Render molecule in 2D

KNIME Analytics Platform
1

Hi,

I'm retrieving some data from a server in Mol2 format and converting it into a table of molecules.  We want to output this as a report, including molecular diagrams.  I'm using a "Renderer to Image" node to create the diagrams with the "Marvin" renderer.  However, this is producing 3D diagrams - which are not very useful as rings are sometimes tilted so that you can only see the edge.  

Is there a way to tell the renderer to produce a 2D diagram by default? I've looked at the preferences but there doesn't seem to be an option for this.

Thanks,

Stephen

2

Convert to smiles using marvinconverter then pipe to report. Molecule -> RDKIT->Molecule(smiles) can be used as well. Similarly indigo and cdk could be used too. If original column is retained it will have to be removed using the filter column node before using the renderer to image.

3

Perfect - thank you!

 

4

You can also change the default molecule renderer for all molecule datatypes by going into KNIME Menu, File/Preferences/KNIME/Chemistry and choosing alternative renderers from the dropdowns.

 

Simon.

5

Hi guys,

I have a similar issue here. I want to display the molecule structures present in my table with 2D graphs, even if the underying structures have 3D coordinates. I would to do it in any table, without having to transform them in SMILES format. Is that possible?

I've tried to change rendering at File/Preferences/KNIME/Chemistry as Simon suggested by I'm not able to switch from 3D to 2D rendering.

Any hints?

Gio

6

The BioSolveIT Naomi Molecular Sketcher should be able to do what you want.

http://www.biosolveit.de/KNIME

Alastair

7

Thanks Alastair,

Does it exists only this commercial solution? There are no way to see the 2D molecular graphs in all the default knime tables?

Gio