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Some modeling tools (e.g., Boltz-2) write CIF files that we can't currently parse. The CIF standard lists `_atom_site.label_atom_id` as a required field, but we use `_atom_site.auth_atom_id`. This allows both. It also makes `_atom_site.pdbx_formal_charge` optional. Reference: https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/atom_site.html#
Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## master #78 +/- ##
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Coverage 95.29% 95.29%
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Files 14 14
Lines 2125 2125
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Looks good, merge when ready. |
timholy
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This is a follow-up to #78, ensuring that all optional fields in the in the `_atom_site` category are handled correctly. This also adds tests for files written by two external tools.
timholy
added a commit
that referenced
this pull request
Sep 4, 2025
This is a follow-up to #78, ensuring that all optional fields in the in the `_atom_site` category are handled correctly. This also adds tests for files written by two external tools.
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Some modeling tools (e.g., Boltz-2) write CIF files that we can't
currently parse. The CIF standard lists
_atom_site.label_atom_idas arequired field, but we use
_atom_site.auth_atom_id. This allows both.It also makes
_atom_site.pdbx_formal_chargeoptional.Reference:
https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Categories/atom_site.html#