How to read in SMARTS for the Substructure counter that aren't full molecules.


I've been testing SMARTS using the Substructure Filter and Substructure Counter.  With the Filter, I can specify [c;r6] to look for systems containing a six membered aromatic ring with at least one carbon - that works fine. If I however use that as a table entry for the substructure counter, using the File Reader node to read in my text file of SMARTS the Molecule to RDKit  node fails to parse the [c;r6] as a molecule (which is fair as it's not) and so I can't use it in the Substructure counter. I note that the Substructure Counter doesn't refer to SMARTS in the documentation which might be a warning sign that I'm really using the wrong node....Advice?

You need to use the "Molecule Type Cast" node in order to "convert" the Smarts strings to real Smarts.


Thanks - that worked - I found another solution using the Indigo toolkit using the Query molecule to Indigo - but having both solutions is best.