Bacting 0.0.2

Exposed a few more APIs, introducing the cdx manager and a few more methods. The combination of bioclipse.sparqlRemote() and rdf.processSPARQLXML() skips the Jena parsing of the SPARQL:

Core managers

• bioclipse.sparqlRemote(String serviceURL, String sparqlQueryString)
• ui.open(String file) (does not do anything)

Cheminformatics managers

• cdk.fromCml(String molstring)
• cdk.asCDKMolecule(IMolecule)
• cdk.loadMolecule(InputStream, IChemFormat)
• cdx.perceiveCDKAtomTypes(IMolecule)

Other managers

• rdf.processSPARQLXML(byte[] queryResults, String originalQuery)

Bacting 0.0.1

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)