Reset repository and upload final project (part 27)

.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

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

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"
+    }
+  ]
+}

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

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

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

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
+

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
+

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

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]

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

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

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

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

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

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

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

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

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

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

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

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",
+      "candidate_ligand": false
+    },
+    {
+      "resname": "HOH",
+      "chain": "A",
+      "residue_id": "583",
+      "atom_count": 1,
+      "heavy_atom_count": 1,
+      "ignored": true,
+      "ignored_reason": "solvent",
+      "candidate_ligand": false
+    },
+    {
+      "resname": "HOH",
+      "chain": "A",
+      "residue_id": "604",
+      "atom_count": 1,
+      "heavy_atom_count": 1,
+      "ignored": true,
+      "ignored_reason": "solvent",
+      "candidate_ligand": false
+    },
+    {
+      "resname": "HOH",
+      "chain": "A",
+      "residue_id": "700",
+      "atom_count": 1,
+      "heavy_atom_count": 1,
+      "ignored": true,
+      "ignored_reason": "solvent",
+      "candidate_ligand": false
+    },
+    {
+      "resname": "HOH",
+      "chain": "A",
+      "residue_id": "701",
+      "atom_count": 1,
+      "heavy_atom_count": 1,
+      "ignored": true,
+      "ignored_reason": "solvent",
+      "candidate_ligand": false
+    },
+    {
+      "resname": "HOH",
+      "chain": "A",
+      "residue_id": "702",
+      "atom_count": 1,
+      "heavy_atom_count": 1,
+      "ignored": true,
+      "ignored_reason": "solvent",
+      "candidate_ligand": false
+    },
+    {
+      "resname": "HOH",
+      "chain": "A",
+      "residue_id": "703",
+      "atom_count": 1,
+      "heavy_atom_count": 1,
+      "ignored": true,
+      "ignored_reason": "solvent",
+      "candidate_ligand": false
+    },
+    {
+      "resname": "HOH",
+      "chain": "A",
+      "residue_id": "704",
+      "atom_count": 1,
+      "heavy_atom_count": 1,
+      "ignored": true,
+      "ignored_reason": "solvent",
+      "candidate_ligand": false
+    },
+    {
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data/datasets/rdock_3PTB_50k_pubchem_local/ligands/all_ligands.sdf

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