| accounting: |
| checkpoint_dir: /sharefs/qiukeyue/project/logs/qiukeyue_bfn_sbdd/train_multi_kekulize/4b71cc6_26712/checkpoints |
| dump_config_path: /sharefs/qiukeyue/project/logs/qiukeyue_bfn_sbdd/train_multi_kekulize/4b71cc6_26712/config.yaml |
| generated_mol_dir: /sharefs/qiukeyue/project/logs/qiukeyue_bfn_sbdd/train_multi_kekulize/4b71cc6_26712/generated_mol |
| logdir: /sharefs/qiukeyue/project/logs/qiukeyue_bfn_sbdd/train_multi_kekulize/4b71cc6_26712 |
| test_outputs_dir: /sharefs/qiukeyue/project/logs/qiukeyue_bfn_sbdd/train_multi_kekulize/4b71cc6_26712/test_outputs |
| wandb_logdir: /sharefs/qiukeyue/project/logs/qiukeyue_bfn_sbdd/train_multi_kekulize/4b71cc6_26712 |
| best_ckpt: val_loss |
| ckpt_path: null |
| data: |
| atom_decoder: |
| - H |
| - C |
| - N |
| - O |
| - F |
| - P |
| - S |
| - Cl |
| colors_dic: |
| - '#FFFFFF99' |
| - C7 |
| - C0 |
| - C3 |
| - C1 |
| - C4 |
| - C8 |
| - C9 |
| name: pl |
| normalizer_dict: |
| pos: 2.0 |
| path: /sharefs/share/sbdd_data/crossdocked_v1.1_rmsd1.0_pocket10 |
| radius_dic: |
| - 0.3 |
| - 0.6 |
| - 0.6 |
| - 0.6 |
| - 0.6 |
| - 0.6 |
| - 0.6 |
| - 0.6 |
| smiles_path: /sharefs/share/sbdd_data/crossdocked_v1.1_rmsd1.0_pocket10_smiles.pkl |
| split: /sharefs/share/sbdd_data/crossdocked_pose_split_kekulize.pt |
| transform: |
| ligand_atom_mode: add_aromatic |
| version: kekulize |
| with_split: true |
| debug: false |
| decouple_mode: none |
| dynamics: |
| beta1: 1.0 |
| beta1_aromatic: 3.0 |
| beta1_bond: 1.0 |
| beta1_charge: 1.5 |
| bond_net_type: lin |
| center_pos_mode: protein |
| destination_prediction: true |
| discrete_steps: 1000 |
| ligand_atom_aromatic_dim: 2 |
| ligand_atom_charge_dim: 3 |
| ligand_atom_feature_dim: 13 |
| ligand_atom_type_dim: 8 |
| net_config: |
| act_fn: relu |
| adaptive_norm: false |
| cutoff_mode: knn |
| dropout: 0.1 |
| edge_feat_dim: 4 |
| h_node_in_bond_net: true |
| hidden_dim: 128 |
| knn: 32 |
| n_heads: 16 |
| name: unio2net_bond |
| norm: true |
| num_blocks: 1 |
| num_bond_classes: 4 |
| num_layers: 4 |
| num_r_gaussian: 20 |
| r_max: 10.0 |
| sync_twoup: false |
| x2h_out_fc: false |
| node_indicator: true |
| pos_init_mode: zero |
| pred_connectivity: false |
| pred_given_all: false |
| protein_atom_feature_dim: 27 |
| sampling_strategy: end_back_pmf |
| self_condition: true |
| sigma1_coord: 0.05 |
| t_min: 0.0001 |
| time_emb_dim: 0 |
| time_emb_mode: simple |
| use_discrete_t: true |
| empty_folder: false |
| evaluation: |
| batch_size: 100 |
| docking_config: |
| exhaustiveness: 16 |
| mode: vina_score |
| protein_root: /sharefs/share/sbdd_data/test_set |
| fix_bond: false |
| ligand_path: 'null' |
| num_samples: 10 |
| protein_path: 'null' |
| sample_num_atoms: ref |
| sample_steps: 100 |
| time_scheduler_path: 'null' |
| exp_name: train_multi_kekulize |
| logging_level: warning |
| no_wandb: false |
| project_name: qiukeyue_bfn_sbdd |
| revision: 4b71cc6_26712 |
| seed: 1234 |
| test_only: false |
| time_decoupled: false |
| timewarp: |
| decay: 0.0 |
| num_bins: 100 |
| num_cat_features: 1 |
| num_cont_features: 1 |
| sigma_max_cat: 1 |
| sigma_max_cont: 1 |
| sigma_min_cat: 0 |
| sigma_min_cont: 0 |
| timewarp_type: bytype |
| train: |
| batch_size: 4 |
| bond_loss_weight: 10 |
| ckpt_freq: 1 |
| ema_decay: 0.999 |
| epochs: 15 |
| log_gradient_scale_interval: 100 |
| max_grad_norm: Q |
| num_workers: 8 |
| optimizer: |
| beta1: 0.95 |
| beta2: 0.999 |
| lr: 0.0005 |
| type: adam |
| weight_decay: 0 |
| pos_noise_std: 0 |
| random_rot: false |
| resume: false |
| scheduler: |
| factor: 0.6 |
| max_iters: 20000 |
| min_lr: 1.0e-06 |
| patience: 10 |
| type: plateau |
| v_loss_weight: 1 |
| val_freq: 1000 |
| val_mode: sample |
| visual: |
| save_mols: false |
| visual_chain: false |
| visual_nums: 10 |
| wandb_resume_id: null |
|
|
