Why are some buttons of the Molecule Widget inactive (in grey)?

Hi there,
In some workflows I’m using the Molecule Widget to input a molecule from the WebPortal. In general the Molecule Widget (currently based on Ketcher version2.0.0-RC) works great but I wonder why there are some buttons on the horizontal top toolbar (e.g. aromatize, dearomatize, check structure) that are inactive and displayed in grey.
Does anybody know how to use them?

Hello @gcincilla ,
Unfortunately, I don’t have much experience with the Molecule Widget. Would you mind sharing an example workflow so that we can have a look?

Hi Emilio,
Thanks for your reply. I’m referring the the 9 inactive buttons on the top right of the Molecule Widget. Please see them highlighted in red in the attached image.

molecule_widget_inactive_buttons.knwf (6.9 KB)

P.S.: the attached workflow contains just the molecule widget.

Hi @gcincilla

The underlying sketcher is the open-source Ketcher. For full functionality and actually doing chemistry (the greyed out buttons), it would need to talk to a Server in the background (Remote mode). However this is not implemented in this application (Standalone mode). It’s the same reason why it cannot deal with a plain SMILES string, but requires pre-calculated 2D coordinates of molecules.

Does that answer your question?

Hi @Alice_Krebs, thanks for your prompt reply!
Now it’s more clear. I was confused because in this page the Ketcher Team talks about the Ketcher Standalone version where all the functionalities are available.

Would it be possible to connect the Ketcher version currently deployed as the KNIME Molecule Widget to a Server? Is it possible to use the KNIME server for that purpose?

Thanks again.

Hey @gcincilla,

we already have a new version of the Molecule Widget which is currently called Molecule Widget (labs). This new node makes use of ketcher 2.7.x and has some other advantages compared to the current Molecule Widget (mainly it is working on KNIME Hub but there are also other smaller tweaks). This node is already available in 4.7.4 (might be in 4.7.3 already). Please give it a try and give us feedback if you are missing anything.



Thank you @DanielBog, the Ketcher version implemented in the Molecule Widget (labs) seems awesome!

I can confirm that already with the version present in KNIME AP 4.7.3 the buttons I was referring to are enabled and allow me to use the functions they were designed for.

Just as a curiosity: where is the calculation performed to enable these chemical functionalities?

Hey @gcincilla,

great to hear that this helps. All of the calculation itself is happening on the ketcher side.


@DanielBog, the Molecule Widget (Labs) is certainly a great step forward compared to the Molecule Widget. Nevertheless I’ve noticed that it doesn’t work on the WebPortal. If I include it in a component I have the following errors on the WebPortal (see attached pictures).
Do you know why this happens? Should I open a new thread for that?

The problem is, that this feature is not yet there on the WebPortal. I just verified that it is in the new version we will release next week.


1 Like

That’s a wonderful news. Thank you @DanielBog.
What version will be the one you are referring to?

Hey @gcincilla,

the new versions will be 5.1 (AP) and 4.16.5 (Server)


1 Like

Perfect. Thank you @DanielBog .

This topic was automatically closed 7 days after the last reply. New replies are no longer allowed.