Hi all,
I am having an issue using the Smarts based Reaction transformations in
RDKit. This is a weird transformation, but I wanted to replace any or all
of the protons on an aromatic ring with an F.
The original transformation that I tried was:
ccc>>cc(F)c
But that didn't work. So then I tried a couple of other transformations:
[c:1][c:2][c:3]>>[c:1][c:2]([F])[c:3]
That failed (as these things generally were failing):
>>> ps = rxn.RunReactants(mol1)
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
Boost.Python.ArgumentError: Python argument types in
ChemicalReaction.RunReactants(ChemicalReaction, Mol)
did not match C++ signature:
RunReactants(class RDKit::ChemicalReaction *, class boost::python::list)
RunReactants(class RDKit::ChemicalReaction *, class
boost::python::tuple)
Then I got desperate:
[#6:1][#6:2]([#1])[#6:3].[H][#9:4]>>[#6:1][#6:2]([#9:4])[#6:3]
Any mention of an explicit H caused issues, so then I dropped it and re-ran
things again.
No luck. I should mention that I am using the pre-built python RDKit
wrappers for windows, and if I use the java wrappers on linux I get
different errors but the same outcome.
I should add, that the molecule that I read (and the molecule for HF) were
both loaded without issue.
Anyone else try to do something like this?
Matthew
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