sdf file problem

Community Extensions RDKit
#1

I'm newbie in KNIME and I have a problem with sdf files. I downloaded small part of ZINC database in sdf format. When I try to read this file in SDF Reader and after that use RDKit From Molecule, in the console I can see message: „Neither SMILES, SMARTS nor SDF compatible column in input table.”

What can be wrong with my sdf file? Could you please give me some advice?

 

Cheers,

Dominika

#2

Dear Dominika,

could you please attach a little workflow (with SDF Reader and RDKit Node) with a concrete file that demonstrates the issue?

Kind regards,

Manuel

#3

Had a similar problem, by splitting up the file in pieces smaller and smaller eventually found several badly drawn compounds.

It was not with Zinc, but still, might very well be a similar issue.