VAE-based molecule generation and translation

This is a joint PyTorch implementation of three papers in VAE-based molecule generation and translation. The papers and the official repos are as follows:

• Junction Tree Variational Autoencoder for Molecular Graph Generation (ICML 2018)
• Learning Multimodal Graph-to-Graph Translation for Molecular Optimization (ICLR 2019)
• Hierarchical Generation of Molecular Graphs using Structural Motifs (ICML 2020)

The master branch works with PyTorch 1.8+.

MolVAE has been tested under Python 3.7 with PyTorch 1.11 on cuda 11.4

Installation

1. Create an Anaconda environment

   conda create --name vae_py37 python=3.7
   conda activate vae_py37

2. Install RDKit

   conda install rdkit -c rdkit

3. Install PyTorch following official instructions, e.g. PyTorch on GPU platforms:

   conda install pytorch torchvision -c pytorch

4. Install other requirements:

   pip install -r requirements.txt

5. Install Chemprop (from source, additional dependency for property-guided finetuning)

   git clone https://github.com/chemprop/chemprop.git
   cd chemprop
   pip install -e .

Data Format

• For molecule generation, each line of a training file is a molecule in SMILES representation.
  • benchmark/moses and benchmark/polymers are used for generation.
• For molecule translation, each line of a training file is a pair of molecules (molA, molB). The target is to translate from molA towards molB, as molB has better chemical properties.
  • benchmark/drd2, benchmark/logp04, benchmark/logp06 and benchmark/qed are used for translation.

Training

1. Select config file and raw data according to task and appraoch.

   • For molecule generation, go to configs/moses or configs/polymers.
     • For junction tree approach, use configs/*/jtvae.json.
     • For hierarchical substructure approach, use configs/*/hiervae.json.
   • For molecule translation, go to configs/drd2 , configs/logp04, configs/logp06 or configs/qed
     • For junction tree approach, according to with or without GAN loss, use config/*/vjtnn_gan.json or configs/*/vjtnn.json
     • For hierarchical substructure approach, use configs/*/hiervgnn.json

2. Extract vocabularies from a given set of molecules and preprocess training data. Add the --get_vocab argument if you have not extracted the vocabulary before. Replace xxx with your selected json file.

   python tools/preprocess.py --config configs/xxx

3. Train the model

   • Without GAN loss

     python tools/train.py --config configs/xxx

   • With GAN loss (only for junction tree approach for molecule translation)

     python tools/train_gan.py --config configs/xxx

Testing

• For molecule generation, replace yyy with your selected model in ckpt/moses or ckpt/polymers.

  python tools/generate.py --config configs/xxx --model ckpt/yyy

• For molecule translation, replace yyy with your selected model in ckpt/drd2, ckpt/logp04, ckpt/logp06 or ckpt/qed.

  python tools/translate.py --config configs/xxx --model ckpt/yyy

Evaluation

Calculate metrics on testing result file and replace zzz with your result file in results/*.

python tools/eval.py --config configs/xxx --result results/zzz