| all_atoms: true | |
| atom_max_neighbors: 8 | |
| atom_radius: 5 | |
| balance: false | |
| batch_size: 8 | |
| batch_size_preprocessing: 1 | |
| best_model_save_frequency: 5 | |
| c_alpha_max_neighbors: 24 | |
| cache_creation_id: 1 | |
| cache_ids_to_combine: | |
| - '1' | |
| cache_path: data/large_cache_confidence | |
| chain_cutoff: 10 | |
| ckpt: best_model.pt | |
| confidence_dropout: 0.0 | |
| confidence_no_batchnorm: false | |
| config: null | |
| cross_distance_embed_dim: 32 | |
| cross_max_distance: 80 | |
| data_dir: data/zincbind_cleaned_processed | |
| distance_embed_dim: 32 | |
| dropout: 0.1 | |
| dynamic_max_cross: true | |
| embedding_scale: 10000 | |
| embedding_type: sinusoidal | |
| esm_embeddings_path: data/esm2_3billion_embeddings.pt | |
| inference_steps: 20 | |
| limit_complexes: 0 | |
| log_dir: workdir | |
| lr: 0.001 | |
| main_metric: confidence_loss | |
| main_metric_goal: min | |
| matching_maxiter: 20 | |
| matching_popsize: 20 | |
| max_lig_size: null | |
| max_radius: 5.0 | |
| model_save_frequency: 0 | |
| multiplicity: 1 | |
| n_epochs: 100 | |
| no_batch_norm: false | |
| no_torsion: false | |
| ns: 24 | |
| num_conformers: 1 | |
| num_conv_layers: 5 | |
| num_workers: 1 | |
| nv: 6 | |
| original_model_dir: workdir/large_all_atoms_model | |
| original_pdb_dir: workdir | |
| project: diffdock_confidence | |
| receptor_radius: 15.0 | |
| remove_hs: true | |
| restart_dir: null | |
| rmsd_classification_cutoff: 5.0 | |
| rmsd_prediction: false | |
| run_name: large_confidence_model | |
| samples_per_complex: 1 | |
| scale_by_sigma: true | |
| scheduler: plateau | |
| scheduler_patience: 50 | |
| sigma_embed_dim: 32 | |
| split_test: data/splits/test_metal3d.txt | |
| split_train: data/splits/train.txt | |
| split_val: data/splits/val.txt | |
| transfer_weights: false | |
| use_original_model_cache: false | |
| use_second_order_repr: false | |
| w_decay: 0.0 | |
| wandb: true | |