Error with OpenBabel on Mac

Groups Cheminformatics
1

Hey, 

I'm a Mac user (MacOS Sierra v10.12.4) and are working with KNIME 3.3.2. I cannot make OpenBabel work.

I have used "Chemical Identifier Resolver" to generate smiles from chemical names and then I want to generate SDFs from the smiles. But when I connect CIR with OpenBabel and wants to configurate OpenBabel, I get the error "Error while executing '/Applications/KNIME 3.3.2.app/Contents/Eclipse/plugins/org.knime.ext.chem.openbabel.bin.macosx.x66_64_2.3.1.v201409161231/macosx/x86_64/babel':dyd: Library not loaded: url/local/lib/libopenbabel.4.dylib Reference from:  '/Applications/KNIME 3.3.2.app/Contents/Eclipse/plugins/org.knime.ext.chem.openbabel.bin.macosx.x66_64_2.3.1.v201409161231/macosx/x86_64/babel' Reason: image not found"

I found one person with the same problem (https://tech.knime.org/forum/knime-general/issue-with-openbabel-translation-node) but the link to ChemSpotlight was no longer available. Instead, I installed OpenBabel 2.0.2 from https://sourceforge.net/projects/openbabel/ as well as iBabel as GUI but that did not solve the problem. I tried to figure out how to change the settings in KNIME so that it would be directed to the correct Babel execution file, but without luck. 

Any suggestions as how to solve this?

/Signe

 

2

Hi Signe,

Thanks for the detailed bug description. I verified the issue on my mac and have opened a ticket for our developers to look into.

There is a workaround where you could use the molecule typecast node to convert the smiles to sdf.

Best,

Jon

3

Dear Signe,

you should be able to generate SDF from chemical name directly using CIR.

Best,

Andrea