The charge is assigned by estimate_amino_acid_charges incorrectly if heteroresidue is bonded to functional group

[dargen3]

Hello,

I'd like to report a potential bug. If I assign formal charges to the amino acids in protein 1rcm using the function hydride.estimate_amino_acid_charges(..., ph=10), the charges -1 are also assigned to the sulfur atoms to which the acetic acid (ACY) is bonded and the formal charge should be therefore 0.

I looked into https://github.com/biotite-dev/hydride/blob/main/src/hydride/charge.py and if I understand correctly the case where a hetero-residue is bonded to a functional group is not treated.

[dargen3]

Even sulfurs in a disulfide bond have a charge of -1.

[dargen3]

If I'm not mistaken, it might be enough to check if the atoms are not involved in an interresidual bond.

[padix-key]

Your analysis seems to be totally correct 👍, thanks for reporting. Would you like to create a fix PR for it?

[dargen3]

I can if you want, but not until January. The end of the year is crazy in the academic world. I'll also add the selenocysteine and pyrolysine as i mentioned in issue 19.