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a-r-j / graphein

Protein Graph Library
https://graphein.ai/
MIT License
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deprotonate pdb structure #198

Closed EyalRozenberg1 closed 2 years ago

EyalRozenberg1 commented 2 years ago

On Deprotonation process on the PDB file, I see that you choose to deprotonate the file according to 'atom_name' field rather than element_symbol field.

see here: https://github.com/a-r-j/graphein/blob/553fd2615e69fcad74c6c2659b795faf6d1c798b/graphein/protein/graphs.py#L152

Is there a reason why not to deprotonate according to element_symbol? Your approach lives some H atoms in the PDB file. I could not find any explanation why they are more important than those that were deprotonated. Thanks

a-r-j commented 2 years ago

Thanks for the report, Eyal! Should be fixed in 1.5.1 :)