configs/evaluate.yml

# ============================================================================
# DiffDock CGModel Dataset Evaluation Configuration
#
# IMPORTANT: Update all filesystem paths below to match your environment.
#
# Supported dataset values: pdbbind | moad | generalisation
#
# External dependencies (optional):
#   gnina_minimize=true  → requires `gnina` executable on PATH
#   RMSD computations     → requires `spyrmsd` (pip install spyrmsd)
# ============================================================================

runtime:
  run_name: diffdock_eval_example
  project: diffdock
  device: auto
  out_dir: examples/biosciences/diffdock/outputs/evaluate
  wandb: false
  num_cpu: null
  restrict_cpu: false

model:
  model_dir: /public/home/liuyx19/modelscope/diffdock/outputs/train/diffdock_pdbbind_smoke100_val20_cpu
  ckpt: best_model.pt
  old_score_model: false  # must stay false; old_* score-model paths are intentionally not migrated
  no_model: false
  force_fixed_center_conv: false

confidence:
  confidence_model_dir: null
  confidence_ckpt: best_model.pt
  old_confidence_model: false  # must stay false; old confidence-model paths are intentionally not migrated

data:
  dataset: pdbbind  # supported: pdbbind | moad | generalisation; unsupported: pdbsidechain | distillation
  cache_path: /public/home/liuyx19/modelscope/diffdock/cache
  data_dir: /public/share/sugonhpcapp01/onestore/onedatasets/diffdock/datasets/PDBBind_processed
  split_path: /public/share/sugonhpcapp01/onestore/onedatasets/diffdock/datasets/splits/timesplit_no_lig_overlap_val
  split: val
  limit_complexes: 0
  num_workers: 1
  chain_cutoff: null
  protein_file: protein_processed
  ligand_file: ligand
  esm_embeddings_path: null
  moad_esm_embeddings_sequences_path: null
  not_knn_only_graph: false
  include_miscellaneous_atoms: false
  triple_training: false  # unsupported in the current migration; will fail fast if set true
  unroll_clusters: false
  remove_pdbbind: false
  min_ligand_size: 0
  max_receptor_size: null
  remove_promiscuous_targets: null
  matching_popsize: 40
  matching_maxiter: 40

sampling:
  batch_size: 20
  inference_steps: 20
  actual_steps: null
  samples_per_complex: 10
  no_random: false
  no_final_step_noise: true
  ode: false
  sigma_schedule: expbeta
  inf_sched_alpha: 1.0
  inf_sched_beta: 1.0
  pocket_knowledge: false
  no_random_pocket: false
  pocket_tr_max: 3.0
  pocket_cutoff: 5.0
  different_schedules: false
  resample_rdkit: false
  skip_matching: false
  initial_noise_std_proportion: -1.0
  choose_residue: false
  limit_failures: 5
  tqdm: true
  temp_sampling_tr: 1.0
  temp_psi_tr: 0.0
  temp_sigma_data_tr: 0.5
  temp_sampling_rot: 1.0
  temp_psi_rot: 0.0
  temp_sigma_data_rot: 0.5
  temp_sampling_tor: 1.0
  temp_psi_tor: 0.0
  temp_sigma_data_tor: 0.5

outputs:
  save_visualisation: false
  save_complexes: false
  complexes_save_path: null

gnina:
  gnina_minimize: false
  gnina_path: gnina
  gnina_full_dock: false
  save_gnina_metrics: false
  gnina_autobox_add: 4.0
  gnina_poses_to_optimize: 1