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


#5

Hey @rsherhod,

You need to install the standalone version of openBabel, as described here: https://openbabel.org/wiki/Category:Macintosh

openBabel uses a lot of different configuration files, which are perfectly handled by the installer and the standalone version. While this is easy to setup on Windows and Linux, the Mac version is quite different. So although it might seem more complicated, just installing the pkg from the website is the smoother and easier way.

Cheers,
Ferry


#6

Hi Ferry,

Thanks, that worked.

The installer linked to on that page is for a very old version of OpenBabel, which didn’t work. However I managed to find a more recent installer in OpenBabel’s SourceForge project.

Unfortunately the most recent mac binary is still only version 2.3.1, from way back in 2011. Unless you know otherwise, it seems the OpenBabel team aren’t interested in making mac binaries. Since the node is part of the core chemistry plug in, it would be really helpful for KNIME to start bundling mac binaries. Alternatively could you share some details about how to get an OpenBabel installation working in KNIME, when built from source or installed through conda?

Cheers,

Richard