Handle missing pdbx_PDB_ins_code in mmCIF parser#877
Merged
padix-key merged 1 commit intobiotite-dev:mainfrom Mar 19, 2026
Merged
Handle missing pdbx_PDB_ins_code in mmCIF parser#877padix-key merged 1 commit intobiotite-dev:mainfrom
padix-key merged 1 commit intobiotite-dev:mainfrom
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The pdbx_PDB_ins_code column is optional per the PDBx dictionary, but get_structure() assumed it was always present. Fall back to empty insertion codes when the column is missing. Closes biotite-dev#869
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Mar 18, 2026
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Looks good, thanks for the fix. This is also a good template for fixing the other optional fields in _atom_site that are still required as mandatory.
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The failing test in |
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Thanks for the review! Yes, please go ahead and merge. Happy to help — and good to know this can serve as a template for the other optional fields in |
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What
Handle missing optional
pdbx_PDB_ins_codecolumn when parsing mmCIF files.Why
get_structure()unconditionally accessesatom_site["pdbx_PDB_ins_code"], raising aKeyErrorfor structures that lack this optional column (e.g., IHM entries like 8ZZ4, 9A0P, 9A8I).How
Added a conditional check: if
pdbx_PDB_ins_codeexists inatom_site, use it as before; otherwise, fill theins_codeannotation with empty strings (the default value).Testing
Added a test that removes
pdbx_PDB_ins_codefrom a CIF file's atom_site category and verifiesget_structure()succeeds with all-empty insertion codes.Closes #869