| 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 | |