Thanks for the feedback and code example!
I understand that it works to make a third query mol using MCS that matches
both the original mols to then match with. However, this seems like overkill
(overly expensive) for this particular problem – as I understand it MCS can be
very expensive depending on the compounds you are comparing. Would it not work
to simply override the atom.Match function with one that will always match
dummies no matter what the other atom is? I am not planning to compare SMARTSy
queries with my matching with any complexity beyond simply dummy atoms. In
fact, as I understand it, my example compounds are not made up of any query
atoms when they are read into rdkit – the dummies are just made into queries
after the read by the QueryParameters code. I am definitely not interested in
doing generic query to query matching.
- Kovas
From: Christos Kannas <chriskan...@gmail.com>
Date: Thursday, August 23, 2018 at 7:53 AM
To: Kovas Palunas <kovas.palu...@arzeda.com>
Cc: RDKit <rdkit-discuss@lists.sourceforge.net>, Paolo Tosco
<paolo.tosco.m...@gmail.com>
Subject: Re: [Rdkit-discuss] Matching Generalized Compounds
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 removed by sender. View Christos Kannas's profile on
LinkedIn]<http://cy.linkedin.com/in/christoskannas>
On Thu, 23 Aug 2018 at 12:36, Paolo Tosco
<paolo.tosco.m...@gmail.com<mailto:paolo.tosco.m...@gmail.com>> 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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