#689·alphafold

inconsistency in aatype mapping

Author: dakpinarogluCreated Jan 29, 2023Updated Jan 14, 2026
Labelsfeature request

restype_order made from restypes does not match the values stored in HHBLITS_AA_TO_ID. For example, the aatype when a pdb is read using pdb_from_string returns the value 7 for 'G'. Later on, when aatype is converted to string type or ultimately one-hot, ID_TO_HHBLITS_AA would return the value 'I' for 7, not 'G'. The dictionaries are not consistent. Instead of using restype_order, HHBLITS_AA_TO_ID would map to aatype while staying consistent with ID_TO_HHBLITS_AA for reading pdbs in protein.py. This also would eliminate the use of residue_constants.MAP_HHBLITS_AATYPE_TO_OUR_AATYPE.

Thanks!

Source: google-deepmind/alphafold