Labs External Tool: Does not read properties in SDF

The Knime Labs external tool does not read the properties in a generated SD-File.

How can this be done? If not possible, this would be a very important feature.

Why not use the SDF reader in the chemistry section. This takes in all SDF properties.


Because the labs external tools handles multiprocessing. I can create x instances of the external tool and it automatically joins together all output files. With a 4 core CPU that matters a lot in this specific case.

Yes, your suggestion would somehow work as a workaround but ultimately the external tool should also read in all the properties, especially the new ones.

The node reads the SDF file as-is and does not change its contents. If the read SDF does not contain properties then the output file of the external command didn't contain any properties.

The external procedure adds a new property and it is clearly visible in the output sd-file. however knime does not read it back in.

Are you aware of the SDF Extractor node?  If the property is there, you should be able to get at it with this. 


Ok, that works except that the structure appears twice per row (can be easily filtered)

But another issue occurs now. namley that bit strings (fingerprints) are automatically evaluated as numbers which they should not. And the evaluation fails (infinity)