Automated addition of R-groups to scaffolds


Is there a way to automatically add R-groups to any given ring structure? For instance, if I present cyclohexane, the process would return:

but if I presented piperidine, it would return:

Thanks for your help!

HI @mbrunavs ,
could you provide, please, a bit more input: which node you refer to?
Does the second screenshot represents the desired input?

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Hi @darspir

Apologies if my original post was unclear.

My goal is to achieve the following structural transformation:

To add more context, here’s what I’d like to happen if thiazole was the input ring system:

Regarding which nodes to use, I don’t know! That’s the point of my question. What node(s) are available in KNIME that could achieve this, and how would I configure them?

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Hi @mbrunavs ,
The attached workflow uses a python scripting node and the RDKit to do what I think you are trying to do.
You need to have the RDKit KNIME nodes installed and to have the RDKit installed in the conda environment that you use inside of KNIME.


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Looks like I forgot the workflow… sorry about that!

Add R groups.knwf (10.9 KB)


Thanks @greglandrum. This works really nicely. The R-group numbering wasn’t quite what I expected but I can work with this as long as those numbers are generated in a consistent manner for any one ring, run-to-run. Much obliged!

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