Thanks to both for your replies. That's more or less what I was thinking of - I
just wanted to make sure that there was not something already available before
starting coding :-) I will get back to the list once I have something ready.
Cheers,
p.
> On 31 Oct 2014, at 05:17, Greg Landrum <greg.land...@gmail.com> wrote:
>
> The reply that Ling forwards has one approach to doing this.
>
> It's a bit easier for someone who is willing to do some C++ work.[1]
>
> One could imagine writing a function prepareForResonanceFormMatching(ROMol
> &m) (or some such thing) that would be applied to the *query* molecule that
> does the following:
> - identifies the groups that need to be resonance-symmetrized
> - changes the resonance bonds to Query bonds that match single or double
> (possibly also aromatic?)
> - neutralizes any charges on resonating atoms in the group.
>
> The last step is important because the query C(O)O matches the molecule
> C(O)[O-] twice, but C(O)[O-] only matches once:
>
> In [11]:
> Chem.MolFromSmiles('C(O)[O-]').GetSubstructMatches(Chem.MolFromSmiles('C(O)O'),uniquify=False)
> Out[11]: ((0, 1, 2), (0, 2, 1))
>
> In [12]:
> Chem.MolFromSmiles('C(O)[O-]').GetSubstructMatches(Chem.MolFromSmiles('C([O-])O'),uniquify=False)
>
> Out[12]: ((0, 2, 1),)
>
> I suspect such a function would be useful to multiple people.
>
> For identifying the groups that are resonance symmetrized: though this could
> be done using a set of particular patterns, it may be better to think about
> doing it more generally by having it find resonance systems.[2] The flag
> Bond.getIsConjugated(), set during sanitization, is probably useful for this.
>
>
> -greg
> [1] well, to the extent that anything is ever "easier" in C++
> [2] this would allow finding the substructure matches within molecules like
> C1=C(C)C=CC=CC=C1
>
>
>> On Fri, Oct 31, 2014 at 2:09 AM, S.L. Chan <slch...@yahoo.com> wrote:
>> Dear Paolo,
>>
>> I have asked a very similar question last year. This was what Greg said.
>>
>> Ling
>>
>> Re: [Rdkit-discuss] atom equivalence for substructure matching
>>
>>
>>
>>
>>
>>
>>
>>
>> Re: [Rdkit-discuss] atom equivalence for substructure ma...
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>>
>> From: Paolo Tosco <paolo.to...@unito.it>
>> To: "rdkit-discuss@lists.sourceforge.net"
>> <rdkit-discuss@lists.sourceforge.net>
>> Sent: Thursday, October 30, 2014 4:26 PM
>> Subject: [Rdkit-discuss] GetSubstructMatches() and resonance structures
>>
>> Dear all,
>>
>> The following code snippet compares two resonance structures of formate
>> anion:
>>
>> import rdkit
>> from rdkit import Chem
>>
>> mol1=Chem.MolFromSmiles('C([O-])=O')
>> mol2=Chem.MolFromSmiles('C(=O)[O-]')
>> mol1.GetSubstructMatches(mol2, uniquify = False)
>> ((0, 2, 1),)
>>
>> mol1.GetSubstructMatches(mol1, uniquify = False)
>> ((0, 1, 2),)
>>
>> I would rather like to get, in both cases, the following output:
>> ((0, 1, 2),(0, 2, 1))
>>
>> which would account for the carboxylate group symmetry due to resonance.
>> The same applies to amidinium, guanidinium, etc.
>>
>> Is that currently feasible within the RDKit API?
>>
>> Thanks in advance, cheers
>> Paolo
>>
>>
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