc3c2)n1 in at most 5 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CS(=O)(=O)Cc1cc(N2CCOCC2)nc(-c2ccc3[nH]ncc3c2)n1\", \"reactants\": [\"Cc1ccc(S(=O)(=O)n2ncc3cc(-c4nc(CS(C)(=O)=O)cc(N5CCOCC5)n4)ccc32)cc1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"Cc1ccc(S(=O)(=O)n2ncc3cc(-c4nc(CS(C)(=O)=O)cc(N5CCOCC5)n4)ccc32)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"RDGRUHHCVUXNAE-UHFFFAOYSA-N>>BNSIQRVSCPOBMK-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"CS(=O)(=O)Cc1cc(N2CCOCC2)nc(-c2ccc3[nH]ncc3c2)n1\", \"reactants\": [\"Cc1ccc(S(=O)(=O)n2ncc3cc(-c4nc(CS(C)(=O)=O)cc(N5CCOCC5)n4)ccc32)cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"Cc1ccc(S(=O)(=O)n2ncc3cc(-c4nc(CS(C)(=O)=O)cc(N5CCOCC5)n4)ccc32)cc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"Cc1ccc(S(=O)(=O)n2ncc3cc(-c4nc(CS(C)(=O)=O)cc(N5CCOCC5)n4)ccc32)cc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Cc1ccc(S(=O)(=O)n2ncc3cc(-c4nc(CS(C)(=O)=O)cc(N5CCOCC5)n4)ccc32)cc1\", \"reactants\": [\"CS(=O)(=O)Cc1cc(N2CCOCC2)nc(Cl)n1\", \"Cc1ccc(S(=O)(=O)n2ncc3cc(B4OC(C)(C)C(C)(C)O4)ccc32)cc1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CS(=O)(=O)Cc1cc(N2CCOCC2)nc(Cl)n1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"Cc1ccc(S(=O)(=O)n2ncc3cc(B4OC(C)(C)C(C)(C)O4)ccc32)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"GUACFAIZFHQZLF-UHFFFAOYSA-N.OPKHZOCWVOFTRM-UHFFFAOYSA-N>>RDGRUHHCVUXNAE-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"Cc1ccc(S(=O)(=O)n2ncc3cc(-c4nc(CS(C)(=O)=O)cc(N5CCOCC5)n4)ccc32)cc1\", \"reactants\": [\"CS(=O)(=O)Cc1cc(N2CCOCC2)nc(Cl)n1\", \"Cc1ccc(S(=O)(=O)n2ncc3cc(B4OC(C)(C)C(C)(C)O4)ccc32)cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CS(=O)(=O)Cc1cc(N2CCOCC2)nc(Cl)n1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"Cc1ccc(S(=O)(=O)n2ncc3cc(B4OC(C)(C)C(C)(C)O4)ccc32)cc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"CS(=O)(=O)Cc1cc(N2CCOCC2)nc(Cl)n1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CS(=O)(=O)Cc1cc(N2CCOCC2)nc(Cl)n1\", \"reactants\": [\"C1COCCN1\", \"CS(=O)(=O)Cc1cc(Cl)nc(Cl)n1\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"C1COCCN1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"CS(=O)(=O)Cc1cc(Cl)nc(Cl)n1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"XWBKVIYQDHDRBZ-UHFFFAOYSA-N.YNAVUWVOSKDBBP-UHFFFAOYSA-N>>GUACFAIZFHQZLF-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"CS(=O)(=O)Cc1cc(N2CCOCC2)nc(Cl)n1\", \"reactants\": [\"C1COCCN1\", \"CS(=O)(=O)Cc1cc(Cl)nc(Cl)n1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"C1COCCN1\", \"results\": [{\"inchikey\": \"YNAVUWVOSKDBBP-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"C1COCCN1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"CS(=O)(=O)Cc1cc(Cl)nc(Cl)n1\", \"results\": [{\"inchikey\": \"XWBKVIYQDHDRBZ-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CS(=O)(=O)Cc1cc(Cl)nc(Cl)n1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"Cc1ccc(S(=O)(=O)n2ncc3cc(B4OC(C)(C)C(C)(C)O4)ccc32)cc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Cc1ccc(S(=O)(=O)n2ncc3cc(B4OC(C)(C)C(C)(C)O4)ccc32)cc1\", \"reactants\": [\"CC1(C)OB(B2OC(C)(C)C(C)(C)O2)OC1(C)C\", \"Cc1ccc(S(=O)(=O)n2ncc3cc(Br)ccc32)cc1\"]}","name":"validate_disconnection"},"id":"call_4_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC1(C)OB(B2OC(C)(C)C(C)(C)O2)OC1(C)C\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_1","type":"function"},{"function":{"arguments":"{\"query\": \"Cc1ccc(S(=O)(=O)n2ncc3cc(Br)ccc32)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"BYPKUFOWXIYICX-UHFFFAOYSA-N.IPWKHHSGDUIRAH-UHFFFAOYSA-N>>OPKHZOCWVOFTRM-UHFFFAOYSA-N\", \"model_turns_remaining\": 12, \"product\": \"Cc1ccc(S(=O)(=O)n2ncc3cc(B4OC(C)(C)C(C)(C)O4)ccc32)cc1\", \"reactants\": [\"CC1(C)OB(B2OC(C)(C)C(C)(C)O2)OC1(C)C\", \"Cc1ccc(S(=O)(=O)n2ncc3cc(Br)ccc32)cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_4_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"CC1(C)OB(B2OC(C)(C)C(C)(C)O2)OC1(C)C\", \"results\": [{\"inchikey\": \"IPWKHHSGDUIRAH-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CC1(C)OB(B2OC(C)(C)C(C)(C)O2)OC1(C)C\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"Cc1ccc(S(=O)(=O)n2ncc3cc(Br)ccc32)cc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_2"},{"content":"Cc1ccc(S(=O)(=O)n2ncc3cc(Br)ccc32)cc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Cc1ccc(S(=O)(=O)n2ncc3cc(Br)ccc32)cc1\", \"reactants\": [\"Brc1ccc2[nH]ncc2c1\", \"Cc1ccc(S(=O)(=O)Cl)cc1\"]}","name":"validate_disconnection"},"id":"call_5_0","type":"function"},{"function":{"arguments":"{\"query\": \"Brc1ccc2[nH]ncc2c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_5_1","type":"function"},{"function":{"arguments":"{\"query\": \"Cc1ccc(S(=O)(=O)Cl)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_5_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"STVHMYNPQCLUNJ-UHFFFAOYSA-N.YYROPELSRYBVMQ-UHFFFAOYSA-N>>BYPKUFOWXIYICX-UHFFFAOYSA-N\", \"model_turns_remaining\": 11, \"product\": \"Cc1ccc(S(=O)(=O)n2ncc3cc(Br)ccc32)cc1\", \"reactants\": [\"Brc1ccc2[nH]ncc2c1\", \"Cc1ccc(S(=O)(=O)Cl)cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_5_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 11, \"query\": \"Brc1ccc2[nH]ncc2c1\", \"results\": [{\"inchikey\": \"STVHMYNPQCLUNJ-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Brc1ccc2[nH]ncc2c1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_5_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 11, \"query\": \"Cc1ccc(S(=O)(=O)Cl)cc1\", \"results\": [{\"inchikey\": \"YYROPELSRYBVMQ-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Cc1ccc(S(=O)(=O)Cl)cc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_5_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CS(=O)(=O)Cc1cc(N2CCOCC2)nc(-c2ccc3[nH]ncc3c2)n1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"Cc1ccc(S(=O)(=O)n2ncc3cc(-c4nc(CS(C)(=O)=O)cc(N5CCOCC5)n4)ccc32)cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"Cc1ccc(S(=O)(=O)n2ncc3cc(-c4nc(CS(C)(=O)=O)cc(N5CCOCC5)n4)ccc32)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CS(=O)(=O)Cc1cc(N2CCOCC2)nc(Cl)n1\": \"precursor\", \"Cc1ccc(S(=O)(=O)n2ncc3cc(B4OC(C)(C)C(C)(C)O4)ccc32)cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CS(=O)(=O)Cc1cc(N2CCOCC2)nc(Cl)n1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"C1COCCN1\": \"precursor\", \"CS(=O)(=O)Cc1cc(Cl)nc(Cl)n1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"C1COCCN1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"CS(=O)(=O)Cc1cc(Cl)nc(Cl)n1\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"Cc1ccc(S(=O)(=O)n2ncc3cc(B4OC(C)(C)C(C)(C)O4)ccc32)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC1(C)OB(B2OC(C)(C)C(C)(C)O2)OC1(C)C\": \"precursor\", \"Cc1ccc(S(=O)(=O)n2ncc3cc(Br)ccc32)cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC1(C)OB(B2OC(C)(C)C(C)(C)O2)OC1(C)C\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"Cc1ccc(S(=O)(=O)n2ncc3cc(Br)ccc32)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"Brc1ccc2[nH]ncc2c1\": \"precursor\", \"Cc1ccc(S(=O)(=O)Cl)cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"Brc1ccc2[nH]ncc2c1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"Cc1ccc(S(=O)(=O)Cl)cc1\", \"in_stock\": true, \"children\": []}]}]}]}]}]}]}]}]}]}}","name":"emit_routes"},"id":"call_6_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"CS(=O)(=O)Cc1cc(N2CCOCC2)nc(-c2ccc3[nH]ncc3c2)n1","task_id":"retro_f0a7a9822ce0aa0f7e0f","tool_calls":15,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":6}
{"exact_match":true,"id":"retro_f0ed56f190f6a830f9ed:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target C[C@@H]1COCCN1C(=O)c1ccc(Nc2cc(Br)cn(C)c2=O)nc1 in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"C[C@@H]1COCCN1C(=O)c1ccc(Nc2cc(Br)cn(C)c2=O)nc1\", \"reactants\": [\"C[C@@H]1COCCN1C(=O)c1ccc(N)nc1\", \"Cn1cc(Br)cc(Br)c1=O\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"C[C@@H]1COCCN1C(=O)c1ccc(N)nc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"Cn1cc(Br)cc(Br)c1=O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"AOJAJTJZSBVNPU-UHFFFAOYSA-N.YZMCJDBGTVGDNZ-MRVPVSSYSA-N>>ANCQUDFEMAOCFC-LLVKDONJSA-N\", \"model_turns_remaining\": 15, \"product\": \"C[C@@H]1COCCN1C(=O)c1ccc(Nc2cc(Br)cn(C)c2=O)nc1\", \"reactants\": [\"C[C@@H]1COCCN1C(=O)c1ccc(N)nc1\", \"Cn1cc(Br)cc(Br)c1=O\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"C[C@@H]1COCCN1C(=O)c1ccc(N)nc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"Cn1cc(Br)cc(Br)c1=O\", \"results\": [{\"inchikey\": \"AOJAJTJZSBVNPU-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Cn1cc(Br)cc(Br)c1=O\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"C[C@@H]1COCCN1C(=O)c1ccc(N)nc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"C[C@@H]1COCCN1C(=O)c1ccc(N)nc1\", \"reactants\": [\"C[C@@H]1COCCN1\", \"Nc1ccc(C(=O)O)cn1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"C[C@@H]1COCCN1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"Nc1ccc(C(=O)O)cn1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"SFWWGMKXCYLZEG-RXMQYKEDSA-N.ZCIFWRHIEBXBOY-UHFFFAOYSA-N>>YZMCJDBGTVGDNZ-MRVPVSSYSA-N\", \"model_turns_remaining\": 14, \"product\": \"C[C@@H]1COCCN1C(=O)c1ccc(N)nc1\", \"reactants\": [\"C[C@@H]1COCCN1\", \"Nc1ccc(C(=O)O)cn1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"C[C@@H]1COCCN1\", \"results\": [{\"inchikey\": \"SFWWGMKXCYLZEG-RXMQYKEDSA-N\", \"similarity\": 1.0, \"smiles\": \"C[C@@H]1COCCN1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"Nc1ccc(C(=O)O)cn1\", \"results\": [{\"inchikey\": \"ZCIFWRHIEBXBOY-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Nc1ccc(C(=O)O)cn1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"C[C@@H]1COCCN1C(=O)c1ccc(Nc2cc(Br)cn(C)c2=O)nc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"C[C@@H]1COCCN1C(=O)c1ccc(N)nc1\": \"precursor\", \"Cn1cc(Br)cc(Br)c1=O\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"C[C@@H]1COCCN1C(=O)c1ccc(N)nc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"C[C@@H]1COCCN1\": \"precursor\", \"Nc1ccc(C(=O)O)cn1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"C[C@@H]1COCCN1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"Nc1ccc(C(=O)O)cn1\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"Cn1cc(Br)cc(Br)c1=O\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"C[C@@H]1COCCN1C(=O)c1ccc(Nc2cc(Br)cn(C)c2=O)nc1","task_id":"retro_f0ed56f190f6a830f9ed","tool_calls":7,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_f11f4b29247e8b4464e0:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target NCCN1CCC[C@@H]1CO in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"NCCN1CCC[C@@H]1CO\", \"reactants\": [\"NCC(=O)N1CCC[C@@H]1CO\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"NCC(=O)N1CCC[C@@H]1CO\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"NBKHGGGZPVKEKG-ZCFIWIBFSA-N>>JCCWMSYGCHUCQE-SSDOTTSWSA-N\", \"model_turns_remaining\": 15, \"product\": \"NCCN1CCC[C@@H]1CO\", \"reactants\": [\"NCC(=O)N1CCC[C@@H]1CO\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"NCC(=O)N1CCC[C@@H]1CO\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"NCC(=O)N1CCC[C@@H]1CO was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"NCC(=O)N1CCC[C@@H]1CO\", \"reactants\": [\"CC(C)(C)OC(=O)NCC(=O)O\", \"OC[C@H]1CCCN1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)OC(=O)NCC(=O)O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"OC[C@H]1CCCN1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"HVVNJUAVDAZWCB-RXMQYKEDSA-N.VRPJIFMKZZEXLR-UHFFFAOYSA-N>>NBKHGGGZPVKEKG-ZCFIWIBFSA-N\", \"model_turns_remaining\": 14, \"product\": \"NCC(=O)N1CCC[C@@H]1CO\", \"reactants\": [\"CC(C)(C)OC(=O)NCC(=O)O\", \"OC[C@H]1CCCN1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CC(C)(C)OC(=O)NCC(=O)O\", \"results\": [{\"inchikey\": \"VRPJIFMKZZEXLR-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CC(C)(C)OC(=O)NCC(=O)O\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"OC[C@H]1CCCN1\", \"results\": [{\"inchikey\": \"HVVNJUAVDAZWCB-RXMQYKEDSA-N\", \"similarity\": 1.0, \"smiles\": \"OC[C@H]1CCCN1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"NCCN1CCC[C@@H]1CO\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"NCC(=O)N1CCC[C@@H]1CO\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"NCC(=O)N1CCC[C@@H]1CO\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)(C)OC(=O)NCC(=O)O\": \"precursor\", \"OC[C@H]1CCCN1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)OC(=O)NCC(=O)O\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"OC[C@H]1CCCN1\", \"in_stock\": true, \"children\": []}]}]}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"NCCN1CCC[C@@H]1CO","task_id":"retro_f11f4b29247e8b4464e0","tool_calls":6,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_f2d7ecde40929057e0e3:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CCOC(=O)C(CC=C(C)C[N+](=O)[O-])C(=O)OCC in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCOC(=O)C(CC=C(C)C[N+](=O)[O-])C(=O)OCC\", \"reactants\": [\"CC(=CCBr)C[N+](=O)[O-]\", \"CCOC(=O)CC(=O)OCC\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(=CCBr)C[N+](=O)[O-]\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"CCOC(=O)CC(=O)OCC\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"IYXGSMUGOJNHAZ-UHFFFAOYSA-N.WUCDMBAKYZOCRA-UHFFFAOYSA-N>>FDISKQVWIKEOOS-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"CCOC(=O)C(CC=C(C)C[N+](=O)[O-])C(=O)OCC\", \"reactants\": [\"CC(=CCBr)C[N+](=O)[O-]\", \"CCOC(=O)CC(=O)OCC\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CC(=CCBr)C[N+](=O)[O-]\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CCOC(=O)CC(=O)OCC\", \"results\": [{\"inchikey\": \"IYXGSMUGOJNHAZ-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CCOC(=O)CC(=O)OCC\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"CC(=CCBr)C[N+](=O)[O-] was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(=CCBr)C[N+](=O)[O-]\", \"reactants\": [\"BrP(Br)Br\", \"CC(=CCO)C[N+](=O)[O-]\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"BrP(Br)Br\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"CC(=CCO)C[N+](=O)[O-]\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"IPNPIHIZVLFAFP-UHFFFAOYSA-N.WMVLBIKHKJXLKX-UHFFFAOYSA-N>>WUCDMBAKYZOCRA-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"CC(=CCBr)C[N+](=O)[O-]\", \"reactants\": [\"BrP(Br)Br\", \"CC(=CCO)C[N+](=O)[O-]\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"BrP(Br)Br\", \"results\": [{\"inchikey\": \"IPNPIHIZVLFAFP-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"BrP(Br)Br\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CC(=CCO)C[N+](=O)[O-]\", \"results\": [{\"inchikey\": \"WMVLBIKHKJXLKX-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CC(=CCO)C[N+](=O)[O-]\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CCOC(=O)C(CC=C(C)C[N+](=O)[O-])C(=O)OCC\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(=CCBr)C[N+](=O)[O-]\": \"precursor\", \"CCOC(=O)CC(=O)OCC\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(=CCBr)C[N+](=O)[O-]\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"BrP(Br)Br\": \"precursor\", \"CC(=CCO)C[N+](=O)[O-]\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"BrP(Br)Br\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"CC(=CCO)C[N+](=O)[O-]\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"CCOC(=O)CC(=O)OCC\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"CCOC(=O)C(CC=C(C)C[N+](=O)[O-])C(=O)OCC","task_id":"retro_f2d7ecde40929057e0e3","tool_calls":7,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_f31db4840cc5ece0e228:reference-expert:a0","kind":"single_route","max_steps":3,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target Cc1ccn2cc(-c3cc(=O)c4cc(N5CCN(C(=O)OC(C)(C)C)CC5)ccc4o3)nc2c1 in at most 3 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Cc1ccn2cc(-c3cc(=O)c4cc(N5CCN(C(=O)OC(C)(C)C)CC5)ccc4o3)nc2c1\", \"reactants\": [\"CC(C)(C)OC(=O)N1CCNCC1\", \"Cc1ccn2cc(-c3cc(=O)c4cc(Br)ccc4o3)nc2c1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)OC(=O)N1CCNCC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"Cc1ccn2cc(-c3cc(=O)c4cc(Br)ccc4o3)nc2c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"CWXPZXBSDSIRCS-UHFFFAOYSA-N.RRYYBXPHESNUEJ-UHFFFAOYSA-N>>CHCJNVOCNQHGJS-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"Cc1ccn2cc(-c3cc(=O)c4cc(N5CCN(C(=O)OC(C)(C)C)CC5)ccc4o3)nc2c1\", \"reactants\": [\"CC(C)(C)OC(=O)N1CCNCC1\", \"Cc1ccn2cc(-c3cc(=O)c4cc(Br)ccc4o3)nc2c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CC(C)(C)OC(=O)N1CCNCC1\", \"results\": [{\"inchikey\": \"CWXPZXBSDSIRCS-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CC(C)(C)OC(=O)N1CCNCC1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"Cc1ccn2cc(-c3cc(=O)c4cc(Br)ccc4o3)nc2c1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"Cc1ccn2cc(-c3cc(=O)c4cc(Br)ccc4o3)nc2c1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Cc1ccn2cc(-c3cc(=O)c4cc(Br)ccc4o3)nc2c1\", \"reactants\": [\"Cc1ccnc(N)c1\", \"O=C(CBr)c1cc(=O)c2cc(Br)ccc2o1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"Cc1ccnc(N)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=C(CBr)c1cc(=O)c2cc(Br)ccc2o1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"KHKGJVKSLLKGNM-UHFFFAOYSA-N.ORLGLBZRQYOWNA-UHFFFAOYSA-N>>RRYYBXPHESNUEJ-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"Cc1ccn2cc(-c3cc(=O)c4cc(Br)ccc4o3)nc2c1\", \"reactants\": [\"Cc1ccnc(N)c1\", \"O=C(CBr)c1cc(=O)c2cc(Br)ccc2o1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"Cc1ccnc(N)c1\", \"results\": [{\"inchikey\": \"ORLGLBZRQYOWNA-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Cc1ccnc(N)c1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"O=C(CBr)c1cc(=O)c2cc(Br)ccc2o1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"O=C(CBr)c1cc(=O)c2cc(Br)ccc2o1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"O=C(CBr)c1cc(=O)c2cc(Br)ccc2o1\", \"reactants\": [\"BrBr\", \"CC(=O)c1cc(=O)c2cc(Br)ccc2o1\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"BrBr\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"CC(=O)c1cc(=O)c2cc(Br)ccc2o1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"GDTBXPJZTBHREO-UHFFFAOYSA-N.INNBUWMERBNXAM-UHFFFAOYSA-N>>KHKGJVKSLLKGNM-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"O=C(CBr)c1cc(=O)c2cc(Br)ccc2o1\", \"reactants\": [\"BrBr\", \"CC(=O)c1cc(=O)c2cc(Br)ccc2o1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"BrBr\", \"results\": [{\"inchikey\": \"GDTBXPJZTBHREO-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"BrBr\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"CC(=O)c1cc(=O)c2cc(Br)ccc2o1\", \"results\": [{\"inchikey\": \"INNBUWMERBNXAM-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CC(=O)c1cc(=O)c2cc(Br)ccc2o1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"Cc1ccn2cc(-c3cc(=O)c4cc(N5CCN(C(=O)OC(C)(C)C)CC5)ccc4o3)nc2c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)(C)OC(=O)N1CCNCC1\": \"precursor\", \"Cc1ccn2cc(-c3cc(=O)c4cc(Br)ccc4o3)nc2c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)OC(=O)N1CCNCC1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"Cc1ccn2cc(-c3cc(=O)c4cc(Br)ccc4o3)nc2c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"Cc1ccnc(N)c1\": \"precursor\", \"O=C(CBr)c1cc(=O)c2cc(Br)ccc2o1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"Cc1ccnc(N)c1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=C(CBr)c1cc(=O)c2cc(Br)ccc2o1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"BrBr\": \"precursor\", \"CC(=O)c1cc(=O)c2cc(Br)ccc2o1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"BrBr\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"CC(=O)c1cc(=O)c2cc(Br)ccc2o1\", \"in_stock\": true, \"children\": []}]}]}]}]}]}]}]}}","name":"emit_routes"},"id":"call_4_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"Cc1ccn2cc(-c3cc(=O)c4cc(N5CCN(C(=O)OC(C)(C)C)CC5)ccc4o3)nc2c1","task_id":"retro_f31db4840cc5ece0e228","tool_calls":10,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":4}
{"exact_match":true,"id":"retro_f3c80b5d054d76b30ced:reference-expert:a0","kind":"single_route","max_steps":5,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target COc1cc2c(c(N3CCN(C)CC3)c1)OC(C(=O)Nc1ccc(N3CCCN(C)C3=O)cc1)CC2 in at most 5 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COc1cc2c(c(N3CCN(C)CC3)c1)OC(C(=O)Nc1ccc(N3CCCN(C)C3=O)cc1)CC2\", \"reactants\": [\"CN1CCCN(c2ccc(N)cc2)C1=O\", \"COc1cc2c(c(N3CCN(C)CC3)c1)OC(C(=O)O)CC2\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CN1CCCN(c2ccc(N)cc2)C1=O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"COc1cc2c(c(N3CCN(C)CC3)c1)OC(C(=O)O)CC2\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"DXYGWLQTBWIHQL-UHFFFAOYSA-N.KCCVVHGYACCRHY-UHFFFAOYSA-N>>LCFRSVVXIIAQCQ-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"COc1cc2c(c(N3CCN(C)CC3)c1)OC(C(=O)Nc1ccc(N3CCCN(C)C3=O)cc1)CC2\", \"reactants\": [\"CN1CCCN(c2ccc(N)cc2)C1=O\", \"COc1cc2c(c(N3CCN(C)CC3)c1)OC(C(=O)O)CC2\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CN1CCCN(c2ccc(N)cc2)C1=O\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"COc1cc2c(c(N3CCN(C)CC3)c1)OC(C(=O)O)CC2\", \"results\": [{\"inchikey\": \"KCCVVHGYACCRHY-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"COc1cc2c(c(N3CCN(C)CC3)c1)OC(C(=O)O)CC2\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"CN1CCCN(c2ccc(N)cc2)C1=O was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CN1CCCN(c2ccc(N)cc2)C1=O\", \"reactants\": [\"CN1CCCN(c2ccc([N+](=O)[O-])cc2)C1=O\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CN1CCCN(c2ccc([N+](=O)[O-])cc2)C1=O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"BZDXVIZTMVAHNM-UHFFFAOYSA-N>>DXYGWLQTBWIHQL-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"CN1CCCN(c2ccc(N)cc2)C1=O\", \"reactants\": [\"CN1CCCN(c2ccc([N+](=O)[O-])cc2)C1=O\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CN1CCCN(c2ccc([N+](=O)[O-])cc2)C1=O\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"CN1CCCN(c2ccc([N+](=O)[O-])cc2)C1=O was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CN1CCCN(c2ccc([N+](=O)[O-])cc2)C1=O\", \"reactants\": [\"CI\", \"O=C1NCCCN1c1ccc([N+](=O)[O-])cc1\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"CI\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=C1NCCCN1c1ccc([N+](=O)[O-])cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"BPJHXPWKTKEXNL-UHFFFAOYSA-N.INQOMBQAUSQDDS-UHFFFAOYSA-N>>BZDXVIZTMVAHNM-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"CN1CCCN(c2ccc([N+](=O)[O-])cc2)C1=O\", \"reactants\": [\"CI\", \"O=C1NCCCN1c1ccc([N+](=O)[O-])cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"CI\", \"results\": [{\"inchikey\": \"INQOMBQAUSQDDS-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CI\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"O=C1NCCCN1c1ccc([N+](=O)[O-])cc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"O=C1NCCCN1c1ccc([N+](=O)[O-])cc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"O=C1NCCCN1c1ccc([N+](=O)[O-])cc1\", \"reactants\": [\"O=C(NCCCCl)Nc1ccc([N+](=O)[O-])cc1\"]}","name":"validate_disconnection"},"id":"call_4_0","type":"function"},{"function":{"arguments":"{\"query\": \"O=C(NCCCCl)Nc1ccc([N+](=O)[O-])cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"ISWLORBKQPKENA-UHFFFAOYSA-N>>BPJHXPWKTKEXNL-UHFFFAOYSA-N\", \"model_turns_remaining\": 12, \"product\": \"O=C1NCCCN1c1ccc([N+](=O)[O-])cc1\", \"reactants\": [\"O=C(NCCCCl)Nc1ccc([N+](=O)[O-])cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_4_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"O=C(NCCCCl)Nc1ccc([N+](=O)[O-])cc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_1"},{"content":"O=C(NCCCCl)Nc1ccc([N+](=O)[O-])cc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"O=C(NCCCCl)Nc1ccc([N+](=O)[O-])cc1\", \"reactants\": [\"NCCCCl\", \"O=C=Nc1ccc([N+](=O)[O-])cc1\"]}","name":"validate_disconnection"},"id":"call_5_0","type":"function"},{"function":{"arguments":"{\"query\": \"NCCCCl\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_5_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=C=Nc1ccc([N+](=O)[O-])cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_5_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_complete\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"BZFKSWOGZQMOMO-UHFFFAOYSA-N.GFNKTLQTQSALEJ-UHFFFAOYSA-N>>ISWLORBKQPKENA-UHFFFAOYSA-N\", \"model_turns_remaining\": 11, \"product\": \"O=C(NCCCCl)Nc1ccc([N+](=O)[O-])cc1\", \"reactants\": [\"NCCCCl\", \"O=C=Nc1ccc([N+](=O)[O-])cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_5_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 11, \"query\": \"NCCCCl\", \"results\": [{\"inchikey\": \"BZFKSWOGZQMOMO-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"NCCCCl\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_5_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 11, \"query\": \"O=C=Nc1ccc([N+](=O)[O-])cc1\", \"results\": [{\"inchikey\": \"GFNKTLQTQSALEJ-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=C=Nc1ccc([N+](=O)[O-])cc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_5_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"COc1cc2c(c(N3CCN(C)CC3)c1)OC(C(=O)Nc1ccc(N3CCCN(C)C3=O)cc1)CC2\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CN1CCCN(c2ccc(N)cc2)C1=O\": \"precursor\", \"COc1cc2c(c(N3CCN(C)CC3)c1)OC(C(=O)O)CC2\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CN1CCCN(c2ccc(N)cc2)C1=O\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CN1CCCN(c2ccc([N+](=O)[O-])cc2)C1=O\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CN1CCCN(c2ccc([N+](=O)[O-])cc2)C1=O\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CI\": \"precursor\", \"O=C1NCCCN1c1ccc([N+](=O)[O-])cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CI\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=C1NCCCN1c1ccc([N+](=O)[O-])cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"O=C(NCCCCl)Nc1ccc([N+](=O)[O-])cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"O=C(NCCCCl)Nc1ccc([N+](=O)[O-])cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"NCCCCl\": \"precursor\", \"O=C=Nc1ccc([N+](=O)[O-])cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"NCCCCl\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=C=Nc1ccc([N+](=O)[O-])cc1\", \"in_stock\": true, \"children\": []}]}]}]}]}]}]}]}]}, {\"type\": \"mol\", \"smiles\": \"COc1cc2c(c(N3CCN(C)CC3)c1)OC(C(=O)O)CC2\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_6_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"COc1cc2c(c(N3CCN(C)CC3)c1)OC(C(=O)Nc1ccc(N3CCCN(C)C3=O)cc1)CC2","task_id":"retro_f3c80b5d054d76b30ced","tool_calls":14,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":6}
{"exact_match":true,"id":"retro_f3fc7c269afab6fb4203:reference-expert:a0","kind":"single_route","max_steps":3,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CC(C)(C)OC(=O)NCCC(Nc1cccc(-c2cnc3c(NCCN4CCOCC4)nccn23)n1)c1cccc(Cl)c1 in at most 3 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(C)(C)OC(=O)NCCC(Nc1cccc(-c2cnc3c(NCCN4CCOCC4)nccn23)n1)c1cccc(Cl)c1\", \"reactants\": [\"Brc1cccc(-c2cnc3c(NCCN4CCOCC4)nccn23)n1\", \"CC(C)(C)OC(=O)NCCC(N)c1cccc(Cl)c1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"Brc1cccc(-c2cnc3c(NCCN4CCOCC4)nccn23)n1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)OC(=O)NCCC(N)c1cccc(Cl)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"BEHXDYNILYMKOM-UHFFFAOYSA-N.ZFJQCQPXYORCMT-UHFFFAOYSA-N>>HJVWSANEZUHTHC-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"CC(C)(C)OC(=O)NCCC(Nc1cccc(-c2cnc3c(NCCN4CCOCC4)nccn23)n1)c1cccc(Cl)c1\", \"reactants\": [\"Brc1cccc(-c2cnc3c(NCCN4CCOCC4)nccn23)n1\", \"CC(C)(C)OC(=O)NCCC(N)c1cccc(Cl)c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"Brc1cccc(-c2cnc3c(NCCN4CCOCC4)nccn23)n1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CC(C)(C)OC(=O)NCCC(N)c1cccc(Cl)c1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"Brc1cccc(-c2cnc3c(NCCN4CCOCC4)nccn23)n1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Brc1cccc(-c2cnc3c(NCCN4CCOCC4)nccn23)n1\", \"reactants\": [\"Clc1nccn2c(-c3cccc(Br)n3)cnc12\", \"NCCN1CCOCC1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"Clc1nccn2c(-c3cccc(Br)n3)cnc12\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"NCCN1CCOCC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"RWIVICVCHVMHMU-UHFFFAOYSA-N.UZEFZKDDIXXZRU-UHFFFAOYSA-N>>BEHXDYNILYMKOM-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"Brc1cccc(-c2cnc3c(NCCN4CCOCC4)nccn23)n1\", \"reactants\": [\"Clc1nccn2c(-c3cccc(Br)n3)cnc12\", \"NCCN1CCOCC1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"Clc1nccn2c(-c3cccc(Br)n3)cnc12\", \"results\": [{\"inchikey\": \"UZEFZKDDIXXZRU-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Clc1nccn2c(-c3cccc(Br)n3)cnc12\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"NCCN1CCOCC1\", \"results\": [{\"inchikey\": \"RWIVICVCHVMHMU-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"NCCN1CCOCC1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"CC(C)(C)OC(=O)NCCC(N)c1cccc(Cl)c1 was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(C)(C)OC(=O)NCCC(N)c1cccc(Cl)c1\", \"reactants\": [\"CC(C)(C)OC(=O)NCCC(c1cccc(Cl)c1)N1C(=O)c2ccccc2C1=O\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)(C)OC(=O)NCCC(c1cccc(Cl)c1)N1C(=O)c2ccccc2C1=O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"OIUQFDOMUGQRRN-UHFFFAOYSA-N>>ZFJQCQPXYORCMT-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"CC(C)(C)OC(=O)NCCC(N)c1cccc(Cl)c1\", \"reactants\": [\"CC(C)(C)OC(=O)NCCC(c1cccc(Cl)c1)N1C(=O)c2ccccc2C1=O\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"CC(C)(C)OC(=O)NCCC(c1cccc(Cl)c1)N1C(=O)c2ccccc2C1=O\", \"results\": [{\"inchikey\": \"OIUQFDOMUGQRRN-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CC(C)(C)OC(=O)NCCC(c1cccc(Cl)c1)N1C(=O)c2ccccc2C1=O\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)OC(=O)NCCC(Nc1cccc(-c2cnc3c(NCCN4CCOCC4)nccn23)n1)c1cccc(Cl)c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"Brc1cccc(-c2cnc3c(NCCN4CCOCC4)nccn23)n1\": \"precursor\", \"CC(C)(C)OC(=O)NCCC(N)c1cccc(Cl)c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"Brc1cccc(-c2cnc3c(NCCN4CCOCC4)nccn23)n1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"Clc1nccn2c(-c3cccc(Br)n3)cnc12\": \"precursor\", \"NCCN1CCOCC1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"Clc1nccn2c(-c3cccc(Br)n3)cnc12\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"NCCN1CCOCC1\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"CC(C)(C)OC(=O)NCCC(N)c1cccc(Cl)c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)(C)OC(=O)NCCC(c1cccc(Cl)c1)N1C(=O)c2ccccc2C1=O\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)(C)OC(=O)NCCC(c1cccc(Cl)c1)N1C(=O)c2ccccc2C1=O\", \"in_stock\": true, \"children\": []}]}]}]}]}]}}","name":"emit_routes"},"id":"call_4_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"CC(C)(C)OC(=O)NCCC(Nc1cccc(-c2cnc3c(NCCN4CCOCC4)nccn23)n1)c1cccc(Cl)c1","task_id":"retro_f3fc7c269afab6fb4203","tool_calls":9,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":4}
{"exact_match":true,"id":"retro_f4d706c14afa583b5e6a:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CCNc1cccc([N+](=O)[O-])c1 in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCNc1cccc([N+](=O)[O-])c1\", \"reactants\": [\"CC(=O)Nc1cccc([N+](=O)[O-])c1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(=O)Nc1cccc([N+](=O)[O-])c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"KFTYNYHJHKCRKU-UHFFFAOYSA-N>>HTVZQOWXJLNSFO-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"CCNc1cccc([N+](=O)[O-])c1\", \"reactants\": [\"CC(=O)Nc1cccc([N+](=O)[O-])c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CC(=O)Nc1cccc([N+](=O)[O-])c1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"CC(=O)Nc1cccc([N+](=O)[O-])c1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(=O)Nc1cccc([N+](=O)[O-])c1\", \"reactants\": [\"CC(=O)OC(C)=O\", \"Nc1cccc([N+](=O)[O-])c1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(=O)OC(C)=O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"Nc1cccc([N+](=O)[O-])c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"WFDIJRYMOXRFFG-UHFFFAOYSA-N.XJCVRTZCHMZPBD-UHFFFAOYSA-N>>KFTYNYHJHKCRKU-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"CC(=O)Nc1cccc([N+](=O)[O-])c1\", \"reactants\": [\"CC(=O)OC(C)=O\", \"Nc1cccc([N+](=O)[O-])c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CC(=O)OC(C)=O\", \"results\": [{\"inchikey\": \"WFDIJRYMOXRFFG-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CC(=O)OC(C)=O\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"Nc1cccc([N+](=O)[O-])c1\", \"results\": [{\"inchikey\": \"XJCVRTZCHMZPBD-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Nc1cccc([N+](=O)[O-])c1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CCNc1cccc([N+](=O)[O-])c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(=O)Nc1cccc([N+](=O)[O-])c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(=O)Nc1cccc([N+](=O)[O-])c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(=O)OC(C)=O\": \"precursor\", \"Nc1cccc([N+](=O)[O-])c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(=O)OC(C)=O\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"Nc1cccc([N+](=O)[O-])c1\", \"in_stock\": true, \"children\": []}]}]}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"CCNc1cccc([N+](=O)[O-])c1","task_id":"retro_f4d706c14afa583b5e6a","tool_calls":6,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_f6a40cc8e4a78ec9f36a:reference-expert:a0","kind":"single_route","max_steps":5,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CCOc1cc(Oc2ccc(NS(=O)(=O)c3ccc(C)cc3)c(C(=O)O)c2)ccc1NS(=O)(=O)c1ccc(C)cc1 in at most 5 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCOc1cc(Oc2ccc(NS(=O)(=O)c3ccc(C)cc3)c(C(=O)O)c2)ccc1NS(=O)(=O)c1ccc(C)cc1\", \"reactants\": [\"CCOc1cc(Oc2ccc(NS(=O)(=O)c3ccc(C)cc3)c(C(=O)OC)c2)ccc1NS(=O)(=O)c1ccc(C)cc1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCOc1cc(Oc2ccc(NS(=O)(=O)c3ccc(C)cc3)c(C(=O)OC)c2)ccc1NS(=O)(=O)c1ccc(C)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"KEBIJDXBJAUQTQ-UHFFFAOYSA-N>>SPEHOCUREUHEOZ-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"CCOc1cc(Oc2ccc(NS(=O)(=O)c3ccc(C)cc3)c(C(=O)O)c2)ccc1NS(=O)(=O)c1ccc(C)cc1\", \"reactants\": [\"CCOc1cc(Oc2ccc(NS(=O)(=O)c3ccc(C)cc3)c(C(=O)OC)c2)ccc1NS(=O)(=O)c1ccc(C)cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CCOc1cc(Oc2ccc(NS(=O)(=O)c3ccc(C)cc3)c(C(=O)OC)c2)ccc1NS(=O)(=O)c1ccc(C)cc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"CCOc1cc(Oc2ccc(NS(=O)(=O)c3ccc(C)cc3)c(C(=O)OC)c2)ccc1NS(=O)(=O)c1ccc(C)cc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCOc1cc(Oc2ccc(NS(=O)(=O)c3ccc(C)cc3)c(C(=O)OC)c2)ccc1NS(=O)(=O)c1ccc(C)cc1\", \"reactants\": [\"CCOc1cc(Oc2ccc(NS(=O)(=O)c3ccc(C)cc3)c(C(=O)OC)c2)ccc1N\", \"Cc1ccc(S(=O)(=O)Cl)cc1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCOc1cc(Oc2ccc(NS(=O)(=O)c3ccc(C)cc3)c(C(=O)OC)c2)ccc1N\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"Cc1ccc(S(=O)(=O)Cl)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"DGIDKLSOJYHWDT-UHFFFAOYSA-N.YYROPELSRYBVMQ-UHFFFAOYSA-N>>KEBIJDXBJAUQTQ-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"CCOc1cc(Oc2ccc(NS(=O)(=O)c3ccc(C)cc3)c(C(=O)OC)c2)ccc1NS(=O)(=O)c1ccc(C)cc1\", \"reactants\": [\"CCOc1cc(Oc2ccc(NS(=O)(=O)c3ccc(C)cc3)c(C(=O)OC)c2)ccc1N\", \"Cc1ccc(S(=O)(=O)Cl)cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CCOc1cc(Oc2ccc(NS(=O)(=O)c3ccc(C)cc3)c(C(=O)OC)c2)ccc1N\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"Cc1ccc(S(=O)(=O)Cl)cc1\", \"results\": [{\"inchikey\": \"YYROPELSRYBVMQ-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Cc1ccc(S(=O)(=O)Cl)cc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"CCOc1cc(Oc2ccc(NS(=O)(=O)c3ccc(C)cc3)c(C(=O)OC)c2)ccc1N was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCOc1cc(Oc2ccc(NS(=O)(=O)c3ccc(C)cc3)c(C(=O)OC)c2)ccc1N\", \"reactants\": [\"CCOc1cc(Oc2ccc(NS(=O)(=O)c3ccc(C)cc3)c(C(=O)OC)c2)ccc1[N+](=O)[O-]\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCOc1cc(Oc2ccc(NS(=O)(=O)c3ccc(C)cc3)c(C(=O)OC)c2)ccc1[N+](=O)[O-]\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"QUKRVUUIMMNSIB-UHFFFAOYSA-N>>DGIDKLSOJYHWDT-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"CCOc1cc(Oc2ccc(NS(=O)(=O)c3ccc(C)cc3)c(C(=O)OC)c2)ccc1N\", \"reactants\": [\"CCOc1cc(Oc2ccc(NS(=O)(=O)c3ccc(C)cc3)c(C(=O)OC)c2)ccc1[N+](=O)[O-]\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"CCOc1cc(Oc2ccc(NS(=O)(=O)c3ccc(C)cc3)c(C(=O)OC)c2)ccc1[N+](=O)[O-]\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"CCOc1cc(Oc2ccc(NS(=O)(=O)c3ccc(C)cc3)c(C(=O)OC)c2)ccc1[N+](=O)[O-] was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCOc1cc(Oc2ccc(NS(=O)(=O)c3ccc(C)cc3)c(C(=O)OC)c2)ccc1[N+](=O)[O-]\", \"reactants\": [\"CCOc1cc(F)ccc1[N+](=O)[O-]\", \"COC(=O)c1cc(O)ccc1NS(=O)(=O)c1ccc(C)cc1\"]}","name":"validate_disconnection"},"id":"call_4_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCOc1cc(F)ccc1[N+](=O)[O-]\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_1","type":"function"},{"function":{"arguments":"{\"query\": \"COC(=O)c1cc(O)ccc1NS(=O)(=O)c1ccc(C)cc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_4_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"LEMJFSSYFHTFFP-UHFFFAOYSA-N.RCZSJZZAARPGRT-UHFFFAOYSA-N>>QUKRVUUIMMNSIB-UHFFFAOYSA-N\", \"model_turns_remaining\": 12, \"product\": \"CCOc1cc(Oc2ccc(NS(=O)(=O)c3ccc(C)cc3)c(C(=O)OC)c2)ccc1[N+](=O)[O-]\", \"reactants\": [\"CCOc1cc(F)ccc1[N+](=O)[O-]\", \"COC(=O)c1cc(O)ccc1NS(=O)(=O)c1ccc(C)cc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_4_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"CCOc1cc(F)ccc1[N+](=O)[O-]\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 12, \"query\": \"COC(=O)c1cc(O)ccc1NS(=O)(=O)c1ccc(C)cc1\", \"results\": [{\"inchikey\": \"RCZSJZZAARPGRT-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"COC(=O)c1cc(O)ccc1NS(=O)(=O)c1ccc(C)cc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_4_2"},{"content":"CCOc1cc(F)ccc1[N+](=O)[O-] was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCOc1cc(F)ccc1[N+](=O)[O-]\", \"reactants\": [\"CCI\", \"O=[N+]([O-])c1ccc(F)cc1O\"]}","name":"validate_disconnection"},"id":"call_5_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCI\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_5_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=[N+]([O-])c1ccc(F)cc1O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_5_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"HVTICUPFWKNHNG-UHFFFAOYSA-N.QQURWFRNETXFTN-UHFFFAOYSA-N>>LEMJFSSYFHTFFP-UHFFFAOYSA-N\", \"model_turns_remaining\": 11, \"product\": \"CCOc1cc(F)ccc1[N+](=O)[O-]\", \"reactants\": [\"CCI\", \"O=[N+]([O-])c1ccc(F)cc1O\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_5_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 11, \"query\": \"CCI\", \"results\": [{\"inchikey\": \"HVTICUPFWKNHNG-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CCI\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_5_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 11, \"query\": \"O=[N+]([O-])c1ccc(F)cc1O\", \"results\": [{\"inchikey\": \"QQURWFRNETXFTN-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=[N+]([O-])c1ccc(F)cc1O\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_5_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CCOc1cc(Oc2ccc(NS(=O)(=O)c3ccc(C)cc3)c(C(=O)O)c2)ccc1NS(=O)(=O)c1ccc(C)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCOc1cc(Oc2ccc(NS(=O)(=O)c3ccc(C)cc3)c(C(=O)OC)c2)ccc1NS(=O)(=O)c1ccc(C)cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCOc1cc(Oc2ccc(NS(=O)(=O)c3ccc(C)cc3)c(C(=O)OC)c2)ccc1NS(=O)(=O)c1ccc(C)cc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCOc1cc(Oc2ccc(NS(=O)(=O)c3ccc(C)cc3)c(C(=O)OC)c2)ccc1N\": \"precursor\", \"Cc1ccc(S(=O)(=O)Cl)cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCOc1cc(Oc2ccc(NS(=O)(=O)c3ccc(C)cc3)c(C(=O)OC)c2)ccc1N\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCOc1cc(Oc2ccc(NS(=O)(=O)c3ccc(C)cc3)c(C(=O)OC)c2)ccc1[N+](=O)[O-]\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCOc1cc(Oc2ccc(NS(=O)(=O)c3ccc(C)cc3)c(C(=O)OC)c2)ccc1[N+](=O)[O-]\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCOc1cc(F)ccc1[N+](=O)[O-]\": \"precursor\", \"COC(=O)c1cc(O)ccc1NS(=O)(=O)c1ccc(C)cc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCOc1cc(F)ccc1[N+](=O)[O-]\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCI\": \"precursor\", \"O=[N+]([O-])c1ccc(F)cc1O\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCI\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=[N+]([O-])c1ccc(F)cc1O\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"COC(=O)c1cc(O)ccc1NS(=O)(=O)c1ccc(C)cc1\", \"in_stock\": true, \"children\": []}]}]}]}]}, {\"type\": \"mol\", \"smiles\": \"Cc1ccc(S(=O)(=O)Cl)cc1\", \"in_stock\": true, \"children\": []}]}]}]}]}]}}","name":"emit_routes"},"id":"call_6_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"CCOc1cc(Oc2ccc(NS(=O)(=O)c3ccc(C)cc3)c(C(=O)O)c2)ccc1NS(=O)(=O)c1ccc(C)cc1","task_id":"retro_f6a40cc8e4a78ec9f36a","tool_calls":14,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":6}
{"exact_match":true,"id":"retro_f74ee60e70a4dd6914d6:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target O=C(OCc1ccccc1)N1CCC(c2nc3ccccc3[nH]2)CC1 in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"O=C(OCc1ccccc1)N1CCC(c2nc3ccccc3[nH]2)CC1\", \"reactants\": [\"Nc1ccccc1NC(=O)C1CCN(C(=O)OCc2ccccc2)CC1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"Nc1ccccc1NC(=O)C1CCN(C(=O)OCc2ccccc2)CC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"JYRDFEZOSSMCPS-UHFFFAOYSA-N>>JKKQBCJFYXQLMF-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"O=C(OCc1ccccc1)N1CCC(c2nc3ccccc3[nH]2)CC1\", \"reactants\": [\"Nc1ccccc1NC(=O)C1CCN(C(=O)OCc2ccccc2)CC1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"Nc1ccccc1NC(=O)C1CCN(C(=O)OCc2ccccc2)CC1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"Nc1ccccc1NC(=O)C1CCN(C(=O)OCc2ccccc2)CC1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Nc1ccccc1NC(=O)C1CCN(C(=O)OCc2ccccc2)CC1\", \"reactants\": [\"Nc1ccccc1N\", \"O=C(O)C1CCN(C(=O)OCc2ccccc2)CC1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"Nc1ccccc1N\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=C(O)C1CCN(C(=O)OCc2ccccc2)CC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"GEYOCULIXLDCMW-UHFFFAOYSA-N.URTPNQRAHXRPMP-UHFFFAOYSA-N>>JYRDFEZOSSMCPS-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"Nc1ccccc1NC(=O)C1CCN(C(=O)OCc2ccccc2)CC1\", \"reactants\": [\"Nc1ccccc1N\", \"O=C(O)C1CCN(C(=O)OCc2ccccc2)CC1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"Nc1ccccc1N\", \"results\": [{\"inchikey\": \"GEYOCULIXLDCMW-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Nc1ccccc1N\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"O=C(O)C1CCN(C(=O)OCc2ccccc2)CC1\", \"results\": [{\"inchikey\": \"URTPNQRAHXRPMP-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=C(O)C1CCN(C(=O)OCc2ccccc2)CC1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"O=C(OCc1ccccc1)N1CCC(c2nc3ccccc3[nH]2)CC1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"Nc1ccccc1NC(=O)C1CCN(C(=O)OCc2ccccc2)CC1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"Nc1ccccc1NC(=O)C1CCN(C(=O)OCc2ccccc2)CC1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"Nc1ccccc1N\": \"precursor\", \"O=C(O)C1CCN(C(=O)OCc2ccccc2)CC1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"Nc1ccccc1N\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=C(O)C1CCN(C(=O)OCc2ccccc2)CC1\", \"in_stock\": true, \"children\": []}]}]}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"O=C(OCc1ccccc1)N1CCC(c2nc3ccccc3[nH]2)CC1","task_id":"retro_f74ee60e70a4dd6914d6","tool_calls":6,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_f80538350d52eef91c46:reference-expert:a0","kind":"single_route","max_steps":3,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target COc1cc(OC)c(Cl)c(-c2c(-c3ccccc3F)nnc(C)c2-c2c(F)cc(F)cc2F)c1 in at most 3 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COc1cc(OC)c(Cl)c(-c2c(-c3ccccc3F)nnc(C)c2-c2c(F)cc(F)cc2F)c1\", \"reactants\": [\"COc1cc(OC)cc(-c2c(-c3ccccc3F)nnc(C)c2-c2c(F)cc(F)cc2F)c1\", \"O=C1CCC(=O)N1Cl\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"COc1cc(OC)cc(-c2c(-c3ccccc3F)nnc(C)c2-c2c(F)cc(F)cc2F)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=C1CCC(=O)N1Cl\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"GEHCEECTKUATLG-UHFFFAOYSA-N.JRNVZBWKYDBUCA-UHFFFAOYSA-N>>BAYAEZVSNZUXFF-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"COc1cc(OC)c(Cl)c(-c2c(-c3ccccc3F)nnc(C)c2-c2c(F)cc(F)cc2F)c1\", \"reactants\": [\"COc1cc(OC)cc(-c2c(-c3ccccc3F)nnc(C)c2-c2c(F)cc(F)cc2F)c1\", \"O=C1CCC(=O)N1Cl\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"COc1cc(OC)cc(-c2c(-c3ccccc3F)nnc(C)c2-c2c(F)cc(F)cc2F)c1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"O=C1CCC(=O)N1Cl\", \"results\": [{\"inchikey\": \"JRNVZBWKYDBUCA-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=C1CCC(=O)N1Cl\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"COc1cc(OC)cc(-c2c(-c3ccccc3F)nnc(C)c2-c2c(F)cc(F)cc2F)c1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COc1cc(OC)cc(-c2c(-c3ccccc3F)nnc(C)c2-c2c(F)cc(F)cc2F)c1\", \"reactants\": [\"CB1OB(C)OB(C)O1\", \"COc1cc(OC)cc(-c2c(-c3ccccc3F)nnc(Cl)c2-c2c(F)cc(F)cc2F)c1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CB1OB(C)OB(C)O1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"COc1cc(OC)cc(-c2c(-c3ccccc3F)nnc(Cl)c2-c2c(F)cc(F)cc2F)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"GBBSAMQTQCPOBF-UHFFFAOYSA-N.ZRSFHIBIWOXOIW-UHFFFAOYSA-N>>GEHCEECTKUATLG-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"COc1cc(OC)cc(-c2c(-c3ccccc3F)nnc(C)c2-c2c(F)cc(F)cc2F)c1\", \"reactants\": [\"CB1OB(C)OB(C)O1\", \"COc1cc(OC)cc(-c2c(-c3ccccc3F)nnc(Cl)c2-c2c(F)cc(F)cc2F)c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CB1OB(C)OB(C)O1\", \"results\": [{\"inchikey\": \"GBBSAMQTQCPOBF-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CB1OB(C)OB(C)O1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"COc1cc(OC)cc(-c2c(-c3ccccc3F)nnc(Cl)c2-c2c(F)cc(F)cc2F)c1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"COc1cc(OC)cc(-c2c(-c3ccccc3F)nnc(Cl)c2-c2c(F)cc(F)cc2F)c1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COc1cc(OC)cc(-c2c(-c3ccccc3F)nnc(Cl)c2-c2c(F)cc(F)cc2F)c1\", \"reactants\": [\"COc1cc(OC)cc(-c2c(-c3ccccc3F)n[nH]c(=O)c2-c2c(F)cc(F)cc2F)c1\", \"O=P(Cl)(Cl)Cl\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"COc1cc(OC)cc(-c2c(-c3ccccc3F)n[nH]c(=O)c2-c2c(F)cc(F)cc2F)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=P(Cl)(Cl)Cl\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"MEHIYVMHIZTYKP-UHFFFAOYSA-N.XHXFXVLFKHQFAL-UHFFFAOYSA-N>>ZRSFHIBIWOXOIW-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"COc1cc(OC)cc(-c2c(-c3ccccc3F)nnc(Cl)c2-c2c(F)cc(F)cc2F)c1\", \"reactants\": [\"COc1cc(OC)cc(-c2c(-c3ccccc3F)n[nH]c(=O)c2-c2c(F)cc(F)cc2F)c1\", \"O=P(Cl)(Cl)Cl\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"COc1cc(OC)cc(-c2c(-c3ccccc3F)n[nH]c(=O)c2-c2c(F)cc(F)cc2F)c1\", \"results\": [{\"inchikey\": \"MEHIYVMHIZTYKP-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"COc1cc(OC)cc(-c2c(-c3ccccc3F)n[nH]c(=O)c2-c2c(F)cc(F)cc2F)c1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"O=P(Cl)(Cl)Cl\", \"results\": [{\"inchikey\": \"XHXFXVLFKHQFAL-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=P(Cl)(Cl)Cl\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"COc1cc(OC)c(Cl)c(-c2c(-c3ccccc3F)nnc(C)c2-c2c(F)cc(F)cc2F)c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COc1cc(OC)cc(-c2c(-c3ccccc3F)nnc(C)c2-c2c(F)cc(F)cc2F)c1\": \"precursor\", \"O=C1CCC(=O)N1Cl\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COc1cc(OC)cc(-c2c(-c3ccccc3F)nnc(C)c2-c2c(F)cc(F)cc2F)c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CB1OB(C)OB(C)O1\": \"precursor\", \"COc1cc(OC)cc(-c2c(-c3ccccc3F)nnc(Cl)c2-c2c(F)cc(F)cc2F)c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CB1OB(C)OB(C)O1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"COc1cc(OC)cc(-c2c(-c3ccccc3F)nnc(Cl)c2-c2c(F)cc(F)cc2F)c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COc1cc(OC)cc(-c2c(-c3ccccc3F)n[nH]c(=O)c2-c2c(F)cc(F)cc2F)c1\": \"precursor\", \"O=P(Cl)(Cl)Cl\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COc1cc(OC)cc(-c2c(-c3ccccc3F)n[nH]c(=O)c2-c2c(F)cc(F)cc2F)c1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=P(Cl)(Cl)Cl\", \"in_stock\": true, \"children\": []}]}]}]}]}, {\"type\": \"mol\", \"smiles\": \"O=C1CCC(=O)N1Cl\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_4_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"COc1cc(OC)c(Cl)c(-c2c(-c3ccccc3F)nnc(C)c2-c2c(F)cc(F)cc2F)c1","task_id":"retro_f80538350d52eef91c46","tool_calls":10,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":4}
{"exact_match":true,"id":"retro_f890bf55f8b6f939ad2a:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target Nc1cc(C(F)(F)F)ccc1N1CCOCC1 in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Nc1cc(C(F)(F)F)ccc1N1CCOCC1\", \"reactants\": [\"O=[N+]([O-])c1cc(C(F)(F)F)ccc1N1CCOCC1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"O=[N+]([O-])c1cc(C(F)(F)F)ccc1N1CCOCC1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"UNDXPKDBFOOQFC-UHFFFAOYSA-N>>CNVOJNRNRNAOOP-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"Nc1cc(C(F)(F)F)ccc1N1CCOCC1\", \"reactants\": [\"O=[N+]([O-])c1cc(C(F)(F)F)ccc1N1CCOCC1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"O=[N+]([O-])c1cc(C(F)(F)F)ccc1N1CCOCC1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"O=[N+]([O-])c1cc(C(F)(F)F)ccc1N1CCOCC1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"O=[N+]([O-])c1cc(C(F)(F)F)ccc1N1CCOCC1\", \"reactants\": [\"C1COCCN1\", \"O=[N+]([O-])c1cc(C(F)(F)F)ccc1F\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"C1COCCN1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=[N+]([O-])c1cc(C(F)(F)F)ccc1F\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"HLDFCCHSOZWKAA-UHFFFAOYSA-N.YNAVUWVOSKDBBP-UHFFFAOYSA-N>>UNDXPKDBFOOQFC-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"O=[N+]([O-])c1cc(C(F)(F)F)ccc1N1CCOCC1\", \"reactants\": [\"C1COCCN1\", \"O=[N+]([O-])c1cc(C(F)(F)F)ccc1F\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"C1COCCN1\", \"results\": [{\"inchikey\": \"YNAVUWVOSKDBBP-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"C1COCCN1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"O=[N+]([O-])c1cc(C(F)(F)F)ccc1F\", \"results\": [{\"inchikey\": \"HLDFCCHSOZWKAA-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=[N+]([O-])c1cc(C(F)(F)F)ccc1F\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"Nc1cc(C(F)(F)F)ccc1N1CCOCC1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"O=[N+]([O-])c1cc(C(F)(F)F)ccc1N1CCOCC1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"O=[N+]([O-])c1cc(C(F)(F)F)ccc1N1CCOCC1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"C1COCCN1\": \"precursor\", \"O=[N+]([O-])c1cc(C(F)(F)F)ccc1F\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"C1COCCN1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=[N+]([O-])c1cc(C(F)(F)F)ccc1F\", \"in_stock\": true, \"children\": []}]}]}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"Nc1cc(C(F)(F)F)ccc1N1CCOCC1","task_id":"retro_f890bf55f8b6f939ad2a","tool_calls":6,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_f957c91d9e435d724a62:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target O=C1NC(=O)C2(CC[C@@H](C(=O)O)C2)N1 in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"O=C1NC(=O)C2(CC[C@@H](C(=O)O)C2)N1\", \"reactants\": [\"O=C1NC(=O)C2(CC[C@@H](C(=O)OCc3ccccc3)C2)N1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"O=C1NC(=O)C2(CC[C@@H](C(=O)OCc3ccccc3)C2)N1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"VNUNNKHSNUOHPN-ZRKZCGFPSA-N>>IDLOULSKJDVSKX-WZIMWHJTSA-N\", \"model_turns_remaining\": 15, \"product\": \"O=C1NC(=O)C2(CC[C@@H](C(=O)O)C2)N1\", \"reactants\": [\"O=C1NC(=O)C2(CC[C@@H](C(=O)OCc3ccccc3)C2)N1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"O=C1NC(=O)C2(CC[C@@H](C(=O)OCc3ccccc3)C2)N1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"O=C1NC(=O)C2(CC[C@@H](C(=O)OCc3ccccc3)C2)N1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"O=C1NC(=O)C2(CC[C@@H](C(=O)OCc3ccccc3)C2)N1\", \"reactants\": [\"C#N\", \"N\", \"O=C(O)O\", \"O=C1CC[C@@H](C(=O)OCc2ccccc2)C1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"C#N\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"N\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"},{"function":{"arguments":"{\"query\": \"O=C(O)O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_3","type":"function"},{"function":{"arguments":"{\"query\": \"O=C1CC[C@@H](C(=O)OCc2ccccc2)C1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_4","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"BVKZGUZCCUSVTD-UHFFFAOYSA-N.LELOWRISYMNNSU-UHFFFAOYSA-N.QGZKDVFQNNGYKY-UHFFFAOYSA-N.UJDODTGHYKJEAA-LLVKDONJSA-N>>VNUNNKHSNUOHPN-ZRKZCGFPSA-N\", \"model_turns_remaining\": 14, \"product\": \"O=C1NC(=O)C2(CC[C@@H](C(=O)OCc3ccccc3)C2)N1\", \"reactants\": [\"C#N\", \"N\", \"O=C(O)O\", \"O=C1CC[C@@H](C(=O)OCc2ccccc2)C1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"C#N\", \"results\": [{\"inchikey\": \"LELOWRISYMNNSU-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"C#N\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"N\", \"results\": [{\"inchikey\": \"QGZKDVFQNNGYKY-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"N\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"O=C(O)O\", \"results\": [{\"inchikey\": \"BVKZGUZCCUSVTD-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=C(O)O\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_3"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"O=C1CC[C@@H](C(=O)OCc2ccccc2)C1\", \"results\": [{\"inchikey\": \"UJDODTGHYKJEAA-LLVKDONJSA-N\", \"similarity\": 1.0, \"smiles\": \"O=C1CC[C@@H](C(=O)OCc2ccccc2)C1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_4"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"O=C1NC(=O)C2(CC[C@@H](C(=O)O)C2)N1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"O=C1NC(=O)C2(CC[C@@H](C(=O)OCc3ccccc3)C2)N1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"O=C1NC(=O)C2(CC[C@@H](C(=O)OCc3ccccc3)C2)N1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"C#N\": \"precursor\", \"N\": \"precursor\", \"O=C(O)O\": \"precursor\", \"O=C1CC[C@@H](C(=O)OCc2ccccc2)C1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"C#N\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"N\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=C(O)O\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=C1CC[C@@H](C(=O)OCc2ccccc2)C1\", \"in_stock\": true, \"children\": []}]}]}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"O=C1NC(=O)C2(CC[C@@H](C(=O)O)C2)N1","task_id":"retro_f957c91d9e435d724a62","tool_calls":8,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_fb1ea9312b6c7583320a:reference-expert:a0","kind":"single_route","max_steps":3,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target COC(=O)Cc1cccc(NC(=O)c2ccc(-c3cccc(C(F)(F)F)c3)o2)c1 in at most 3 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COC(=O)Cc1cccc(NC(=O)c2ccc(-c3cccc(C(F)(F)F)c3)o2)c1\", \"reactants\": [\"COC(=O)Cc1cccc(NC(=O)c2ccc(Br)o2)c1\", \"OB(O)c1cccc(C(F)(F)F)c1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"COC(=O)Cc1cccc(NC(=O)c2ccc(Br)o2)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"OB(O)c1cccc(C(F)(F)F)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"QMQYEZQFXDLRKQ-UHFFFAOYSA-N.WOAORAPRPVIATR-UHFFFAOYSA-N>>BYBXTSMEOHXRPZ-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"COC(=O)Cc1cccc(NC(=O)c2ccc(-c3cccc(C(F)(F)F)c3)o2)c1\", \"reactants\": [\"COC(=O)Cc1cccc(NC(=O)c2ccc(Br)o2)c1\", \"OB(O)c1cccc(C(F)(F)F)c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"COC(=O)Cc1cccc(NC(=O)c2ccc(Br)o2)c1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"OB(O)c1cccc(C(F)(F)F)c1\", \"results\": [{\"inchikey\": \"WOAORAPRPVIATR-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"OB(O)c1cccc(C(F)(F)F)c1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"COC(=O)Cc1cccc(NC(=O)c2ccc(Br)o2)c1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COC(=O)Cc1cccc(NC(=O)c2ccc(Br)o2)c1\", \"reactants\": [\"COC(=O)Cc1cccc(N)c1\", \"O=C(O)c1ccc(Br)o1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"COC(=O)Cc1cccc(N)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=C(O)c1ccc(Br)o1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"BVKGNQRDVFGNIW-UHFFFAOYSA-N.YVTQHZDUDUCGRD-UHFFFAOYSA-N>>QMQYEZQFXDLRKQ-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"COC(=O)Cc1cccc(NC(=O)c2ccc(Br)o2)c1\", \"reactants\": [\"COC(=O)Cc1cccc(N)c1\", \"O=C(O)c1ccc(Br)o1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"COC(=O)Cc1cccc(N)c1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"O=C(O)c1ccc(Br)o1\", \"results\": [{\"inchikey\": \"YVTQHZDUDUCGRD-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=C(O)c1ccc(Br)o1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"COC(=O)Cc1cccc(N)c1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COC(=O)Cc1cccc(N)c1\", \"reactants\": [\"CO\", \"Nc1cccc(CC(=O)O)c1\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"CO\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"Nc1cccc(CC(=O)O)c1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"OKKJLVBELUTLKV-UHFFFAOYSA-N.XUSKZLBLGHBCLD-UHFFFAOYSA-N>>BVKGNQRDVFGNIW-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"COC(=O)Cc1cccc(N)c1\", \"reactants\": [\"CO\", \"Nc1cccc(CC(=O)O)c1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"CO\", \"results\": [{\"inchikey\": \"OKKJLVBELUTLKV-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CO\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"Nc1cccc(CC(=O)O)c1\", \"results\": [{\"inchikey\": \"XUSKZLBLGHBCLD-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Nc1cccc(CC(=O)O)c1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"COC(=O)Cc1cccc(NC(=O)c2ccc(-c3cccc(C(F)(F)F)c3)o2)c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COC(=O)Cc1cccc(NC(=O)c2ccc(Br)o2)c1\": \"precursor\", \"OB(O)c1cccc(C(F)(F)F)c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COC(=O)Cc1cccc(NC(=O)c2ccc(Br)o2)c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COC(=O)Cc1cccc(N)c1\": \"precursor\", \"O=C(O)c1ccc(Br)o1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COC(=O)Cc1cccc(N)c1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CO\": \"precursor\", \"Nc1cccc(CC(=O)O)c1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CO\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"Nc1cccc(CC(=O)O)c1\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"O=C(O)c1ccc(Br)o1\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"OB(O)c1cccc(C(F)(F)F)c1\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_4_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"COC(=O)Cc1cccc(NC(=O)c2ccc(-c3cccc(C(F)(F)F)c3)o2)c1","task_id":"retro_fb1ea9312b6c7583320a","tool_calls":10,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":4}
{"exact_match":true,"id":"retro_fcd26acaea89bd9909f6:reference-expert:a0","kind":"single_route","max_steps":3,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CC(C)[C@H](NC(=O)OC(C)(C)C)C(=O)Nc1cccnc1Nc1ccccc1 in at most 3 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(C)[C@H](NC(=O)OC(C)(C)C)C(=O)Nc1cccnc1Nc1ccccc1\", \"reactants\": [\"CC(C)[C@H](NC(=O)OC(C)(C)C)C(=O)O\", \"Nc1cccnc1Nc1ccccc1\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)[C@H](NC(=O)OC(C)(C)C)C(=O)O\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"Nc1cccnc1Nc1ccccc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"OLQLKEGDKARDNO-UHFFFAOYSA-N.SZXBQTSZISFIAO-ZETCQYMHSA-N>>UXJNFKZERPZUPY-KRWDZBQOSA-N\", \"model_turns_remaining\": 15, \"product\": \"CC(C)[C@H](NC(=O)OC(C)(C)C)C(=O)Nc1cccnc1Nc1ccccc1\", \"reactants\": [\"CC(C)[C@H](NC(=O)OC(C)(C)C)C(=O)O\", \"Nc1cccnc1Nc1ccccc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CC(C)[C@H](NC(=O)OC(C)(C)C)C(=O)O\", \"results\": [{\"inchikey\": \"SZXBQTSZISFIAO-ZETCQYMHSA-N\", \"similarity\": 1.0, \"smiles\": \"CC(C)[C@H](NC(=O)OC(C)(C)C)C(=O)O\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"Nc1cccnc1Nc1ccccc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"Nc1cccnc1Nc1ccccc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"Nc1cccnc1Nc1ccccc1\", \"reactants\": [\"O=[N+]([O-])c1cccnc1Nc1ccccc1\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"O=[N+]([O-])c1cccnc1Nc1ccccc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"PCCSYAWZVABITQ-UHFFFAOYSA-N>>OLQLKEGDKARDNO-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"Nc1cccnc1Nc1ccccc1\", \"reactants\": [\"O=[N+]([O-])c1cccnc1Nc1ccccc1\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"O=[N+]([O-])c1cccnc1Nc1ccccc1\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"O=[N+]([O-])c1cccnc1Nc1ccccc1 was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"O=[N+]([O-])c1cccnc1Nc1ccccc1\", \"reactants\": [\"Nc1ccccc1\", \"O=[N+]([O-])c1cccnc1Cl\"]}","name":"validate_disconnection"},"id":"call_3_0","type":"function"},{"function":{"arguments":"{\"query\": \"Nc1ccccc1\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_1","type":"function"},{"function":{"arguments":"{\"query\": \"O=[N+]([O-])c1cccnc1Cl\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_3_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"PAYRUJLWNCNPSJ-UHFFFAOYSA-N.UUOLETYDNTVQDY-UHFFFAOYSA-N>>PCCSYAWZVABITQ-UHFFFAOYSA-N\", \"model_turns_remaining\": 13, \"product\": \"O=[N+]([O-])c1cccnc1Nc1ccccc1\", \"reactants\": [\"Nc1ccccc1\", \"O=[N+]([O-])c1cccnc1Cl\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_3_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"Nc1ccccc1\", \"results\": [{\"inchikey\": \"PAYRUJLWNCNPSJ-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Nc1ccccc1\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 13, \"query\": \"O=[N+]([O-])c1cccnc1Cl\", \"results\": [{\"inchikey\": \"UUOLETYDNTVQDY-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"O=[N+]([O-])c1cccnc1Cl\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_3_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CC(C)[C@H](NC(=O)OC(C)(C)C)C(=O)Nc1cccnc1Nc1ccccc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)[C@H](NC(=O)OC(C)(C)C)C(=O)O\": \"precursor\", \"Nc1cccnc1Nc1ccccc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)[C@H](NC(=O)OC(C)(C)C)C(=O)O\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"Nc1cccnc1Nc1ccccc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"O=[N+]([O-])c1cccnc1Nc1ccccc1\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"O=[N+]([O-])c1cccnc1Nc1ccccc1\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"Nc1ccccc1\": \"precursor\", \"O=[N+]([O-])c1cccnc1Cl\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"Nc1ccccc1\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"O=[N+]([O-])c1cccnc1Cl\", \"in_stock\": true, \"children\": []}]}]}]}]}]}]}]}}","name":"emit_routes"},"id":"call_4_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"CC(C)[C@H](NC(=O)OC(C)(C)C)C(=O)Nc1cccnc1Nc1ccccc1","task_id":"retro_fcd26acaea89bd9909f6","tool_calls":9,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":4}
{"exact_match":true,"id":"retro_fe0dd3946558681f7274:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target CC(C)n1ncnc1-c1nc2c(s1)CCOc1cc(C3CN(S(C)(=O)=O)C3)ccc1-2 in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(C)n1ncnc1-c1nc2c(s1)CCOc1cc(C3CN(S(C)(=O)=O)C3)ccc1-2\", \"reactants\": [\"CC(C)n1ncnc1-c1nc2c(s1)CCOc1cc(C3CNC3)ccc1-2\", \"CS(=O)(=O)Cl\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)n1ncnc1-c1nc2c(s1)CCOc1cc(C3CNC3)ccc1-2\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"CS(=O)(=O)Cl\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"QARBMVPHQWIHKH-UHFFFAOYSA-N.UYNXWBXISXVSIW-UHFFFAOYSA-N>>VUZDGNCBQGICTG-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"CC(C)n1ncnc1-c1nc2c(s1)CCOc1cc(C3CN(S(C)(=O)=O)C3)ccc1-2\", \"reactants\": [\"CC(C)n1ncnc1-c1nc2c(s1)CCOc1cc(C3CNC3)ccc1-2\", \"CS(=O)(=O)Cl\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CC(C)n1ncnc1-c1nc2c(s1)CCOc1cc(C3CNC3)ccc1-2\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CS(=O)(=O)Cl\", \"results\": [{\"inchikey\": \"QARBMVPHQWIHKH-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CS(=O)(=O)Cl\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"CC(C)n1ncnc1-c1nc2c(s1)CCOc1cc(C3CNC3)ccc1-2 was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CC(C)n1ncnc1-c1nc2c(s1)CCOc1cc(C3CNC3)ccc1-2\", \"reactants\": [\"CC(C)n1ncnc1-c1nc2c(s1)CCOc1cc(C3CN(C(=O)OC(C)(C)C)C3)ccc1-2\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CC(C)n1ncnc1-c1nc2c(s1)CCOc1cc(C3CN(C(=O)OC(C)(C)C)C3)ccc1-2\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"UXLCVQIOSVIMIF-UHFFFAOYSA-N>>UYNXWBXISXVSIW-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"CC(C)n1ncnc1-c1nc2c(s1)CCOc1cc(C3CNC3)ccc1-2\", \"reactants\": [\"CC(C)n1ncnc1-c1nc2c(s1)CCOc1cc(C3CN(C(=O)OC(C)(C)C)C3)ccc1-2\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CC(C)n1ncnc1-c1nc2c(s1)CCOc1cc(C3CN(C(=O)OC(C)(C)C)C3)ccc1-2\", \"results\": [{\"inchikey\": \"UXLCVQIOSVIMIF-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CC(C)n1ncnc1-c1nc2c(s1)CCOc1cc(C3CN(C(=O)OC(C)(C)C)C3)ccc1-2\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"CC(C)n1ncnc1-c1nc2c(s1)CCOc1cc(C3CN(S(C)(=O)=O)C3)ccc1-2\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)n1ncnc1-c1nc2c(s1)CCOc1cc(C3CNC3)ccc1-2\": \"precursor\", \"CS(=O)(=O)Cl\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)n1ncnc1-c1nc2c(s1)CCOc1cc(C3CNC3)ccc1-2\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CC(C)n1ncnc1-c1nc2c(s1)CCOc1cc(C3CN(C(=O)OC(C)(C)C)C3)ccc1-2\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CC(C)n1ncnc1-c1nc2c(s1)CCOc1cc(C3CN(C(=O)OC(C)(C)C)C3)ccc1-2\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"CS(=O)(=O)Cl\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"CC(C)n1ncnc1-c1nc2c(s1)CCOc1cc(C3CN(S(C)(=O)=O)C3)ccc1-2","task_id":"retro_fe0dd3946558681f7274","tool_calls":6,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_ff0dc718ce2331409893:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target COc1c(OCCCN2CCOCC2)ccc(C2=NCCN2)c1N in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COc1c(OCCCN2CCOCC2)ccc(C2=NCCN2)c1N\", \"reactants\": [\"COc1c(OCCCN2CCOCC2)ccc(C#N)c1N\", \"NCCN\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"COc1c(OCCCN2CCOCC2)ccc(C#N)c1N\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"},{"function":{"arguments":"{\"query\": \"NCCN\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"PIICEJLVQHRZGT-UHFFFAOYSA-N.XRVBOUAQFSGOFT-UHFFFAOYSA-N>>ZROYKUBDBPTBSM-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"COc1c(OCCCN2CCOCC2)ccc(C2=NCCN2)c1N\", \"reactants\": [\"COc1c(OCCCN2CCOCC2)ccc(C#N)c1N\", \"NCCN\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"COc1c(OCCCN2CCOCC2)ccc(C#N)c1N\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"NCCN\", \"results\": [{\"inchikey\": \"PIICEJLVQHRZGT-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"NCCN\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_2"},{"content":"COc1c(OCCCN2CCOCC2)ccc(C#N)c1N was not found in stock, so it needs its own disconnection. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"COc1c(OCCCN2CCOCC2)ccc(C#N)c1N\", \"reactants\": [\"COc1c(OCCCN2CCOCC2)ccc(C#N)c1[N+](=O)[O-]\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"COc1c(OCCCN2CCOCC2)ccc(C#N)c1[N+](=O)[O-]\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"SSUVMPBASIJFQF-UHFFFAOYSA-N>>XRVBOUAQFSGOFT-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"COc1c(OCCCN2CCOCC2)ccc(C#N)c1N\", \"reactants\": [\"COc1c(OCCCN2CCOCC2)ccc(C#N)c1[N+](=O)[O-]\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"COc1c(OCCCN2CCOCC2)ccc(C#N)c1[N+](=O)[O-]\", \"results\": [{\"inchikey\": \"SSUVMPBASIJFQF-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"COc1c(OCCCN2CCOCC2)ccc(C#N)c1[N+](=O)[O-]\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"COc1c(OCCCN2CCOCC2)ccc(C2=NCCN2)c1N\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COc1c(OCCCN2CCOCC2)ccc(C#N)c1N\": \"precursor\", \"NCCN\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COc1c(OCCCN2CCOCC2)ccc(C#N)c1N\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"COc1c(OCCCN2CCOCC2)ccc(C#N)c1[N+](=O)[O-]\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"COc1c(OCCCN2CCOCC2)ccc(C#N)c1[N+](=O)[O-]\", \"in_stock\": true, \"children\": []}]}]}, {\"type\": \"mol\", \"smiles\": \"NCCN\", \"in_stock\": true, \"children\": []}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"COc1c(OCCCN2CCOCC2)ccc(C2=NCCN2)c1N","task_id":"retro_ff0dc718ce2331409893","tool_calls":6,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}
{"exact_match":true,"id":"retro_ff3dd6ceba68db7e50fe:reference-expert:a0","kind":"single_route","max_steps":2,"messages":[{"content":"You are a retrosynthesis planning agent. Use tools, validate cuts, confirm every stock leaf by exact lookup, and finish only with emit_routes. You have at most 16 model turns and must reserve the final turn for emit_routes even if the routes are incomplete. Pass emit_routes.submission as a JSON object, not as a string. Do not reveal chain-of-thought; put short evidence-based explanations in reaction metadata.","role":"system"},{"content":"Plan retrosyntheses for the target OCC(F)(F)c1ccccc1Cl in at most 2 step(s).\nReturn 1 to 1 molecule/reaction trees by calling emit_routes\nexactly once. The stock is not in this prompt: stock_retrieve is its only access\nsurface and a leaf may claim in_stock=true only after an exact lookup hit.\n\nEach tree must alternate molecule -> reaction -> molecule. A molecule has\n{\"type\":\"mol\",\"smiles\":\"...\",\"in_stock\":false,\"children\":[]}. A reaction has\ntype=\"reaction\", is_reaction=true, metadata (explanation, reaction_class,\nconfidence as a numeric value from 0 to 1, literature as a list, precursor_roles\nas an object), and molecule children. Distinct routes\nmust differ at the first cut. Every item in submission.routes must be the root\nmolecule object directly: never wrap it in route, root, tree, or route_id keys.\nValidate proposed cuts before emitting. Dataset\nsupport is not proof that a reaction will work experimentally.","role":"user"},{"content":"Start with the first disconnection of the target. Validate the cut and look up the new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"OCC(F)(F)c1ccccc1Cl\", \"reactants\": [\"CCOC(=O)C(F)(F)c1ccccc1Cl\"]}","name":"validate_disconnection"},"id":"call_1_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCOC(=O)C(F)(F)c1ccccc1Cl\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_1_1","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"RTPZPIXDNPGMRW-UHFFFAOYSA-N>>RBFOBWKGRFPAQH-UHFFFAOYSA-N\", \"model_turns_remaining\": 15, \"product\": \"OCC(F)(F)c1ccccc1Cl\", \"reactants\": [\"CCOC(=O)C(F)(F)c1ccccc1Cl\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_1_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 15, \"query\": \"CCOC(=O)C(F)(F)c1ccccc1Cl\", \"results\": [], \"returned\": 0, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_1_1"},{"content":"CCOC(=O)C(F)(F)c1ccccc1Cl was not found in stock, so it needs its own disconnection. Validate the cut and look up each new precursor in the stock.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"product_smiles\": \"CCOC(=O)C(F)(F)c1ccccc1Cl\", \"reactants\": [\"CCOC(=O)C(F)(F)Br\", \"Clc1ccccc1I\"]}","name":"validate_disconnection"},"id":"call_2_0","type":"function"},{"function":{"arguments":"{\"query\": \"CCOC(=O)C(F)(F)Br\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_1","type":"function"},{"function":{"arguments":"{\"query\": \"Clc1ccccc1I\", \"mode\": \"exact\", \"limit\": 1}","name":"stock_retrieve"},"id":"call_2_2","type":"function"}]},{"content":"{\"atom_conservation\": \"reference_mapping_partial\", \"checks\": {\"atom_inventory_conserved\": true, \"dataset_or_template_support\": true, \"no_product_leakage\": true, \"reaction_class_compatible\": true, \"valid_structures\": true}, \"errors\": [], \"matched_reaction_id\": \"IRSJDVYTJUCXRV-UHFFFAOYSA-N.MPEOPBCQHNWNFB-UHFFFAOYSA-N>>RTPZPIXDNPGMRW-UHFFFAOYSA-N\", \"model_turns_remaining\": 14, \"product\": \"CCOC(=O)C(F)(F)c1ccccc1Cl\", \"reactants\": [\"CCOC(=O)C(F)(F)Br\", \"Clc1ccccc1I\"], \"support\": \"dataset_exact\", \"valid\": true}","name":"validate_disconnection","role":"tool","tool_call_id":"call_2_0"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"CCOC(=O)C(F)(F)Br\", \"results\": [{\"inchikey\": \"IRSJDVYTJUCXRV-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"CCOC(=O)C(F)(F)Br\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_1"},{"content":"{\"mode\": \"exact\", \"model_turns_remaining\": 14, \"query\": \"Clc1ccccc1I\", \"results\": [{\"inchikey\": \"MPEOPBCQHNWNFB-UHFFFAOYSA-N\", \"similarity\": 1.0, \"smiles\": \"Clc1ccccc1I\"}], \"returned\": 1, \"truncated\": false}","name":"stock_retrieve","role":"tool","tool_call_id":"call_2_2"},{"content":"Every leaf was found by exact stock lookup. Emitting the route.","role":"assistant","tool_calls":[{"function":{"arguments":"{\"submission\": {\"routes\": [{\"type\": \"mol\", \"smiles\": \"OCC(F)(F)c1ccccc1Cl\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCOC(=O)C(F)(F)c1ccccc1Cl\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCOC(=O)C(F)(F)c1ccccc1Cl\", \"in_stock\": false, \"children\": [{\"type\": \"reaction\", \"is_reaction\": true, \"metadata\": {\"explanation\": \"Cut supported by validate_disconnection; precursors checked by exact stock lookup.\", \"reaction_class\": \"unclassified\", \"confidence\": 0.9, \"literature\": [], \"precursor_roles\": {\"CCOC(=O)C(F)(F)Br\": \"precursor\", \"Clc1ccccc1I\": \"precursor\"}}, \"children\": [{\"type\": \"mol\", \"smiles\": \"CCOC(=O)C(F)(F)Br\", \"in_stock\": true, \"children\": []}, {\"type\": \"mol\", \"smiles\": \"Clc1ccccc1I\", \"in_stock\": true, \"children\": []}]}]}]}]}]}}","name":"emit_routes"},"id":"call_3_0","type":"function"}]}],"provider":"reference","reward":1.0,"source":"reference-expert","target_smiles":"OCC(F)(F)c1ccccc1Cl","task_id":"retro_ff3dd6ceba68db7e50fe","tool_calls":6,"tools":"[{\"function\": {\"description\": \"Inspect a molecule with RDKit.\", \"name\": \"inspect_molecule\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}}, \"required\": [\"smiles\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Canonicalize a SMILES or query the frozen molecule cache.\", \"name\": \"pubchem_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"The only stock access. Search exact SMILES/InChIKey, class, SMARTS, or similarity; at most 20 results.\", \"name\": \"stock_retrieve\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"mode\": {\"default\": \"auto\", \"enum\": [\"auto\", \"exact\", \"inchikey\", \"class\", \"substructure\", \"similarity\"], \"type\": \"string\"}, \"query\": {\"type\": \"string\"}}, \"required\": [\"query\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find reaction analogues from training-visible records.\", \"name\": \"reaction_precedent_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 10, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Validate one proposed product-to-reactants cut against hidden evidence.\", \"name\": \"validate_disconnection\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Name the class of an agent-supplied supported cut.\", \"name\": \"reaction_class_lookup\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}}, \"required\": [\"product_smiles\", \"reactants\"], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Find frozen reported conditions for a cut or analogue.\", \"name\": \"reaction_conditions_search\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reactants\": {\"items\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"minItems\": 1, \"type\": \"array\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Search frozen citation metadata attached to training precedents.\", \"name\": \"search_literature\", \"parameters\": {\"additionalProperties\": false, \"properties\": {\"limit\": {\"default\": 5, \"maximum\": 20, \"minimum\": 1, \"type\": \"integer\"}, \"product_smiles\": {\"description\": \"A SMILES string.\", \"type\": \"string\"}, \"reaction_class\": {\"type\": \"string\"}}, \"required\": [], \"type\": \"object\"}}, \"type\": \"function\"}, {\"function\": {\"description\": \"Terminal call. Emit the required renderable molecule/reaction trees.\", \"name\": \"emit_routes\", \"parameters\": {\"$defs\": {\"metadata\": {\"additionalProperties\": true, \"description\": \"Evidence and confidence for this disconnection.\", \"properties\": {\"classification\": {\"type\": \"string\"}, \"conditions\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"confidence\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"explanation\": {\"type\": \"string\"}, \"literature\": {\"items\": {\"type\": \"object\"}, \"type\": \"array\"}, \"policy_probability\": {\"maximum\": 1, \"minimum\": 0, \"type\": \"number\"}, \"precursor_roles\": {\"additionalProperties\": {\"type\": \"string\"}, \"type\": \"object\"}, \"reaction_class\": {\"type\": \"string\"}, \"source\": {\"type\": \"string\"}}, \"required\": [\"explanation\", \"reaction_class\", \"confidence\", \"literature\", \"precursor_roles\"], \"type\": \"object\"}, \"mol\": {\"additionalProperties\": false, \"description\": \"A molecule node. Expanded nodes have one reaction child and in_stock=false; leaves have no children.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/reaction\"}, \"maxItems\": 1, \"type\": \"array\"}, \"in_stock\": {\"type\": \"boolean\"}, \"smiles\": {\"minLength\": 1, \"type\": \"string\"}, \"type\": {\"const\": \"mol\"}}, \"required\": [\"type\", \"smiles\", \"in_stock\", \"children\"], \"type\": \"object\"}, \"reaction\": {\"additionalProperties\": false, \"description\": \"A reaction whose children are its precursor molecules.\", \"properties\": {\"children\": {\"items\": {\"$ref\": \"#/$defs/mol\"}, \"minItems\": 1, \"type\": \"array\"}, \"is_reaction\": {\"const\": true}, \"metadata\": {\"$ref\": \"#/$defs/metadata\"}, \"type\": {\"const\": \"reaction\"}}, \"required\": [\"type\", \"is_reaction\", \"metadata\", \"children\"], \"type\": \"object\"}}, \"additionalProperties\": false, \"properties\": {\"submission\": {\"properties\": {\"routes\": {\"description\": \"Root molecule nodes directly; do not wrap them in route/root/tree objects.\", \"items\": {\"$ref\": \"#/$defs/mol\"}, \"maxItems\": 5, \"minItems\": 1, \"type\": \"array\"}, \"schema_version\": {\"type\": \"string\"}}, \"required\": [\"routes\"], \"type\": \"object\"}}, \"required\": [\"submission\"], \"type\": \"object\"}}, \"type\": \"function\"}]","toolset":"full","turns":3}