Add opencadd.structure.subpockets module

[dominiquesydow]

Description

Add opencadd.structure.subpockets module that calculates subpocket centers based on input residue PDB IDs (anchor residues). Add nglviewer visualization of subpockets.

Use kissim code: https://github.com/volkamerlab/kissim/blob/master/kissim/encoding.py

Todos

• [x] Add Residue class that handles retrieval of anchor residue center (what happens if input atoms associated with input residue PDB ID is missing?)
• [x] Add Subpocket class that calculated a subpocket center based on input anchor residues.
• [x] Add Pocket class that holds all subpockets and user-defined regions (e.g. if the user wants to highlight important pocket regions like the hinge region in kinases and/or regions that were used to define anchor residues); this class will handle also the visualization of subpockets and regions.
• [x] Unit testing

Questions

• [x] Where shall the parser module code (currently in klifs and subpockets) live? In opencadd.core? > This code lives now in opencadd.io

Status

• [x] Ready to go

[dominiquesydow]

Merge this branch into add_io_klifs_subpockets branch, see PR #44.