Render MOL to image without Marvin

Now that ChemAxon is charging for Marvin nodes, is there another opensource node that will render MOL data into images in a table? Previously I used a Molecule Type Cast and Render to Image node to do this.

Hi @kuenzifr

I do not have ChemAxon installed on my laptop and I just tried the -Render to Image- node which worked without any dependency to ChemAxon, as showned below:

The -Render to Image- node is directly provided by KNIME:

image

It should work on its own.

Hope this helps.

Best,

Ael

3 Likes

Hi aworker,
What is the output of the “PROTOCOL” node? I have a table with multiline string “MOL” format and another column with the structures rendered as SMILES. Neither of these are converted to PNGs with either “multiline string” or “string” as the renderer.

image
image

Hi @kuenzifr

Do you have at least one of the other chemo-informatics plugins installed, such as RDKiT ? I believe this is the problem.

If you have it, the following option should appear on the Renderer configuration options of the -Render to Image- node:

image

EDIT: I’m starting from the smiles column. If you start from a MOL or SDF type column, may br you would need to use first the -RDKiT to Molecule- node :

image

Hope this helps.

Best

Ael

1 Like

Hi @kuenzifr

I’m just curious whether the solution I suggested solved your problem ? Thanks for your feedback.

Best

Ael

Thanks,
I found the CDK community toolkit had a “Molecule to CDK” which put the data in a format that the “Render to Image” could use. That is similar to your reply.
Regards,
Fred

1 Like

My pleasure. Good to know it worked.

Best,

Ael

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