Getting MarvinJS to work with ChemAxon web services


I am currently looking at ways of drawing chemical structures especially reactions into workflows via the web portal. MarvinJS looks to have the features that we require but some of these need to call the ChemAxon web services to convert the output of the sketch tool into SMILES for example.

The Chemaxon webservices cannot be installed on TomEE along side the sketcher. Has anyone been able to set up this connection?


Hi Gary,

For general questions about ChemAxon tools (aside from the KNIME nodes), I would encourage you to contact

Best regards,


1 Like

Hi @gnugent, I have a similar need and found out I was able to deploy the JChem Web Service Classic on the Knime apache server along side the sketcher. What you need to do is to unzip the content of the archive under <knime_installation_dir>/apache-tomcat-9.0.36/webapps. For the 20.19.1-10-b2303 version I deployed, this resulted in a webservices.war file and me_assets folder. You will also need to copy a valid ChemAxon license file under the .chemaxon directory of the home directory of the user who runs the Knime server. You can verify the installation is successful by visiting https://your_knime_server/sketcher.marvinJS/marvinJS/editorws.html and importing a chemical name or SMILES into the sketcher.

However, I still have a question for the Knime development team. The “Molecule String Input” node under Quickforms is hardcoded to use the webapps/sketcher.marvinJS/marvinJS/editor.html file as opposed to editorws.html. Can we introduce a parameter to let the user choose which file? Only editorws.html allows communicating with the JChem Web Services to translate between different chemical structure formats.


this should not be a problem as the sketcher support for MarvinJS is a separate war file that needs to be deployed on the server. The code of the Quickform just makes use of that. You could simply download the war file from the downloads page, extract it and change the html file to point to editorws.html and then deploy the changed file on your Tomcat. Is there a reason to use the other file, or can editorws be used for all scenarios?
I don’t know anything about the Chemaxon web services, but I hope this helps already.


Thanks, I will look into modifying the MarvinJS war file directly.

On the difference between editor.html and editorws.html, if we deploy the latter without deploying JChem Web Services, the sketcher will show additional chemical formats as supported but will display an error when a user attempts to import a structure from SMILES for example.