Currently the code will throw a warning if it finds any non-protein atoms in the residue selection. However the "protein residue" definition in MDA is quite loose, my understanding is that propka only really accepts these:
What would we think about making the check more stringent so that if it finds anything not in that dictionary it throws a warning to telling users to consider renaming residues to their standard value if necessary?
orbeckst
commented
4 years ago
Currently the code will throw a warning if it finds any non-protein atoms in the residue selection. However the "protein residue" definition in MDA is quite loose, my understanding is that propka only really accepts these:
https://github.com/jensengroup/propka/blob/831e7380689b05892645012766671e2df8a644d8/propka/lib.py#L20-L23
What would we think about making the check more stringent so that if it finds anything not in that dictionary it throws a warning to telling users to consider renaming residues to their standard value if necessary?