Generate fingerprint from PDB file + pocket indices

[dominiquesydow]

Currently, we generate fingerprints from structure KLIFS IDs.
Add API to generate fingerprint from a PDB ID + indices for 85 binding site residues.

• Rename kissim.io.data.KlifsToKissimData to KissimData with the following methods
  • KissimData.from_structure_klifs_id(structure_klifs_id, klifs_session)
  • KissimData.from_pdb(pdb_id_or_file, chain_id, alternate_model_id, residue_ids, residue_ixs, kinase_name)
  • Update kissim.io.biopython.PocketBioPython and kissim.io.dataframe.DataFrame
• Rename KissimData attribute structure_klifs_id > structure_id
• Add Fingerprint.from_pdb
• Add FingerprintGenerator.from_pdb
• Add kissim.encoding.features.BaseFeature.from_pdb

[dominiquesydow]

Dunbrack UniProt-based remuneration of protein PDB residues

• https://github.com/volkamerlab/plipify/blob/proj03-av/projects/03/main.ipynb
• http://dunbrack3.fccc.edu/PDBrenum/