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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