Error in workflow execution with Padel

[AKUM]

I have recently downloaded the padel descriptor to include in knime node. When I am connecting it with excel reader containing SMILES string it is showing error as ERROR PaDEL-Descriptor 0:10 Execute failed: (“ArrayIndexOutOfBoundsException”): null.
Even I connected it to the output port of openbabel (connected to excel reader containing SMILES string of the molecule) which contained molecule structure in sdf format, the same error comes on execution. What is the solution?

[Alice_Krebs]

Hi @AKUM

I assume in general you would need to add the Molecule to CDK node, but that only results in another error. Unfortunately this is a known issue for quite a long time:

PaDEL Issue

I'd like to read a SMILES or SDF file in and used PaDEL to generate descriptors however a) When using PaDEL's own Compounds Reader to read an SDF file I get the error: "ERROR Compounds Reader     2:15       Execute failed: Error while writing to buffer, failed to write to file "knime_container_20170720_6246293811033658750.bin.gz": org.openscience.cdk.knime.type.CDKCell cannot be cast to org.openscience.cdk.knime.type.CDKCell" b) I can read in SMILES, File Reader -> RDKit From Molecule -> RDK…

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…

and probably has something to do with the underlying CDK.
These are community nodes not developed by KNIME but PaDEL, so there is not much we at KNIME can do about it, I’m sorry.
Maybe the workaround using the Linux command line mentioned in the first forum link works for you.

Best,
Alice

[AKUM]

I had added both nodes sdf reader and string to molecule nodes containing molecules to molecule to CDK node but in each case error output ws there.

[Alastair2]

I think the PaDEL nodes have not been maintained for quite some time, and even some years ago there were problems with the version of CDK in the background.

Maybe try Mold2 as an alternative, although it is not the most KNIME friendly node, and only has 2D descriptors.
https://www.fda.gov/science-research/bioinformatics-tools/mold2