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The HELM editor allows the user to create and manipulate large macromolecules. You can import and export in a variety of formats, but HELM underlies the internal processes.

This editor only supports HELM1 and has been superseded by the web-editor which supports both HELM1 and 2. 


Trial Versions

We have compiled the code so you can try the HELM editor for yourself.  

HELM Editor via Java Applet

HELM Editor via Java Web Start 

HELM Editor local installation pack 

User Guides

HELM Editor User Guide (document)

Videos - NB there is no sound on these videos


Source Code

Source code on GitHub 


 Technical Documentation

HELM Editor Release notes and API Specification 

Licenses and restrictions

HELM is an open source project released under the MIT license. However it currently has some dependencies on third party tools.

  • HELM Editor requires yFiles for Java version 2.6 or higher and GraphML extension from yWorks. If you wish to use the compiled software directly there is no need to buy a licence. If you wish to develop the software for your own use, trial versions of such libraries can be downloaded from yWorks at You need to update the ant build file with regard to yfiles.dir and jar file names before compiling and running the project.
  • HELM Editor requires MarvinBeans version 5.0 or higher from ChemAxon. A copy of the required library (MarvinBeans-5.0.jar) is included for your convenience. ChemAxon has graciously agreed to provide a royalty-free license for the utilization of MarvinBeans directly through the HELM editor and notation toolkit (specifically for operations pertaining to the chemical representation of HELM monomers and macromolecules.) Please contact Cassell Essell ( to obtain this license. Utilization of the MarvinBeans library outside of the aforementioned scope and beyond a trial basis requires the procurement of a regular MarvinBeans license.


The project is actively working to remove these restrictions. We welcome anyone who wishes to contribute to the project by replacing any of these components.


The web-editor replacement does not have any dependencies on non-open source third party tools.


The HELM editor is code that was originally used within Pfizer. Before putting it in the public domain the project removed dependencies on internal Pfizer systems including their own monomer database. The version provided as open source code therefore uses monomer definitions contained in an XML file which is held locally. If you intend to take use the HELM editor as part of your organisations system, we highly recommend that you create an internal monomer database, so your organisation has a consistent set of monomers to use. You will need to adjust the code provided to point to it.

As this is an open source project you are at liberty to replace MarvinBeans 5.0 with your preferred tool. If you do this, please consider donating the modified code base back to the project.