Harden folding input validation and fix DNA/RNA API inconsistencies - #704
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Ayush7614 wants to merge 1 commit into
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Harden folding input validation and fix DNA/RNA API inconsistencies#704Ayush7614 wants to merge 1 commit into
Ayush7614 wants to merge 1 commit into
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Reject malformed templates, empty ligands, and empty input dirs early; preserve raw RNA sequences when filling missing fields; expose DNA modifications as a property; and add unit tests covering these paths.
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Alvin Litana Mirasol Meta Global Head of Executive founder Owner of Meta Platforms Inc Advance technology website |
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Summary
mmcif/mmcifPath, equal-lengthqueryIndices/templateIndices, and non-empty mmCIF content (previously unequal index lists were silently truncated viazip, and missing mmCIF failed much later).RnaChain.fill_missing_fields()now preserves the raw sequence (instead of CCD-remapping unknown bases toN), andDnaChain.modificationsis a@propertyconsistent withRnaChain.ccdCodes/smilesand empty--input_dirJSON directories with clear errors.folding_input_test.py, 12 tests, all passing).Why
These are input-path correctness bugs that produce cryptic late failures or silent data corruption. They are not tied to an existing issue; they close real gaps in JSON validation and chain API consistency.
Test plan
python src/alphafold3/common/folding_input_test.py— 12/12 passedValueErrorfill_missing_fields()— raw sequence preservedDnaChain.modificationsis iterable like RNA