Similarity Search node error: Execute failed: Iterator at end

Hello everybody,

I'm trying to perform a similarity search using CDK extended fingerprints nodes. I'm searching the 10 nearest neighbors of a target compound. I calculate their extended fingerprints without problems using CDK fingerprints node. Then I passed the fingerprints to the Similarity Search node. I'm obtaining the following error:

ERROR Similarity Search Execute failed: Iterator at end

Do you have any suggestion?

Thanks,

Gio

Hi Gio,

I tried reproducing it but it works for me. Can you provide me with the workflow or some example to diagnose it?

Thanks,
  Bernd

Hi Bernd,

Thanks for your help. I wanted to export the workflow for your diagnosis. As the database on which I wanted to perform the similarity search is large (several hundreds thousands of compounds), I limited the sdf reading to just 10 molecules. Doing this I just realized that:

  • If the DB on which the search is performed was 10,000 molecules or smaller, than the error given by the Similarity Search node was: "ERROR Similarity Search Execute failed: No more rows in buffer"

  • If the DB on which the search is performed was 100,000 molecules or larger, than the error given by the Similarity Search node was: "ERROR Similarity Search Execute failed: Iterator at end"

Hence I thought that the problem could be related with some molecules and I better checked my workflow.

Finally I realized I didn't filter out those molecules whose fingerprints failed to be calculated, and this was causing the problem. If I filter those molecule out using the regular Row Filter, I avoid the problem. I'm sorry if I didn't realized the error sooner. Anyway thanks again for your help!

Gio