Write _atom_site.occupancy in mmCIF output (Fix #331)#341
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Write _atom_site.occupancy in mmCIF output (Fix #331)#341faustomilletari wants to merge 1 commit into
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Biotite only emits an _atom_site column when the corresponding annotation is present on the AtomArray. Our writers set b_factor but not occupancy, so the occupancy column was omitted entirely. This broke downstream parsers that require it (e.g. BioPython's MMCIFParser, which raises KeyError: '_atom_site.occupancy'). Set occupancy=1.0 on atoms in ProteinChain.atom_array / atom_array_no_insertions (also covers ProteinComplex, which reuses chain.atom_array) and on the manually-built AtomArray in MolecularComplex.to_mmcif. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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Biotite only emits an _atom_site column when the corresponding annotation is present on the AtomArray. Our writers set b_factor but not occupancy, so the occupancy column was omitted entirely. This broke downstream parsers that require it (e.g. BioPython's MMCIFParser, which raises KeyError: '_atom_site.occupancy').
Set occupancy=1.0 on atoms in ProteinChain.atom_array / atom_array_no_insertions (also covers ProteinComplex, which reuses chain.atom_array) and on the manually-built AtomArray in MolecularComplex.to_mmcif.