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We have updated the toolkit so it now includes the ability to parse and use the ambiguity definition and we have created a new API which allows you to add the chemistry engine of your choice. We have implemented two chemistry engines: CDK and MarvinBeans, but you can add your own. If you do, please consider donating the code back to the project so others can benefit.

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HELM Toolkit v1.x

The HELM editor (original thick client) and HAbE are designed to work with the HELM toolkit v 1.x, so we are keeping this in place until we replace both with web-based versions.

Source code -

Release Notes and API Specification - 

HELM Toolkit v2.0

The new This version that adds ambiguity support and allows you to access its functionality via the HELM2webservices. We recommend you use this for new applications as the older version will only be updated on a limited basis. 

V2.0 Source code - 


However, you may find the test page more convenient

Licenses and restrictions

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

HELM toolkit v1.1 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.

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.We have removed this dependency from the HELM2NotationToolkit so you don't need to worry about licences if you use this newer version.