While this doesn't answer your core question of can RDKit do what you want
without manually editing the smarts strings, if you do end up hacking it
using 'C[CX3v4](~O)~O' might be cleaner than 'CC(~O)~O)' as it would
exclude the case where both Os were singly bonded.
Yours,
Toby Wright
--
InhibOx Ltd
On 30 October 2013 01:12, S.L. Chan <[email protected]> wrote:
> 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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