Identifying fragments of a multi-fragment structure

Given a set of structures such as

I would like to be able to say ‘this molecule has 5 molecules of water.’ (There is a list of known salt counterions and solvents to use for matching fragments.)
I’ve gotten part of the way using the RDKit Molecule Extractor, which creates a new record for each fragment.
The next step is to put a name (or identifier) on each fragment.
The RDKit Molecule Substructure almost works.
It tells me that the the extracted water molecules match ‘[OH2]’ but [OH2] also matches the parent fragment, which is not what my team is looking for.

How can I perform an exact match of a set of generated fragments against a set of known molecules?


Hi @ChemMitch

I have to admit I am not sure I understood your question correctly, or if I did maybe your given SMILES is not the best example. But maybe that workflow will help you.

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Thank you, Alice!
That approach works well for me.


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A follow-up question: it looks like the Molecular Substructure Filter is ignoring double bond stereochemistry. Fumarate and maleate match each other.
Is there a way to distinguish between them?


Hi Mitch,
Though the RDKit supports using stereochemistry, that functionality is not yet exposed in the KNIME nodes.
This is something we can/should change… I will put it on the list.