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