SMILES conversion?

It has been a while since I ran KNIME, but I’m finding that the latest version has a number of changes that alter the function of my previous workflows.

The workflow of interest does a global pairwise comparison of all input compounds. If the pair is above a specified Tannimoto similarity, the pair is kept and a comparison of activity values is reported. The final report has two columns of molecules and associated columns of activity data for comparison purposes. The premise is to help mine large sets of compounds for SAR data. I generate an text file as output that consists of SMILES, molecule ID, activity, SMILES (molecule 2), molecule 2 ID, molecule 2 activity for visualization in other software tools.

Is there no longer a CDK to SMILES conversion node? I have this node in a previous version of my workflow, but the current version of KNIME does not seem to have this any longer.

It seems that now all of my SMILES have explicit hydrogen atoms in place. This makes visualization quite messy in other tools. Is there no hydrogen stripping tool?

Any help is appreciated.


KNIME now has generic CDK->Molecule and Molecule->CDK nodes which can convert from/to a number of different formats.
Hydrogens stripping is currently not possible with KNIME, but that is a good point, I will put it on the feature request list.