Deep Learning Toolchain for Drug Discovery and Quantum Chemistry

• openbabel
• pandas
• rdkit
• boost
• joblib
• sklearn
• numpy
• theano
• keras
• six
• dill
• ipyparallel
• mdtraj
• tensorflow

deepchem currently requires Python 2.7, and is not supported on any platforms except 64 bit linux. Please make sure you follow the directions below precisely. While you may already have system versions of some of these packages, there is no guarantee that deepchem will work with alternate versions than those specified below. This is especially true for the keras library, where deepchem is known not to work with the latest default version.

1. Anaconda 2.7 Download the 64-bit Python 2.7 version of Anaconda for linux here.
   Follow the installation instructions

2. openbabel

   conda install -c omnia openbabel

3. pandas

   conda install pandas 

4. rdkit

   conda install -c omnia rdkit

5. boost

   conda install -c omnia boost=1.59.0

6. joblib

   conda install joblib 

7. theano

   conda install -c omnia theano

8. keras

   conda install -c omnia keras

9. six

   conda install six

10. dill

    conda install dill

11. ipyparallel

    conda install ipyparallel

12. mdtraj

conda install -c omnia mdtraj

13. tensorflow: Installing tensorflow on older versions of Linux (which have glibc < 2.17) can be very challenging. For these older Linux versions, contact your local sysadmin to work out a custom installation. If your version of Linux is recent, then the following command will work:

    conda install -c https://conda.anaconda.org/jjhelmus tensorflow
    

14. deepchem: Clone the deepchem github repo:

    git clone https://github.com/deepchem/deepchem.git

    cd into the deepchem directory and execute

    python setup.py install

15. If installation has been successful, all tests in test suite should pass:

    nosetests -v deepchem --nologcapture