Highlighting atoms by substructure

I'm trying to use the 'RDKit Highlighting Atoms' node to show MCSS among a series of compounds.  The node seems to require a column containing a collection of atom numbers.  How do I extract these atom numbers from a substructure?  The only description I found in the forums is to use it with the 'Substructure Filter' node.  However, this only takes in SMARTS queries.  There's two additional challenges with this: 1) SMARTS doesn't seem to be a format supported by the OpenBabel conversion tool (my compounds are in SMILES format), and 2) the 'RDKit Substructure Filter' node only allows hard-coded SMARTS queries (I can't change it dynamically with a Flow Variable).



You can get to smarts by using the free Marvin extensions, the desired node is called MolConverter.


Hi George,

I do not understand why it would be impossible to feed in SMARTS values to the Substructure Filter node via flow variables. I just did exactly that and it worked fine. BTW, as SMILES are a subset of SMARTS you can use the KNIME node "Molecule Type Cast" to convert your SMILES into SMARTS. That is what I did in my sample workflow. Hope this helps you to accomplish what you have in mind.