Dear All,
I have been exploring some interactivity between PyMOL and RDKit
recently, and at the moment am ferrying molecules between the two in MOL
format. However, I have come up against a bit of a problem that I
wondered if anyone could help with?
PyMOL does a pretty good job of setting bond valences automatically for
ligands read-in as part of PDB files, and most of the time these ligands
exported in MOL format are recognised fine by RDKit (a little bit of
parsing is necessary to change things like 'Cl' being capitalised in
some PDB files, etc!). However, it seems that when there is ambiguity
about how to tautomerise 5-membered heteroaromatics, RDKit fails to
create a mol object from the molfile. I have included an example
Molfile below (a pyrazolopyrimidine).
Ideally (from my point of view at least!) it would be great if in these
situations RDKit yielded an arbitrary explicit H to 'mend' the problem.
However, I am definitely open to workaround suggestions (including "go
post on the PyMOL lists" :-) ). Maybe this is something that is
relatively trivial to tackle using PyMOL's ChemPy module? (which I know
very little about!).
untitled
ChemPy 3D 0
9 10 0 0 1 0 0 0 0 0999 V2000
16.6400 15.1940 18.3320 C 0 0 0 0 0 0 0 0 0 0 0 0
16.6190 14.6050 17.0520 C 0 0 0 0 0 0 0 0 0 0 0 0
16.7200 15.3750 15.9600 N 0 0 0 0 0 0 0 0 0 0 0 0
16.8570 16.7060 16.1150 C 0 0 0 0 0 0 0 0 0 0 0 0
16.8760 17.3110 17.3320 N 0 0 0 0 0 0 0 0 0 0 0 0
16.7640 16.5880 18.4530 C 0 0 0 0 0 0 0 0 0 0 0 0
16.4970 14.1830 19.1960 C 0 0 0 0 0 0 0 0 0 0 0 0
16.3960 13.0610 18.4470 N 0 0 0 0 0 0 0 0 0 0 0 0
16.4690 13.2930 17.2130 N 0 0 0 0 0 0 0 0 0 0 0 0
1 6 4 0 0 0 0
2 1 4 0 0 0 0
2 9 4 0 0 0 0
3 2 4 0 0 0 0
4 3 4 0 0 0 0
4 5 4 0 0 0 0
5 6 4 0 0 0 0
7 1 4 0 0 0 0
8 7 4 0 0 0 0
9 8 4 0 0 0 0
M END
Kind regards
James
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