AlphaPulldown/test/test_data/features/test_input.json at main - AlphaPulldown - Gitea: Git with a cup of tea

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Dima fc41c1a5eb AF3 templates: fix mmCIF parsing by removing synthetic _entity_poly_seq and mapping only present residues

- Strip _entity_poly_seq from generated template mmCIF so AF3 reconstructs _pdbx_poly_seq_scheme from _atom_site, avoiding UNK/gap mismatches
- Build query_to_template_map using only residues with atoms to prevent OOB indexing in template features
- Add --debug_templates flag to optionally dump generated template mmCIFs into templates_debug/
- Keep templates enabled; test test__chopped_dimer now passes

2025-08-12 14:04:33 +02:00

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 {
   "version": 1,
   "name": "test_input",
   "dialect": "alphafold3",
   "modelSeeds": [42],
   "sequences": [
     {"id": "C", "type": "protein"}
   ],
   "bondedAtomPairs": [],
   "userCCD": null
 }