Upload mol pilot config

crossdocked_pose_split_kekulize.pt

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:f078600c2f38b6718f5a5bd49c95171b7b08646252ae19054d778320517df7f6
+size 425199

molpilot_config.yaml

@@ -0,0 +1,157 @@
+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