Publish n1-n5-single-step-v1

.gitattributes

@@ -58,3 +58,7 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
 # Video files - compressed
 *.mp4 filter=lfs diff=lfs merge=lfs -text
 *.webm filter=lfs diff=lfs merge=lfs -text
+releases/n1-n5-single-step-v1/payload/single_step/reaction_provenance.jsonl filter=lfs diff=lfs merge=lfs -text
+releases/n1-n5-single-step-v1/payload/single_step/reactions.smi filter=lfs diff=lfs merge=lfs -text
+releases/n1-n5-single-step-v1/payload/single_step/single_step.stereo.jsonl filter=lfs diff=lfs merge=lfs -text
+releases/n1-n5-single-step-v1/payload/splits/single_step/assignments.jsonl filter=lfs diff=lfs merge=lfs -text

releases/n1-n5-single-step-v1/payload/single_step/policy_product_normalization.jsonl

@@ -0,0 +1,22 @@
+{"canonical": "Cc1cc(ccc1)Cc2[nH]nc(N)c2", "original": "[nH]1c(N)cc(Cc2cc(C)ccc2)n1", "row_index": 2571, "rule_id": 3321}
+{"canonical": "C1(=O)C(=O)Nc2c(cc(c(c2[N+](=O)[O-])N)Cl)N1", "original": "c12c(c([N+]([O-])=O)c(c(Cl)c1)N)nc(O)c(n2)O", "row_index": 6753, "rule_id": 3564}
+{"canonical": "C1(C(Nc2c3[nH]cnc3c(Cl)cc2N1)=O)=O", "original": "c1c2c(c3nc[nH]c3c1Cl)nc(O)c(n2)O", "row_index": 7161, "rule_id": 6070}
+{"canonical": "C1CN(CCC1OC)CCCNC2=N[N+](c3c(N2[O-])cc4c(CCC4)c3)=O", "original": "C1CN(CCC1OC)CCCNC2=N[N+](=O)C=3C(=CC=4CCCC=4C=3)N2[O-]", "row_index": 13591, "rule_id": 6686}
+{"canonical": "C1CN(CCO1)CCCNC=2[N+](=O)c3cc4CCCOc4cc3N(N=2)[O-]", "original": "C1CN(CCO1)CCCNC2=NN(C=3C(=CC4=C(OCCC4)C=3)[N+]2=O)[O-]", "row_index": 14381, "rule_id": 6757}
+{"canonical": "CC(C)(C)OC(CC(CCCC1CCCCC1)C(ONC(=N)Cc2ccncc2)=O)=O", "original": "CC(C)(C)OC(=O)CC(CCCC1CCCCC1)C(ON=C(N)Cc2ccncc2)=O", "row_index": 18182, "rule_id": 4075}
+{"canonical": "CC(C)(C)OC(N(C)C(C(NO)=N)CCCC(O)C)=O", "original": "CC(C)(C)OC(N(C)C(C(=NO)N)CCCC(O)C)=O", "row_index": 21798, "rule_id": 609}
+{"canonical": "CC(C)(C)OC(NC(C)C(=N)NOC(=O)C)=O", "original": "CC(C)(C)OC(=O)NC(C(N)=NOC(C)=O)C", "row_index": 23314, "rule_id": 7533}
+{"canonical": "CC(C)(C)[Si](C)(C)OC(c1ccc(cc1)C(NO)=N)CN2CC(C(OCC)=O)CCC2", "original": "CC(C)(C)[Si](C)(C)OC(CN1CC(C(OCC)=O)CCC1)c2ccc(cc2)C(N)=NO", "row_index": 24711, "rule_id": 253}
+{"canonical": "c1ccccc1-c2nn(c3C4(CC(C(=O)C(C)C4CCc23)C=O)c5ccccc5)C", "original": "c1ccccc1C23CC(C(=O)C(C2CCc4c3n(nc4-c5ccccc5)C)C)=CO", "row_index": 31188, "rule_id": 4500}
+{"canonical": "c1cc(ccc1)C23C(CCc4c2nc(nc4OC)-c5ccccc5OC)C(C)C(C(C3)C=O)=O", "original": "c1ccccc1C23c4nc(-c5ccccc5OC)nc(c4CCC2C(C)C(C(C3)=CO)=O)OC", "row_index": 31189, "rule_id": 4500}
+{"canonical": "c1c(-c2cc(ccc2)OC)[nH]nc1N", "original": "[nH]1c(N)cc(-c2cc(ccc2)OC)n1", "row_index": 33551, "rule_id": 1941}
+{"canonical": "c1(Cc2[nH]nc(NC=C3c4ccccc4NC3=O)c2)cc(ccc1)C", "original": "c12C(=CNc3[nH]nc(c3)Cc4cc(ccc4)C)C(Nc1cccc2)=O", "row_index": 34523, "rule_id": 4604}
+{"canonical": "Cc1nc(Cl)c(c(c1Cl)C)C(NO)=N", "original": "Cc1nc(Cl)c(C(=NO)N)c(c1Cl)C", "row_index": 34649, "rule_id": 4610}
+{"canonical": "N=C(Cc1cccnc1)NO", "original": "ON=C(Cc1cccnc1)N", "row_index": 41314, "rule_id": 609}
+{"canonical": "c12c(cccc1)CN(C2)C(=O)Nc3ccc(cc3)C(NO)=N", "original": "c12c(cccc1)CN(C2)C(=O)Nc3ccc(cc3)C(=NO)N", "row_index": 47057, "rule_id": 253}
+{"canonical": "c1cc(ccc1C(=N)NO)-c2nc3c([nH]2)cccc3", "original": "c1cc(ccc1-c2nc3c(cccc3)[nH]2)C(N)=NO", "row_index": 47105, "rule_id": 253}
+{"canonical": "c1cc(ccc1C(NO)=N)C2CC3(C(N(C(N3)=O)C)=O)CC2", "original": "c1cc(ccc1C(=NO)N)C2CC3(C(N(C(N3)=O)C)=O)CC2", "row_index": 47107, "rule_id": 253}
+{"canonical": "c1ccccc1C(F)(F)C(NO)=N", "original": "FC(F)(C(N)=NO)c1ccccc1", "row_index": 47172, "rule_id": 609}
+{"canonical": "c12c(cc3CCCc3c1)[N+](=O)N=C(NCCN(C)CCCOC)N2[O-]", "original": "C(N(CCN=C1N[N+](=O)C=2C(=CC=3CCCC=3C=2)N1[O-])C)CCOC", "row_index": 47324, "rule_id": 10315}
+{"canonical": "N(c1cc([nH]n1)-c2cc(ccc2)OC)C=C3c4ccccc4NC3=O", "original": "c1(cc([nH]n1)NC=C2c3ccccc3NC2=O)-c4cc(ccc4)OC", "row_index": 50097, "rule_id": 4604}
+{"canonical": "c1cc(ccc1-c2ccccc2S(C)=O)CC(c3ncc(CC(C)(C)CC)[nH]3)(O)C", "original": "c1cc(ccc1-c2ccccc2S(C)=O)CC(O)(C)c3nc(c[nH]3)CC(C)(C)CC", "row_index": 53242, "rule_id": 5050}

releases/n1-n5-single-step-v1/payload/single_step/preparation.json

@@ -0,0 +1,53 @@
+{
+  "config": "9dc216f8693e444a93a70339faed2ae899595dc7d43948a5753d476124568cca",
+  "deduplication": "stereo-free reactant/product multisets; reagents excluded",
+  "duplicates": 13804,
+  "excluded_reaction_count": 0,
+  "inputs": [
+    {
+      "path": "../route-inspector/data/clean/n1_routes.json",
+      "sha256": "c1e396cd71228e3ab113412428571d223ef943835c3793f91b994b3341359439"
+    },
+    {
+      "path": "../route-inspector/data/clean/n5_routes.json",
+      "sha256": "5a27be2e0199f2bacd66556122f50906a24e27946bb30b1d9472d55d725e71af"
+    },
+    {
+      "path": "configs/rule_extraction.yaml",
+      "sha256": "9dc216f8693e444a93a70339faed2ae899595dc7d43948a5753d476124568cca"
+    }
+  ],
+  "kind": "single-step",
+  "outputs": {
+    "policy_product_normalization.jsonl": "af78b3ad35018a52ddc916f0bd05f7ed77e37b8853a59a25581ab0ea94d2a977",
+    "reaction_provenance.jsonl": "be1b5196a03829773fd1faa5687d6ce14cbf72d19087deb9586119e53458175e",
+    "reactions.smi": "e8ffb9ba9837a6e19f269fefe6bb1b5c2c4b3b097fed783ebd505897572d1cbd",
+    "single_step.audit.tsv": "7e768b6bcef28f43dbf69ef0075aba95e7d1abc47650bd379681fc460b257435",
+    "single_step.errors.tsv": "0d185fc10c2c9b91d1f2bf8fb8c98ac2cc1f6a102aed967599ab45cadec5aa6c",
+    "single_step.manifest.json": "4c3d152ee67763ef3219bd9a6fecd1b2fc313810d6a46eb70823b6decb93d572",
+    "single_step.stereo.jsonl": "a2e8df9a9a7cb0ac15cc8b6a7486d4825d65005d679464799c71c5554a4e79ab",
+    "single_step.tsv": "479d34a98d8e670f889f6ee29405a802d432a97bd1a4280d0b9bdd98642d3ac5",
+    "single_step_policy_data.native.tsv": "8e5c637f61ec5a9312056c5d54a86ffd0d1dd5994cdfd29b4cf712c5a9b38c55",
+    "single_step_policy_data.tsv": "24fe9bb31584e10c66f490788c42d43244d5284c4b6434e368b7fc9f5c99a805"
+  },
+  "policy_product_normalization": {
+    "changed_rows": 22,
+    "native_rows": "single_step_policy_data.native.tsv",
+    "policy": "retrocomposite.molecule_key; same as stock and grouped splitting",
+    "rows": 57381
+  },
+  "policy_rows": 57381,
+  "reaction_occurrences": 71185,
+  "retained_reaction_count": 57381,
+  "rule_count": 11209,
+  "schema": "retrocomposite-preparation/1",
+  "software": {
+    "SynPlanner": "1.8.0",
+    "chython-synplan": "1.108",
+    "retrocomposite": "0.1.0",
+    "route-inspector": "3.0.0.dev0"
+  },
+  "stereo": "ignored",
+  "unique_reactions": 57381,
+  "workers": 1
+}

releases/n1-n5-single-step-v1/payload/single_step/reaction_provenance.jsonl

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:be1b5196a03829773fd1faa5687d6ce14cbf72d19087deb9586119e53458175e
+size 32200325

releases/n1-n5-single-step-v1/payload/single_step/reactions.smi

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:e8ffb9ba9837a6e19f269fefe6bb1b5c2c4b3b097fed783ebd505897572d1cbd
+size 20381108

releases/n1-n5-single-step-v1/payload/single_step/single_step.audit.tsv

@@ -0,0 +1 @@
+# reaction_index	original_smiles	source_info	stage	error_type	error_message

releases/n1-n5-single-step-v1/payload/single_step/single_step.errors.tsv

@@ -0,0 +1 @@
+# original_smiles	source_info	stage	error_type	error_message

releases/n1-n5-single-step-v1/payload/single_step/single_step.manifest.json

@@ -0,0 +1,11 @@
+{
+  "chython_version": "1.108",
+  "input_sha256": "e8ffb9ba9837a6e19f269fefe6bb1b5c2c4b3b097fed783ebd505897572d1cbd",
+  "policy_compatibility": "requires the exact ordered rule vocabulary used for training",
+  "preserve_stereo": false,
+  "rule_count": 11209,
+  "rules_sha256": "479d34a98d8e670f889f6ee29405a802d432a97bd1a4280d0b9bdd98642d3ac5",
+  "schema": "synplan-rules/2",
+  "source_stereo_file": "single_step.stereo.jsonl",
+  "stereo_schema": 1
+}

releases/n1-n5-single-step-v1/payload/single_step/single_step.stereo.jsonl

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:a2e8df9a9a7cb0ac15cc8b6a7486d4825d65005d679464799c71c5554a4e79ab
+size 34339740

releases/n1-n5-single-step-v1/payload/splits/single_step/assets/single_step.manifest.json

@@ -0,0 +1,11 @@
+{
+  "chython_version": "1.108",
+  "input_sha256": "e8ffb9ba9837a6e19f269fefe6bb1b5c2c4b3b097fed783ebd505897572d1cbd",
+  "policy_compatibility": "requires the exact ordered rule vocabulary used for training",
+  "preserve_stereo": false,
+  "rule_count": 11209,
+  "rules_sha256": "479d34a98d8e670f889f6ee29405a802d432a97bd1a4280d0b9bdd98642d3ac5",
+  "schema": "synplan-rules/2",
+  "source_stereo_file": "single_step.stereo.jsonl",
+  "stereo_schema": 1
+}

releases/n1-n5-single-step-v1/payload/splits/single_step/assignments.jsonl

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:3ff9cb8e97a985e805a1a583dbc586f020ce817483c4400617a0236031f9ee83
+size 18351243

releases/n1-n5-single-step-v1/payload/splits/single_step/preparation.json

@@ -0,0 +1,35 @@
+{
+  "implementation": "d28dd250d6b2f7c83d4091b802d71338a54cc7d84ee6ec52ac9c94462a8dd880",
+  "inputs": [
+    {
+      "path": "/Users/almazgil/Developer/projects/retrocomposite/data/single_step/preparation.json",
+      "sha256": "4a86c1e61ab7bf421acba34847442b0c5ef2bb3136bcdf288ae91d879ead559d"
+    },
+    {
+      "path": "/Users/almazgil/Developer/projects/retrocomposite/data/single_step/single_step.tsv",
+      "sha256": "479d34a98d8e670f889f6ee29405a802d432a97bd1a4280d0b9bdd98642d3ac5"
+    },
+    {
+      "path": "/Users/almazgil/Developer/projects/retrocomposite/data/single_step/single_step_policy_data.tsv",
+      "sha256": "24fe9bb31584e10c66f490788c42d43244d5284c4b6434e368b7fc9f5c99a805"
+    }
+  ],
+  "kind": "grouped-split",
+  "outputs": {
+    "assets/single_step.manifest.json": "4c3d152ee67763ef3219bd9a6fecd1b2fc313810d6a46eb70823b6decb93d572",
+    "assets/single_step.tsv": "479d34a98d8e670f889f6ee29405a802d432a97bd1a4280d0b9bdd98642d3ac5",
+    "assets/single_step_policy_data.tsv": "24fe9bb31584e10c66f490788c42d43244d5284c4b6434e368b7fc9f5c99a805",
+    "assignments.jsonl": "3ff9cb8e97a985e805a1a583dbc586f020ce817483c4400617a0236031f9ee83",
+    "split.json": "4c92de820de291abdcf4593760920f522d1a6ea12522adb142dbdacc40a6c70d",
+    "train.tsv": "7450dcc1eb9cdae6d1414f6a53c6fae3f1cd659672179e1af02849cb2f458f72",
+    "validation.tsv": "2267a9d8be9186b5ed8d4a14027d939422b1f9b469b1b919c30ddbaa56b57741"
+  },
+  "schema": "retrocomposite-preparation/1",
+  "software": {
+    "SynPlanner": "1.8.0",
+    "chython-synplan": "1.108",
+    "retrocomposite": "0.1.0",
+    "route-inspector": "3.0.0.dev0"
+  },
+  "stereo": "ignored"
+}

releases/n1-n5-single-step-v1/payload/stock/preparation.json

@@ -0,0 +1,39 @@
+{
+  "inputs": [
+    {
+      "path": "../route-inspector/data/clean/n1_routes.json",
+      "sha256": "c1e396cd71228e3ab113412428571d223ef943835c3793f91b994b3341359439"
+    },
+    {
+      "path": "../route-inspector/data/clean/n5_routes.json",
+      "sha256": "5a27be2e0199f2bacd66556122f50906a24e27946bb30b1d9472d55d725e71af"
+    }
+  ],
+  "kind": "leaf-stock",
+  "outputs": {
+    "leaves.jsonl": "6df9fff75641f3a45d717e7c570aed53c202e249e7749d53a9f012d2ba0f4873",
+    "n1.smi": "13d01086e9388eed7ad082f586f74d78e88fa57a242b68e2f4248a96798b459a",
+    "n1_targets.smi": "38b13cd678b3e6bd1c1154ba294dbda23a7c655504e7a5bc2e2155a574146596",
+    "n5.smi": "b3099bec1799a9980bb4ea8463ea8a8f2facac92ccfdc8531308c948f26eb012",
+    "n5_targets.smi": "ebe8865e8290a850e06c3d10c160f600493de8b5295d80beae8b2f8d1113d781",
+    "union.smi": "877608f2cd05e3a2a0f0c027579a2c0b259ea50c4d8d25753ff9f2f70b596ae3"
+  },
+  "routes": {
+    "n1": 10000,
+    "n5": 10000
+  },
+  "schema": "retrocomposite-preparation/1",
+  "software": {
+    "SynPlanner": "1.8.0",
+    "chython-synplan": "1.108",
+    "retrocomposite": "0.1.0",
+    "route-inspector": "3.0.0.dev0"
+  },
+  "stereo": "ignored",
+  "stock_counts": {
+    "n1": 13308,
+    "n5": 13195
+  },
+  "terminal_policy": "molecule node without children; ignore stored stock flags",
+  "union_count": 20087
+}

releases/n1-n5-single-step-v1/release.json

@@ -0,0 +1,34 @@
+{
+  "dataset": null,
+  "files": {
+    "single_step/policy_product_normalization.jsonl": "af78b3ad35018a52ddc916f0bd05f7ed77e37b8853a59a25581ab0ea94d2a977",
+    "single_step/preparation.json": "4a86c1e61ab7bf421acba34847442b0c5ef2bb3136bcdf288ae91d879ead559d",
+    "single_step/reaction_provenance.jsonl": "be1b5196a03829773fd1faa5687d6ce14cbf72d19087deb9586119e53458175e",
+    "single_step/reactions.smi": "e8ffb9ba9837a6e19f269fefe6bb1b5c2c4b3b097fed783ebd505897572d1cbd",
+    "single_step/single_step.audit.tsv": "7e768b6bcef28f43dbf69ef0075aba95e7d1abc47650bd379681fc460b257435",
+    "single_step/single_step.errors.tsv": "0d185fc10c2c9b91d1f2bf8fb8c98ac2cc1f6a102aed967599ab45cadec5aa6c",
+    "single_step/single_step.manifest.json": "4c3d152ee67763ef3219bd9a6fecd1b2fc313810d6a46eb70823b6decb93d572",
+    "single_step/single_step.stereo.jsonl": "a2e8df9a9a7cb0ac15cc8b6a7486d4825d65005d679464799c71c5554a4e79ab",
+    "single_step/single_step.tsv": "479d34a98d8e670f889f6ee29405a802d432a97bd1a4280d0b9bdd98642d3ac5",
+    "single_step/single_step_policy_data.native.tsv": "8e5c637f61ec5a9312056c5d54a86ffd0d1dd5994cdfd29b4cf712c5a9b38c55",
+    "single_step/single_step_policy_data.tsv": "24fe9bb31584e10c66f490788c42d43244d5284c4b6434e368b7fc9f5c99a805",
+    "splits/single_step/assets/single_step.manifest.json": "4c3d152ee67763ef3219bd9a6fecd1b2fc313810d6a46eb70823b6decb93d572",
+    "splits/single_step/assets/single_step.tsv": "479d34a98d8e670f889f6ee29405a802d432a97bd1a4280d0b9bdd98642d3ac5",
+    "splits/single_step/assets/single_step_policy_data.tsv": "24fe9bb31584e10c66f490788c42d43244d5284c4b6434e368b7fc9f5c99a805",
+    "splits/single_step/assignments.jsonl": "3ff9cb8e97a985e805a1a583dbc586f020ce817483c4400617a0236031f9ee83",
+    "splits/single_step/preparation.json": "1294e8683a250814dd94b4169bffd8bb2270d0c0c405424186a0afe1149ee23a",
+    "splits/single_step/split.json": "4c92de820de291abdcf4593760920f522d1a6ea12522adb142dbdacc40a6c70d",
+    "splits/single_step/train.tsv": "7450dcc1eb9cdae6d1414f6a53c6fae3f1cd659672179e1af02849cb2f458f72",
+    "splits/single_step/validation.tsv": "2267a9d8be9186b5ed8d4a14027d939422b1f9b469b1b919c30ddbaa56b57741",
+    "stock/leaves.jsonl": "6df9fff75641f3a45d717e7c570aed53c202e249e7749d53a9f012d2ba0f4873",
+    "stock/n1.smi": "13d01086e9388eed7ad082f586f74d78e88fa57a242b68e2f4248a96798b459a",
+    "stock/n1_targets.smi": "38b13cd678b3e6bd1c1154ba294dbda23a7c655504e7a5bc2e2155a574146596",
+    "stock/n5.smi": "b3099bec1799a9980bb4ea8463ea8a8f2facac92ccfdc8531308c948f26eb012",
+    "stock/n5_targets.smi": "ebe8865e8290a850e06c3d10c160f600493de8b5295d80beae8b2f8d1113d781",
+    "stock/preparation.json": "ac8bff58717d523c8e62d3f35dbd54bb430789e184ed272847af529d0c921173",
+    "stock/union.smi": "877608f2cd05e3a2a0f0c027579a2c0b259ea50c4d8d25753ff9f2f70b596ae3"
+  },
+  "kind": "dataset",
+  "release": "n1-n5-single-step-v1",
+  "schema": "retrocomposite-hub-release/1"
+}