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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