<commit_before>﻿# DeepChem
[![Build Status](https://travis-ci.org/deepchem/deepchem.svg?branch=master)](https://travis-ci.org/deepchem/deepchem)
[![Coverage Status](https://coveralls.io/repos/github/deepchem/deepchem/badge.svg?branch=master)](https://coveralls.io/github/deepchem/deepchem?branch=master)
[![Anaconda-Server Badge](https://anaconda.org/deepchem/deepchem/badges/version.svg)](https://anaconda.org/deepchem/deepchem)
[![PyPI version](https://badge.fury.io/py/deepchem.svg)](https://badge.fury.io/py/deepchem)


DeepChem aims to provide a high quality open-source toolchain that
democratizes the use of deep-learning in drug discovery, materials science, quantum chemistry, and biology.

### Table of contents:

* [Requirements](#requirements)
* [Installation](#installation)
    * [Easy Install with Conda](#easy-install-with-conda)
    * [Conda Environment](#using-a-conda-environment)
    * [Docker](#using-a-docker-image)
* [FAQ and Troubleshooting](#faq-and-troubleshooting)
* [Getting Started](#getting-started)
* [Contributing to DeepChem](/CONTRIBUTING.md)
    * [Code Style Guidelines](/CONTRIBUTING.md#code-style-guidelines)
    * [Documentation Style Guidelines](/CONTRIBUTING.md#documentation-style-guidelines)
    * [Gitter](#gitter)
* [DeepChem Publications](#deepchem-publications)
* [Examples](/examples)
* [About Us](#about-us)
* [Citing DeepChem](#citing-deepchem)

## Requirements
* [pandas](http://pandas.pydata.org/)
* [joblib](https://pypi.python.org/pypi/joblib)
* [sklearn](https://github.com/scikit-learn/scikit-learn.git)
* [numpy](https://store.continuum.io/cshop/anaconda/)
* [tensorflow](https://www.tensorflow.org/)

### Soft Requirements
DeepChem has a number of "soft" requirements. These are packages which are needed for various submodules of DeepChem but not for the package as a whole.

* [RDKit](http://www.rdkit.org/docs/Install.html)
* [six](https://pypi.python.org/pypi/six)
* [MDTraj](http://mdtraj.org/)
* [PDBFixer](https://github.com/pandegroup/pdbfixer)
* [Pillow](https://pillow.readthedocs.io/en/stable/)

### Super easy install via pip3

```bash
pip3 install joblib pandas sklearn tensorflow pillow deepchem
```

### Easy Install via Conda

```bash
conda install -c deepchem -c rdkit -c conda-forge -c omnia deepchem=2.2.0
```
If you want GPU support:
```bash
conda install -c deepchem -c rdkit -c conda-forge -c omnia deepchem-gpu=2.2.0
```

**Note:** The above commands install the latest stable version of `deepchem` and _do not install from source_. If you need to install from source make sure you follow the steps [here](#using-a-conda-environment).

### Using a Docker Image
Using a docker image requires an NVIDIA GPU.  If you do not have a GPU please follow the directions for [using a conda environment](#using-a-conda-environment)
In order to get GPU support you will have to use the [nvidia-docker](https://github.com/NVIDIA/nvidia-docker) plugin.
``` bash
# This will the download the latest stable deepchem docker image into your images
docker pull deepchemio/deepchem

# This will create a container out of our latest image with GPU support
nvidia-docker run -i -t deepchemio/deepchem

# You are now in a docker container whose python has deepchem installed
# For example you can run our tox21 benchmark
cd deepchem/examples
python benchmark.py -d tox21

# Or you can start playing with it in the command line
pip install jupyter
ipython
import deepchem as dc
```

### Installing from source in a conda environment
You can install deepchem in a new conda environment using the conda commands in scripts/install_deepchem_conda.sh
Installing via this script will ensure that you are **installing from the source**.

```bash
git clone https://github.com/deepchem/deepchem.git      # Clone deepchem source code from GitHub<commit_msg>Updated installation instructions to specify 2.3<commit_after>﻿# DeepChem
[![Build Status](https://travis-ci.org/deepchem/deepchem.svg?branch=master)](https://travis-ci.org/deepchem/deepchem)
[![Coverage Status](https://coveralls.io/repos/github/deepchem/deepchem/badge.svg?branch=master)](https://coveralls.io/github/deepchem/deepchem?branch=master)
[![Anaconda-Server Badge](https://anaconda.org/deepchem/deepchem/badges/version.svg)](https://anaconda.org/deepchem/deepchem)
[![PyPI version](https://badge.fury.io/py/deepchem.svg)](https://badge.fury.io/py/deepchem)


DeepChem aims to provide a high quality open-source toolchain that
democratizes the use of deep-learning in drug discovery, materials science, quantum chemistry, and biology.

### Table of contents:

* [Requirements](#requirements)
* [Installation](#installation)
    * [Easy Install with Conda](#easy-install-with-conda)
    * [Conda Environment](#using-a-conda-environment)
    * [Docker](#using-a-docker-image)
* [FAQ and Troubleshooting](#faq-and-troubleshooting)
* [Getting Started](#getting-started)
* [Contributing to DeepChem](/CONTRIBUTING.md)
    * [Code Style Guidelines](/CONTRIBUTING.md#code-style-guidelines)
    * [Documentation Style Guidelines](/CONTRIBUTING.md#documentation-style-guidelines)
    * [Gitter](#gitter)
* [DeepChem Publications](#deepchem-publications)
* [Examples](/examples)
* [About Us](#about-us)
* [Citing DeepChem](#citing-deepchem)

## Requirements
* [pandas](http://pandas.pydata.org/)
* [joblib](https://pypi.python.org/pypi/joblib)
* [sklearn](https://github.com/scikit-learn/scikit-learn.git)
* [numpy](https://store.continuum.io/cshop/anaconda/)
* [tensorflow](https://www.tensorflow.org/)

### Soft Requirements
DeepChem has a number of "soft" requirements. These are packages which are needed for various submodules of DeepChem but not for the package as a whole.

* [RDKit](http://www.rdkit.org/docs/Install.html)
* [six](https://pypi.python.org/pypi/six)
* [MDTraj](http://mdtraj.org/)
* [PDBFixer](https://github.com/pandegroup/pdbfixer)
* [Pillow](https://pillow.readthedocs.io/en/stable/)

### Super easy install via pip3

```bash
pip3 install joblib pandas sklearn tensorflow pillow deepchem
```

### Easy Install via Conda

```bash
conda install -c deepchem -c rdkit -c conda-forge -c omnia deepchem=2.3.0
```
If you want GPU support:
```bash
conda install -c deepchem -c rdkit -c conda-forge -c omnia deepchem-gpu=2.3.0
```

**Note:** The above commands install the latest stable version of `deepchem` and _do not install from source_. If you need to install from source make sure you follow the steps [here](#using-a-conda-environment).

### Using a Docker Image
Using a docker image requires an NVIDIA GPU.  If you do not have a GPU please follow the directions for [using a conda environment](#using-a-conda-environment)
In order to get GPU support you will have to use the [nvidia-docker](https://github.com/NVIDIA/nvidia-docker) plugin.
``` bash
# This will the download the latest stable deepchem docker image into your images
docker pull deepchemio/deepchem

# This will create a container out of our latest image with GPU support
nvidia-docker run -i -t deepchemio/deepchem

# You are now in a docker container whose python has deepchem installed
# For example you can run our tox21 benchmark
cd deepchem/examples
python benchmark.py -d tox21

# Or you can start playing with it in the command line
pip install jupyter
ipython
import deepchem as dc
```

### Installing from source in a conda environment
You can install deepchem in a new conda environment using the conda commands in scripts/install_deepchem_conda.sh
Installing via this script will ensure that you are **installing from the source**.

```bash
git clone https://github.com/deepchem/deepchem.git      # Clone deepchem source code from GitHub
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