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julie-forman-kay-lab / IDPConformerGenerator

Build conformational representations of Intrinsically Disordered Proteins and Regions by a guided sampling of the protein torsion space
https://idpconformergenerator.readthedocs.io/
Apache License 2.0
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`HIP` instead of `HIS` #234

Open joaomcteixeira opened 1 year ago

joaomcteixeira commented 1 year ago

IDPCG is generating HIP residues by default instead of HIS, and even if -dsd is given. A user has reported.

@menoliu can you help me here to sort this out? It should be HIS unless HIPis provided in the fasta with the letter p.

Is there any reason why this is like this that I may not be remembering?

Thanks so much! If you can, please give priority to this issue.

menoliu commented 1 year ago

Yes I have realized that but I assumed it was intentional to accommodate double protonation? I should have asked what you meant here in libparse.py lines 379-390:

# TODO: correct for HIS/HIE/HID/HIP
def translate_seq_to_3l(input_seq, histidine_protonation="HIS"):
    """
    Translate 1-letter sequence to 3-letter sequence.

    Currently translates 'H' to 'HIP', to accommodate double protonation.
    """
    return [
        histidine_protonation if _res == 'H' else aa1to3[_res]
        for _res in input_seq
        ]