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…t str Previous code would wrap the list in double quotes, resulting in Boltz2 not being able to unwrap the three elements.
… mode Boltz2 would raise an error when no MSA files are provided and `--use_msa_server` is not passed.
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This pull request refactors and improves the clarity and correctness of the Boltz2-related code, particularly in how bonded atom pairs are processed and YAML output is generated. It also adds a special case for handling single-sequence mode in the YAML output.
Refactoring and code clarity:
bonded_atom_pairs_to_yamlto use named variables (atom1,atom2) instead of indexing intopair, improving readability and reducing the risk of errors.YAML output improvements:
add_key_and_valueto handle both strings and lists as values, only quoting the value if it is a string, which improves the correctness of the generated YAML.sequence_to_yaml, added special handling for single-sequence mode (whenmsa_fileisNoneand the sequence type is "protein") by inserting an explicitmsa: emptyline in the YAML output.