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HELMNotationToolkit Requirements

HELMNotationToolkit 1.0

  • Java 1.6
  • MarvinBeans 5.0

HELMNotationToolkit 1.1

  • Java 1.6
  • MarvinBeans 5.0

HELMNotationToolkit 1.2

  • Java 1.6
  • MarvinBeans 5.0

HELMNotationToolkit 2.0

  • Java 1.7
  • MarvinBeans 5.0

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 MARVIN.

chemistry=org.helm.chemtoolkit.chemaxon.ChemaxonManipulator

or

chemistry=org.helm.chemtoolkit.cdk.CDKManipulator

The MonomerStoreConfig.properties contains the information if you want to use a webservice to do 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