| # ============================================================================ | |
| # DiffDock CGModel Sampling Configuration | |
| # | |
| # IMPORTANT: Update all filesystem paths below to match your environment. | |
| # - model_dir: must contain a CGModel checkpoint + model_parameters.yml | |
| # - protein_path: path to receptor PDB | |
| # - ligand_description: SMILES string or path to .sdf/.mol2 | |
| # | |
| # CSV batch mode: | |
| # Set protein_ligand_csv instead of the single-complex fields. | |
| # CSV columns: complex_name, protein_path, ligand_description, protein_sequence | |
| # | |
| # Confidence rerank: | |
| # Set confidence_model_dir to a CGModel-based confidence checkpoint dir. | |
| # ============================================================================ | |
| runtime: | |
| device: auto | |
| loglevel: INFO | |
| out_dir: examples/biosciences/diffdock/outputs/sample | |
| model: | |
| model_dir: ${ONESCIENCE_DATASETS_DIR}/diffdock/score_model | |
| ckpt: best_ema_inference_epoch_model.pt | |
| old_score_model: false | |
| confidence: | |
| confidence_model_dir: ${ONESCIENCE_DATASETS_DIR}/diffdock/confidence_model | |
| confidence_ckpt: best_model_epoch75.pt | |
| old_confidence_model: false | |
| input: | |
| protein_ligand_csv: null | |
| complex_name: 6o5u_test | |
| protein_path: examples/biosciences/diffdock/data/6o5u_protein_processed.pdb | |
| protein_sequence: null | |
| ligand_description: examples/biosciences/diffdock/data/6o5u_ligand.sdf | |
| lm_embeddings: null | |
| sampling: | |
| samples_per_complex: 10 | |
| batch_size: 10 | |
| inference_steps: 20 | |
| actual_steps: null | |
| sigma_schedule: expbeta | |
| inf_sched_alpha: 1.0 | |
| inf_sched_beta: 1.0 | |
| no_random: false | |
| no_final_step_noise: true | |
| ode: false | |
| choose_residue: false | |
| initial_noise_std_proportion: 1.0 | |
| 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 | |