Getting the OpenBabel node to work on macOS


#1

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:

/anaconda3/pkgs/openbabel-2.4.1-py35_5/bin/babel

…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.


#2

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.

Best,
Anna


#3

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.


#4

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

Best,
Daria