Embedded usage of CDK1.4

Hi all,

    I am using a third party open source descripter calculator called PaDEL from the Univ. of Singapore. This requires a CDK 1.4 MoleculetoCDK node which is supplied along with the PaDEL node. The PaDEL node fails under CDK 1.5.

    There is no problem until I save the workflow and reopen. Then this CDK1.4 node gets reset to the corresponding CDK 1.5 node and the workflow fails. So the workflow cannot be used in production.

   Is there anyway to fix it so that this doesn't happen and the CDK1.4 MoleculetoCDK node gets loaded on reopening?



Hi John,

I don't think there is an easy and good way around this. In theory, PaDEL and KNIME-CDK shouldn't use different versions of CDK but that's unfortunately how it is for now. I will try to resolve this issue with the next major version of CDK.

If the current situation is very inconvenient for you, you could remove KNIME-CDK and carry on with PaDEL alone for now.

Best regards,


A work around woulds be the following sequence:

  1. Convert your structure to mol/SDF*
  2. Create a temporary directory 
  3. Write a temporary SDF file*
  4. Read in the temp SDF file using the Padel file reader*
  5. Process these CDK structure through PaDEL

This could all be bundled into a meta node. Without easy saving of meta nodes it's more of a pain to use however.

I would guess that the converter node was copied in PaDEL and the ID not changed?




* Or does it read molfiles?

That's a good work around. Thanks.

Yes, I assume that's the case. Let's see if we can get PaDEL and CDK on identical versions in the near future.



Thanks, that workaround worked just fine.



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