Hi Kovas,
You have two fuzzy compounds that you try to match them, because our
intuition says that any atom notation [*:1] from m1 should match the
Fluorine [F:11] in m2 and any atom [*:14] in m2 should match Carbon [CH3:4]
in m1.
The issue here is that you create two query compounds from m1 and m2 which
will match their own specific substructures. Query to query matching is not
trivial.
In order to do what you want you need a query compound that combines their
characteristic, which is what Paolo showed.
Paolo with MCS and modifying atom properties created that query compound
'[*:1]-[CH2:2]-[C:3](-[*:4])=[CH2:5]' or
'[*:1]-[CH2X4:2]-[CX3:3](-[*:4])=[CH2X3:5]'
Also bare in mind that Paolo's approach changed the starting compounds, as
now they resemble the generic query compound that combines their fuzzy
atoms.
https://gist.github.com/CKannas/ac1a4791dec909552d7c8899cfaff030
Best,
Christos
Christos Kannas
Chem[o]informatics Researcher & Software Developer
[image: View Christos Kannas's profile on LinkedIn]
<http://cy.linkedin.com/in/christoskannas>
On Thu, 23 Aug 2018 at 12:36, Paolo Tosco <[email protected]>
wrote:
> Dear Kovas,
>
> It looks like GetSubstructMatch() only finds a match if the dummy atom is
> in the query, not if it is in the molecule they you are matching the query
> against.
>
> This notebook present a possible solution off the top of my head:
>
> https://gist.github.com/ptosco/a35ac28a14103b47096f6d6af1aec831
>
> which does not involve changes to the C++ layer, even though it is
> computationally more expensive and will fail with disconnected fragments as
> it uses FindMCS(). There may be better solutions - this is what I came out
> with yesterday night in the little time I had available.
>
> Cheers,
> P.
>
> On 08/22/18 19:34, Kovas Palunas wrote:
>
> Hi All,
>
>
>
> I’m interested in having GetSubstructMatches return non-“null” results in
> the following example. The results should lead to a match where atom 1
> maps to atom 11, 2 to 12, etc.
>
>
>
> m1 = Chem.MolFromSmiles('[*:1][CH2:2][C:3]([CH3:4])=[CH2:5]')
>
> m2 = Chem.MolFromSmiles('[F:11][CH2:12][C:13]([*:14])=[CH2:15]')
>
>
>
> ### do something here so that the mols will match ###
>
> qp = Chem.AdjustQueryParameters()
>
> qp.makeDummiesQueries = True
>
> m1 = Chem.AdjustQueryProperties(m1, qp)
>
> m2 = Chem.AdjustQueryProperties(m2, qp)
>
>
>
> # I’d like both of the following to return results
>
> m1.GetSubstructMatches(m2)
>
> m2.GetSubstructMatches(m1)
>
>
>
> My understanding of why these mols currently do not match is as follows:
> because only the dummy atoms are made queries (based on my query parameter
> adjustment), when one mol is matched to another dummy 1 may match to F:11,
> but dummy 14 will then not match to methyl:14. This is because (as I
> understand), normal atoms can only be matched by queries, and cannot match
> them themselves.
>
>
>
> Potential ideas to make this work as I’d like:
>
> 1. Override atom.Match in the python code – not sure that this would
> work since the C++ version of this function is what would be called during
> GetSubstructMatches
> 2. Override atom.Match in the C++ code – not quite sure how to do
> this, or what side affects it might have. Ideally the changes I make would
> only affect this example (and other similar ones)
> 3. Make all atoms in both molecules QueryAtoms, but otherwise leave
> them unchanged. I’m not quite sure how to do this!
>
>
>
> Does anyone have any ideas for what the best approach here would be, or
> knows if there is already built in functionality for something like this?
> I’d prefer to not use SMARTS to construct my molecules if possible, since I
> don’t really think of them as queries, just as other molecules in the
> system that happen to not be fully specified.
>
>
>
> - Kovas
>
>
>
>
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