Add support for parsing custom CIF files as PLINDER systems

[Ninjani]

• Allows parsing any cif files with Entry.from_custom_cif_file
• Bump BindingDB version
• Fix BindingDB to PDB mapping (based on 100% pocket sequence coverage and identity)
• Better handling of counts for pocket residues, interactions etc only considering proper ligands
• Release date fix (needs data regen)
• Use proper_ligand-based counts for scoring
• PDB conversion fix, rename residues with >3 characters
• Residue export, add auth_number
• Fallible rdkit parsing
• crystal contact detection within asymmetric units

Closes #102

[yusuf1759]

@Ninjani I thought the new Openstructure update should handle this. I remember you mentioned that at some point

[yusuf1759]

Still a problem to get it into conda ?

[github-actions]

Coverage report

Click to see where and how coverage changed

File	Statements	Missing	Coverage	Coverage (new stmts)	Lines missing
src/plinder/core/index
system.py					364-367
src/plinder/core/structure
atoms.py					247-251
src/plinder/core/utils
io.py					80
src/plinder/data/pipeline
io.py
transform.py
src/plinder/data/utils/annotations
aggregate_annotations.py					287, 547, 1070-1137
get_similarity_scores.py					431-443, 773-775
interaction_utils.py					222
ligand_utils.py
rdkit_utils.py					41, 144-146
save_utils.py					39
Project Total

This report was generated by python-coverage-comment-action

[weitse-hsu]

Hi @Ninjani, thanks so much for working on this PR to address #102—really appreciate the progress so far. I noticed most of the checklist is complete and just wanted to check in on any updates.

Also, is there a plan for supporting custom PDB files in the codebase? Thanks a lot!