This code is forked from this repository.
Additional requirements:
pandas rdkit torch_geometric h5py ray- a few biochemistry programs, see
mols/Programs/README
For rdkit in particular we found it to be easier to install through (mini)conda, but rdkit-pypi also works on pip in a vanilla python virtual environment. torch_geometric has non-trivial installation instructions.
If you have CUDA 10.1 configured, you can run pip install -r requirements.txt. You can also change requirements.txt to match your CUDA version. (Replace cu101 to cuXXX, where XXX is your CUDA version).
We compress the 300k molecule dataset for size. To uncompress it, run cd mols/data/; gunzip docked_mols.h5.gz.