Is there a work-around for the "can not calculate implicit hydrogens on aromatic N" glitch in the Indigo Substructure Match Counter (and other nodes)? e.g. target molecule theophyline, C[n]1c2c([n](c([n](C)c2nc1)=O)C)=O fails and just generates a missing value.
I have tried the old trick of adding a Dearomatizer node, but this does not help.
Even an imperfectly represented molecule would be better than failing to a missing value, perhaps a not very chemically realistic kekule structure would do.
I have hundreds of these compounds in the database I'm using, so it would be unrealistic to manually tinker with the SMILES string.
I would recommend using the ChemAxon MolConverter node - you can generate kekulised SMILES (or other formats) by using "-a" (without the quotes) as the output option. I have tested with your example and it kekulised fine.
Tried both - still did not work. Molecules were kekularized properly, but the Indigo Substructure Counter Node still gave out the errors - almost as if the molecules were being re-aromatized.
Indigo Substructure Counter Node seemed to require the "Molecule to Indigo" and the "Query Molecule to Indigo" nodes, so it might be these that are re-aromatizing the molecules.
Switching to the RDKit Substructure Counter node seemed to work better.