substructure node cannot deal with explicit hydrogens

Dear CDK team,

I would like to use your substructure search node.
Unfortunately it cannot deal with explicit hydrogens. But that is really crucial to my search, as I need to limit in which direction my molecule is “growing”.

here examples for query and molecule:



is this a bug or a missing feature? :slight_smile:
would be great if this would work.

2nd question for understanding:
does the node automatically also create the tautomers of the molecules that are compared in order not to miss a match that is “hidden” in tautomerization?

best regards,

Hi Jan,

I can reproduce your example with the explicit hydrogens and I can’t find a way to include them. The answer to the tautomer question I don’t know.
I have forwarded your questions to the developers of the toolkit and waiting for their feedback.

Kind regards,


I forwarded to question (substructure node cannot deal with explicit hydrogens · Issue #21 · cdk/nodes4knime · GitHub).

A process has started to make a CDK2.x-based node set. That will likely solve this isse.


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