Refactor pocket module

[dominiquesydow]

Description

This PR started with me realizing that so far I have only allowed anchor residue definitions by residue PDB IDs but not by residue KLIFS IDs (which is needed for e.g. the kissim module).

Then this PR evolved into a bigger refactoring, where the methods of the classes Subpocket and AnchorResidue are moved to Pocket, since only Pocket contains the full atomic data, which is needed to calculate anchor residues and subpockets. Subpocket and AnchorResidue mainly contain attributes and properties (but no methods).

Todos

• [x] Move AnchorResidue to its own anchor module
• [x] Move methods from Subpocket and AnchorResidue to Pocket
• [x] Allow anchor residue calculation from residue PDB and KLIFS ID
• [x] Move Pocket.visualize method to its own class Viewer in module viewer to allow visualization of multiple pockets at once
• [x] Update unit tests; almost done - missing: Pocket.centroid/subpockets/regions/anchor_residues
• [x] Refactor Region class
• [x] Rerun tutorial

Questions

None.

Status

• [x] Ready to go

[codecov-io]

Codecov Report

Merging #59 (6b2dd68) into master (a9da35e) will decrease coverage by 1.91%. The diff coverage is 65.74%.

[dominiquesydow]

This PR is superseded by #66 (contains latest changes from master).