SmartCyp in knime?

Hi all,

I wonder if it is possible to include SmartCyp into Knime (or had that been done already)?

This software uses chemical structure data (.sdf, .smi, you name it, depending on OpenBabel) as an input. It comes either as a .jar executable or as a set of source code scripts. The external tool node failed - the input file generated from the data stream was not readible because of the "" signs Knime puts around the field content. Is it possible to run the source code within the JavaSnippet? Apparently, this node does not unterstand the package and the import sections.

Can anybody give me a hint how to deal with this (or find information how to deal with this?)


Thanks a lot,



Just to clarify input/output of SMARTCyp.

smartcyp is run as a commandline java program

input should be sdf or smiles file (other formats have to be converted first)

output is csv file with a line for each atom, with ranks, scores etc. which can be imported easily into most programs.

more info at

/Patrik, SMARTCyp developer

Hi patrick,

thanks a lot for your feedback!

Basically, the input requirements are the biggest problem when trying to include SmartCYP via the "external-tool" node which by default writes the data stream as a csv file. Do you have any suggestions how to include SmartCYP in a KNIME workflow?


I guess one could write a wrapper which takes the structural information from the cvs (if it's in sdf or smiles format), runs SMARTCyp, and then puts the SMARTCyp output into the cvs.

You may try out the External tool node from KNIME Labs category (needs to be installed explictely). This one has support for SDF and Mol2 files.

indeed, this was a valuable hint :-) .... Thanks!

However, as it seems, I need a more complex statement than simply run SmartCYP. Something like an execution batch. Unfortunately, this seems not to work with the external tool node. Do you have an idea how to manage that (So far, I´ve been running KNIME on a Win machine, but could also switch to LINUX).

cheers, aks