toxsmi

PyTorch implementation of toxsmi, a package for toxicity prediction models from SMILES.

Requirements

• conda>=3.7

Installation

The library itself has few dependencies (see setup.py) with loose requirements.

Create a conda environment:

conda env create -f conda.yml

Activate the environment:

conda activate toxsmi

Install in editable mode for development:

pip install -e .

Example usage

In the scripts directory is a training script train_tox.py that makes use of toxsmi.

Download sample data from the Tox21 database and store it in a folder called data here.

(toxsmi) $ python3 scripts/train_tox.py data/tox21_train.csv \
data/tox21_score.csv data/tox21.smi data/smiles_language_tox21.pkl \
models params/mca.json test --embedding_path data/smiles_vae_embeddings.pkl

Type python scripts/train_tox.py -h for further help.