Yep, this is what I think I need. Many thanks Greg!
And thank Toby for the tips too.
Ling
>________________________________
> From: Greg Landrum <[email protected]>
>To: S.L. Chan <[email protected]>
>Cc: "[email protected]"
><[email protected]>
>Sent: Wednesday, October 30, 2013 6:08 AM
>Subject: Re: [Rdkit-discuss] atom equivalence for substructure matching
>
>
>
>Hi Ling,
>
>
>
>On Wed, Oct 30, 2013 at 2:12 AM, 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?
>
>
>This is an interesting question.
>
>
>There's no super-easy way that I can think of to get what you want, but there
>is an approach that will probably work.
>
>
>What you can do is edit the molecule to replace the substructures in question
>with something that gives the appropriate matching behavior.
>Here's one way of doing that which preserves atom types:
>
>
>In [17]: repl = Chem.MolFromSmiles('C(O)O')
>In [18]: repl.GetBondWithIdx(0).SetBondType(Chem.BondType.ONEANDAHALF)
>
>In [19]: repl.GetBondWithIdx(1).SetBondType(Chem.BondType.ONEANDAHALF)
>
>In [20]: m = Chem.MolFromSmiles('CC(C(=O)O)C(C(=O)O)C')
>
>In [21]: m.GetSubstructMatches(m,uniquify=False)
>
>Out[21]: ((0, 1, 2, 3, 4, 5, 6, 7, 8, 9), (9, 5, 6, 7, 8, 1, 2, 3, 4, 0))
>In [25]: nm =
>Chem.ReplaceSubstructs(m,Chem.MolFromSmarts('C(=O)[OH,O-]'),repl,replaceAll=True)
>In [28]: nm[0].GetSubstructMatches(nm[0],uniquify=False)
>Out[28]:
>((0, 1, 2, 3, 4, 5, 6, 7, 8, 9),
> (0, 1, 2, 3, 4, 5, 6, 7, 9, 8),
> (0, 1, 2, 3, 4, 6, 5, 7, 8, 9),
> (0, 1, 2, 3, 4, 6, 5, 7, 9, 8),
> (3, 2, 1, 0, 7, 8, 9, 4, 5, 6),
> (3, 2, 1, 0, 7, 8, 9, 4, 6, 5),
> (3, 2, 1, 0, 7, 9, 8, 4, 5, 6),
> (3, 2, 1, 0, 7, 9, 8, 4, 6, 5))
>
>
>
>
>Note that the problem with this is that it changes the atom numbering. If you
>want to preserve atom numbering, it's a bit more complex:
>
>
>
>
>In [45]: q = Chem.MolFromSmarts('C(=O)[OH,O-]')
>In [46]: m = Chem.MolFromSmiles('CC(C(=O)O)C(C(=O)O)C')
>
>In [48]: qmatch = m.GetSubstructMatches(q)
>
>In [50]: for match in qmatch:
>
> b = m.GetBondBetweenAtoms(match[0],match[1])
> b.SetBondType(Chem.BondType.ONEANDAHALF)
> b = m.GetBondBetweenAtoms(match[0],match[2])
> b.SetBondType(Chem.BondType.ONEANDAHALF)
> m.GetAtomWithIdx(match[2]).SetFormalCharge(0)
> m.GetAtomWithIdx(match[2]).SetNoImplicit(False)
> m.GetAtomWithIdx(match[2]).SetNumExplicitHs(0)
>
>
>In [52]: m.GetSubstructMatches(m,uniquify=False)
>Out[52]:
>((0, 1, 2, 3, 4, 5, 6, 7, 8, 9),
> (0, 1, 2, 3, 4, 5, 6, 8, 7, 9),
> (0, 1, 2, 4, 3, 5, 6, 7, 8, 9),
> (0, 1, 2, 4, 3, 5, 6, 8, 7, 9),
> (9, 5, 6, 7, 8, 1, 2, 3, 4, 0),
> (9, 5, 6, 7, 8, 1, 2, 4, 3, 0),
> (9, 5, 6, 8, 7, 1, 2, 3, 4, 0),
> (9, 5, 6, 8, 7, 1, 2, 4, 3, 0))
>
>
>In all the above I'm showing how to solve the problem for carboxyls. Handling
>other groups is left as an exercise to the reader. ;-)
>
>
>
>Is that doing what you're looking for?
>-greg
>
>
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