HELM2 Notation Toolkit

The HELM2NotationToolkit contains functionality to parse HELM2 notation and create a HELM2Notation object. This allows the user to perform calculations, validate HELM strings and manipulate HELM molecules via the toolkit.

The toolkit is normally accessed via the HELM2Webservice and calls other packages for some processes. See

Getting started

Releases can be found in the Nexus repository

• Dependency information can be found in the POM
• Object model information can be found in the Java doc.

Please check version numbers carefully.

Configuration

There are two new configuration files in .helm.

The Chemistry.property contains the information which Chemistry plugin you want to use. The default one is CDK.

chemistry=org.helm.chemtoolkit.cdk.CDKManipulator

The MonomerStoreConfig.properties contains the information if you want to use a webservice to perform monomer management actions.

use.webservice=false update.automatic=true webservice.monomers.url=http://localhost:8080
webservice.monomers.path=DemoWebserver/service/monomerStore?
polymerType=#webservice.monomers.put.path=path/monomerToolkit 
webservice.monomers.put.path=DemoWebserver/service/monomerStore 
webservice.nucleotides.url=http://localhost:8080 webservice.nucleotides.path=DemoWebserver/service/nucleotideStore #webservice.nucleotides.put.path=path/nucleotideTemplate 
webservice.nucleotides.put.path=DemoWebserver/service/nucleotidestore 
webservice.editor.categorization.url=http://localhost:8080 
webservice.editor.categorization.path=path/monomerStoreEditorCategories

Defects

Please let us know by logging in the issue list. Even better - send us a fix via a pull request!

Further information

See the HELM wiki for additional documentation and user guides