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]