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Bacting 0.0.1
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@egonw egonw released this 13 Apr 08:18
bacting-0.0.1
9ed146c

DOI

First release of Bacting, a first working prototype for running Bioclipse scripts in on the command line with a regular Groovy installation. This version allows me to run an extended script to convert a SMILES to Wikidata content. The following manager APIs are supported:

Core managers

  • bioclipse.fullPath(String file) (uses a workspace-relative file path)
  • bioclipse.assumeOnline()
  • bioclipse.isOnline()
  • ui.fileExists(String file)
  • ui.newFile(String file)
  • ui.newFile(String file, String content)
  • ui.remove(String file)
  • ui.append(String file, String content)

Cheminformatics managers

  • cdk.createMoleculeList() (which returns a List<ICDKMolecule>)
  • cdk.fromSMILES(String smiles)
  • cdk.molecularFormulaObject(ICDKMolecule mol) (returns a IMolecularFormula)
  • cdk.molecularFormula(ICDKMolecule mol) (returns a string)
  • inchi.generate(IMolecule molecule) (returns a InChI object)
  • inchi.check(String inchi)
  • inchi.checkStrict(String inchi)
  • pubchem.search(String query) (which returns a List<Integer>)

Other managers

  • rdf.createInMemoryStore() (which returns a IRDFStore)
  • rdf.createInMemoryStore(boolean ontologyModel) (which returns a IRDFStore)
  • rdf.sparqlRemote(String serviceURL, String sparqlQueryString) (which returns a StringMatrix)
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