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@egonw egonw released this Jul 13, 2019 · 3 commits to master since this release

DOI

First release after 0.0.5 and the second one available from Maven Central. This release ported a first method from the chemspider manager, the bridgedb manager with BridgeDb, and the report manager. For searching in ChemSpider, identifier mapping, and creating HTML reports.

Core managers

  • bioclipse.version()
  • report.createReport()
  • report.asHTML(IReport report)

Cheminformatics managers

  • chemspider.resolve(String inchiKey)

Other managers

  • bridgedb.getSource(String source)
  • bridgedb.getSourceFromName(String name)
  • bridgedb.listAllSources()
  • bridgedb.listAllOrganisms()
  • bridgedb.search(IDMapper database, String query, int limit)
  • bridgedb.guessIdentifierType(String identifier)
  • bridgedb.map(String restService, String identifier, String source)
  • bridgedb.map(IDMapper database, String identifier, String source)
  • bridgedb.map(String restService, String identifier, String source, String target)
  • bridgedb.map(IDMapper database, String identifier, String source, String target)
  • bridgedb.map(IDMapper database, Xref source)
  • bridgedb.map(IDMapper database, Xref source, String target)
Assets 2
Jul 13, 2019
[maven-release-plugin] copy for tag bacting-0.0.6

@egonw egonw released this Jun 22, 2019 · 15 commits to master since this release

DOI

Major release as it is the first one available from OSSRH, simplying the use. This release changed the groupId to accomodate for this. In Groovy you can now use:

@GrabResolver(name='ossrh', root='https://oss.sonatype.org/content/groups/public')
@Grab(group='io.github.egonw.bacting', module='managers-cdk', version='0.0.5')

This release also introduces a new manager, excel, which allows reading of Excel files. Otherwise, it ported a few more methods from Bioclipse 2.6.

Core managers

  • bioclipse.version()
  • bioclipse.requireVersion("2.8.0.2")

Other managers

  • rdf.sparql(IRDFStore store, String sparql)
  • rdf.size(IRDF store)
  • rdf.importFile(IRDFStore store, String rdfFile, String format)
  • rdf.importFromStream(IRDFStore store, InputStream rdfStream, String format)
  • rdf.importFromString(IRDFStore store, String rdfContent, String format)
Assets 2

@egonw egonw released this Apr 30, 2019 · 35 commits to master since this release

DOI

Not that many updates, since the current set of methods already runs a good many of the methods I seem to be using and also of the A lot of Bioclipse Scripting Language examples booklet. This release includes two new methods which help with populating Wikidata with clean structures, which are not yet ported back to Bioclipse (pending a bit more testing). This release also depends on a newer Eclipse library version.

Cheminformatics managers

  • cdk.getAtomsWithDefinedStereo(IMolecule)
  • cdk.getAtomsWithUndefinedStereo(IMolecule)

Other managers

  • rdf.createStore(String tripleStoreDirectoryPath) (which creates an on disk store using Apache Jena's TDB)
Assets 2

@egonw egonw released this Apr 20, 2019 · 44 commits to master since this release

DOI

Exposed a more APIs (see below), introducing the opsin manager.
If you have used an earlier version, please note that the group and artifacts identifiers have
changed.

Core managers

  • bioclipse.download(String url)
  • bioclipse.download(String url, String mimetype)
  • bioclipse.downloadAsFile(String url, String filename)
  • bioclipse.downloadAsFile(String url, String mimetype, String filename)
  • bioclipse.downloadAsFile(String url, String mimetype, String filename, Map<String,String> extraHeaders)

Cheminformatics managers

  • opsin.parseIUPACName(String name)
  • opsin.parseIUPACNameAsCML(String name)
  • opsin.parseIUPACNameAsSMILES(String name)
Assets 2

@egonw egonw released this Apr 14, 2019 · 58 commits to master since this release

DOI

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)
Assets 2

@egonw egonw released this Apr 13, 2019 · 68 commits to master since this release

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)
Assets 2
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