/PyTorch-DeNovoDesign

Primary LanguagePython

De novo design

The codes below are confirmed for normal operation with AWS Deep Learning AMI (Ubuntu 18.04) Version 32.0 under the pytorch_p36 conda environment. Codes are slightly adpated from the following githubs : REINVENT, GENTRL, MOSES. After activating pytorch environment, you have to install rdkit package

conda install -c conda-forge rdkit

REINVENT

  1. Pre-train
    Run train_prior.py
  2. RL-train
    Run main.py --scoring-function tanimoto --num-steps 1000
    (we also can use --scoring-function activity_model, but we have to train classifier for target activity model in advance)

GENTRL

  1. Pre-train
    Run pretrain.py
  2. RL-train
    Run rltrain.py
  3. sampling
    Run sampling.py

MOSES

We use part of this code for the moleclue metrics.