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affinity.ckpt

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+version https://git-lfs.github.com/spec/v1
+oid sha256:324ea3d206fa1418da1b83b4ebd9fe32c3c2eb1996b10ad7a9604503a2089b2d
+size 43388406

affinity4.ckpt

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+version https://git-lfs.github.com/spec/v1
+oid sha256:29781a85bce4a71d8b21b857c1ea125d7f90bed312076721d11a97c735eada01
+size 19587991

affinity4.yaml

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+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