Thanks to you both for the help, I will have a look and see if I can sort it
out.
I did check the forum before I posted, obviously missed that one, sorry for the
time wasting.
Best,
Nick
Nicholas Firth, Ph.D. Student
Institute of Cancer Research
15 Cotswold Road
Belmont
Surrey
SM2 5NG
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On 6 Jun 2012, at 13:40, Greg Landrum wrote:
Hi Nick,
On Wed, Jun 6, 2012 at 12:27 PM, Nicholas Firth
<[email protected]<mailto:[email protected]>> 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.
Any help, whether it be programming advice or RDKit function advice would be
very helpful.
This is related to a question that came up a while ago about
automatically fixing kekulization problems:
http://www.mail-archive.com/[email protected]/msg01901.html
That code, which is Python, is probably a good start. If you're using
C++, you will need to translate a bit, but it should be
"straightforward". Note that you can skip the whole thing with the
EditableMol in C++.
-greg
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