OpenChem

OpenChem is a deep learning toolkit for Computational Chemistry with PyTorch backend. The goal of OpenChem is to make Deep Learning models an easy-to-use tool for Computational Chemistry and Drug Design Researchers.

Main features

Modular design with unified API, modules can be easily combined with each other.
OpenChem is easy-to-use: new models are built with only configuration file.
Fast training with multi-gpu support.
Utilities for data preprocessing.
Tensorboard support.

Documentation

Check out OpenChem documentation here.

Supported functionality

Tasks:

Classification (binary or multi-class)
Regression
Multi-task (such as N binary classification tasks)
Generative models

Data types

Sequences of characters such as SMILES strings or amino-acid sequences
Molecular graphs. OpenChem takes care of converting SMILES strings into molecular graphs

Modules:

Token embeddings
Recurrent neural network encoders
Graph convolution neural network encoders
Multi-layer perceptrons

We are working on populating OpenChem with more models and other building blocks.

Installation

Requirements

In order to get started you need:

Modern NVIDIA GPU, compute capability 3.5 or newer.
Python 3.5 or newer (we recommend Anaconda distribution)
CUDA 9.0 or newer

General installation

If you installed your Python with Anaconda you can run the following commands to get started:

git clone https://github.com/Mariewelt/OpenChem.git
cd OpenChem
conda create --name OpenChem python=3.7
conda activate OpenChem
conda install --yes --file requirements.txt
conda install -c rdkit rdkit nox cairo
conda install pytorch torchvision -c pytorch
pip install -e .

If your CUDA version is older than 9.0, check Pytorch website for different installation instructions.

Installation with Docker

Alternative way of installation is with Docker. We provide a Dockerfile, so you can run your models in a container that already has all the necessary packages installed. You will also need nvidia-docker in order to run models on GPU.

Acknowledgements

OpenChem is sponsored by the University of North Carolina at Chapel Hill and NVIDIA Corp.

qize/OpenChem