Fix/rfd3 duplicate cif atom ids#248
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DeltaDesign wants to merge 2 commits intoRosettaCommons:productionfrom
Open
Fix/rfd3 duplicate cif atom ids#248DeltaDesign wants to merge 2 commits intoRosettaCommons:productionfrom
DeltaDesign wants to merge 2 commits intoRosettaCommons:productionfrom
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…#148) PadTokensWithVirtualAtoms copies CB's atom_id to virtual atom slots. After cleanup removes the virtual atoms, sidechain atoms retain the duplicated atom_id. The CIF writer uses these values for _atom_site.id, producing non-conformant output with duplicate IDs. Strip atom_id before CIF serialization so the writer auto-generates unique sequential 1..N IDs. Two sites: - _cleanup_virtual_atoms_and_assign_atom_name_elements: strips after filtering virtual atoms (covers Python API consumers) - RFD3Output._strip_atom_id: strips in dump() before every to_cif_file() call (covers trajectories and cleanup_virtual_atoms=False) Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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Summary
Fixes #148.
What changed and why
PadTokensWithVirtualAtomscopies the central atom (CB) to create virtual atom positions, including CB'satom_idannotation. After cleanup removes the virtual atoms, sidechain atoms retain CB's duplicatedatom_id. The CIF writer uses these values for_atom_site.id, producing non-conformant output with duplicate IDs._atom_site.iduniqueness is required by the mmCIF dictionary specification — downstream parsers (PyMOL, ChimeraX, Phenix) may silently drop or misassign atoms when IDs collide.The fix strips
atom_idbefore CIF serialization so the writer auto-generates unique sequential 1..N IDs. Two sites:_cleanup_virtual_atoms_and_assign_atom_name_elements— strips after filtering virtual atoms (covers Python API consumers)RFD3Output._strip_atom_id— strips indump()before everyto_cif_file()call (covers trajectories andcleanup_virtual_atoms=Falsepath)How tested
Two new tests in
models/rfd3/tests/test_cif_duplicate_ids.py:test_cleanup_strips_atom_id— verifies cleanup removes the duplicated annotationtest_cif_output_has_unique_ids— verifies CIF output has unique sequential_atom_site.idvaluesruff checkpasses on all 3 changed files.