Bacting 0.0.22

Bacting 0.0.22 completes the Bioclipse 2.6 PubChem manager and upgrades the RDF manager to use the most recent Apache Jena 4.1.0 library.

Cheminformatics managers

• pubchem.loadCompoundRDF()
• pubchem.loadCompound()
• pubchem.loadCompound3d()
• pubchem.download3d()
• pubchem.download3dAsString()
• pubchem.download(List)
• pubchem.download3d(List)

Bacting 0.0.21

Bacting 0.0.21 adds a new CDK method to generate SVG, updates to the latest BridgeDb version, but mostly improves the test coverage.

Cheminformatics managers

• cdk.asSVG(IMolecule) which returns a String

Bacting 0.0.20

Bacting 0.0.20 ports a few methods (see below), disables the chemspider manager because the service was down, improves the test coverage, and the rdf.importURL() method now follows HTTP redirects, improving the usefulness greatly. PS, the paper is out!

Core managers

• ui.append(String path, InputStream toWrite)

Cheminformatics managers

• cdk.getFormat(format) which returns a IChemFormat
• pubchem.download(cid)
• pubchem.downloadRDF(cid)

Other managers

• rdf.getForPredicate(IRDFStore store, String resourceURI, String predicate)
• rdf.allOwlSameAs(IRDFStore store, String resourceURI)
• rdf.allOwlEquivalentClass(IRDFStore store, String resourceURI, String predicate)

Bacting 0.0.19

Bacting 0.0.19 updates the URLs of the BridgeDb webservice (if you use it, you need to upgrade to this version), and now requires Java 11, as one of the dependencies does.

JOSS paper v3

Second revision, applying some editorial text suggestions.

Bacting 0.0.18

Bacting 0.0.18 updated the dependencies to CDK 2.5 and BridgeDb 3.0.4. It also ports the OscarManager with the below functionality:

Other managers

• oscar.findNamedEntities(String) which returns a list of strings
• oscar.findResolvedNamedEntities() which returns a list of IMolecules
• oscar.extractText() which takes a HTML string and extract the text content

Bacting 0.0.17

Minor release that adds documentation on how to use Bacting in Python with scyjava and removes a duplicate plugin declaration in the pom.xml.

Bacting 0.0.16

This release fixes a few JavaDoc issues, and adds two methods that needed to be ported to allow comparing chemical structures from the new CAS Common Chemistry with Wikidata (doi:10.5281/zenodo.4682767).

Cheminformatics managers

• cdk.isValidCAS(String)
• cdk.partition(IMolecule molecule) (which returns a List<IAtomContainer>)

Bacting 0.0.15

This release mostly improved test coverage and adds some further documentation. It adds an initial Biojava manager (based on version 1.9.4) with a minimal amount of ported functionality and fixed an issues in that bridgedb.guessIdentifierType() did not always provide expected output. The following new functionality was ported in this release, along with the Bioclipse domain objects IDNA, ISequence, IProtein, and IRNA:

Bioinformatics managers

• biojava.DNAfromPlainSequence(dnaString)
• biojava.DNAfromPlainSequence(dnaString, name)
• biojava.proteinFromPlainSequence(proteinString)
• biojava.proteinFromPlainSequence(proteinString, name)

Cheminformatics managers

• pubchem.downloadAsString()
• inchi.options()
• inchi.generate(molecule, options)

Bacting 0.0.14

This release mostly improved documentation, adds test coverage with JaCoCo, and updates versions of dependencies:

• Eclipse Core Runtime (3.20.0) and Resources (3.13.900)
• BridgeDb 2.3.10
• OPSIN 2.5.0

Furthermore, it fixes a few small issues:

• reported manager names of the pubchem and cdx managers
• BridgeDb mapping with the REST webservice