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Feat/mmcif input - #208
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maciek-wisniewski wants to merge 2 commits into
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Feat/mmcif input#208maciek-wisniewski wants to merge 2 commits into
maciek-wisniewski wants to merge 2 commits into
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September 24, 2026 09:18
- read mmCIF as a single file (-f complex.cif) or as separate receptor and ligand files (--receptor, --ligand); files are merged with biotite and routed through PDB text into the existing OpenBabel pipeline (docs/adr/0001) - each ligand file is one ligand without filtering; a file with a single metal atom is a cofactor kept in the surroundings - chain options accept original multi-character chain IDs; reports show original chain IDs and residue names plus the chain mapping - new --npz output with atom pairs indexed per input file - new plip.profile.profile_system API - require Python >= 3.10 and biotite >= 1.2.0
A ligand file with a single metal ion is now profiled as a ligand of type ION, as PLIP does for PDB input, instead of being kept in the surroundings as a cofactor. PLIP only detects metal complexes for metals that belong to the profiled ligand, so cofactors never showed any metal coordination and split input differed from single-file input. Removes the cofactor arrays from the NPZ output and the cofactor sections from the reports.
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