Hi Gonzalo,
SmilesToMol has a sanitize flag which you can set to False. However - I am not
sure how well you molecule fingerprints will work with an unsanitized molecule.
I would imagine that you will run into all sorts of funny problems wrt
aromaticity detection etc.
Not sure if this helps in your case – but if you write out the molecules as
non-aromatic (ie alternating ring bonds) maybe this would help with your
approach? How do you fragment your molecules? Do you need the vendor code or
could you just do the same in RDKit – eg using BRICS or similar?
Ciao
Nik
From: Gonzalo Colmenarejo-Sanchez
<[email protected]<mailto:[email protected]>>
Date: Tue, 7 Aug 2012 09:50:30 +0000
To:
"[email protected]<mailto:[email protected]>"
<[email protected]<mailto:[email protected]>>
Subject: [Rdkit-discuss] matching substructures to molecules
Hi,
I have a vendor fragmentation algorithm and I want to evaluate the presence of
the fragments/substructures in a list of molecules with the RDKit C++ API. In
order to avoid a slow SubstructMatch comparison of n fragments x m molecules I
first SmilesToMol the fragment, generate a fingerprint, calculate the Tversky
similarity with the molecule fingerprint, and only if the value is high a
SubstructMatch is run. This makes the process extremely fast.
The problem I observe is that for many SmilesToMol of the substructures I’m
getting exceptions like
[10:34:46] Can't kekulize mol
[10:34:46] non-ring atom 4 marked aromatic
Is there a way to “force” SmilesToMol to accept the fragment SMILES so that a
fingerprint of the fragment graph can be generated (btw, I don’t understand why
a kekulization is performed) even when the fragment is not a complete molecule?
Thanks a lot,
Gonzalo
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