OneScience-Group/DiffDock

1# ============================================================================2# DiffDock CGModel Dataset Evaluation Configuration3#4# IMPORTANT: Update all filesystem paths below to match your environment.5#6# Supported dataset values: pdbbind | moad | generalisation7#8# External dependencies (optional):9#   gnina_minimize=true  → requires `gnina` executable on PATH10#   RMSD computations     → requires `spyrmsd` (pip install spyrmsd)11# ============================================================================12 13runtime:14  run_name: diffdock_eval_example15  project: diffdock16  device: auto17  out_dir: examples/biosciences/diffdock/outputs/evaluate18  wandb: false19  num_cpu: null20  restrict_cpu: false21 22model:23  model_dir: /public/home/liuyx19/modelscope/diffdock/outputs/train/diffdock_pdbbind_smoke100_val20_cpu24  ckpt: best_model.pt25  old_score_model: false  # must stay false; old_* score-model paths are intentionally not migrated26  no_model: false27  force_fixed_center_conv: false28 29confidence:30  confidence_model_dir: null31  confidence_ckpt: best_model.pt32  old_confidence_model: false  # must stay false; old confidence-model paths are intentionally not migrated33 34data:35  dataset: pdbbind  # supported: pdbbind | moad | generalisation; unsupported: pdbsidechain | distillation36  cache_path: /public/home/liuyx19/modelscope/diffdock/cache37  data_dir: /public/share/sugonhpcapp01/onestore/onedatasets/diffdock/datasets/PDBBind_processed38  split_path: /public/share/sugonhpcapp01/onestore/onedatasets/diffdock/datasets/splits/timesplit_no_lig_overlap_val39  split: val40  limit_complexes: 041  num_workers: 142  chain_cutoff: null43  protein_file: protein_processed44  ligand_file: ligand45  esm_embeddings_path: null46  moad_esm_embeddings_sequences_path: null47  not_knn_only_graph: false48  include_miscellaneous_atoms: false49  triple_training: false  # unsupported in the current migration; will fail fast if set true50  unroll_clusters: false51  remove_pdbbind: false52  min_ligand_size: 053  max_receptor_size: null54  remove_promiscuous_targets: null55  matching_popsize: 4056  matching_maxiter: 4057 58sampling:59  batch_size: 2060  inference_steps: 2061  actual_steps: null62  samples_per_complex: 1063  no_random: false64  no_final_step_noise: true65  ode: false66  sigma_schedule: expbeta67  inf_sched_alpha: 1.068  inf_sched_beta: 1.069  pocket_knowledge: false70  no_random_pocket: false71  pocket_tr_max: 3.072  pocket_cutoff: 5.073  different_schedules: false74  resample_rdkit: false75  skip_matching: false76  initial_noise_std_proportion: -1.077  choose_residue: false78  limit_failures: 579  tqdm: true80  temp_sampling_tr: 1.081  temp_psi_tr: 0.082  temp_sigma_data_tr: 0.583  temp_sampling_rot: 1.084  temp_psi_rot: 0.085  temp_sigma_data_rot: 0.586  temp_sampling_tor: 1.087  temp_psi_tor: 0.088  temp_sigma_data_tor: 0.589 90outputs:91  save_visualisation: false92  save_complexes: false93  complexes_save_path: null94 95gnina:96  gnina_minimize: false97  gnina_path: gnina98  gnina_full_dock: false99  save_gnina_metrics: false100  gnina_autobox_add: 4.0101  gnina_poses_to_optimize: 1102