HELM Toolkit

The HELM toolkit contains the basic calculations and parsers required to use HELM. Other tools can then be built using the toolkit as a foundation.

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.

HELM Toolkit v1.x

The HELM editor (original thick client) and HAbE are designed to work with the HELM toolkit v 1.x.

Source code - https://github.com/PistoiaHELM/HELMNotationToolkit

Release Notes and API Specification - http://pistoiahelm.github.io/HELM_Notation_Toolkit_Release_Notes.html 

HELM Toolkit v2.0

This version 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 - https://github.com/PistoiaHELM/HELM2NotationToolkit 

Public Maven repository for components https://oss.sonatype.org/#nexus-search;quick~org.pistoiaalliance.helm.

A ‘getting started’ guide is available:


And you can try out many of the functions via this test page http://webeditor.openhelm.org/WebService/FirstPage.html

Web service documentation

For a full technical description of RESTful web-services, see this document.

Technical presentation on HELM Toolkit V2.0




Validation Tool

A basic UI has been developed which allows the user to convert HELM1 to HELM2 or JSON. This has the side-effect of providing a validation tool, since if the input HELM is not valid, it will not be converted.

However, you may find the test page http://webeditor.openhelm.org/WebService/FirstPage.html more convenient. 

Licenses and restrictions

HELM is an open source project released under the MIT license. However 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 (cessell@chemaxon.com) 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.

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