ArrayIndexOutOfBounds when connecting 'Molecule to CDK' to 'PaDEL-Descriptor'

 Alright I'm completely stumped.  I'm attempting to use 'Molecules to CDK' - 'PaDEL-Descriptor' nodes and keep getting the following error:

     ArrayIndexOutOfBoundsException = -1 (or) NULL

The first time I connect these nodes together and execute the entire workflow, the workflow works.  The second time I execute the workflow everything works...  Now, the odd thing is once I save the workflow, exit it, then re-open the workflow - I get the above error.  There is a way around this which is to delete the 'Molecule to CDK' node and relace it with the exact same node and then the error will go away.  It works every time.

Any thoughts on how to resolve this error?


Thanks all,



Well I figured out what's happening.  

CDK's 'Molecule to CDK' -> PaDEL-Descriptor  won't work due to a version issue.

PaDEL's 'Molecule to CDK' -> PaDEL-Descriptor works just fine.

When exiting and saving a workflow with the following node configuration: PaDEL's 'Molecule to CDK' -> PaDEL-Descriptor, during the next loading of the workflow - PaDEL's node will be replaced with CDK's which will result in an error due to version differences.

I'm still looking for a solution to this issue.  I may end up uninstalling CDK's node as a fix, but I'm reporting this issue because it's cost me a good bit of time to figure out what's going on and may help someone in the future.



Hi Christopher,

thanks for the summary. That hopefully helps other users to save some time.

The PaDEL KNIME extension is unfortunately not compatible with the currenct CDK version we use. The topics have also been discussed in some other places.:

I'm would love to align PaDEL and CDK in KNIME but PaDEL is still on the old 'stable' CDK 1.4 build. I believe they upgrade upon the release of CDK 1.6.



In fact I have been trying to work with connecting mol converter node which contain sdf structure in its output to molecule to CDK node and connecting this to Padel descriptor node .However, no node is successfully working.As aresult I am unable to get Padel descriptors.
Can anyone suggest how to obtain Padel descriptors for smiles string kept in an excel file.I need it urgently as I am in a midst of QSAR project.