diff --git a/.gitattributes b/.gitattributes index 5c674fb6a3aea3ff4a417c9d74e7c261c501a90e..bd02da05819412aa03bfc0cc0c68f39ca5e98c7d 100644 --- a/.gitattributes +++ b/.gitattributes @@ -204,3 +204,5 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text .venv_haddock/lib/python3.12/site-packages/scipy/stats/_stats_pythran.cpython-312-darwin.so filter=lfs diff=lfs merge=lfs -text .venv_haddock/lib/python3.12/site-packages/scipy/stats/_unuran/unuran_wrapper.cpython-312-darwin.so filter=lfs diff=lfs merge=lfs -text .venv_haddock/lib/python3.12/site-packages/yaml/_yaml.cpython-312-darwin.so filter=lfs diff=lfs merge=lfs -text +data/datasets/rdock_3PTB_50k_pubchem_local/ligands/all_ligands.sdf filter=lfs diff=lfs merge=lfs -text +data/datasets/rdock_3PTB_50k_pubchem_local/ligands/ligand_metadata.csv filter=lfs diff=lfs merge=lfs -text diff --git a/configs/._known_good_pdb_complexes.yaml b/configs/._known_good_pdb_complexes.yaml new file mode 100644 index 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b/configs/._ppi_sanity_check.yaml differ diff --git a/configs/._reference_free_triage_bandit_defaults.yaml b/configs/._reference_free_triage_bandit_defaults.yaml new file mode 100644 index 0000000000000000000000000000000000000000..ee537d225f1b1eed0d0f4ed0b171fdc63ca71d82 Binary files /dev/null and b/configs/._reference_free_triage_bandit_defaults.yaml differ diff --git a/configs/._smoke_test.yaml b/configs/._smoke_test.yaml new file mode 100644 index 0000000000000000000000000000000000000000..ee537d225f1b1eed0d0f4ed0b171fdc63ca71d82 Binary files /dev/null and b/configs/._smoke_test.yaml differ diff --git a/configs/_tmp_smoke_check.yaml b/configs/_tmp_smoke_check.yaml new file mode 100644 index 0000000000000000000000000000000000000000..08f982e5fbc835b22a0f3497b36e7a1c4d5bc1dd --- /dev/null +++ b/configs/_tmp_smoke_check.yaml @@ -0,0 +1,27 @@ +backend: + allow_mock_if_missing: true + n_runs: 3 + type: rdock +clustering: + butina_cutoff: 0.4 + n_hyperclusters: 2 +data: + benchmark_metadata: data/benchmarks/smoke_metadata.json + ligand_table: data/ligands/smoke_ligands.csv + target_id: smoke_mdm2 + target_path: data/targets/smoke_target.pdb +encoding: + fingerprint_bits: 512 + fingerprint_radius: 2 + generate_3d: false +run: + max_batches: 2 + name: smoke_test + output_dir: results/smoke_check + random_seed: 7 +scheduler: + batch_size: 4 + conservative_deprioritize: false + init_coverage_fraction: 0.5 +scoring: + interface_weight: 1.0 diff --git a/configs/benchmarks/._three_pdb_targets.yaml b/configs/benchmarks/._three_pdb_targets.yaml new file mode 100644 index 0000000000000000000000000000000000000000..ee537d225f1b1eed0d0f4ed0b171fdc63ca71d82 Binary files /dev/null and b/configs/benchmarks/._three_pdb_targets.yaml differ diff --git a/configs/benchmarks/three_pdb_targets.yaml b/configs/benchmarks/three_pdb_targets.yaml new file mode 100644 index 0000000000000000000000000000000000000000..09e096de3754ebafd1c07a2eb29b4ff43a221dce --- /dev/null +++ b/configs/benchmarks/three_pdb_targets.yaml @@ -0,0 +1,31 @@ +{ + "targets": [ + { + "target_id": "mdm2_4hg7", + "pdb_id": "4HG7", + "pdb_path": "data/targets/prelim_set_mdm2_4hg7/mdm2_4hg7.pdb", + "receptor_chain": "A", + "reference_ligand_resname": "NUT", + "reference_ligand_chain": "A", + "ligands_csv": "data/ligands/prelim_set_mdm2_4hg7/shared_library_dedup.csv" + }, + { + "target_id": "egfr_4wkq", + "pdb_id": "4WKQ", + "pdb_path": "data/targets/prelim_set_egfr_4wkq/egfr_4wkq.pdb", + "receptor_chain": "A", + "reference_ligand_resname": "IRE", + "reference_ligand_chain": "A", + "ligands_csv": "data/ligands/prelim_set_egfr_4wkq/shared_library_dedup.csv" + }, + { + "target_id": "abl1_1iep", + "pdb_id": "1IEP", + "pdb_path": "data/targets/prelim_set_abl1_1iep/abl1_1iep.pdb", + "receptor_chain": "A", + "reference_ligand_resname": "STI", + "reference_ligand_chain": "A", + "ligands_csv": "data/ligands/prelim_set_abl1_1iep/shared_library_dedup.csv" + } + ] +} diff --git a/configs/budget_efficiency_benchmark.yaml b/configs/budget_efficiency_benchmark.yaml new file mode 100644 index 0000000000000000000000000000000000000000..11a3981962992ccf032f88da8f031ae5dd0e66c1 --- /dev/null +++ b/configs/budget_efficiency_benchmark.yaml @@ -0,0 +1,140 @@ +run: + name: budget_efficiency_benchmark + output_dir: results/budget_efficiency_benchmark + random_seed: 20260416 + batch_size: 64 + allow_resume: true + max_batches: 500 + budgets: [100, 500, 2500, 5000, 10000] + time_importance_values: [0.0, 0.5, 1.0] + +backend: + type: rdock + require_real_backend: true + n_runs: 1 + mapper_radius: 6.0 + command_timeout_seconds: 240 + parallel_jobs: auto-minus-4 + allow_skip_failed_ligands: true + max_failed_ligands: 200 + +encoding: + fingerprint_radius: 2 + fingerprint_bits: 1024 + generate_3d: false + +feature_extraction: + compute_partial_charges: false + compute_sasa: false + +clustering: + butina_cutoff: 0.35 + n_hyperclusters: 40 + +scheduler: + init_coverage_fraction: 0.35 + conservative_deprioritize: true + surrogate: + prefer_xgboost: true + n_estimators: 180 + min_train_samples: 20 + max_depth_small: 3 + max_depth_large: 6 + model_weight_schedule: + sample_knots: [20, 50, 100, 200, 500] + weight_knots: [0.1, 0.3, 0.5, 0.7, 0.9] + max_weight: 0.9 + min_weight: 0.05 + instability_threshold: 2.0 + instability_decay: 0.25 + +early_stop: + min_evaluated: 600 + patience_rounds: 8 + min_model_weight: 0.35 + quantile: 0.15 + uncertainty_weight: 0.2 + min_improvement: 0.02 + exploration_margin: 0.45 + exploitation_margin: 0.1 + reference_evaluations: 10000 + +policies: + adaptive_hard_stop: { enabled: true } + adaptive_soft_stop: + enabled: true + soft_recovery_batches: 16 + soft_threshold_relax: 0.35 + soft_model_weight_cap: 0.45 + soft_exploration_boost: 0.25 + max_soft_recoveries: 1 + adaptive_no_stop: { enabled: true } + adaptive_cluster_bootstrap: + enabled: true + cluster_bootstrap_rounds: 24 + adaptive_soft_stop_cluster_floor: + enabled: true + cluster_bootstrap_rounds: 20 + min_cluster_coverage: 0.60 + min_hypercluster_coverage: 0.55 + soft_recovery_batches: 20 + soft_threshold_relax: 0.40 + soft_model_weight_cap: 0.40 + soft_exploration_boost: 0.30 + pre_floor_model_weight_cap: 0.35 + max_soft_recoveries: 2 + +matrix: + naive_random_seeds: [11, 22, 33] + cluster_naive_seeds: [101, 202, 303] + +disk_guard: + min_free_gb: 10.0 + projected_output_gb: 3.0 + keep_raw_batches: 6 + +dataset_A: + name: dataset_A + protein_name: EGFR + target_id: egfr_budget + docking_reference_pdb: "4WKQ" + docking_target_path: data/targets/budget_efficiency_benchmark_A/egfr_4wkq.pdb + reference_id: ref_gefitinib + pdb_id: "4WKQ" + ligand_comp_id: "IRE" + reference_name: Gefitinib + reference_smiles: "COC1=C(C=C2C(=C1)N=CN=C2NC3=CC(=C(C=C3)F)Cl)OCCCN4CCOCC4" + benchmark_dataset: + output_dir: data/ligands/budget_efficiency_benchmark_A + target_size: 10000 + shuffle_seed: 334455 + reuse_existing: true + min_similarity_keep: 0.00 + pubchem_max_records: 12000 + pubchem_thresholds: [80] + chembl_target_id: CHEMBL203 + chembl_max_rows: 0 + allow_generated_fallback: true + +dataset_B: + name: dataset_B + protein_name: ABL1 + target_id: abl1_budget + docking_reference_pdb: "1IEP" + docking_target_path: data/targets/budget_efficiency_benchmark_B/abl1_1iep.pdb + reference_id: ref_imatinib + pdb_id: "1IEP" + ligand_comp_id: "STI" + reference_name: Imatinib + reference_smiles: "CC1=C(C=C(C=C1)NC(=O)C2=CC=C(C=C2)CN3CCN(CC3)C)NC4=NC=CC(=N4)C5=CN=CC=C5" + benchmark_dataset: + output_dir: data/ligands/budget_efficiency_benchmark_B + target_size: 10000 + shuffle_seed: 556677 + reuse_existing: true + min_similarity_keep: 0.00 + pubchem_max_records: 12000 + pubchem_thresholds: [80] + chembl_target_id: CHEMBL1862 + chembl_max_rows: 0 + allow_generated_fallback: true diff --git a/configs/default.yaml b/configs/default.yaml new file mode 100644 index 0000000000000000000000000000000000000000..24e5cb1a546e408b0d4db969ec19a791fa5f305b --- /dev/null +++ b/configs/default.yaml @@ -0,0 +1,38 @@ +run: + name: default + output_dir: results/demo_run + max_batches: 5 + random_seed: 42 + +data: + target_id: mdm2 + target_path: data/targets/mdm2_1ycr_excerpt.pdb + ligand_table: data/ligands/mdm2_ligands_demo.csv + benchmark_metadata: data/benchmarks/mdm2_demo_metadata.json + +backend: + type: rdock + allow_mock_if_missing: false + require_real_backend: true + n_runs: 5 + mapper_radius: 6.0 + pocket_mode: reference_complex_pocket + pocket_reference_ligand_id: "" + pocket_relaxation_margin: 0.0 + +encoding: + fingerprint_radius: 2 + fingerprint_bits: 1024 + generate_3d: true + +clustering: + butina_cutoff: 0.35 + n_hyperclusters: 4 + +scheduler: + batch_size: 8 + init_coverage_fraction: 0.25 + conservative_deprioritize: true + +scoring: + interface_weight: 1.0 diff --git a/configs/demo_mdm2.yaml b/configs/demo_mdm2.yaml new file mode 100644 index 0000000000000000000000000000000000000000..1422391b0ff2fc03d809b1013ceed26f9d94fdb4 --- /dev/null +++ b/configs/demo_mdm2.yaml @@ -0,0 +1,35 @@ +run: + name: demo_mdm2 + output_dir: results/demo_run + max_batches: 6 + random_seed: 42 + +data: + target_id: mdm2 + target_path: data/targets/mdm2_1ycr_excerpt.pdb + ligand_table: data/ligands/mdm2_ligands_demo.csv + benchmark_metadata: data/benchmarks/mdm2_demo_metadata.json + +backend: + type: rdock + allow_mock_if_missing: false + require_real_backend: true + n_runs: 5 + mapper_radius: 6.0 + +encoding: + fingerprint_radius: 2 + fingerprint_bits: 1024 + generate_3d: true + +clustering: + butina_cutoff: 0.35 + n_hyperclusters: 4 + +scheduler: + batch_size: 8 + init_coverage_fraction: 0.25 + conservative_deprioritize: true + +scoring: + interface_weight: 1.0 diff --git a/configs/discovery_benchmark.yaml b/configs/discovery_benchmark.yaml new file mode 100644 index 0000000000000000000000000000000000000000..6536be28740df1dfefecc10b494ab06419bc69c1 --- /dev/null +++ b/configs/discovery_benchmark.yaml @@ -0,0 +1,100 @@ +run: + name: discovery_benchmark + output_dir: results/discovery_benchmark + random_seed: 20260415 + batch_size: 32 + adaptive_budget: 50000 + baseline_budget: 50000 + max_batches: 2000 + allow_resume: true + enable_adaptive_early_stop: true + +target: + protein_name: MDM2 + target_id: mdm2_discovery + docking_reference_pdb: "4HG7" + docking_target_path: data/targets/discovery_benchmark/mdm2_4hg7.pdb + +reference: + reference_id: ref_nutlin3a + pdb_id: "4HG7" + ligand_comp_id: "NUT" + +benchmark_dataset: + output_dir: data/ligands/discovery_benchmark + target_size: 50000 + shuffle_seed: 424242 + reuse_existing: true + min_similarity_keep: 0.08 + pubchem_max_records: 120000 + pubchem_thresholds: [95, 92, 90, 88, 85, 82, 80, 77, 75, 72, 70, 67, 65, 62, 60, 57, 55, 52, 50, 47, 45, 42, 40, 37, 35, 32, 30] + chembl_target_id: CHEMBL5023 + chembl_max_rows: 120000 + allow_generated_fallback: true + +backend: + type: rdock + require_real_backend: true + n_runs: 5 + mapper_radius: 6.0 + command_timeout_seconds: 300 + parallel_jobs: auto-minus-4 + +encoding: + fingerprint_radius: 2 + fingerprint_bits: 1024 + generate_3d: false + +feature_extraction: + compute_partial_charges: false + compute_sasa: false + +clustering: + butina_cutoff: 0.35 + n_hyperclusters: 50 + +scheduler: + init_coverage_fraction: 0.35 + conservative_deprioritize: true + surrogate: + prefer_xgboost: true + n_estimators: 250 + min_train_samples: 20 + max_depth_small: 3 + max_depth_large: 6 + model_weight_schedule: + sample_knots: [20, 50, 100, 200, 500] + weight_knots: [0.1, 0.3, 0.5, 0.7, 0.9] + max_weight: 0.9 + min_weight: 0.05 + instability_threshold: 2.0 + instability_decay: 0.25 + +matrix: + naive_random_seeds: [11, 22, 33, 44, 55] + cluster_naive_seeds: [101, 202, 303, 404, 505] + include_adaptive_top1_variant: true + include_adaptive: true + include_naive_random: true + include_cluster_naive: true + modes: [docking_only, full_feature] + +analysis: + analog_similarity_threshold: 0.65 + rolling_window: 200 + replicate_subset_size_top: 20 + replicate_subset_size_borderline: 20 + replicate_subset_size_clusters: 20 + replicate_runs: 2 + +early_stop: + min_evaluated: 3000 + patience_rounds: 12 + min_model_weight: 0.4 + quantile: 0.15 + uncertainty_weight: 0.2 + min_improvement: 0.015 + exploration_margin: 0.45 + exploitation_margin: 0.1 + reference_evaluations: 50000 + diff --git a/configs/discovery_benchmark_reduced.yaml b/configs/discovery_benchmark_reduced.yaml new file mode 100644 index 0000000000000000000000000000000000000000..efdefe49b4d059588ce111ccfc73d58a9e21bd2b --- /dev/null +++ b/configs/discovery_benchmark_reduced.yaml @@ -0,0 +1,100 @@ +run: + name: discovery_benchmark_reduced + output_dir: results/discovery_benchmark + random_seed: 20260415 + batch_size: 32 + adaptive_budget: 7500 + baseline_budget: 7500 + max_batches: 500 + allow_resume: true + enable_adaptive_early_stop: true + +target: + protein_name: MDM2 + target_id: mdm2_discovery + docking_reference_pdb: "4HG7" + docking_target_path: data/targets/large_benchmark/mdm2_4hg7.pdb + +reference: + reference_id: ref_nutlin3a + pdb_id: "4HG7" + ligand_comp_id: "NUT" + +benchmark_dataset: + output_dir: data/ligands/discovery_benchmark + target_size: 7500 + shuffle_seed: 424242 + reuse_existing: true + min_similarity_keep: 0.12 + pubchem_max_records: 20000 + pubchem_thresholds: [95, 92, 90, 88, 85, 82, 80, 77, 75, 72, 70, 67, 65, 62, 60, 57, 55, 52, 50, 47, 45, 42, 40, 37, 35] + chembl_target_id: CHEMBL5023 + chembl_max_rows: 40000 + allow_generated_fallback: true + +backend: + type: rdock + require_real_backend: true + n_runs: 5 + mapper_radius: 6.0 + command_timeout_seconds: 300 + parallel_jobs: auto-minus-4 + +encoding: + fingerprint_radius: 2 + fingerprint_bits: 1024 + generate_3d: false + +feature_extraction: + compute_partial_charges: false + compute_sasa: false + +clustering: + butina_cutoff: 0.35 + n_hyperclusters: 30 + +scheduler: + init_coverage_fraction: 0.35 + conservative_deprioritize: true + surrogate: + prefer_xgboost: true + n_estimators: 250 + min_train_samples: 20 + max_depth_small: 3 + max_depth_large: 6 + model_weight_schedule: + sample_knots: [20, 50, 100, 200, 500] + weight_knots: [0.1, 0.3, 0.5, 0.7, 0.9] + max_weight: 0.9 + min_weight: 0.05 + instability_threshold: 2.0 + instability_decay: 0.25 + +matrix: + naive_random_seeds: [11, 22, 33, 44, 55] + cluster_naive_seeds: [101, 202, 303, 404, 505] + include_adaptive_top1_variant: true + include_adaptive: true + include_naive_random: true + include_cluster_naive: true + modes: [docking_only, full_feature] + +analysis: + analog_similarity_threshold: 0.65 + rolling_window: 200 + replicate_subset_size_top: 20 + replicate_subset_size_borderline: 20 + replicate_subset_size_clusters: 20 + replicate_runs: 2 + +early_stop: + min_evaluated: 600 + patience_rounds: 8 + min_model_weight: 0.35 + quantile: 0.15 + uncertainty_weight: 0.2 + min_improvement: 0.02 + exploration_margin: 0.45 + exploitation_margin: 0.1 + reference_evaluations: 7500 + diff --git a/configs/epsilon_regret_benchmark.yaml b/configs/epsilon_regret_benchmark.yaml new file mode 100644 index 0000000000000000000000000000000000000000..308881929c42c09f287845d436ddece071a81dd0 --- /dev/null +++ b/configs/epsilon_regret_benchmark.yaml @@ -0,0 +1,64 @@ +run: + name: epsilon_regret_benchmark + output_dir: results/epsilon_regret_benchmark + random_seed: 20260416 + budgets: [100, 250, 500, 1000] + time_importance: 0.5 + allow_resume: true + +epsilon_regret: + epsilon_quality: 0.10 + acceptable_regret: 0.10 + min_budget: 250 + max_budget: 1000 + min_model_weight: 0.25 + patience_rounds: 6 + min_improvement: 0.02 + uncertainty_multiplier: 0.50 + min_cluster_coverage: 0.20 + min_hypercluster_coverage: 0.20 + +backend: + primary: rdock + secondary: haddock + require_real_backend: true + rdock: + n_runs: 1 + mapper_radius: 6.0 + command_timeout_seconds: 240 + parallel_jobs: auto-minus-4 + haddock: + command_timeout_seconds: 240 + haddock_env_bin_dir: .venv_haddock/bin + calibration_subset_size: 24 + +runtime: + estimated_seconds_per_docking: 0.5 + +datasets: + - name: dataset_A + target_name: EGFR + target_path: data/targets/budget_efficiency_benchmark_A/egfr_4wkq.pdb + shared_library_path: data/ligands/budget_efficiency_benchmark_A/shared_library_shuffled.csv + predock_master_path: results/budget_efficiency_benchmark/dataset_A/bootstrap/predock/parsed_scores_master.csv + adaptive_no_stop_run_path: results/budget_efficiency_benchmark/dataset_A/replay_cache/dataset_A__adaptive_no_stop__ti0.50__evaluated.csv + adaptive_model_events_path: results/budget_efficiency_benchmark/dataset_A/replay_cache/dataset_A__adaptive_no_stop__ti0.50__model.csv + naive_glob: results/budget_efficiency_benchmark/dataset_A/replay_cache/dataset_A__naive_random_s*__evaluated.csv + cluster_glob: results/budget_efficiency_benchmark/dataset_A/replay_cache/dataset_A__cluster_naive_s*__evaluated.csv + source_summary_path: results/budget_efficiency_benchmark/dataset_A_target_selection.md + + - name: dataset_B + target_name: ABL1 + target_path: data/targets/budget_efficiency_benchmark_B/abl1_1iep.pdb + shared_library_path: data/ligands/budget_efficiency_benchmark_B/shared_library_shuffled.csv + predock_master_path: results/budget_efficiency_benchmark/dataset_B/bootstrap/predock/parsed_scores_master.csv + adaptive_no_stop_run_path: results/budget_efficiency_benchmark/dataset_B/replay_cache/dataset_B__adaptive_no_stop__ti0.50__evaluated.csv + adaptive_model_events_path: results/budget_efficiency_benchmark/dataset_B/replay_cache/dataset_B__adaptive_no_stop__ti0.50__model.csv + naive_glob: results/budget_efficiency_benchmark/dataset_B/replay_cache/dataset_B__naive_random_s*__evaluated.csv + cluster_glob: results/budget_efficiency_benchmark/dataset_B/replay_cache/dataset_B__cluster_naive_s*__evaluated.csv + source_summary_path: results/budget_efficiency_benchmark/dataset_B_target_selection.md + +disk_guard: + min_free_gb: 10.0 + projected_output_gb: 1.2 + keep_raw_batches: 4 diff --git a/configs/experimental_benchmark.yaml b/configs/experimental_benchmark.yaml new file mode 100644 index 0000000000000000000000000000000000000000..8546636f645612a562ddd95c65ef53026431db0a --- /dev/null +++ b/configs/experimental_benchmark.yaml @@ -0,0 +1,72 @@ +run: + name: experimental_benchmark + output_dir: results/experimental_benchmark + random_seed: 42 + max_batches: 15 + batch_size: 10 + adaptive_budget: 150 + baseline_budget: 150 + resume: true + +target: + protein_name: MDM2 + target_id: mdm2_experimental + docking_reference_pdb: 4HG7 + docking_target_path: data/targets/experimental_benchmark/mdm2_4hg7.pdb + +references: + complexes: + - pdb_id: 4HG7 + ligand_comp_id: NUT + reference_id: ref_nutlin3a + - pdb_id: 4J7D + ligand_comp_id: I31 + reference_id: ref_ro5045331 + - pdb_id: 4LWU + ligand_comp_id: 20U + reference_id: ref_ro5499252 + +benchmark_dataset: + output_dir: data/ligands/experimental_benchmark + reuse_existing: true + per_reference_target: 1500 + pubchem_similarity_threshold: 80 + pubchem_max_records: 2200 + min_similarity_keep: 0.2 + +backend: + require_real_backend: true + allow_mock_if_missing: false + n_runs: 1 + mapper_radius: 6.0 + command_timeout_seconds: 180 + +encoding: + fingerprint_radius: 2 + fingerprint_bits: 1024 + generate_3d: false + +clustering: + butina_cutoff: 0.35 + n_hyperclusters: 20 + +scheduler: + init_coverage_fraction: 0.35 + conservative_deprioritize: true + model_weight_schedule: + sample_knots: [20, 50, 100, 200] + weight_knots: [0.1, 0.3, 0.5, 0.8] + max_weight: 0.9 + min_weight: 0.05 + instability_threshold: 2.0 + instability_decay: 0.25 + surrogate: + prefer_xgboost: true + n_estimators: 200 + min_train_samples: 12 + max_depth_small: 3 + max_depth_large: 6 + +analysis: + analog_similarity_threshold: 0.65 + topk_values: [10, 25, 50, 100] diff --git a/configs/experimental_benchmark_single_library.yaml b/configs/experimental_benchmark_single_library.yaml new file mode 100644 index 0000000000000000000000000000000000000000..dfb67f8b73e09cb614f707ad7fdf0ef8496ee919 --- /dev/null +++ b/configs/experimental_benchmark_single_library.yaml @@ -0,0 +1,73 @@ +run: + name: experimental_benchmark_single_library + output_dir: results/experimental_benchmark_single_library + random_seed: 42 + adaptive_budget: 1500 + baseline_budget: 1500 + batch_size: 10 + max_batches: 200 + +target: + protein_name: MDM2 + target_id: mdm2_experimental_single_library + docking_reference_pdb: 4HG7 + docking_target_path: data/targets/experimental_benchmark_single_library/mdm2_4hg7.pdb + +references: + complexes: + - pdb_id: 4HG7 + ligand_comp_id: NUT + reference_id: ref_nutlin3a + - pdb_id: 4J7D + ligand_comp_id: I31 + reference_id: ref_ro5045331 + - pdb_id: 4LWU + ligand_comp_id: 20U + reference_id: ref_ro5499252 + +benchmark_dataset: + output_dir: data/ligands/experimental_benchmark_single_library + reuse_existing: true + per_reference_target: 1300 + pubchem_similarity_threshold: 80 + pubchem_max_records: 2500 + min_similarity_keep: 0.2 + shared_library_target_size: 1500 + analog_similarity_threshold: 0.65 + +backend: + require_real_backend: true + allow_mock_if_missing: false + n_runs: 1 + mapper_radius: 6.0 + command_timeout_seconds: 180 + +encoding: + fingerprint_radius: 2 + fingerprint_bits: 1024 + generate_3d: false + +clustering: + butina_cutoff: 0.35 + n_hyperclusters: 20 + +scheduler: + init_coverage_fraction: 0.35 + conservative_deprioritize: true + model_weight_schedule: + sample_knots: [20, 50, 100, 200] + weight_knots: [0.1, 0.3, 0.5, 0.8] + max_weight: 0.9 + min_weight: 0.05 + instability_threshold: 2.0 + instability_decay: 0.25 + surrogate: + prefer_xgboost: true + n_estimators: 200 + min_train_samples: 12 + max_depth_small: 3 + max_depth_large: 6 + +analysis: + rolling_window: 100 + analog_similarity_threshold: 0.65 diff --git a/configs/experimental_validation.yaml b/configs/experimental_validation.yaml new file mode 100644 index 0000000000000000000000000000000000000000..ae993c0a42ff96dec89865b0545c3fdd50d92091 --- /dev/null +++ b/configs/experimental_validation.yaml @@ -0,0 +1,36 @@ +run: + name: experimental_validation + output_dir: results/experimental_validation_strict + max_batches: 2 + random_seed: 42 + +data: + target_id: mdm2_pocket_excerpt + target_path: data/targets/mdm2_1ycr_pocket_excerpt.pdb + ligand_table: data/ligands/mdm2_ligands_validation_strict.csv + benchmark_metadata: data/benchmarks/mdm2_validation_metadata.json + +backend: + type: rdock + allow_mock_if_missing: false + require_real_backend: true + n_runs: 1 + mapper_radius: 6.0 + command_timeout_seconds: 60 + +encoding: + fingerprint_radius: 2 + fingerprint_bits: 1024 + generate_3d: true + +clustering: + butina_cutoff: 0.35 + n_hyperclusters: 4 + +scheduler: + batch_size: 6 + init_coverage_fraction: 0.34 + conservative_deprioritize: true + +scoring: + interface_weight: 1.0 diff --git a/configs/large_benchmark.yaml b/configs/large_benchmark.yaml new file mode 100644 index 0000000000000000000000000000000000000000..9476f34047631a34965c39a47d22f5394a90db49 --- /dev/null +++ b/configs/large_benchmark.yaml @@ -0,0 +1,87 @@ +run: + name: large_benchmark + output_dir: results/large_benchmark + random_seed: 20260415 + batch_size: 32 + adaptive_budget: 7500 + baseline_budget: 7500 + max_batches: 500 + allow_resume: true + +target: + protein_name: MDM2 + target_id: mdm2_large + docking_reference_pdb: "4HG7" + docking_target_path: data/targets/large_benchmark/mdm2_4hg7.pdb + +reference: + reference_id: ref_nutlin3a + pdb_id: "4HG7" + ligand_comp_id: "NUT" + +benchmark_dataset: + output_dir: data/ligands/large_benchmark + target_size: 7500 + shuffle_seed: 424242 + reuse_existing: true + min_similarity_keep: 0.12 + pubchem_max_records: 20000 + pubchem_thresholds: [95, 92, 90, 88, 85, 82, 80, 77, 75, 72, 70, 67, 65, 62, 60, 57, 55, 52, 50, 47, 45, 42, 40, 37, 35] + chembl_target_id: CHEMBL5023 + chembl_max_rows: 40000 + allow_generated_fallback: true + +backend: + type: rdock + require_real_backend: true + n_runs: 5 + mapper_radius: 6.0 + command_timeout_seconds: 300 + parallel_jobs: auto-minus-4 + pocket_mode: reference_complex_pocket + pocket_reference_ligand_id: NUT + pocket_relaxation_margin: 0.0 + +encoding: + fingerprint_radius: 2 + fingerprint_bits: 1024 + generate_3d: false + +feature_extraction: + compute_partial_charges: false + compute_sasa: false + +clustering: + butina_cutoff: 0.35 + n_hyperclusters: 30 + +scheduler: + init_coverage_fraction: 0.35 + conservative_deprioritize: true + surrogate: + prefer_xgboost: true + n_estimators: 250 + min_train_samples: 20 + max_depth_small: 3 + max_depth_large: 6 + model_weight_schedule: + sample_knots: [20, 50, 100, 200, 500] + weight_knots: [0.1, 0.3, 0.5, 0.7, 0.9] + max_weight: 0.9 + min_weight: 0.05 + instability_threshold: 2.0 + instability_decay: 0.25 + +matrix: + naive_random_seeds: [11, 22, 33, 44, 55] + cluster_naive_seeds: [101, 202, 303, 404, 505] + include_adaptive_top1_variant: true + modes: [docking_only, full_feature] + +analysis: + analog_similarity_threshold: 0.65 + rolling_window: 200 + replicate_subset_size_top: 20 + replicate_subset_size_borderline: 20 + replicate_subset_size_clusters: 20 + replicate_runs: 2 diff --git a/configs/multifidelity_regularized.yaml b/configs/multifidelity_regularized.yaml new file mode 100644 index 0000000000000000000000000000000000000000..1d2a32af0fae1d80b4b0511cc6513c5c0f13aeca --- /dev/null +++ b/configs/multifidelity_regularized.yaml @@ -0,0 +1,119 @@ +run: + name: multifidelity_regularized + output_dir: results/multifidelity_regularized + random_seed: 20260416 + budgets: [50, 100, 150, 200, 250, 300, 400, 500, 750, 1000, 1500, 2000, 2500, 5000, 10000] + haddock_budgets: [250] + dynamic_predock_batch_size: 256 + dynamic_predock_max_batches: 4 + dynamic_predock_flush_every_batches: 1 + wall_time_per_dock: 0.5 + max_wall_time_seconds: 7200 + n_baseline_seeds: 3 + allow_resume: true + +parameters: + max_budget: 10000 + min_budget: 100 + epsilon_quality_target: 0.10 + time_importance: 0.6 + shortlist_fraction: 0.35 + haddock_shortlist_size: 4 + +stopping: + target_rank_percentile: 1.0 + peak_patience: 32 + min_improvement_delta: 0.02 + +exploration: + stagnation_patience: 20 + diversity_boost_strength: 0.5 + dominant_window: 128 + +uncertainty: + uncertainty_low_threshold: 0.35 + uncertainty_patience: 32 + expected_gain_threshold: 0.03 + +backend: + require_real_backend: true + rdock: + n_runs: 1 + mapper_radius: 6.0 + command_timeout_seconds: 20 + parallel_jobs: auto-minus-4 + allow_skip_failed_ligands: true + max_failed_ligands: 3000 + haddock: + enabled: false + command_timeout_seconds: 90 + haddock_env_bin_dir: .venv_haddock/bin + +disk_guard: + min_free_gb: 10.0 + projected_output_gb: 3.0 + keep_raw_batches: 4 + +datasets: + A: + name: dataset_A + target_name: EGFR + target_path: data/targets/budget_efficiency_benchmark_A/egfr_4wkq.pdb + shared_library_path: data/ligands/budget_efficiency_benchmark_A/shared_library_shuffled.csv + predock_master_path: results/budget_efficiency_benchmark/dataset_A/bootstrap/predock/parsed_scores_master.csv + adaptive_no_stop_run_path: results/budget_efficiency_benchmark/dataset_A/replay_cache/dataset_A__adaptive_no_stop__ti0.50__evaluated.csv + naive_glob: results/budget_efficiency_benchmark/dataset_A/replay_cache/dataset_A__naive_random_s*__evaluated.csv + cluster_glob: results/budget_efficiency_benchmark/dataset_A/replay_cache/dataset_A__cluster_naive_s*__evaluated.csv + + B: + name: dataset_B + target_name: ABL1 + target_path: data/targets/budget_efficiency_benchmark_B/abl1_1iep.pdb + shared_library_path: data/ligands/budget_efficiency_benchmark_B/shared_library_shuffled.csv + predock_master_path: results/budget_efficiency_benchmark/dataset_B/bootstrap/predock/parsed_scores_master.csv + adaptive_no_stop_run_path: results/budget_efficiency_benchmark/dataset_B/replay_cache/dataset_B__adaptive_no_stop__ti0.50__evaluated.csv + naive_glob: results/budget_efficiency_benchmark/dataset_B/replay_cache/dataset_B__naive_random_s*__evaluated.csv + cluster_glob: results/budget_efficiency_benchmark/dataset_B/replay_cache/dataset_B__cluster_naive_s*__evaluated.csv + + C: + name: dataset_C + target_name: MDM2 + target_id: mdm2_mf_c + target_pdb: "4HG7" + target_path: data/targets/multifidelity_benchmark_C/mdm2_4hg7.pdb + reference_id: ref_nutlin3a_c + reference_name: Nutlin-3a + ligand_comp_id: NUT + reference_smiles: "CC1=C(C(C)=NN1)C2=CC=C(C=C2)C3=NC(C)(C)C4=CC(Cl)=CC(Cl)=C34" + benchmark_dataset: + output_dir: data/ligands/multifidelity_benchmark_C + target_size: 10000 + shuffle_seed: 909001 + reuse_existing: false + min_similarity_keep: 0.0 + pubchem_max_records: 20000 + pubchem_thresholds: [95, 92, 90, 88, 85, 82, 80, 77, 75, 72, 70, 67, 65, 62, 60, 57, 55, 52, 50, 47, 45, 42, 40, 37, 35] + chembl_target_id: CHEMBL5023 + chembl_max_rows: 40000 + allow_generated_fallback: true + + D: + name: dataset_D + target_name: CDK2 + target_id: cdk2_mf_d + target_pdb: "1H1Q" + target_path: data/targets/multifidelity_benchmark_D/cdk2_1h1q.pdb + reference_id: ref_stauro_d + reference_name: Staurosporine + ligand_comp_id: STU + benchmark_dataset: + output_dir: data/ligands/multifidelity_benchmark_D + target_size: 10000 + shuffle_seed: 909101 + reuse_existing: true + min_similarity_keep: 0.0 + pubchem_max_records: 20000 + pubchem_thresholds: [95, 92, 90, 88, 85, 82, 80, 77, 75, 72, 70, 67, 65, 62, 60, 57, 55, 52, 50, 47, 45, 42, 40, 37, 35] + chembl_target_id: CHEMBL301 + chembl_max_rows: 40000 + allow_generated_fallback: true diff --git a/configs/overnight_stop_model.yaml b/configs/overnight_stop_model.yaml new file mode 100644 index 0000000000000000000000000000000000000000..454ff65f20b4724257c5f442c3359bb365e6ac31 --- /dev/null +++ b/configs/overnight_stop_model.yaml @@ -0,0 +1,175 @@ +run: + name: overnight_stop_model + output_dir: results/overnight_stop_model + random_seed: 20260417 + budgets: [50, 100, 150, 200, 250, 300, 400, 500, 750, 1000, 1500, 2000, 2500, 5000, 10000] + include_15000_if_safe: true + dynamic_predock_batch_size: 192 + dynamic_predock_max_batches: 4 + dynamic_predock_flush_every_batches: 1 + wall_time_per_dock: 0.5 + max_wall_time_seconds: 10800 + allow_resume: true + +resource: + min_free_gb: 10.0 + min_free_gb_for_15k: 35.0 + min_ram_gb_for_15k: 24.0 + default_target_size: 10000 + projected_output_gb: 3.5 + +parameters: + max_budget: 10000 + min_budget: 100 + epsilon_quality_target: 0.10 + time_importance: 0.6 + shortlist_fraction: 0.35 + haddock_shortlist_size: 3 + +stopping: + target_rank_percentile: 1.0 + peak_patience: 32 + min_improvement_delta: 0.02 + +exploration: + stagnation_patience: 20 + diversity_boost_strength: 0.5 + dominant_window: 128 + +uncertainty: + uncertainty_low_threshold: 0.35 + uncertainty_patience: 32 + expected_gain_threshold: 0.03 + +stop_models: + target_percentile: 1.0 + probability_threshold: 0.80 + epsilon_quality: 0.10 + min_budget: 100 + gain_threshold: 0.03 + utility_lambda: 0.001 + utility_threshold: 0.0 + uncertainty_threshold: 0.35 + confirmation_window: 24 + min_improvement_delta: 0.02 + +analysis: + objective_functions: + - quality_per_time + - quality_per_docking + - rank_percentile_minimization + - regret_constrained_utility + - target_percentile_attainment + - hybrid_objective + haddock_shortlist_budgets: [250, 1000] + enable_haddock_shortlist: true + uncertainty_weight: 0.5 + +backend: + require_real_backend: true + rdock: + n_runs: 1 + mapper_radius: 6.0 + command_timeout_seconds: 20 + parallel_jobs: auto-minus-4 + allow_skip_failed_ligands: true + max_failed_ligands: 3000 + haddock: + enabled: true + command_timeout_seconds: 90 + haddock_env_bin_dir: .venv_haddock/bin + +disk_guard: + min_free_gb: 10.0 + projected_output_gb: 3.5 + keep_raw_batches: 4 + +datasets: + A: + name: dataset_A + target_name: EGFR + target_path: data/targets/budget_efficiency_benchmark_A/egfr_4wkq.pdb + shared_library_path: data/ligands/budget_efficiency_benchmark_A/shared_library_shuffled.csv + predock_master_path: results/budget_efficiency_benchmark/dataset_A/bootstrap/predock/parsed_scores_master.csv + adaptive_no_stop_run_path: results/budget_efficiency_benchmark/dataset_A/replay_cache/dataset_A__adaptive_no_stop__ti0.50__evaluated.csv + naive_glob: results/budget_efficiency_benchmark/dataset_A/replay_cache/dataset_A__naive_random_s*__evaluated.csv + cluster_glob: results/budget_efficiency_benchmark/dataset_A/replay_cache/dataset_A__cluster_naive_s*__evaluated.csv + + B: + name: dataset_B + target_name: ABL1 + target_path: data/targets/budget_efficiency_benchmark_B/abl1_1iep.pdb + shared_library_path: data/ligands/budget_efficiency_benchmark_B/shared_library_shuffled.csv + predock_master_path: results/budget_efficiency_benchmark/dataset_B/bootstrap/predock/parsed_scores_master.csv + adaptive_no_stop_run_path: results/budget_efficiency_benchmark/dataset_B/replay_cache/dataset_B__adaptive_no_stop__ti0.50__evaluated.csv + naive_glob: results/budget_efficiency_benchmark/dataset_B/replay_cache/dataset_B__naive_random_s*__evaluated.csv + cluster_glob: results/budget_efficiency_benchmark/dataset_B/replay_cache/dataset_B__cluster_naive_s*__evaluated.csv + + C: + name: dataset_C + target_name: MDM2 + target_id: mdm2_mf_c + target_pdb: "4HG7" + target_path: data/targets/multifidelity_benchmark_C/mdm2_4hg7.pdb + reference_id: ref_nutlin3a_c + reference_name: Nutlin-3a + ligand_comp_id: NUT + reference_smiles: "CC1=C(C(C)=NN1)C2=CC=C(C=C2)C3=NC(C)(C)C4=CC(Cl)=CC(Cl)=C34" + reuse_out_dir: results/multifidelity_regularized + benchmark_dataset: + output_dir: data/ligands/multifidelity_benchmark_C + target_size: 10000 + shuffle_seed: 909001 + reuse_existing: true + min_similarity_keep: 0.0 + pubchem_max_records: 20000 + pubchem_thresholds: [95, 92, 90, 88, 85, 82, 80, 77, 75, 72, 70, 67, 65, 62, 60, 57, 55, 52, 50, 47, 45, 42, 40, 37, 35] + chembl_target_id: CHEMBL5023 + chembl_max_rows: 40000 + allow_generated_fallback: true + + D: + name: dataset_D + target_name: CDK2 + target_id: cdk2_mf_d + target_pdb: "1H1Q" + target_path: data/targets/multifidelity_benchmark_D/cdk2_1h1q.pdb + reference_id: ref_stauro_d + reference_name: Staurosporine + ligand_comp_id: STU + reference_smiles: "CN[C@@H]1C[C@H]2O[C@@](C)(N3C=NC4=C3N=CN=C4N)[C@@H]1OC2" + reuse_out_dir: results/multifidelity_regularized + benchmark_dataset: + output_dir: data/ligands/multifidelity_benchmark_D + target_size: 10000 + shuffle_seed: 909101 + reuse_existing: true + min_similarity_keep: 0.0 + pubchem_max_records: 20000 + pubchem_thresholds: [95, 92, 90, 88, 85, 82, 80, 77, 75, 72, 70, 67, 65, 62, 60, 57, 55, 52, 50, 47, 45, 42, 40, 37, 35] + chembl_target_id: CHEMBL301 + chembl_max_rows: 40000 + allow_generated_fallback: true + + E: + name: dataset_E + target_name: MAPK14 + target_id: mapk14_mf_e + target_pdb: "1A9U" + target_path: data/targets/multifidelity_benchmark_E/mapk14_1a9u.pdb + reference_id: ref_sb203580_e + reference_name: SB203580 + ligand_comp_id: SB2 + reference_smiles: "CC(C)Oc1ccc(cc1)c2nc(c(cn2)N)c3cnn(c3)C(C)(C)C" + reuse_out_dir: results/overnight_stop_model + benchmark_dataset: + output_dir: data/ligands/multifidelity_benchmark_E + target_size: 10000 + shuffle_seed: 909201 + reuse_existing: true + min_similarity_keep: 0.0 + pubchem_max_records: 25000 + pubchem_thresholds: [95, 92, 90, 88, 85, 82, 80, 77, 75, 72, 70, 67, 65, 62, 60, 57, 55, 52, 50, 47, 45, 42, 40, 37, 35] + chembl_target_id: CHEMBL260 + chembl_max_rows: 50000 + allow_generated_fallback: true diff --git a/configs/policy_repair_benchmark.yaml b/configs/policy_repair_benchmark.yaml new file mode 100644 index 0000000000000000000000000000000000000000..51194af72bdaa623eb2a466d619e84139ee19725 --- /dev/null +++ b/configs/policy_repair_benchmark.yaml @@ -0,0 +1,98 @@ +run: + name: policy_repair_benchmark + output_dir: results/policy_repair_benchmark + random_seed: 20260416 + batch_size: 32 + adaptive_budget: 7500 + baseline_budget: 7500 + max_batches: 500 + allow_resume: true + +target: + protein_name: MDM2 + target_id: mdm2_discovery + docking_reference_pdb: "4HG7" + docking_target_path: data/targets/large_benchmark/mdm2_4hg7.pdb + +reference: + reference_id: ref_nutlin3a + pdb_id: "4HG7" + ligand_comp_id: "NUT" + +inputs: + source_benchmark_dir: results/discovery_benchmark + shared_library_path: results/discovery_benchmark/shared_library_shuffled.csv + predock_master_path: results/discovery_benchmark/predock/parsed_scores_master.csv + cluster_source_path: results/discovery_benchmark/parsed_scores.csv + features_values_path: results/discovery_benchmark/features_per_ligand.csv + features_masks_path: results/discovery_benchmark/feature_masks.csv + validated_size: 7500 + +backend: + type: rdock + require_real_backend: true + parallel_jobs: auto-minus-4 + +scheduler: + init_coverage_fraction: 0.35 + conservative_deprioritize: true + surrogate: + prefer_xgboost: true + n_estimators: 180 + min_train_samples: 20 + max_depth_small: 3 + max_depth_large: 6 + model_weight_schedule: + sample_knots: [20, 50, 100, 200, 500] + weight_knots: [0.1, 0.3, 0.5, 0.7, 0.9] + max_weight: 0.9 + min_weight: 0.05 + instability_threshold: 2.0 + instability_decay: 0.25 + +matrix: + naive_random_seeds: [11, 22, 33, 44, 55] + cluster_naive_seeds: [101, 202, 303, 404, 505] + +early_stop: + min_evaluated: 600 + patience_rounds: 8 + min_model_weight: 0.35 + quantile: 0.15 + uncertainty_weight: 0.2 + min_improvement: 0.02 + exploration_margin: 0.45 + exploitation_margin: 0.1 + reference_evaluations: 7500 + +policies: + adaptive_hard_stop: + enabled: true + adaptive_soft_stop: + enabled: true + soft_recovery_batches: 16 + soft_threshold_relax: 0.35 + soft_model_weight_cap: 0.45 + soft_exploration_boost: 0.25 + max_soft_recoveries: 1 + adaptive_no_stop: + enabled: true + adaptive_cluster_bootstrap: + enabled: true + cluster_bootstrap_rounds: 24 + adaptive_soft_stop_cluster_floor: + enabled: true + cluster_bootstrap_rounds: 20 + min_cluster_coverage: 0.60 + min_hypercluster_coverage: 0.55 + soft_recovery_batches: 20 + soft_threshold_relax: 0.40 + soft_model_weight_cap: 0.40 + soft_exploration_boost: 0.30 + pre_floor_model_weight_cap: 0.35 + max_soft_recoveries: 2 + +disk_guard: + min_free_gb: 10.0 + projected_output_gb: 1.5 + keep_raw_batches: 6 diff --git a/configs/ppi_benchmark.yaml b/configs/ppi_benchmark.yaml new file mode 100644 index 0000000000000000000000000000000000000000..30cf05bc791790aa809b72a12ea9353d1b2125cf --- /dev/null +++ b/configs/ppi_benchmark.yaml @@ -0,0 +1,25 @@ +run: + name: ppi_benchmark + output_dir: results/ppi_benchmark + random_seed: 20260415 + batch_size: 8 + +benchmark: + benchmark_type: peptide_like + +target: + protein_name: MDM2 + target_id: mdm2_ppi_benchmark + docking_target_path: data/targets/ppi_benchmark/mdm2_1ycr.pdb + +reference: + reference_pdb_id: "1YCR" + receptor_chain_id: "A" + peptide_chain_id: "B" + n_variants: 50 + min_length: 8 + max_length: 20 + +disk_guard: + min_free_gb: 8.0 + force_cleanup: true diff --git a/configs/ppi_sanity_check.yaml b/configs/ppi_sanity_check.yaml new file mode 100644 index 0000000000000000000000000000000000000000..cf6a7f8c6a827b94cc12293636c349375f8f9c8d --- /dev/null +++ b/configs/ppi_sanity_check.yaml @@ -0,0 +1,24 @@ +run: + name: ppi_sanity_check + output_dir: results/ppi_sanity_check + random_seed: 20260415 + batch_size: 8 + +benchmark: + benchmark_type: peptide_like + +target: + protein_name: MDM2 + target_id: mdm2_ppi_sanity + docking_target_path: data/targets/ppi_sanity_check/mdm2_1ycr.pdb + +reference: + reference_pdb_id: "1YCR" + receptor_chain_id: "A" + peptide_chain_id: "B" + n_variants: 40 + min_length: 8 + max_length: 20 + +disk_guard: + min_free_gb: 8.0 diff --git a/configs/reference_free_triage_bandit_defaults.yaml b/configs/reference_free_triage_bandit_defaults.yaml new file mode 100644 index 0000000000000000000000000000000000000000..40ca74e45e970e5408ee90c5a4e75636ecffbe9e --- /dev/null +++ b/configs/reference_free_triage_bandit_defaults.yaml @@ -0,0 +1,42 @@ +strategy: reference_free_triage_bandit_v1 +triage_controller: auto_recall +triage_model: classifier +triage_retain_fraction: 0.02 +triage_target_recall: 0.98 +max_retain_fraction_before_not_useful: 0.5 +classifier_threshold_mode: recall_target +classifier_min_positives: 10 +classifier_holdout_fraction: 0.25 +classifier_fallback: cluster_only +model_fallback_if_worse: union_with_cluster_only +survivor_combination_policy: union +calibration_size: 1000 +calibration_fraction: 0.2 +fidelity_validation_size: 200 +fidelity_levels: + - 5 + - 10 + - 15 + - 30 + - 50 +promotion_policy: conservative +rescue_fraction: 0.05 +uncertainty_weight: 0.35 +diversity_weight: 0.75 +outlier_risk_weight: 2.0 +cluster_min_survivors: 1 +cluster_max_survivors: 50 +classifier_top_percentile: 0.05 +max_per_cluster: 50 +final_fidelity_runs: 50 +min_final_ligands: 20 +min_promotion_per_level: 8 +final_survivor_enumerate_variants: false +variant_stage: none +enumerate_stereoisomers: none +max_stereoisomers_per_parent: 2 +enumerate_tautomers: none +enumerate_protonation: none +max_conformers_per_variant: 1 +max_total_variants_per_parent: 1 +variant_fairness_policy: cap diff --git a/configs/smoke_test.yaml b/configs/smoke_test.yaml new file mode 100644 index 0000000000000000000000000000000000000000..5ec1d231cabc9ab0270431ad4638418e6fde32cd --- /dev/null +++ b/configs/smoke_test.yaml @@ -0,0 +1,39 @@ +run: + name: smoke_test + output_dir: results/smoke_test + max_batches: 2 + random_seed: 7 + +data: + target_id: smoke_3ptb + target_path: data/datasets/rdock_3PTB_10k_pubchem/target/rdock_prm/target_raw.pdb + ligand_table: data/ligands/smoke_ligands.csv + benchmark_metadata: data/benchmarks/smoke_metadata.json + +backend: + type: rdock + allow_mock_if_missing: false + require_real_backend: true + n_runs: 3 + mapper_radius: 6.0 + pocket_mode: user_fixed_pocket + pocket_center: [-1.7591111111111113, 14.461, 16.915777777777777] + pocket_radius: 6.0 + pocket_relaxation_margin: 0.0 + +encoding: + fingerprint_radius: 2 + fingerprint_bits: 512 + generate_3d: false + +clustering: + butina_cutoff: 0.4 + n_hyperclusters: 2 + +scheduler: + batch_size: 4 + init_coverage_fraction: 0.5 + conservative_deprioritize: false + +scoring: + interface_weight: 1.0 diff --git a/conftest.py b/conftest.py new file mode 100644 index 0000000000000000000000000000000000000000..99bace744bdbf3bc0c6d5d83547ed8e9c0c75c25 --- /dev/null +++ b/conftest.py @@ -0,0 +1,42 @@ +from __future__ import annotations + +import os +from pathlib import Path + + +NEW_TEST_FILES = { + "test_docking_pipeline_adaptive.py", + "test_docking_pipeline_failures.py", + "test_docking_pipeline_cli_validation.py", + "test_docking_pipeline_dud_metrics.py", + "test_docking_pipeline_metrics.py", + "test_docking_pipeline_sdf.py", + "test_docking_pipeline_dataset.py", + "test_docking_pipeline_bundle.py", + "test_rdock_validation_smoke.py", + "test_pdb_benchmark_real.py", + "test_legacy_collection_policy.py", + "test_rdock_backend.py", + "test_rdock_feature_parsing.py", + "test_rdock_output_parsing_real.py", + "test_rdock_real_execution.py", + "test_smoke_pipeline.py", +} + + +def pytest_ignore_collect(collection_path, config): # type: ignore[no-untyped-def] + """Keep default collection operational without optional legacy dependencies. + + The historical benchmark suite imports pandas/RDKit/matplotlib/yaml/HADDOCK/smina + modules at collection time. Those tests remain in the tree for reference and can be + re-enabled in a fully provisioned legacy environment with DOCKING_INCLUDE_LEGACY=1. + The strict rDock-first tests are collected by default. + """ + path = Path(str(collection_path)) + if os.environ.get("DOCKING_INCLUDE_LEGACY") == "1": + return False + if path.name.startswith("test_") and path.suffix == ".py" and path.parent.name == "tests": + return path.name not in NEW_TEST_FILES + if path.name == "run_smoke_test.py" and path.parent.name == "pipeline": + return True + return False diff --git a/data/._.DS_Store b/data/._.DS_Store new file mode 100644 index 0000000000000000000000000000000000000000..28c42fb20a1f27e695fb64323501fc6476578b13 Binary files /dev/null and b/data/._.DS_Store differ diff --git a/data/._.cache b/data/._.cache new file mode 100644 index 0000000000000000000000000000000000000000..ee537d225f1b1eed0d0f4ed0b171fdc63ca71d82 Binary files /dev/null and b/data/._.cache differ diff --git a/data/datasets/._.DS_Store 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0000000000000000000000000000000000000000..ee537d225f1b1eed0d0f4ed0b171fdc63ca71d82 Binary files /dev/null and b/data/datasets/rdock_3PTB_50k_pubchem_local/._dataset_manifest.json differ diff --git a/data/datasets/rdock_3PTB_50k_pubchem_local/._ligands b/data/datasets/rdock_3PTB_50k_pubchem_local/._ligands new file mode 100644 index 0000000000000000000000000000000000000000..ee537d225f1b1eed0d0f4ed0b171fdc63ca71d82 Binary files /dev/null and b/data/datasets/rdock_3PTB_50k_pubchem_local/._ligands differ diff --git a/data/datasets/rdock_3PTB_50k_pubchem_local/._logs b/data/datasets/rdock_3PTB_50k_pubchem_local/._logs new file mode 100644 index 0000000000000000000000000000000000000000..ee537d225f1b1eed0d0f4ed0b171fdc63ca71d82 Binary files /dev/null and b/data/datasets/rdock_3PTB_50k_pubchem_local/._logs differ diff --git a/data/datasets/rdock_3PTB_50k_pubchem_local/._qc b/data/datasets/rdock_3PTB_50k_pubchem_local/._qc new file mode 100644 index 0000000000000000000000000000000000000000..ee537d225f1b1eed0d0f4ed0b171fdc63ca71d82 Binary files /dev/null and b/data/datasets/rdock_3PTB_50k_pubchem_local/._qc differ diff --git a/data/datasets/rdock_3PTB_50k_pubchem_local/._target b/data/datasets/rdock_3PTB_50k_pubchem_local/._target new file mode 100644 index 0000000000000000000000000000000000000000..ee537d225f1b1eed0d0f4ed0b171fdc63ca71d82 Binary files /dev/null and b/data/datasets/rdock_3PTB_50k_pubchem_local/._target differ diff --git a/data/datasets/rdock_3PTB_50k_pubchem_local/dataset_manifest.json b/data/datasets/rdock_3PTB_50k_pubchem_local/dataset_manifest.json new file mode 100644 index 0000000000000000000000000000000000000000..30539db3e9784bb0c62ae550468afc49311fbfef --- /dev/null +++ b/data/datasets/rdock_3PTB_50k_pubchem_local/dataset_manifest.json @@ -0,0 +1,907 @@ +{ + "pdb_id": "3PTB", + "receptor_chain": "A", + "reference_ligand_resname": "BEN", + "reference_ligand_chain": "A", + "n_ligands_requested": 50000, + "ligands_prepared": 50000, + "paths": { + "target_mol2": "data/datasets/rdock_3PTB_50k_pubchem_local/target/target.mol2", + "reference_ligand_sdf": "data/datasets/rdock_3PTB_50k_pubchem_local/target/reference_ligand.sdf", + "all_ligands_sdf": "data/datasets/rdock_3PTB_50k_pubchem_local/ligands/all_ligands.sdf", + "rdock_prm_dir": "data/datasets/rdock_3PTB_50k_pubchem_local/target/rdock_prm", + "target_config_yaml": "data/datasets/rdock_3PTB_50k_pubchem_local/target/rdock_prm/target_config.yaml", + "all_ligands_smi": "data/datasets/rdock_3PTB_50k_pubchem_local/ligands/all_ligands.smi" + }, + "versions": { + "obabel": "Open Babel 3.1.0 -- May 8 2020 -- 15:48:11", + "rbdock": "The rDock program is\u00a0licensed under GNU-LGPLv3.0. http://rdock.sourceforge.net/", + "rbcavity": "The rDock program is\u00a0licensed under GNU-LGPLv3.0. http://rdock.sourceforge.net/" + }, + "ligand_source": "pubchem_similarity_collect_only_local_50k", + "reference_ligand_smiles": "c1(ccccc1)C(=N)N", + "pubchem_threshold_ladder": [ + 99, + 98, + 97, + 96, + 95, + 94, + 93, + 92, + 91, + 90, + 89, + 88, + 87, + 86, + 85, + 84, + 83, + 82, + 81, + 80, + 79, + 78, + 77, + 76, + 75, + 74, + 73, + 72, + 71, + 70, + 69, + 68, + 67, + 66, + 65 + ], + "pubchem_diagnostics": { + "source": "pubchem_similarity", + "reference_smiles": "c1(ccccc1)C(=N)N", + "thresholds_tried": [ + 99, + 98, + 97, + 96, + 95, + 94, + 93, + 92, + 91, + 90, + 89, + 88, + 87, + 86, + 85, + 84, + 83, + 82, + 81, + 80, + 79, + 78, + 77, + 76, + 75, + 74, + 73, + 72, + 71, + 70, + 69, + 68, + 67, + 66, + 65, + 64, + 63, + 62, + 61, + 60, + 59, + 58, + 57, + 56, + 55, + 54, + 53, + 52, + 51, + 50 + ], + "requested_ligands": 50000, + "collected_ligands": 50000, + "endpoints_tried": [ + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/fastsimilarity_2d/sdf/cids/JSON (POST form field: sdf=...)", + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/fastidentity/sdf/cids/JSON (POST form field: sdf=...)", + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/fastsimilarity_2d/smiles/{smiles}/cids/JSON", + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/{query}/cids/JSON", + "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/{cids}/property/.../JSON" + ], + "diagnostics": [ + { + "threshold": 99, + "returned_cids": 4, + "accepted_new_smiles": 2, + "collected_total": 2 + }, + { + "threshold": 98, + "returned_cids": 25, + "accepted_new_smiles": 2, + "collected_total": 4 + }, + { + "threshold": 97, + "returned_cids": 36, + "accepted_new_smiles": 0, + "collected_total": 4 + }, + { + "threshold": 96, + "returned_cids": 60, + "accepted_new_smiles": 6, + "collected_total": 10 + }, + { + "threshold": 95, + "returned_cids": 71, + "accepted_new_smiles": 10, + "collected_total": 20 + }, + { + "threshold": 94, + "returned_cids": 133, + "accepted_new_smiles": 32, + "collected_total": 52 + }, + { + "threshold": 93, + "returned_cids": 205, + "accepted_new_smiles": 44, + "collected_total": 96 + }, + { + "threshold": 92, + "returned_cids": 334, + "accepted_new_smiles": 79, + "collected_total": 175 + }, + { + "threshold": 91, + "returned_cids": 471, + "accepted_new_smiles": 95, + "collected_total": 270 + }, + { + "threshold": 90, + "returned_cids": 615, + "accepted_new_smiles": 101, + "collected_total": 371 + }, + { + "threshold": 89, + "returned_cids": 715, + "accepted_new_smiles": 70, + "collected_total": 441 + }, + { + "threshold": 88, + "returned_cids": 1061, + "accepted_new_smiles": 293, + "collected_total": 734 + }, + { + "threshold": 87, + "returned_cids": 1411, + "accepted_new_smiles": 272, + "collected_total": 1006 + }, + { + "threshold": 86, + "returned_cids": 1884, + "accepted_new_smiles": 378, + "collected_total": 1384 + }, + { + "threshold": 85, + "returned_cids": 2443, + "accepted_new_smiles": 463, + "collected_total": 1847 + }, + { + "threshold": 84, + "returned_cids": 3105, + "accepted_new_smiles": 544, + "collected_total": 2391 + }, + { + "threshold": 83, + "returned_cids": 3975, + "accepted_new_smiles": 717, + "collected_total": 3108 + }, + { + "threshold": 82, + "returned_cids": 5045, + "accepted_new_smiles": 898, + "collected_total": 4006 + }, + { + "threshold": 81, + "returned_cids": 6342, + "accepted_new_smiles": 1058, + "collected_total": 5064 + }, + { + "threshold": 80, + "returned_cids": 8440, + "accepted_new_smiles": 1751, + "collected_total": 6815 + }, + { + "threshold": 79, + "returned_cids": 10436, + "accepted_new_smiles": 1634, + "collected_total": 8449 + }, + { + "threshold": 78, + "returned_cids": 13498, + "accepted_new_smiles": 2565, + "collected_total": 11014 + }, + { + "threshold": 77, + "returned_cids": 16892, + "accepted_new_smiles": 2908, + "collected_total": 13922 + }, + { + "threshold": 76, + "returned_cids": 20000, + "accepted_new_smiles": 3507, + "collected_total": 17429 + }, + { + "threshold": 75, + "returned_cids": 20000, + "accepted_new_smiles": 3971, + "collected_total": 21400 + }, + { + "threshold": 74, + "returned_cids": 20000, + "accepted_new_smiles": 3340, + "collected_total": 24740 + }, + { + "threshold": 73, + "returned_cids": 20000, + "accepted_new_smiles": 4454, + "collected_total": 29194 + }, + { + "threshold": 72, + "returned_cids": 20000, + "accepted_new_smiles": 4934, + "collected_total": 34128 + }, + { + "threshold": 71, + "returned_cids": 20000, + "accepted_new_smiles": 4827, + "collected_total": 38955 + }, + { + "threshold": 70, + "returned_cids": 20000, + "accepted_new_smiles": 4498, + "collected_total": 43453 + }, + { + "threshold": 69, + "returned_cids": 20000, + "accepted_new_smiles": 3838, + "collected_total": 47291 + }, + { + "threshold": 68, + "returned_cids": 20000, + "accepted_new_smiles": 2709, + "collected_total": 50000 + } + ], + "errors": [] + }, + "rbcavity_status": "success", + "warnings": [ + "50k dataset assembled locally from collected PubChem ligands and copied 3PTB rDock target bundle", + "qc/preparation_report.md was missing before ligand resume" + ], + "available_hetero_ligands": [ + { + "resname": "BEN", + "chain": "A", + "residue_id": "1", + "atom_count": 9, + "heavy_atom_count": 9, + "ignored": false, + "ignored_reason": "", + "candidate_ligand": true + }, + { + "resname": "CA", + "chain": "A", + "residue_id": "480", + "atom_count": 1, + "heavy_atom_count": 1, + "ignored": true, + "ignored_reason": "ion_or_metal", + "candidate_ligand": false + }, + { + "resname": "HOH", + "chain": "A", + "residue_id": "401", + "atom_count": 1, + "heavy_atom_count": 1, + "ignored": true, + "ignored_reason": "solvent", + "candidate_ligand": false + }, + { + "resname": "HOH", + "chain": "A", + "residue_id": "406", + "atom_count": 1, + "heavy_atom_count": 1, + "ignored": true, + "ignored_reason": "solvent", + "candidate_ligand": false + }, + { + "resname": "HOH", + "chain": "A", + "residue_id": "408", + "atom_count": 1, + "heavy_atom_count": 1, + "ignored": true, + "ignored_reason": "solvent", + "candidate_ligand": false + }, + { + "resname": "HOH", + "chain": "A", + "residue_id": "410", + "atom_count": 1, + "heavy_atom_count": 1, + "ignored": true, + "ignored_reason": "solvent", + "candidate_ligand": false + }, + { + "resname": "HOH", + "chain": "A", + "residue_id": "412", + "atom_count": 1, + "heavy_atom_count": 1, + "ignored": true, + "ignored_reason": "solvent", + "candidate_ligand": false + }, + { + "resname": "HOH", + "chain": "A", + "residue_id": "415", + "atom_count": 1, + "heavy_atom_count": 1, + "ignored": true, + "ignored_reason": "solvent", + "candidate_ligand": false + }, + { + "resname": "HOH", + "chain": "A", + "residue_id": "416", + "atom_count": 1, + "heavy_atom_count": 1, + "ignored": true, + "ignored_reason": "solvent", + "candidate_ligand": false + }, + { + "resname": "HOH", + "chain": "A", + "residue_id": "429", + "atom_count": 1, + "heavy_atom_count": 1, + "ignored": true, + "ignored_reason": "solvent", + "candidate_ligand": false + }, + { + "resname": "HOH", + "chain": "A", + "residue_id": "430", + "atom_count": 1, + "heavy_atom_count": 1, + "ignored": true, + "ignored_reason": "solvent", + "candidate_ligand": false + }, + { + "resname": "HOH", + "chain": "A", + "residue_id": "439", + "atom_count": 1, + "heavy_atom_count": 1, + "ignored": true, + "ignored_reason": "solvent", + "candidate_ligand": false + }, + { + "resname": "HOH", + "chain": "A", + "residue_id": "457", + "atom_count": 1, + "heavy_atom_count": 1, + "ignored": true, + "ignored_reason": "solvent", + "candidate_ligand": false + }, + { + "resname": "HOH", + "chain": "A", + "residue_id": "470", + "atom_count": 1, + "heavy_atom_count": 1, + "ignored": true, + "ignored_reason": "solvent", + "candidate_ligand": false + }, + { + "resname": "HOH", + "chain": "A", + "residue_id": "473", + "atom_count": 1, + "heavy_atom_count": 1, + "ignored": true, + "ignored_reason": "solvent", + "candidate_ligand": false + }, + { + "resname": "HOH", + "chain": "A", + "residue_id": "482", + "atom_count": 1, + "heavy_atom_count": 1, + "ignored": true, + "ignored_reason": "solvent", + "candidate_ligand": false + }, + { + "resname": "HOH", + "chain": "A", + "residue_id": "499", + "atom_count": 1, + "heavy_atom_count": 1, + "ignored": true, + "ignored_reason": "solvent", + "candidate_ligand": false + }, + { + "resname": "HOH", + "chain": "A", + "residue_id": "516", + "atom_count": 1, + "heavy_atom_count": 1, + "ignored": true, + "ignored_reason": "solvent", + "candidate_ligand": false + }, + { + "resname": "HOH", + "chain": "A", + "residue_id": "530", + "atom_count": 1, + "heavy_atom_count": 1, + "ignored": true, + "ignored_reason": "solvent", + "candidate_ligand": false + }, + { + "resname": "HOH", + "chain": "A", + "residue_id": "561", + "atom_count": 1, + "heavy_atom_count": 1, + "ignored": true, + "ignored_reason": "solvent", + "candidate_ligand": false + }, + { + "resname": "HOH", + "chain": "A", + "residue_id": "562", + "atom_count": 1, + "heavy_atom_count": 1, + "ignored": true, + "ignored_reason": "solvent", + 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+[2H]C1=CC=CC(=C1[2H])C([2H])([2H])C([2H])N=C(N)N=C(C)N pubchem_cid_160503712 +[2H]C1=CC=C(C(=C1)C([2H])([2H])C([2H])N=C(N)N=C(C)N)[2H] pubchem_cid_160503713 +[2H]C1=CC(=C(C(=C1)[2H])[2H])C([2H])([2H])CN=C(N)N=C(C)N pubchem_cid_160503714 +[2H]C1=CC=C(C(=C1)C([2H])C([2H])([2H])N=C(N)N=C(C)N)[2H] pubchem_cid_160503715 +[2H]C1=CC=CC(=C1[2H])C([2H])([2H])C([2H])([2H])N=C(N)N=C(C)N pubchem_cid_160503716 +[2H]C1=CC(=CC(=C1)C([2H])([2H])C([2H])([2H])N=C(N)N=C(C)N)[2H] pubchem_cid_160503717 +[2H]C1=CC(=C(C(=C1)[2H])C([2H])([2H])C([2H])N=C(N)N=C(C)N)[2H] pubchem_cid_160503719 +[2H]C1=C(C(=C(C=C1)C([2H])([2H])C([2H])N=C(N)N=C(C)N)[2H])[2H] pubchem_cid_160503720 +[2H]C1=CC(=C(C(=C1C([2H])([2H])CN=C(N)N=C(C)N)[2H])[2H])[2H] pubchem_cid_160503721 +[2H]C1=CC(=C(C(=C1[2H])[2H])[2H])C([2H])([2H])CN=C(N)N=C(C)N pubchem_cid_160503722 +[2H]C1=C(C(=C(C=C1)C([2H])C([2H])([2H])N=C(N)N=C(C)N)[2H])[2H] pubchem_cid_160503723 +[2H]C1=CC(=CC(=C1[2H])[2H])C([2H])C([2H])([2H])N=C(N)N=C(C)N pubchem_cid_160503724 +[2H]C1=CC(=C(C(=C1)[2H])C([2H])([2H])C([2H])([2H])N=C(N)N=C(C)N)[2H] pubchem_cid_160503725 +[2H]C1=C(C(=C(C=C1)C([2H])([2H])C([2H])([2H])N=C(N)N=C(C)N)[2H])[2H] pubchem_cid_160503726 +[2H]C1=CC=C(C(=C1[2H])CC([2H])([2H])N=C(N)N=C(C)N)[2H] pubchem_cid_160503728 +[2H]C1=CC(=C(C(=C1)[2H])[2H])CC([2H])([2H])N=C(N)N=C(C)N pubchem_cid_160503729 +[2H]C1=CC=C(C(=C1)C([2H])([2H])C([2H])([2H])N=C(N)N=C(C)N)[2H] pubchem_cid_160503730 +[2H]C1=C(C=C(C=C1)C([2H])([2H])C([2H])N=C(N)N=C(C)N)[2H] pubchem_cid_160503732 +[2H]C1=C(C(=C(C=C1)C([2H])([2H])CN=C(N)N=C(C)N)[2H])[2H] pubchem_cid_160503733 +[2H]C1=CC(=C(C=C1[2H])C([2H])([2H])CN=C(N)N=C(C)N)[2H] pubchem_cid_160503734 +[2H]C1=CC(=CC(=C1[2H])[2H])C([2H])([2H])CN=C(N)N=C(C)N pubchem_cid_160503735 +[2H]C1=C(C=C(C=C1)C([2H])C([2H])([2H])N=C(N)N=C(C)N)[2H] pubchem_cid_160503736 +[2H]C1=C(C(=C(C=C1)CC([2H])([2H])N=C(N)N=C(C)N)[2H])[2H] pubchem_cid_160503737 +[2H]C1=CC(=C(C=C1[2H])CC([2H])([2H])N=C(N)N=C(C)N)[2H] pubchem_cid_160503738 +[2H]C1=CC(=CC(=C1[2H])[2H])CC([2H])([2H])N=C(N)N=C(C)N pubchem_cid_160503739 +[2H]C1=C(C=C(C=C1)C([2H])([2H])C([2H])([2H])N=C(N)N=C(C)N)[2H] pubchem_cid_160503740 +[2H]C1=CC=C(C=C1)C([2H])([2H])CN=C(N)N=C(C)N pubchem_cid_160503742 +[2H]C1=CC=C(C=C1)CC([2H])([2H])N=C(N)N=C(C)N pubchem_cid_160503743 +[2H]C1=CC=C(C(=C1[2H])C([2H])C([2H])([2H])N=C(N)N=C(C)N)[2H] pubchem_cid_160503744 +[2H]C1=CC(=C(C(=C1)[2H])[2H])C([2H])C([2H])([2H])N=C(N)N=C(C)N pubchem_cid_160503745 +[2H]C1=CC=C(C(=C1[2H])C([2H])([2H])C([2H])([2H])N=C(N)N=C(C)N)[2H] pubchem_cid_160503746 +[2H]C1=CC(=C(C(=C1)[2H])[2H])C([2H])([2H])C([2H])([2H])N=C(N)N=C(C)N pubchem_cid_160503747 +[2H]C1=CC(=C(C(=C1[2H])C([2H])C([2H])([2H])N=C(N)N=C(C)N)[2H])[2H] pubchem_cid_160503748 +[2H]C1=CC(=C(C(=C1[2H])C([2H])([2H])C([2H])([2H])N=C(N)N=C(C)N)[2H])[2H] pubchem_cid_160503749 +[2H]C1=CC(=C(C(=C1)[2H])C([2H])C([2H])([2H])N=C(N)N=C(C)N)[2H] pubchem_cid_160503751 +[2H]C1=CC(=C(C(=C1C([2H])C([2H])N=C(N)N=C(C)N)[2H])[2H])[2H] pubchem_cid_160503752 +[2H]C1=CC(=C(C(=C1[2H])[2H])[2H])C([2H])C([2H])N=C(N)N=C(C)N pubchem_cid_160503753 +[2H]C1=CC(=C(C(=C1C([2H])([2H])C([2H])N=C(N)N=C(C)N)[2H])[2H])[2H] pubchem_cid_160503754 +[2H]C1=CC(=C(C(=C1[2H])[2H])[2H])C([2H])([2H])C([2H])N=C(N)N=C(C)N pubchem_cid_160503755 +[2H]C1=C(C(=C(C(=C1[2H])[2H])C([2H])C([2H])N=C(N)N=C(C)N)[2H])[2H] pubchem_cid_160503756 +[2H]C1=C(C(=C(C(=C1[2H])[2H])C([2H])([2H])C([2H])N=C(N)N=C(C)N)[2H])[2H] pubchem_cid_160503757 +[2H]C1=CC=C(C(=C1)CC([2H])N=C(N)N=C(C)N)[2H] pubchem_cid_160503759 +[2H]C1=CC(=CC(=C1)CC([2H])N=C(N)N=C(C)N)[2H] pubchem_cid_160503760 +[2H]C1=CC=CC(=C1)C([2H])([2H])C([2H])N=C(N)N=C(C)N pubchem_cid_160503761 +[2H]C1=CC=C(C(=C1)C([2H])([2H])CN=C(N)N=C(C)N)[2H] pubchem_cid_160503762 +[2H]C1=CC=CC(=C1[2H])CC([2H])([2H])N=C(N)N=C(C)N pubchem_cid_160503763 +[2H]C1=CC=C(C(=C1)CC([2H])([2H])N=C(N)N=C(C)N)[2H] pubchem_cid_160503764 +[2H]C1=CC(=C(C(=C1)[2H])C([2H])C([2H])N=C(N)N=C(C)N)[2H] pubchem_cid_160503766 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+[2H]C1=CC=C(C(=C1)CCN=C(N)N=C(C)N)[2H] pubchem_cid_160627827 +[2H]C1=C(C=C(C=C1)CCN=C(N)N=C(C)N)[2H] pubchem_cid_160627828 +[2H]C1=CC=C(C=C1)CCN=C(N)N=C(C)N pubchem_cid_160627829 +[2H]C1=CC=CC(=C1[2H])CCN=C(N)N=C(C)N pubchem_cid_160627830 +[2H]C1=CC=C(C=C1)C([2H])CN=C(N)N=C(C)N pubchem_cid_160766292 +[2H]C1=CC=C(C=C1)CC([2H])N=C(N)N=C(C)N pubchem_cid_160766293 +[2H]C1=CC=C(C=C1)C([2H])C([2H])N=C(N)N=C(C)N pubchem_cid_160766294 +[2H]C1=C(C=C(C=C1)C([2H])CN=C(N)N=C(C)N)[2H] pubchem_cid_160766295 +[2H]C1=C(C=C(C=C1)CC([2H])N=C(N)N=C(C)N)[2H] pubchem_cid_160766296 +[2H]C1=CC(=C(C=C1)C([2H])CN=C(N)N=C(C)N)[2H] pubchem_cid_160766298 +[2H]C1=CC(=C(C=C1)CC([2H])N=C(N)N=C(C)N)[2H] pubchem_cid_160766299 +[2H]C1=CC=C(C=C1)C([2H])([2H])C([2H])N=C(N)N=C(C)N pubchem_cid_160766300 +[2H]C1=CC(=C(C=C1)C([2H])([2H])CN=C(N)N=C(C)N)[2H] pubchem_cid_160766301 +[2H]C1=C(C=C(C=C1)C([2H])([2H])CN=C(N)N=C(C)N)[2H] pubchem_cid_160766302 +[2H]C1=CC(=C(C=C1)CC([2H])([2H])N=C(N)N=C(C)N)[2H] pubchem_cid_160766303 +[2H]C1=C(C=C(C=C1)CC([2H])([2H])N=C(N)N=C(C)N)[2H] pubchem_cid_160766304 +[2H]C1=CC=C(C=C1)C([2H])([2H])C([2H])([2H])N=C(N)N=C(C)N pubchem_cid_160766305 +[2H]C1=C(C=CC=C1)CCN=C(N)N=C(C)N pubchem_cid_160766307 +[2H]C1=CC=CC(=C1)CCN=C(N)N=C(C)N pubchem_cid_160766308 +[2H]C1=C(C(=C(C=C1)CCN=C(N)N=C(C)N)[2H])[2H] pubchem_cid_160766309 +[2H]C1=C(C=CC=C1)C([2H])CN=C(N)N=C(C)N pubchem_cid_160766312 +[2H]C1=CC=CC(=C1)C([2H])CN=C(N)N=C(C)N pubchem_cid_160766313 +[2H]C1=C(C=CC=C1)CC([2H])N=C(N)N=C(C)N pubchem_cid_160766315 +[2H]C1=CC=CC(=C1)CC([2H])N=C(N)N=C(C)N pubchem_cid_160766316 +[C-]#[N+]C1=CC=C(C=C1)CC(=N)N pubchem_cid_160792198 +C1=CC=C(C=C1)CCC(=N)CN pubchem_cid_161365613 +[2H]C1=CC(=C(C(=C1C([2H])C([2H])([2H])N=C(N)N=C(C)N)[2H])[2H])[2H] pubchem_cid_161555969 +[2H]C1=CC(=C(C(=C1[2H])[2H])[2H])C([2H])C([2H])([2H])N=C(N)N=C(C)N pubchem_cid_161555970 +[2H]C1=CC(=C(C(=C1C([2H])([2H])C([2H])([2H])N=C(N)N=C(C)N)[2H])[2H])[2H] pubchem_cid_161555971 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pubchem_cid_61567954 +CC(C)N(CCC(=N)N)CC1=CC(=CC=C1)F pubchem_cid_61585555 +C1CC1N(CCC(=N)N)CC2=CC(=CC=C2)F pubchem_cid_61587186 +CC(C)CN(CCC(=N)N)CC1=C(C(=CC=C1)F)F pubchem_cid_61662462 +CCN(CC1=C(C=CC(=C1)F)F)CC(C)C(=N)N pubchem_cid_61677639 +CC(CN(C)CC1=C(C=CC(=C1)F)F)C(=N)N pubchem_cid_61677686 +CC(C)N(CCC(=N)N)CC1=C(C=CC(=C1)F)F pubchem_cid_61677687 +CC(C)CN(CCC(=N)N)CC1=C(C=CC(=C1)F)F pubchem_cid_61677728 +CC(C(=N)N)N(C)CC1=CC(=CC=C1)F pubchem_cid_61691760 +CC(C(=N)N)N(C)CC1=CC=CC=C1F pubchem_cid_61691765 +CC(C(=N)N)N(C)CC1=CC=C(C=C1)F pubchem_cid_61691767 +CN(CCC(=N)N)CC1=CC=C(C=C1)C(F)(F)F pubchem_cid_61692776 +CCN(CCC(=N)N)CC1=CC=C(C=C1)C(F)(F)F pubchem_cid_61692778 +CCC(C(=N)N)N(C)CC1=CC(=CC=C1)F pubchem_cid_61697609 +CCC(C(=N)N)N(C)CC1=CC=CC=C1F pubchem_cid_61697682 +CCC(C(=N)N)N(C)CC1=CC=C(C=C1)F pubchem_cid_61697808 +CN=C(C1=CC(=C(C=C1)F)C(F)(F)F)NN pubchem_cid_61710107 +CCCC(=NCCC1=CC=C(C=C1)F)N pubchem_cid_62049622 +CC1CCCN(C1C)CC2=C(C=C(C=C2)C(=N)N)F 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pubchem_cid_584050 +C1=C(C=C(C(=C1F)CN)F)F pubchem_cid_2777046 +C1=CC=C(C=C1)C(=S)NN pubchem_cid_3361911 +C1=CC(=CC=C1CN=[N+]=[N-])F pubchem_cid_11205864 +C1=CC(=CC=C1C(=N)N)[N+](=O)[O-] pubchem_cid_117475 +C1=CC=C(C=C1)[C@@H](CC#N)N pubchem_cid_66957844 +CC1=CC=C(C=C1)/C(=N/N=C(N)N)/P(O)O pubchem_cid_91896176 +C1/C(=C\C2=CC=C(C=C2)C(=N)N)/C(=O)/C(=C/C3=CC=C(C=C3)C(=N)N)/C1 pubchem_cid_10066101 +C\1C/C(=C/C2=CC=C(C=C2)C(=N)N)/C(=O)/C1=C/C3=CC=C(C=C3)C(=N)N pubchem_cid_10497634 +C1C(C(=NC(=N1)N)N)CC2=CC=CC=C2 pubchem_cid_44344895 +C1=CC=C(C=C1)CNS(=O)(=O)NO pubchem_cid_44401744 +B1(N=C(NO1)C2=CC=CC=C2)C3=CC(=CC=C3)Br pubchem_cid_129886905 +B1(N=C(NO1)C2=CC=CC=C2)C3=CC(=CC=C3)Cl pubchem_cid_129886924 +CC(C)(/C(=N\O)/C1=CC=CC=C1)NO pubchem_cid_5392395 +C1=CC=C(C=C1)CN=C=[Se] pubchem_cid_12506035 +C1C(N=C(C2=C1C=C(C=C2)F)N)C3=CC=C(C=C3)F pubchem_cid_18785788 +C1C(N=C(C2=C1C(=CC=C2)F)N)C3=CC=C(C=C3)F pubchem_cid_18785905 +C1=CC=C(C=C1)C/[N+](=C/C2=CC=CC=C2)/[O-] pubchem_cid_5368368 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+CCC(C(C1=CC=C(C=C1)F)N)N pubchem_cid_86058336 +C1=CC=C(C=C1)CN=CC2=C(C=C(C=C2F)F)F pubchem_cid_86172183 +C1=CC=C(C=C1)CN=CC2=C(C=CC=C2F)F pubchem_cid_101453919 +C1=CC=C(C=C1)CN=CC2=C(C=CC(=C2F)F)F pubchem_cid_101453920 +C1=CC(=CC=C1/C(=C\F)/CN)F pubchem_cid_129705463 +C1=CC=C(C=C1)CN=C(C(F)(F)F)F pubchem_cid_129862122 +C[C@](CC=C)(C1=CC=CC=C1F)N pubchem_cid_130706698 +C[C@H]1CCN=C(N1)C2=CC=CC=C2F pubchem_cid_134861075 +C1CCC(=NCC2=CC=CC=C2)C(C1)F pubchem_cid_135086496 +C1=CC=C(C(=C1)/C=N/C(/N=C/C2=CC=CC=C2F)C3=CC=CC=C3F)F pubchem_cid_139078255 +CCC(C)(C1=CC=CC=C1)[N+]#[C-] pubchem_cid_422123 +CC1(C(=[N+](C(=[N+]1[O-])C2=CC=CC=C2)[O-])C3=CC=CC=C3)C pubchem_cid_2218345 +C1CCC(=NCC1)N/N=C/C2=CC=CC=C2 pubchem_cid_9565653 +CC1=CC(=CC(=C1)/C(=N/OC(=O)C(C)(C)C)/N)/C(=N/OC(=O)C(C)(C)C)/N pubchem_cid_9580594 +CC1=CC=CC=C1/C(=N/C2=NNN=N2)/N pubchem_cid_13897331 +C1=CC=C(C=C1)/C(=C(\C2=CC=CC=C2)/N)/C#N pubchem_cid_54610653 +CCN=C1C2=CC=CC=C2C(=NCC)N1 pubchem_cid_135492822 +CO/N=C(\C1=CC=C(C=C1)CC2=CC=C(C=C2)CC3=CC(=CC=C3)/C(=N/OC)/N)/N pubchem_cid_164626667 +B1(N=C(NO1)C2=CC=C(C=C2)/C=C/3\CCC(C(=C3C)CC)(C)C)C4=CC=CC=C4 pubchem_cid_172447784 +C1=CC(=CC(=C1)F)/C(=C/C#N)/N pubchem_cid_12540166 +C1=CC=C(C=C1)C=C=CCN pubchem_cid_16005219 +C1=CC(=CC(=C1)Cl)CN=C(C2=CC(=CC=C2)F)N pubchem_cid_20706457 +CSC1=NC(=O)NC(=N1)C2=CC=CC=C2 pubchem_cid_15961 +C1=CC=C(C=C1)C2C(=N2)C3=CC=CC=C3 pubchem_cid_140090 +C1=CC=C(C=C1)CC2=NNC(=NN2)CC3=CC=CC=C3 pubchem_cid_725764 +C1CN(C(=N1)C2=CC=CC=C2)CC3=CC=CC=C3 pubchem_cid_11207103 +CC1=CC=C(C=C1)C(=C)CN pubchem_cid_13737670 +C1=CC=C(C=C1)C2=NN=NS2 pubchem_cid_141919 +CC1=NN=C(N=N1)C2=CC=CC=C2 pubchem_cid_750329 +CCC(CN)(C1=CC=CC=C1)N pubchem_cid_21149 +C1=CC(=CC(=C1)Br)CN=C(N)N pubchem_cid_56044 +CCCC(CN)(C1=CC=CC=C1)N pubchem_cid_199817 +C1=CC=C(C=C1)C(=NC2=CC=CC(=C2)C(F)(F)F)N pubchem_cid_211746 +CC1=CC=C(C=C1)CNN pubchem_cid_33348 +C1=CC=C(C=C1)CNCCCN pubchem_cid_83811 +C1=CC=C(C=C1)CC(CN)N pubchem_cid_413434 +CC(C1=CC=CC=C1)[N+]#[C-] pubchem_cid_519905 +C[C@@H](C1=CC=CC=C1)[N+]#[C-] pubchem_cid_10983286 +C1=CC=C(C=C1)C2(N=N2)C(F)(F)F pubchem_cid_11116743 +C1=CC=C(C=C1)[C@@H](C(F)(F)F)N pubchem_cid_11389695 +CONCC1=CC=CC=C1 pubchem_cid_11815413 +CC(C)(C1=CC=C(C=C1)F)N pubchem_cid_13025665 +CC(C)(C1=CC=CC=C1F)N pubchem_cid_13569520 +C1=CC=C(C=C1)/C/2=N/C(=N\N=C(/C=C2)\C3=CC=CC=C3)/N pubchem_cid_9552085 +C1=CC=C2C(=C1)C(=NS(=O)(=O)N2)N pubchem_cid_13330335 +C1=CC(=CC=C1C2=NNN=N2)I pubchem_cid_12288323 +CC(=C)C1=CC(=CC=C1)C(C)(C)N pubchem_cid_14716541 +CC1=CC(=CC=C1)C2C(=NS(=O)(=O)N2)N pubchem_cid_2892683 +C1CC2=CC=CC=C2/C(=N/N=C(N)N)/C1 pubchem_cid_9718990 +C1=CC(=CC(=C1)C(=N)N)C2=CC3=C(C=C2)C=CC(=C3)C4=CC(=CC=C4)C(=N)N pubchem_cid_10338813 +C1=CC(=CC2=C1C=CC(=C2)C(=N)N)C3=CC=C(C=C3)C4=CC=C(C=C4)C(=N)N pubchem_cid_16126642 +C/C(=C(\C1=CC=CC=C1)/Cl)/C=N/N=C(N)N pubchem_cid_25147765 +C1=CC=C(C=C1)C2=CS/C(=C\C3=CC=C(C=C3)F)/C(=N)N=N2 pubchem_cid_40484268 +C1=CC=C(C(=C1)C(=NCC2=CC(=CC=C2)Cl)N)Cl pubchem_cid_44374973 +C1=CC=C(C=C1)/C(=N\N=C(N)N)/C=C/C2=CC=CC=C2F pubchem_cid_52943886 +C1=CC=C(C=C1)/C(=N\N=C(N)N)/C=C/C2=CC=C(C=C2)F pubchem_cid_52946395 +C=CCN1CC(=C(C1=N)C2=CC=CC=C2)O pubchem_cid_135415481 +CC(C)(CC1=CC=CC=C1)N pubchem_cid_4771 +CNC(=NC)NCC1=CC=CC=C1 pubchem_cid_2368 +CN(C)CC1=CC=CC=C1 pubchem_cid_7681 +C1=CC=C(C=C1)CCCN pubchem_cid_16259 +C1=CC=C(C=C1)C(C2=CC=CC=C2)N pubchem_cid_7036 +CN1C(=NNC1=S)C2=CC=CC=C2 pubchem_cid_719799 +C1=CC=C(C=C1)C(=NN)C2=CC=CC=C2 pubchem_cid_79304 +C1=CC=C(C=C1)CCCCN pubchem_cid_83242 +C1=CC=C(C=C1)/C=N/N=C/C2=CC=CC=C2 pubchem_cid_5324610 +C1=CC=C(C=C1)C2=NNC(=O)N2 pubchem_cid_135418902 +C1=CC=C(C=C1)C=NN=CC2=CC=CC=C2 pubchem_cid_92130 +C1=CC(=CC(=C1)C(F)(F)F)CN pubchem_cid_75962 +CCC1=CC=C(C=C1)C(=S)N pubchem_cid_2525970 +CC1=CC=C(C=C1)C2=NNN=N2 pubchem_cid_285164 +C1=CC=C(C=C1)C2=NNC(=S)N2N pubchem_cid_737082 +C1=CC=C(C=C1)CNCCN pubchem_cid_77801 +CC1=NN=C(NC1=O)C2=CC=CC=C2 pubchem_cid_135472887 +C1=CC(=CC(=C1)F)C2=NNN=N2 pubchem_cid_333943 +CC(C)C1=CC=C(C=C1)CN pubchem_cid_138221 +C=CCNCC1=CC=CC=C1 pubchem_cid_521150 +C1=CC=C(C=C1)CN=C=O pubchem_cid_76639 +C1=CC(=C(C(=C1)Cl)CC(=N)N)Cl pubchem_cid_597357 +CC1=CC=C(C=C1)N=C(N)N pubchem_cid_409364 +C1=CC(=CC=C1C2=NC(=S)NN2)C(F)(F)F pubchem_cid_2743573 +C1=CC=C(C=C1)CCN=[N+]=[N-] pubchem_cid_145976 +C1=CC=C(C=C1)CCN=CC2=CC=CC=C2 pubchem_cid_576350 +C1=CC(=CC(=C1)Cl)CN=C(N)N pubchem_cid_41357 +CC(C)C(C1=CC=CC=C1)N pubchem_cid_4962875 +C1=CC=C(C(=C1)C2=NNN=N2)F pubchem_cid_596275 +C1=CC(=CC=C1C2=NNN=N2)F pubchem_cid_766140 +C[Si](C)(C)NCC1=CC=CC=C1 pubchem_cid_519016 +C1=CC=C(C=C1)CCC[NH3+] pubchem_cid_448752 +C1CC(=NC2=CC=CC=C21)N pubchem_cid_4102304 +CC(C)(C)C1=CC=C(C=C1)C2=NNC(=NN2)SC pubchem_cid_2813305 +C1=CC=C(C=C1)N=C2C3=CC=CC=C3C(=N2)N pubchem_cid_705539 +C1=CC(=CC=C1/C=N/N=C(N)N)C#N pubchem_cid_9560224 +C1=CC=C(C=C1)CC=N pubchem_cid_11734968 +C1=CC=C(C=C1)CN=S(F)F pubchem_cid_12211612 +C1=CC=C(C=C1)C([N+](=O)[O-])([N+](=O)[O-])[N+](=O)[O-] pubchem_cid_12503820 +C1=CC=C(C(=C1)C(=N)N)[N+](=O)[O-] pubchem_cid_12535783 +C1=CC=C(C=C1)CNS(=O)(=O)O pubchem_cid_12649342 +C1=CC(=CC=C1CNO)F pubchem_cid_14157467 +CNCC1=CC=C(C=C1)CNC pubchem_cid_14801555 +C1=CC=C(C(=C1)/C=N/N)F pubchem_cid_15514463 +C1=CC(=C(C(=C1C(=S)N)F)F)F pubchem_cid_19800537 +C1=CC(=CC=C1CC[Se]C(=N)N)CC[Se]C(=N)N pubchem_cid_46844534 +C1=CC=C(C=C1)C(C(=N)N)S(=O)(=O)F pubchem_cid_53940806 +C1=CC(=CC=C1C2=NC(=O)C=N2)F pubchem_cid_57092776 +C1=CC=C(C=C1)CNS(=O)(=O)F pubchem_cid_59403787 +C1=CC=C(C=C1)N=C(C2=CC=C(C=C2)C(F)(F)F)N pubchem_cid_72712936 +C1=CC=C(C(=C1)C=NN)F pubchem_cid_77545903 +C1CNC(=NC1)C2=CC=C(C=C2)C(F)(F)F pubchem_cid_101477526 +C1[C@H](C1C2=CC3=C(C=C2)C=C(C=C3)C(=N)N)C4=CC=CC=C4 pubchem_cid_3010978 +C/C(=N\N=C(N)N)/C1=CC(=CC(=C1)/C(=N\N=C(N)N)/C)/C(=N/N=C(N)N)/C pubchem_cid_9574208 +C1=CC=C(C=C1)CC2=NC3=CC=C4C(=NSN4)C3=N2 pubchem_cid_622351 +C1CN(C(=N1)C2=CC=CC=C2)C(=S)N pubchem_cid_977897 +C1=CC=C(C=C1)C2N=C(C(=N2)C3=CC=CC=C3)C4=CC=CC=C4 pubchem_cid_1201557 +C1=CC=C(C=C1)C(N)(P(=O)(O)O)P(=O)(O)O pubchem_cid_438132 +CC1=CC=C(C=C1)N=C(C)N pubchem_cid_352165 +C1CN=C1C2=CC=CC=C2 pubchem_cid_568635 +CC1(C=C(N=N1)C2=CC=CC=C2)C pubchem_cid_582268 +C1=CC=C(C=C1)C=NCC#N pubchem_cid_588729 +CC1(C(=NC(N1)(C)C)C2=CC=CC=C2)C pubchem_cid_604453 +C1CCC(CC1)(C2=CC=CC=C2)N=[N+]=[N-] pubchem_cid_2769487 +C[NH+](C)CC1=CC=CC=C1 pubchem_cid_3661619 +C1CN=C(N1)C2=CC(=CC=C2)C3=NCCN3 pubchem_cid_10536593 +C1=CC=C(C(=C1)CN=[N+]=[N-])CN=[N+]=[N-] pubchem_cid_10877881 +CC1=CC=CC=C1CN=[N+]=[N-] pubchem_cid_11040842 +CC1=CC=C(C=C1)CN=CC2=CC=C(C=C2)C pubchem_cid_11096215 +C1=CC(=C(C=C1/C(=N/O)/N)Cl)Cl pubchem_cid_11264185 +C1CCC(C1)(C2=CC=CC=C2)N=[N+]=[N-] pubchem_cid_12396745 +CC1=CC=CC=C1N=C(C)N pubchem_cid_12866780 +CC1=CC(=CC=C1)N=C(C)N pubchem_cid_12866781 +CCN(CC1=CC=CC=C1)C#N pubchem_cid_13213313 +C1=CC=C(C=C1)C(CN=[N+]=[N-])N=[N+]=[N-] pubchem_cid_13624377 +C1=CC=C(C=C1)/C=C/C(C2=CC=CC=C2)N pubchem_cid_15268441 +C1C2=CC=CC=C2N=C1N pubchem_cid_21597145 +C1=CC=C(C=C1)CC2=CC=C(C=C2)CN pubchem_cid_28344480 +CCCCCC/C(=N\NC1=NC(=C(C1)C)C2=CC=CC=C2)/C pubchem_cid_90665476 +CC(C(=NCC1=CC=CC=C1)N)SS(=O)(=O)O pubchem_cid_302479 +C1CC1/C(=N/N=C(N)N)/C2=CC=C(C=C2)F pubchem_cid_5357139 +CC(C)(C)N1CC2=CC=CC=C2C1=N pubchem_cid_1236973 +C1=CC=C(C=C1)/C(=C(/C2=CC=CC=C2)\N)/C#N pubchem_cid_3003894 +C1=CC=C(C=C1)C#CC2C=CC=CC2=N pubchem_cid_169502365 +C1C2=CC=CC=C2C(=N)N1CC(F)(F)F pubchem_cid_702588 +CC1=CC=C(C=C1)[C@@H]2C(=NS(=O)(=O)N2)N pubchem_cid_2274596 +CCC(C)N1CC2=CC=CC=C2C1=N pubchem_cid_2979958 +CCN(CC)CCN1CC2=CC=CC=C2C1=N pubchem_cid_5206666 +C1=CC=C(C=C1)/C(=N/S(=O)(=O)C2=C(C=C(C=C2)F)F)/N pubchem_cid_9587600 +CC(C)(C)CN=C(C1=CC=CC=C1C2=CC=CC=C2)NO pubchem_cid_56659382 +CC(=O)CC(=O)NC(=N)C1=CC=CC=C1 pubchem_cid_145925504 +B(C1=CC(=CC=C1)CCN=C(N)N)(O)O pubchem_cid_177664409 +B(C1=CC=CC=C1CCN=C(N)N)(O)O pubchem_cid_177664873 +C1=CC=C(C=C1)C(=NOC(=N)C(C(C(C(C(C(C(=N)ON=C(C2=CC=CC=C2)N)(F)F)(F)F)(F)F)(F)F)(F)F)(F)F)N pubchem_cid_4198697 +C1=CC=C(C=C1)/C(=N\OC(=N)C(F)(F)C(F)(F)C(F)(F)C(F)(F)C(F)(F)C(F)(F)C(=N)O/N=C(/N)\C2=CC=CC=C2)/N pubchem_cid_6380497 +C1=CC=C(C=C1)/C(=N/OC(=N)C(F)(F)C(F)(F)C(F)(F)C(F)(F)C(F)(F)C(F)(F)C(=N)O/N=C(\N)/C2=CC=CC=C2)/N pubchem_cid_9614060 +C[C@H]([C@@H](C1=CC=C(C=C1)F)N)N pubchem_cid_9980335 +C1=C(C=C(C=C1CN)C(F)(F)F)CN pubchem_cid_10512372 +CC(C)(C(C1=CC=CC=C1)N)F pubchem_cid_12546700 +C[C@@H]([C@@H](C1=CC=C(C=C1)F)N)N pubchem_cid_130730167 +CC[C@H]([C@@H](C1=CC=C(C=C1)F)N)N pubchem_cid_130882232 +CC1=CC=C(C=C1)CN=C(N)NN pubchem_cid_19068 +C1=CC(=CC=C1CN)[As](=O)(O)O pubchem_cid_224257 +C1=CC(=CC(=C1)F)C=NN=C(N)NO pubchem_cid_371646 +C1=CC(=CC(=C1)C(F)(F)F)C[NH3+] pubchem_cid_1614315 +C1=CC(=C(C(=C1)Cl)CC(=N)N)F pubchem_cid_3288757 +C1=CC(=CC=C1C=NN)F pubchem_cid_4360495 +C(C1=C(C(=C(C(=C1F)F)F)F)F)C(=N)N pubchem_cid_4572332 +CC1=C(C=CC(=C1)C[NH3+])F pubchem_cid_7009359 +C1=CC(=CC=C1CN=C(N)NN)F pubchem_cid_7454260 +C1=CC(=CC(=C1)C(F)(F)F)/C=N\N=C(N)N 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pubchem_cid_53403997 +C1=CC(=CC=C1C(F)F)C(=N)N pubchem_cid_83854591 +C1=CC(=C(C=C1F)I)C(=N)N pubchem_cid_168485081 +C1=CC(=C(C(=C1)F)I)C(=N)N pubchem_cid_168485132 +C1=CC=C(C=C1)/C(=N/S(=O)(=O)N)/N pubchem_cid_9602030 +C1=CC=C(C=C1)C(=NN=C(C2=CC=CC=C2)N)N pubchem_cid_456726 diff --git a/data/datasets/rdock_3PTB_50k_pubchem_local/ligands/obabel_batches/batch_00001/logs/._batch_00001_to_sdf.stderr.log b/data/datasets/rdock_3PTB_50k_pubchem_local/ligands/obabel_batches/batch_00001/logs/._batch_00001_to_sdf.stderr.log new file mode 100644 index 0000000000000000000000000000000000000000..ee537d225f1b1eed0d0f4ed0b171fdc63ca71d82 Binary files /dev/null and b/data/datasets/rdock_3PTB_50k_pubchem_local/ligands/obabel_batches/batch_00001/logs/._batch_00001_to_sdf.stderr.log differ diff --git a/data/datasets/rdock_3PTB_50k_pubchem_local/ligands/obabel_batches/batch_00001/logs/._batch_00001_to_sdf.stdout.log b/data/datasets/rdock_3PTB_50k_pubchem_local/ligands/obabel_batches/batch_00001/logs/._batch_00001_to_sdf.stdout.log new file mode 100644 index 0000000000000000000000000000000000000000..ee537d225f1b1eed0d0f4ed0b171fdc63ca71d82 Binary files /dev/null and b/data/datasets/rdock_3PTB_50k_pubchem_local/ligands/obabel_batches/batch_00001/logs/._batch_00001_to_sdf.stdout.log differ diff --git a/data/datasets/rdock_3PTB_50k_pubchem_local/ligands/obabel_batches/batch_00001/logs/._commands.log b/data/datasets/rdock_3PTB_50k_pubchem_local/ligands/obabel_batches/batch_00001/logs/._commands.log new file mode 100644 index 0000000000000000000000000000000000000000..ee537d225f1b1eed0d0f4ed0b171fdc63ca71d82 Binary files /dev/null and b/data/datasets/rdock_3PTB_50k_pubchem_local/ligands/obabel_batches/batch_00001/logs/._commands.log differ diff --git a/data/datasets/rdock_3PTB_50k_pubchem_local/ligands/obabel_batches/batch_00001/logs/batch_00001_to_sdf.stderr.log b/data/datasets/rdock_3PTB_50k_pubchem_local/ligands/obabel_batches/batch_00001/logs/batch_00001_to_sdf.stderr.log new file mode 100644 index 0000000000000000000000000000000000000000..b1d2072b5861ed9e9e11bfbd73097978d98aa62e --- /dev/null +++ b/data/datasets/rdock_3PTB_50k_pubchem_local/ligands/obabel_batches/batch_00001/logs/batch_00001_to_sdf.stderr.log @@ -0,0 +1,7 @@ +============================== +*** Open Babel Error in Do + 3D coordinate generation failed +============================== +*** Open Babel Warning in WriteMolecule + No 2D or 3D coordinates exist. Stereochemical information will be stored using an Open Babel extension. 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--git a/data/datasets/rdock_3PTB_50k_pubchem_local/ligands/obabel_batches/batch_00005/logs/._batch_00005_to_sdf.stderr.log b/data/datasets/rdock_3PTB_50k_pubchem_local/ligands/obabel_batches/batch_00005/logs/._batch_00005_to_sdf.stderr.log new file mode 100644 index 0000000000000000000000000000000000000000..ee537d225f1b1eed0d0f4ed0b171fdc63ca71d82 Binary files /dev/null and b/data/datasets/rdock_3PTB_50k_pubchem_local/ligands/obabel_batches/batch_00005/logs/._batch_00005_to_sdf.stderr.log differ diff --git a/data/datasets/rdock_3PTB_50k_pubchem_local/ligands/obabel_batches/batch_00005/logs/._batch_00005_to_sdf.stdout.log b/data/datasets/rdock_3PTB_50k_pubchem_local/ligands/obabel_batches/batch_00005/logs/._batch_00005_to_sdf.stdout.log new file mode 100644 index 0000000000000000000000000000000000000000..ee537d225f1b1eed0d0f4ed0b171fdc63ca71d82 Binary files /dev/null and b/data/datasets/rdock_3PTB_50k_pubchem_local/ligands/obabel_batches/batch_00005/logs/._batch_00005_to_sdf.stdout.log differ diff --git a/data/datasets/rdock_3PTB_50k_pubchem_local/ligands/obabel_batches/batch_00005/logs/._commands.log b/data/datasets/rdock_3PTB_50k_pubchem_local/ligands/obabel_batches/batch_00005/logs/._commands.log new file mode 100644 index 0000000000000000000000000000000000000000..ee537d225f1b1eed0d0f4ed0b171fdc63ca71d82 Binary files /dev/null and b/data/datasets/rdock_3PTB_50k_pubchem_local/ligands/obabel_batches/batch_00005/logs/._commands.log differ diff --git a/data/datasets/rdock_3PTB_50k_pubchem_local/ligands/obabel_batches/batch_00005/logs/batch_00005_to_sdf.stderr.log b/data/datasets/rdock_3PTB_50k_pubchem_local/ligands/obabel_batches/batch_00005/logs/batch_00005_to_sdf.stderr.log new file mode 100644 index 0000000000000000000000000000000000000000..59052e9413108527f932a6cbdffbff20ecc26efe --- /dev/null +++ b/data/datasets/rdock_3PTB_50k_pubchem_local/ligands/obabel_batches/batch_00005/logs/batch_00005_to_sdf.stderr.log @@ -0,0 +1,13 @@ +============================== +*** Open Babel Error in Do + 3D coordinate generation failed +============================== +*** Open Babel Warning in WriteMolecule + No 2D or 3D coordinates exist. Stereochemical information will be stored using an Open Babel extension. To generate 2D or 3D coordinates instead use --gen2D or --gen3D. +============================== +*** Open Babel Error in Do + 3D coordinate generation failed +============================== +*** Open Babel Warning in WriteMolecule + No 2D or 3D coordinates exist. Stereochemical information will be stored using an Open Babel extension. To generate 2D or 3D coordinates instead use --gen2D or --gen3D. +250 molecules converted diff --git a/data/datasets/rdock_3PTB_50k_pubchem_local/ligands/obabel_batches/batch_00005/logs/batch_00005_to_sdf.stdout.log b/data/datasets/rdock_3PTB_50k_pubchem_local/ligands/obabel_batches/batch_00005/logs/batch_00005_to_sdf.stdout.log new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/data/datasets/rdock_3PTB_50k_pubchem_local/ligands/obabel_batches/batch_00005/logs/commands.log b/data/datasets/rdock_3PTB_50k_pubchem_local/ligands/obabel_batches/batch_00005/logs/commands.log new file mode 100644 index 0000000000000000000000000000000000000000..4ed513d6d1d15aa906ea04f28fbabe0dcef68072 --- /dev/null +++ b/data/datasets/rdock_3PTB_50k_pubchem_local/ligands/obabel_batches/batch_00005/logs/commands.log @@ -0,0 +1 @@ +{"command": ["/Users/makardorohuntsev/miniconda3/envs/portable-rdock-pipeline/bin/obabel", 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WriteMolecule + No 2D or 3D coordinates exist. Stereochemical information will be stored using an Open Babel extension. To generate 2D or 3D coordinates instead use --gen2D or --gen3D. +============================== +*** Open Babel Error in Do + 3D coordinate generation failed +============================== +*** Open Babel Warning in WriteMolecule + No 2D or 3D coordinates exist. Stereochemical information will be stored using an Open Babel extension. To generate 2D or 3D coordinates instead use --gen2D or --gen3D. +============================== +*** Open Babel Error in Do + 3D coordinate generation failed +============================== +*** Open Babel Warning in WriteMolecule + No 2D or 3D coordinates exist. Stereochemical information will be stored using an Open Babel extension. To generate 2D or 3D coordinates instead use --gen2D or --gen3D. +250 molecules converted diff --git a/data/datasets/rdock_3PTB_50k_pubchem_local/ligands/obabel_batches/batch_00019/logs/batch_00019_to_sdf.stdout.log b/data/datasets/rdock_3PTB_50k_pubchem_local/ligands/obabel_batches/batch_00019/logs/batch_00019_to_sdf.stdout.log new file mode 100644 index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 diff --git a/data/datasets/rdock_3PTB_50k_pubchem_local/ligands/obabel_batches/batch_00019/logs/commands.log b/data/datasets/rdock_3PTB_50k_pubchem_local/ligands/obabel_batches/batch_00019/logs/commands.log new file mode 100644 index 0000000000000000000000000000000000000000..6701aadec32d049adf40a8e8221a726d2f95ee76 --- /dev/null +++ b/data/datasets/rdock_3PTB_50k_pubchem_local/ligands/obabel_batches/batch_00019/logs/commands.log @@ -0,0 +1 @@ +{"command": ["/Users/makardorohuntsev/miniconda3/envs/portable-rdock-pipeline/bin/obabel", 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