Thank you again for your useful suggestions. We can add the "Number of aromatic rings" into the next build, but I am wondering whether it should be all rings or just SSSR (smallest set of smallest rings)? In other words, take naphtalene: should Indigo report 2 or 3 aromatic rings for it?
As for the HBAs, HBDs, and rotatable bonds: Indigo can not calculate them directly, but you can get the result by using the Substructure Match Counter node with a SMARTS string as a query. You just connect your molecule(s) source to the first input of the Substructure Match Counter node, while to the second one you should pass a query molecule which you can obtain in the following way:
Table Creator (enter your SMARTS expression there) -->
Molecule Type Cast (cast it to the SMARTS type) -->
Query Molecule to Indigo (parse the SMARTS) -->
(to the second slot of the Substructure Match Counter)
There are known SMARTS expressions for HBAs and HBDs, and also for the number of rotatable bonds.
Moreover, you can calculate the TPSA this way! (you asked about the Polar Surface Area before -- is that what you want?). However, this is a bit more complicated as it involves summing the substructure match counters (multiplied by coefficients) for different SMARTS. Good news: you can download an example of TPSA calculation from the KNIME Example Flow Server, look there into 099_Community/07_Indigo/09907006_indigo-tpsa-example. There are other examples there, too.