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
------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
