Hi All,
I'm having some issues with getting some more 'interesting' ring systems to
kekulize. I'm creating the molecule in RDKit by individually adding all the
atoms and bonds from a graph. However I have found similar issue when trying to
initialise a molecule from smiles.
Two examples of molecules which won't kekulize are:
n1nnnn1
c1cccp1
however, when adding hydrogens to these smiles, so
n1n[nH]nn1
c1ccc[pH]1
These will work perfectly fine. This is a problem as the graph structure I have
does not include any hydrogens. For a fix I have tried to addHs to my molecule,
however I'm having issue with these functions because I'm writing in C++ and
want to return this value, so don't have any pointers as this results in a
memory leak.
Any help, whether it be programming advice or RDKit function advice would be
very helpful.
Best,
Nick
Nicholas Firth, Ph.D. Student
Institute of Cancer Research
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Belmont
Surrey
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