Dear RDKitters,
I have a set of ligands in mol2 format which contain phosphate groups. I am
reading them in by typing:
rdkMol = Chem.MolFromMol2File(inmol2file, sanitize=True, removeHs=False)
and get the following warning message: "warning - O.co2 with non C.2 or
S.o2 neighbor."
The reason for the message is that I have P.3 atoms bound to O.co2's and
Mol2FileParser.cpp (in $RDKIT/Code/GraphMol/FileParsers) is (at least in my
version) only postprocessing carboxylates or sulphates groups.
Changing line 292 in Mol2FileParser.cpp into ' if (tATT=="C.2" ||
tATT=="S.o2" || tATT=="P.3"){ '
allows me to postprocess the phosphate containing ligands. If my change is
only part of the solution I would be really grateful to hear about it. In
any case I guess it's s.th. which should be changed in the code
distribution.
Kind regards,
Simone
--
Dr. Simone Fulle
Post-doctoral Researcher
InhibOx, Ltd
Oxford Centre for Innovation, Suites F14-F16
New Road
Oxford, OX1 1BY, UK
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