Good evening,
I would like to get an exhaustive substructure matching of a molecule onto
itself. Generally I could use the GetSubstructMatches function with the
"uniquify=False" option. However, if there is a carboxylate or a guanidinium
head around, this would give only "one side" of the match since the two oxygens
/ nitrogens are not considered equivalent:
>>> mol = Chem.MolFromSmiles('CC(=O)[O-]')
>>> patt = Chem.MolFromSmarts('CC(=O)[O-]')
>>> print mol.GetSubstructMatches(patt,uniquify=False)
((0,1,2,3),)
Now, I suppose I could do an ugly (could in principle match two single bonds)
hack to achieve my purpose:
>>> mol = Chem.MolFromSmiles('CC(=O)[O-]')
>>> patt = Chem.MolFromSmarts('CC(~O)~O')
>>> print mol.GetSubstructMatches(patt,uniquify=False)
((0,1,2,3), (0,1,3,2))
However, this would mean that I would need to manually edit the smarts string
for all molecules. I just wonder if there is something similar to the
"Kekulize" command that would make the two oxygens equivalent? Or are there
other ways around this?
Ling
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