Problems parsing molecules from SMILES to CDK

Hi CDK lovers,

I'm a CDK lover too but I have a problem importing molecules to CDK from SMILES.

I have the following flow:

SDF reader → OpenBabel → Molecule type cast → molecule to CDK (reading from SMI)

The flow is correctly executed giving no errors and no warnings. Anyway when I open up the table with the parsed molecules in molecule to CDK node, in the CDK molecule column I have an Object missing ('?') statement. Do you have idea why this could happen?

If I import the same molecules in CDK directly form sdf, I have no problem. Anyway this is not what I want because the original molecules have 3D coordinates and I need to see them in 2D coordinates during my workflow. This is why I'm converting them to SMILES.



Hi Gio,

I update the nightly a bit later today: in the Molecule to CDK node existing 2D coordinates will be overriden if the force option is used or simply added to already existing 3D coordinates if not present. That should solve your problem and is the correct behaviour for the node option in the first place. :) When you display the molecules, the 2D coordinates are used.

There appears to be another problem with the rendering of molecules though. If you select the String renderer in your broken workflow, can you see the SMILES string? Can you display the molecules using the Marvin renderer or successfully convert them back to SMILES?

Thanks for your help,


I have updated the nightly build. The renderer should now also handle difficult 3D depictions correctly. Before it ran into issues with missing 2D coordinates for Stereo perception.

Please let me know if that solves your problem.



Hi Stephan,

Thank you for your quick reply and for the solution. You guys are great!

Effectively now, with the nightly build implementation, I can correctly see the 2D molecule structures as I wanted. Both if I parse them form SMILES or SDF (with the force generation option).

Maybe the expected user behavior, when he have 3D structures and he want to render them in 2D, is to use the force generation option from the SDF. Anyway I still prefer the rendering obtained from SMILES as the structures are rendered in a much more clear way to me.

Thanks again,


This topic was automatically closed 90 days after the last reply. New replies are no longer allowed.