Simple Streaming and Rdkit

Hi everybody,

When I try to use some nodes of RDKit to clean a library (for instance salt stripping, canonicalization ecc… ) or to do a similarity search along with the Simple Streaming I got the following error:

java.lang.IllegalThreadStateException: The current thread is not taken out of a thread pool

I know that there are already a couple of threads on this since it is a known bug, but they all have been closed years ago without a solution.

What can be done about it?

My system is:
Windows 11
Knime 5.2.1
RDKIT 2023.09.2

Thank you so much for your help!

@saltalamacchia , look if this node from Palladian can help you

It is streamable.

Thank you for your suggestion, but unfortunately I have this problem with multiple nodes of RDKit. moreover I prefer to stick with one library in order to be consistent in the processing of the molecules.

I hope that this bug will be fixed sooner or later!

I tried as well and could reproduce your error. The error has been reported, thank you.

In the meantime, I can offer two workarounds.
One is to pull the nodes that are not compatible with streaming out of the component, and leave only the one that are compatible in the streamed component. In the RDKit extension, it seems that SMILES canonicalization and fingerprint creation are examples of streaming-compatible nodes.

The other is to use a chunk loop to separate the data (Chunk Loop Start and Loop End). A chunk size can then be set accordingly.

I hope that one of these options is suitable.
Best regards,