| accounting: |
| checkpoint_dir: /sharefs/qiukeyue/project/logs/qiukeyue_bfn_molopt/train_prop/affinity_3e8bf31_2796/checkpoints |
| dump_config_path: /sharefs/qiukeyue/project/logs/qiukeyue_bfn_molopt/train_prop/affinity_3e8bf31_2796/config.yaml |
| generated_mol_dir: /sharefs/qiukeyue/project/logs/qiukeyue_bfn_molopt/train_prop/affinity_3e8bf31_2796/generated_mol |
| logdir: /sharefs/qiukeyue/project/logs/qiukeyue_bfn_molopt/train_prop/affinity_3e8bf31_2796 |
| test_outputs_dir: /sharefs/qiukeyue/project/logs/qiukeyue_bfn_molopt/train_prop/affinity_3e8bf31_2796/test_outputs |
| wandb_logdir: /sharefs/qiukeyue/project/logs/qiukeyue_bfn_molopt/train_prop/affinity_3e8bf31_2796 |
| data: |
| atom_decoder: |
| - H |
| - C |
| - N |
| - O |
| - F |
| - P |
| - S |
| - Cl |
| colors_dic: |
| - '#FFFFFF99' |
| - C7 |
| - C0 |
| - C3 |
| - C1 |
| - C4 |
| - C8 |
| - C9 |
| name: pl_tr |
| 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 |
| split: /sharefs/share/sbdd_data/crossdocked_pocket10_pose_split.pt |
| transform: |
| ligand_atom_mode: add_aromatic |
| with_split: true |
| debug: false |
| dynamics: |
| beta1: 1.5 |
| center_pos_mode: protein |
| destination_prediction: true |
| discrete_steps: 1000 |
| ligand_atom_feature_dim: 13 |
| net_config: |
| act_fn: relu |
| cutoff_mode: knn |
| edge_feat_dim: 4 |
| ew_net_type: global |
| hidden_dim: 128 |
| knn: 32 |
| n_heads: 16 |
| name: unio2net |
| norm: true |
| num_blocks: 1 |
| num_h2x: 1 |
| num_layers: 4 |
| num_node_types: 8 |
| num_r_gaussian: 20 |
| num_x2h: 1 |
| r_max: 10.0 |
| sync_twoup: false |
| x2h_out_fc: false |
| node_indicator: true |
| pos_init_mode: zero |
| prop_name: affinity |
| protein_atom_feature_dim: 27 |
| sampling_strategy: end_back_pmf |
| sigma1_coord: 0.03 |
| t_min: 0.0001 |
| time_emb_dim: 1 |
| 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 |
| last_ckpt: false |
| ligand_path: 'null' |
| num_samples: 10 |
| protein_path: 'null' |
| sample_num_atoms: prior |
| sample_steps: 100 |
| save_traj: false |
| exp_name: train_prop |
| logging_level: warning |
| no_wandb: false |
| project_name: qiukeyue_bfn_molopt |
| revision: affinity_3e8bf31_2796 |
| seed: 1234 |
| test_only: false |
| train: |
| batch_size: 8 |
| ckpt_freq: 1 |
| ema_decay: 0.999 |
| epochs: 15 |
| 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 |
| visual: |
| save_mols: true |
| visual_chain: false |
| visual_nums: 10 |
| wandb_resume_id: null |
|
|
