OneScience-Group/DiffDock

1# ============================================================================2# DiffDock CGModel Sampling Configuration3#4# IMPORTANT: Update all filesystem paths below to match your environment.5#   - model_dir: must contain a CGModel checkpoint + model_parameters.yml6#   - protein_path: path to receptor PDB7#   - ligand_description: SMILES string or path to .sdf/.mol28#9# CSV batch mode:10#   Set protein_ligand_csv instead of the single-complex fields.11#   CSV columns: complex_name, protein_path, ligand_description, protein_sequence12#13# Confidence rerank:14#   Set confidence_model_dir to a CGModel-based confidence checkpoint dir.15# ============================================================================16 17runtime:18  device: auto19  loglevel: INFO20  out_dir: examples/biosciences/diffdock/outputs/sample21 22model:23  model_dir: ${ONESCIENCE_DATASETS_DIR}/diffdock/score_model24  ckpt: best_ema_inference_epoch_model.pt25  old_score_model: false26 27confidence:28  confidence_model_dir: ${ONESCIENCE_DATASETS_DIR}/diffdock/confidence_model29  confidence_ckpt: best_model_epoch75.pt30  old_confidence_model: false31 32input:33  protein_ligand_csv: null34  complex_name: 6o5u_test35  protein_path: examples/biosciences/diffdock/data/6o5u_protein_processed.pdb36  protein_sequence: null37  ligand_description: examples/biosciences/diffdock/data/6o5u_ligand.sdf38  lm_embeddings: null39 40sampling:41  samples_per_complex: 1042  batch_size: 1043  inference_steps: 2044  actual_steps: null45  sigma_schedule: expbeta46  inf_sched_alpha: 1.047  inf_sched_beta: 1.048  no_random: false49  no_final_step_noise: true50  ode: false51  choose_residue: false52  initial_noise_std_proportion: 1.053  temp_sampling_tr: 1.054  temp_psi_tr: 0.055  temp_sigma_data_tr: 0.556  temp_sampling_rot: 1.057  temp_psi_rot: 0.058  temp_sigma_data_rot: 0.559  temp_sampling_tor: 1.060  temp_psi_tor: 0.061  temp_sigma_data_tor: 0.562