google-deepmind / google-deepmind/alphafold

inconsistency in aatype mapping

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feature request
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Python
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Description

`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`.

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