Protein/Ligand Preparation for Docking

[rbharath]

This repo is intended to start where deepchem.dock left off. It's factored into a separate repo to allow for more flexibility in maintaining a separate codebase that handles issues with docking.

One thing we'll need to get right in this repo is having robust protein/ligand preparation for docking. This is a complex issue with lots of factors to consider. This old DeepChem issue has a good amount of discussion: deepchem/deepchem#368

Let's continue the conversation here.