Possible bug in Openbabel node while converting molecule to mol2 format

Dear KNIMErs,

I found a problem while I was using the Openbabel node to convert a molecule to mol2 format. As you can see in the attached workflow (using the “Mol2 string render”), when I use the Openbabel KNIME node (using the bundled version of openbabel) it results in a mol2 format structure where atom types are not correct. They miss points (e.g. “Car” instead of “C.ar, Npl instead of N.pl, etc.). This results in invalid structure that cannot be well displayed by the molecule renders.

I also checked that the problem is not due to openbabel itself because if I run the transformation by an external version of Openbabel (through the External Tool Lab node) the resulting format is correct.

So in my opinion this could represent a bug. Can you please confirm that?



P.S.: I'm using the last current version of "KNIME Base Chemistry Types & Nodes" (3.2.2.v201609201941)

Did you use the same version of OpenBabel in both cases? We are simply calling the external executable so it's more likely a bug in OpenBabel than in our code. The version we bundle is rather old.

Hi Thor,

Thanks for the information. You're right, the bug seems to be on the OpenBabel side. I have it also if I externally use the KNIME-bundled-version of OpenBabel, so it doesn't depend on the node. The current KNIME bundled version seems to be the 2.3.1 of May 16th 2012. While externally I was using the new version 2.4.0 of Sep 22 2016.

It would be great if the new OpenBabel version could be included in the next KNIME release.