On 06/06/12 12:27, Nicholas Firth wrote:
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.
I guess I'm missing something. addHs() returns an ROMol - it is not
clear to me why that gives you pointer issues/problems.
P.
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