Standard and Extended fingerprints are not being calculated for the attached drug molecules. Pubchem, MACCS work.
the standard and extended fingerprints are linear fingerprints. The current search depth is 8. If more than 150 paths are created for a molecule, the fingerprinter fails to save time and returns an emtpy fingerprint.
We could increase the max. paths limit but that would only postpone the problem until larger molecule are run. The exception thrown by CDK indicates that people are working on making the method faster. I have added a warning message to the node that warns users about empty fingerprints.