// download all GPML files for a species, and save those in /WikiPathways/data/ dataMap = bioclipse.fullPath("/WikiPathways/data/") gpmlFiles = new File(dataMap).listFiles() structureList = cdk.createMoleculeList() gpmlFiles.each { file -> def data = new XmlParser().parse(file) def metabolites = data.DataNode.findAll{ it.'@Type'.contains('Metabolite') } metabolites.each() { node -> name = node.'@TextLabel'.trim() try { molecule = opsin.parseIUPACName(name) js.print("IUPAC name found: $name \n") structureList.add(molecule) } catch (Exception exception) { // OK, it was not an IUPAC name } } } ui.open(structureList)