Cleaning 2D chemical structures


I'm looking to have KNIME perform 2 specific clean-ups on a set of structures:

1) Remove hydrogen atoms that are not used to specify stereochemical configuration.

2) Flatten out any 3D structures in the set and clean the 2D coordinates.

RDKit Remove Hs and RDKit Generate Coords do most of what I need BUT they remove stereochemical bond designations.

Are there any known KNIME components that remove H but not when it's used for stereochemistry or that clean up 2D structures?

Best regards,


You can use the  Marvins ChemAxon MolConverter node and in the option box put -H to remove hydrogens.


For your reference, other available options in this node are;

options box you can add;

-a               General Dearomatisation

-a_huckel    Huckel Dearomatisation

a                General Aromatisation

a_bas         Basic Aromatisation

a_loose       Loose Aromatisation

a_ambig      Ambiguous Aromatisation

H               Add Explicit Hydrogens

-H              Remove Explicit Hydrogens



For other options for getting new 2D coordinates, Indigo nodes do a version, I am not sure if this retains stereo bond assignments, you will need to try it out.


Without losing the 3D coordinates, and getting the molecules displayed in 2D you can use The BioSolveIT Naomi Molecular Sketcher Renderer in the Knime preferences under Knime/renderer (I think).

You can also click on the molecule column header in a table and choose the Naomi renderer that way.

If you don't have it installed, you can visit biosolve IT below for it.  Although their nodes are commercial nodes, I believe the Naomi Render node and option is free. It gives you the site address you need to add into the Knime updating section.




Thanks, Simon! That works nicely.