Problem with nitrile coordinates generated by Molecule to CDK node

Dear CDK lovers,

I'm experiencing an odd behavior with the Molecule to CDK node for which I would like you to confirm whether it is a bug. There are some molecule for which the 2D coordinates of their nitrile groups are not correctly generated by Molecule to CDK node. In the depiction it seems that the nitrogen atom overlap the carbon atom of the nitrile. Nevertheless the correct atom connection is maintained. An example workflow is attached.

Thanks in advance for any feedback.


Dear Gio,

thanks for the demo workflow. I can confirm that this is a bug. As you have already pointed out, the connectivity of the molecule is not affected.

I'll check whether the issue stems from the core library or the KNIME plug-in and submit a bug report.

Kind regards,


Dear Stephan,

Thank you for the feedback and for taking care of submitting the bug.



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