Enable pocket retrieval from local pdb files

[dominiquesydow]

Description

opencadd.databases.klifs allows interaction with local KLIFS data. So far, it was only possible to get pocket information (i.e. residue PDB ID to KLIFS index mapping) based on mol2 files. In this PR, we add the same based on pdb files (KLIFS offers both mol2 and pdb files as download).

Todos

• [x] Add extension argument to Pockets.from_structure_klifs_id signature
• [x] Generalize all variables with mol2 mention that now refer to pdb- or mol2-based data (e.g. mol2_df > dataframe or mol2_path > filepath)
• [x] Add unit tests for local pocket from pdb file
• [x] Pin parso version to 0.8.1 to resolve conflict with jedi

Questions

None

Status

• [x] Ready to go

[codecov-io]

Codecov Report

Merging #64 (a8dd154) into master (c860671) will not change coverage. The diff coverage is 100.00%.

[dominiquesydow]

Fixed CI / docs fails as described here: https://github.com/volkamerlab/opencadd/issues/65