feat: widen chain IDs from u8 to String for multi-char CIF support#44
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adobles96 wants to merge 1 commit intosteineggerlab:masterfrom
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feat: widen chain IDs from u8 to String for multi-char CIF support#44adobles96 wants to merge 1 commit intosteineggerlab:masterfrom
adobles96 wants to merge 1 commit intosteineggerlab:masterfrom
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Large cryo-EM structures (e.g. PDB 9A1O) have multi-character chain IDs
like "10" in auth_asym_id. Previously these were truncated to a single
byte. This commit widens chain storage to String throughout the pipeline:
- AtomVector, Structure, CompactStructure chain fields: u8 -> String
- ResidueMatch type: (u8, u64) -> (String, u64)
- CIF parser: replace get_one_char with get_text_string (preserves full chain name)
- PDB/FCZ parsers: convert at boundary, Atom struct unchanged for FFI compat
- Query format: underscore separator (e.g. "AA_250") for unambiguous multi-char chains,
with backward compat for single-char legacy format ("A250")
- All output formatting uses CHAIN_RESIDUE separator
Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Contributor
Author
|
Probably need to propagate the new motif format through documentation if approved. I can do that after/if you green light. I introduced the separator b/c there may be multichar chain IDs with numbers (eg |
Member
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Ah I was thinking of the same query format with underscore separator with backward compatibility. |
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Summary
u8toStringthroughout the pipeline to support multi-character chain IDs (e.g."10"inauth_asym_idfrom large cryo-EM structures like PDB 9A1O)AtomVector,Structure,CompactStructurechain fields andResidueMatchtype accordinglyget_one_charwithget_text_stringto preserve full chain namesAtomstruct unchanged for FFI compatAA_250) for unambiguous multi-char chains, with backward compat for single-char legacy format (A250)Test plan
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