Getting the OpenBabel node to work on macOS


I’m trying to use the OpenBabel node on a Mac and not having any luck getting it to work. Apparently you can’t use the bundled OpenBabel (why?) so I’ve pointed the node to:


…but it won’t load the available formats into the node dialogue and throws a NullPointerException when it tries to run.
Any pointers on where I’m going wrong would be very helpful.


Hi @rsherhod,

Which version of KNIME are you using?

Can you attach a sample workflow please so we can try to reproduce the problem?

Thank you.



KNIME 3.6.0 on macOS 10.13.6. OpenBabel 2.4.1 was installed into my Anaconda (Python 3.5) directory, via conda, into the location I quoted. It’s possible that’s just the wrong binary, but can’t find it anywhere else.

I can share a workflow if you like but it’s just a MarvinSketch node that generates a SMILES, followed by the OpenBabel node.

Out of interest, why is the bundled version of OpenBabel not available on the mac? That’d save me a right headache.


Hi Rscherhod,
The workflow would be very helpful. Thank you.