Hi,
it seems that nitrogen atoms in aromatic rings are being assigned
faulty valences. See example below:
>>> from rdkit import Chem
>>> pyrrole = Chem.MolFromSmiles('C1=CNC=C1')
>>> for atom in pyrrole.GetAtoms():
... print atom.GetSymbol(), atom.GetExplicitValence(),
atom.GetNumImplicitHs()
...
C 3 1
C 3 1
N 3 0
C 3 1
C 3 1
The nitrogen should have a valence of two and one implicit hydrogen.
If we reduce one C=C double bond, it works correctly:
>>> m = Chem.MolFromSmiles('C1=CNCC1')
>>> for atom in m.GetAtoms():
... print atom.GetSymbol(), atom.GetExplicitValence(),
atom.GetNumImplicitHs()
...
C 3 1
C 3 1
N 2 1
C 2 2
C 2 2
I've seen this with several other compounds as well; I'm not exactly
sure that the error is strictly associated with aromaticity though.
Sorry if this is a known issue, but I couldn't find it mentioned
anywhere.
Best regards, Michael
--
Michael Palmer
University of Waterloo
Waterloo, Canada
science.uwaterloo.ca/~mpalmer
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