SMILES_BindEvaluator/config.yaml

defaults:
  - _self_

compute:
  ngpus: 2  
  nodes: 4

training:
  seed: 42
  kl_weight: 0.1

optim:
  weight_decay: 0.03
  optimizer: AdamW
  lr: 1e-4
  beta1: 0.9
  beta2: 0.95
  eps: 1e-8
  grad_clip: 1.0
  eta_min_ratio: 0.1
  fused: false
  max_epochs: 50
  warmup_ratio: 0.1

model:
  n_layers: 8
  d_model: 128
  d_hidden: 128
  n_head: 8
  d_inner: 64 
  d_k: 64
  d_v: 128
  dropout: 0.3

work_dir: /scratch/pranamlab/tong/SMILES_BindEvaluator/outs

inference:
  ckpt: /scratch/pranamlab/tong/SMILES_BindEvaluator/outs/mcc_lr=1e-4_nlayers=8_dmodel=128_nhead=8_dinner=64_kl0.1/model-epoch=23-val_mcc=0.64.ckpt
  binder: 'CN2C(=O)[C@@H](CS)C(=O)N1CCC[C@H]1NC(=O)[C@@H](CCC(=O)O)NC(=O)[C@@H](CS)NC(=O)[C@@H](CC(=O)O)NC(=O)[C@@H](CCC(=O)OCC=C)NC(=O)[C@@H](CSC(C1=CC=CC=C1)(C2=CC=CC=C2)C3=CC=C(OC)C=C3)NC(=O)[C@@H](CC(=O)N)NC(=O)[C@@H](C(C)C)C(=O)2'
  target: MEPSATPGAQMGVPPGSREPSPVPPDYEDEFLRYLWRDYLYPKQYEWVLIAAYVAVFVVALVGNTLVCLAVWRNHHMRTVTNYFIVNLSLADVLVTAICLPASLLVDITESWLFGHALCKVIPYLQAVSVSVAVLTLSFIALDRWYAICHPLLFKSTARRARGSILGIWAVSLAIMVPQAAVMECSSVLPELANRTRLFSVCDERWADDLYPKIYHSCFFIVTYLAPLGLMAMAYFQIFRKLWGRQIPGTTSALVRNWKRPSDQLGDLEQGLSGEPQPRARAFLAEVKQMRARRKTAKMLMVVLLVFALCYLPISVLNVLKRVFGMFRQASDREAVYACFTFSHWLVYANSAANPIIYNFLSGKFREQFKAAFSCCLPGLGPCGSLKAPSPRSSASHKSLSLQSRCSISKISEHVVLTSVTTVLP
  ground_truth: 126-130
  threshold: 0.918