configs/overnight_stop_model.yaml

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