fix: ligand extraction from cif works

[sg-s]

No description provided.

[Copilot]

Pull request overview

This pull request fixes ligand extraction from CIF files by implementing proper CIF-to-PDB conversion before HETATM parsing, and enhances water molecule filtering to include additional water residue names (WAT, H2O) beyond just HOH.

Changes:

• Enhanced extract_ligand() to handle CIF files by temporarily converting them to PDB format
• Expanded default water molecule exclusion to include HOH, WAT, and H2O residue names
• Added uppercase normalization for residue name comparisons to ensure consistent filtering
• Added comprehensive test coverage for water filtering and CIF file ligand extraction

Reviewed changes

Copilot reviewed 3 out of 4 changed files in this pull request and generated 1 comment.

File	Description
src/drug_discovery/structures/protein.py	Implemented CIF-to-PDB conversion for ligand extraction, added uppercase normalization for residue names, and expanded default water exclusion list
tests/test_protein.py	Added three new tests covering water filtering, custom exclude_resnames, and CIF file ligand extraction scenarios
docs/dd/how-to/proteins.md	Added documentation note explaining automatic water exclusion and the exclude_resnames parameter usage

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[Copilot]

This import of module os is redundant, as it was previously imported on line 1.

Suggested change

import os