Whenever I convert certain molecules from SMILES into SDF using the ChemAxon MolConverter component, some molecule show up with the symbol "IMPL_H1" when the renderer in KNIME is used.
This at least seems to prevent the Indigo components from creating InChi from them (though I bet there's more, but I haven't tested). Has anyone else had this?
I'm rather reluctant to post any examples with the molecules as it's using the WOMBAT dataset (which last time I checked, is proprietary). Though if needed I may try to reproduce the issue with ChEMBL compounds.
I'm really sorry that I need example data to reproduce the problem...
I've attached a screenshot of the workflow, and the workflow itself. Hope that demonstrates the issue.
Note that I've used the EMBL-EBI ChEMBL nodes, which you'll need installed (I'm reluctant to attach any datasets for now).
On KNIME 2.8.0 (my version), 3 of the 50 molecules retrieved have this wierd issue when converted to SDF with MolConverter.
The ChemAxon MolConverter creates SDF which contains the "IMPL_H1" as SED (Data sgroup data end of line) property.
Then, I'm not sure, but the Indigo nodes seems to convert it to the symbol...
(I'm really not sure whether this is bug or not...)
However, in your example flow, you don't need to use the MolConverter.
Because the Indigo node can convert the smiles to indigo directly.