ligand_fixes

[OleinikovasV]

Ligand related fixes

• removeHs more systemically in data processing and in loader
• minor bugfix in rascalMCES unmatched bond masking in get_template_to_mol_matches and in get_matched_template_v2
• increase rascal_opts.maxBondMatchPairs to 5000 in get_matched_template_v2
• remove code that is not used from smallmolecules.py
• move useful rdkit functions from data to core
• Ligand MMP similarity scoring in test stratification
• introduce ligand uncharger for improved ligand protonation state consistency
• cleanup some unused test files
• upgrade to rdkit 2024
• patch entry_release_date values

[github-actions]

Coverage report

Click to see where and how coverage changed

File	Statements	Missing	Coverage	Coverage (new stmts)	Lines missing
src/plinder/core/scores
index.py
links.py					44, 47
src/plinder/core/structure
atoms.py
smallmols_similarity.py					74-77, 83-126, 130-139
smallmols_utils.py					38-39, 82-90, 147, 149, 154-159, 203-209, 213-220, 234, 258-259, 278-281, 285, 327-357, 374-381, 442-443, 495-496, 557
structure.py
src/plinder/data
final_structure_qc.py
src/plinder/data/pipeline
tasks.py					410, 425
utils.py
src/plinder/data/utils/annotations
aggregate_annotations.py					1276
interface_gap.py					166, 187
mmpdb_utils.py
rdkit_utils.py					77, 100, 135, 159
src/plinder/eval/docking
stratify_test_set.py					133-134, 139-141, 147
Project Total

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