Index

A B C D E F G H I J L M N O P Q R S T U V W X Z
All Classes and Interfaces|All Packages

A

addDataProperty(IRDFStore, String, String, String) - Method in class net.bioclipse.managers.RDFManager

Creates a new RDF data triple in the given triple store.

addObjectProperty(IRDFStore, String, String, String) - Method in class net.bioclipse.managers.RDFManager

Creates a new RDF object triple in the given triple store.

addPrefix(IRDFStore, String, String) - Method in class net.bioclipse.managers.RDFManager

Adds a prefix definition to the given triple store.

addPropertyInLanguage(IRDFStore, String, String, String, String) - Method in class net.bioclipse.managers.RDFManager

Creates a new RDF data triple in the given triple store.

addTypedDataProperty(IRDFStore, String, String, String, String) - Method in class net.bioclipse.managers.RDFManager

Creates a new RDF data triple in the given triple store.

allOwlEquivalentClass(IRDFStore, String) - Method in class net.bioclipse.managers.RDFManager

Lists all resources that are owl:equivalentClass as the given resource.

allOwlSameAs(IRDFStore, String) - Method in class net.bioclipse.managers.RDFManager

Lists all resources that are owl:sameAs as the given resource.

append(String, byte[]) - Method in class net.bioclipse.managers.UIManager

Appends the new content to write to a new or existing file in the Bioclipse workspace.

append(String, InputStream) - Method in class net.bioclipse.managers.UIManager

Appends the new content to write to a new or existing file in the Bioclipse workspace.

append(String, String) - Method in class net.bioclipse.managers.UIManager

Appends the new content to write to a new or existing file in the Bioclipse workspace.

appendToSDF(String, ICDKMolecule) - Method in class net.bioclipse.managers.CDKManager

Extends the given SD file with an molfile entry for the given ICDKMolecule.

asCDKMolecule() - Method in class net.bioclipse.wikidata.domain.WikidataMolecule

asCDKMolecule(IMolecule) - Method in class net.bioclipse.managers.CDKManager

Helper function that casts or converts the input IMolecule to an ICDKMolecule.

asHTML(IReport) - Method in class net.bioclipse.managers.ReportManager

Serializes the content of the given report into HTML.

asMarkdown(IReport) - Method in class net.bioclipse.managers.ReportManager

Serializes the content of the given report into Markdown.

asRDFN3(IRDFStore) - Method in class net.bioclipse.managers.RDFManager

Serializes the triples in the triple store as Notation3.

asString(ShexReport) - Method in class net.bioclipse.managers.RDFManager

Converts a ShexReport into a String.

assumeOnline() - Method in class net.bioclipse.managers.BioclipseManager

Tests if there is an active internet connection and throws an BioclipseException if not.

asSVG(IMolecule) - Method in class net.bioclipse.managers.CDKManager

asTurtle(IRDFStore) - Method in class net.bioclipse.managers.RDFManager

Serializes the triples in the triple store as Turtle.

B

BioclipseManager - Class in net.bioclipse.managers

Bioclipse manager providing core functionality.

BioclipseManager(String) - Constructor for class net.bioclipse.managers.BioclipseManager

Creates a new BioclipseManager.

BiojavaDNA - Class in net.bioclipse.biojava.domain

BiojavaDNA() - Constructor for class net.bioclipse.biojava.domain.BiojavaDNA

BiojavaDNA(Sequence) - Constructor for class net.bioclipse.biojava.domain.BiojavaDNA

BiojavaManager - Class in net.bioclipse.managers

Bioclipse manager that provides BioJava functionality.

BiojavaManager(String) - Constructor for class net.bioclipse.managers.BiojavaManager

Creates a new BiojavaManager.

BiojavaProtein - Class in net.bioclipse.biojava.domain

BiojavaProtein() - Constructor for class net.bioclipse.biojava.domain.BiojavaProtein

BiojavaProtein(Sequence) - Constructor for class net.bioclipse.biojava.domain.BiojavaProtein

BiojavaSequence - Class in net.bioclipse.biojava.domain

BiojavaSequence() - Constructor for class net.bioclipse.biojava.domain.BiojavaSequence

BiojavaSequence(Sequence) - Constructor for class net.bioclipse.biojava.domain.BiojavaSequence

Create a BiojavaSequence from a Sequence.

BridgedbManager - Class in net.bioclipse.managers

Bioclipse manager that provides identifier mapping functionality using the BridgeDb framework.

BridgedbManager(String) - Constructor for class net.bioclipse.managers.BridgedbManager

Creates a new BridgedbManager.

C

calculateMajorIsotopeMass(IMolecule) - Method in class net.bioclipse.managers.CDKManager

calculateMass(IMolecule) - Method in class net.bioclipse.managers.CDKManager

calculateSMILES(IMolecule) - Method in class net.bioclipse.managers.CDKManager

Returns the SMILES for a molecule.

CDKDebugManager - Class in net.bioclipse.managers.cdkdebug

Bioclipse manager that provides functionality by the Chemistry Development Kit that give access to less used functionality and exposes more details of the underlying data model.

CDKDebugManager(String) - Constructor for class net.bioclipse.managers.cdkdebug.CDKDebugManager

Creates a new CDKDebugManager.

CDKManager - Class in net.bioclipse.managers

Bioclipse manager that provides cheminformatics functionality using the Chemistry Development Kit database.

CDKManager(String) - Constructor for class net.bioclipse.managers.CDKManager

Creates a new CDKManager.

check(String) - Method in class net.bioclipse.managers.InChIManager

Checks the validity of the InChI.

checkKey(String) - Method in class net.bioclipse.managers.InChIManager

Checks the validity of the InChIkey.

checkStrict(String) - Method in class net.bioclipse.managers.InChIManager

Checks the validity of the InChI using more strict rules.

ChemspiderManager - Class in net.bioclipse.managers

Bioclipse manager that provides functionality to interact with the ChemSpider database.

ChemspiderManager(String) - Constructor for class net.bioclipse.managers.ChemspiderManager

Creates a new ChemspiderManager.

CONNECT_TIME_OUT - Static variable in class net.bioclipse.managers.RDFManager

convertTo(Quantity, Unit) - Method in class net.bioclipse.managers.QUDTManager

Converts a quantity from one unit to another.

convertTo(Quantity, String) - Method in class net.bioclipse.managers.QUDTManager

Converts a quantity from one unit to another.

createInMemoryStore() - Method in class net.bioclipse.managers.RDFManager

Creates a triple store that is fully stored in memory.

createInMemoryStore(boolean) - Method in class net.bioclipse.managers.RDFManager

Creates an ontology triple store that is fully stored in memory.

createMoleculeList() - Method in class net.bioclipse.managers.CDKManager

Create a new Java List for storing ICDKMolecule.

createReport() - Method in class net.bioclipse.managers.ReportManager

Creates a new IReport object.

createStore(String) - Method in class net.bioclipse.managers.RDFManager

Creates a triple store that is fully stored on disk.

curie(String) - Method in class net.bioclipse.managers.BridgedbManager

Creates a Xref object for the given Bioregistry.io compact identifier.

D

determineIChemFormat(String) - Method in class net.bioclipse.managers.CDKManager

Determines the file format of the given input.

determineIChemFormatOfString(String) - Method in class net.bioclipse.managers.CDKManager

Determines the file format of the given input.

diff(ICDKMolecule, ICDKMolecule) - Method in class net.bioclipse.managers.cdkdebug.CDKDebugManager

Returns the differences between the two molecules.

DNAfromPlainSequence(String) - Method in class net.bioclipse.managers.BiojavaManager

DNAfromPlainSequence(String, String) - Method in class net.bioclipse.managers.BiojavaManager

doi() - Method in interface io.github.egonw.bacting.IBactingManager

Lists the DOIs of the articles associated to this manager.

doi() - Method in class net.bioclipse.managers.BioclipseManager

doi() - Method in class net.bioclipse.managers.BiojavaManager

doi() - Method in class net.bioclipse.managers.BridgedbManager

doi() - Method in class net.bioclipse.managers.cdkdebug.CDKDebugManager

doi() - Method in class net.bioclipse.managers.CDKManager

doi() - Method in class net.bioclipse.managers.ChemspiderManager

doi() - Method in class net.bioclipse.managers.DOIManager

doi() - Method in class net.bioclipse.managers.DuckDuckGoManager

doi() - Method in class net.bioclipse.managers.ExcelManager

doi() - Method in class net.bioclipse.managers.InChIManager

doi() - Method in class net.bioclipse.managers.JSoupManager

doi() - Method in class net.bioclipse.managers.NanoManager

doi() - Method in class net.bioclipse.managers.OpsinManager

doi() - Method in class net.bioclipse.managers.OscarManager

doi() - Method in class net.bioclipse.managers.PubChemManager

doi() - Method in class net.bioclipse.managers.PubmedManager

doi() - Method in class net.bioclipse.managers.QUDTManager

doi() - Method in class net.bioclipse.managers.ReportManager

doi() - Method in class net.bioclipse.managers.SitemapManager

doi() - Method in class net.bioclipse.managers.UIManager

doi() - Method in class net.bioclipse.managers.WikidataManager

doi() - Method in class net.bioclipse.managers.XMLManager

doi() - Method in class net.bioclipse.managers.ZenodoManager

DOIManager - Class in net.bioclipse.managers

DOIManager(String) - Constructor for class net.bioclipse.managers.DOIManager

Creates a new DOIManager.

download(Integer) - Method in class net.bioclipse.managers.ChemspiderManager

Downloads the molecular for the given ChemSpider identifier as a IMolecule object.

download(Integer) - Method in class net.bioclipse.managers.PubChemManager

download(String) - Method in class net.bioclipse.managers.BioclipseManager

Downloads the content of the page located by the given URL string as a Java String.

download(String, String) - Method in class net.bioclipse.managers.BioclipseManager

Downloads the content of the page located by the given URL string as a Java String in the given mimetype (if provided by the webserver).

download(String, String, Map<String, String>) - Method in class net.bioclipse.managers.BioclipseManager

Downloads the content of the page located by the given URL string as a Java String in the given mimetype (if provided by the webserver).

download(List<Integer>) - Method in class net.bioclipse.managers.PubChemManager

download3d(Integer) - Method in class net.bioclipse.managers.PubChemManager

download3d(List<Integer>) - Method in class net.bioclipse.managers.PubChemManager

download3dAsString(Integer) - Method in class net.bioclipse.managers.PubChemManager

downloadAsFile(String, String) - Method in class net.bioclipse.managers.BioclipseManager

Downloads the content of the page located by the given URL string as a file in the Bioclipse workspace and return the path as String.

downloadAsFile(String, String, String) - Method in class net.bioclipse.managers.BioclipseManager

Downloads the content of the page located by the given URL string as a file in the given mimetype (if provided by the webserver) in the Bioclipse workspace and return the path as String.

downloadAsFile(String, String, String, Map<String, String>) - Method in class net.bioclipse.managers.BioclipseManager

Downloads the content of the page located by the given URL string as a file in the given mimetype (if provided by the webserver) in the Bioclipse workspace and return the path as String.

downloadAsString(Integer) - Method in class net.bioclipse.managers.ChemspiderManager

Downloads the molecular for the given ChemSpider identifier as an SD file.

downloadAsString(Integer) - Method in class net.bioclipse.managers.PubChemManager

downloadRDF(Integer, IRDFStore) - Method in class net.bioclipse.managers.PubChemManager

DuckDuckGoManager - Class in net.bioclipse.managers

Bioclipse manager that provides functionality around the Resource Description Framework standard.

DuckDuckGoManager(String) - Constructor for class net.bioclipse.managers.DuckDuckGoManager

Creates a new DuckDuckGoManager.

DummyErrorHandler - Class in net.bioclipse.xml.business

Dummy error handler that ignores all problems.

DummyErrorHandler() - Constructor for class net.bioclipse.xml.business.DummyErrorHandler

E

error(SAXParseException) - Method in class net.bioclipse.xml.business.DummyErrorHandler

ExcelManager - Class in net.bioclipse.managers

ExcelManager(String) - Constructor for class net.bioclipse.managers.ExcelManager

extractText(String) - Method in class net.bioclipse.managers.OscarManager

Extracts plain text from a HTML document.

F

factory - Variable in class net.bioclipse.managers.InChIManager

fatalError(SAXParseException) - Method in class net.bioclipse.xml.business.DummyErrorHandler

fetchInfo(String) - Method in class net.bioclipse.managers.DOIManager

fetchInfo(String) - Method in class net.bioclipse.managers.PubmedManager

fileExists(String) - Method in class net.bioclipse.managers.UIManager

Determines if the given file exists in the Bioclipse workspace.

findNamedEntities(String) - Method in class net.bioclipse.managers.OscarManager

Extracts named entities from a text.

findResolvedNamedEntities(String) - Method in class net.bioclipse.managers.OscarManager

Extracts molecules from a text for which the corresponding named entities are recognized as chemicals.

findUnits(String) - Method in class net.bioclipse.managers.QUDTManager

Returns a list of zero or more units matching the given unit.

fromCml(String) - Method in class net.bioclipse.managers.CDKManager

Creates a new ICDKMolecule from CML in the given String.

fromSMILES(String) - Method in class net.bioclipse.managers.CDKManager

Creates a new ICDKMolecule from the SMILES in the given String.

fromString(String) - Method in class net.bioclipse.managers.CDKManager

Creates a new ICDKMolecule from the content of the given String, but guesses the format the input is in.

fullPath(String) - Method in class net.bioclipse.managers.BioclipseManager

Converts a Bioclipse workspace path for the given file to an operating system level absolute path.

G

generate(IMolecule) - Method in class net.bioclipse.managers.InChIManager

Generates an InChI for the given IMolecule.

generate(IMolecule, String) - Method in class net.bioclipse.managers.InChIManager

Generates an InChI for the given IMolecule, using the given options.

generateInChI(IMaterial) - Method in class net.bioclipse.managers.NanoManager

getAdapter(Class) - Method in class net.bioclipse.biojava.domain.BiojavaSequence

getAdapter(Class) - Method in class net.bioclipse.wikidata.domain.WikidataMolecule

getAtomsWithDefinedStereo(IMolecule) - Method in class net.bioclipse.managers.CDKManager

Determine the atoms for which the stereochemistry is defined.

getAtomsWithUndefinedStereo(IMolecule) - Method in class net.bioclipse.managers.CDKManager

Determine the atoms for which the stereochemistry is not fully defined.

getConformers() - Method in class net.bioclipse.wikidata.domain.WikidataMolecule

getEntityID(String) - Method in class net.bioclipse.managers.WikidataManager

Return a work with the given DOI, or throws an BioclipseException when it does not exist.

getEntityID(InChI) - Method in class net.bioclipse.managers.WikidataManager

Returns the Wikidata entity ID for the molecule with the given InChI.

getEntityIDs(List<InChI>) - Method in class net.bioclipse.managers.WikidataManager

Returns the Wikidata entity IDs for the molecules with the given InChIs.

getEntityIDsForDOIs(List<String>) - Method in class net.bioclipse.managers.WikidataManager

Returns the Wikidata entity IDs for the works with the given DOIs.

getEntityIDsForType(String) - Method in class net.bioclipse.managers.WikidataManager

Returns the Wikidata entity IDs for entities instance of a certain type (P31).

getFormat(String) - Method in class net.bioclipse.managers.CDKManager

getFormats() - Method in class net.bioclipse.managers.CDKManager

getForPredicate(IRDFStore, String, String) - Method in class net.bioclipse.managers.RDFManager

Lists all resources or literals for the resource and predicate.

getId() - Method in interface net.bioclipse.wikidata.domain.IWikidataMolecule

getId() - Method in class net.bioclipse.wikidata.domain.WikidataMolecule

getIDMapper(String) - Method in class net.bioclipse.managers.BridgedbManager

Returns the IDMapper for the given provider.

getInternalModel() - Method in class net.bioclipse.managers.domain.Material

getManagerName() - Method in class net.bioclipse.managers.BioclipseManager

getManagerName() - Method in class net.bioclipse.managers.BiojavaManager

getManagerName() - Method in class net.bioclipse.managers.BridgedbManager

getManagerName() - Method in class net.bioclipse.managers.cdkdebug.CDKDebugManager

getManagerName() - Method in class net.bioclipse.managers.CDKManager

getManagerName() - Method in class net.bioclipse.managers.ChemspiderManager

getManagerName() - Method in class net.bioclipse.managers.DOIManager

getManagerName() - Method in class net.bioclipse.managers.DuckDuckGoManager

getManagerName() - Method in class net.bioclipse.managers.ExcelManager

getManagerName() - Method in class net.bioclipse.managers.InChIManager

getManagerName() - Method in class net.bioclipse.managers.JSoupManager

getManagerName() - Method in class net.bioclipse.managers.NanoManager

getManagerName() - Method in class net.bioclipse.managers.OpsinManager

getManagerName() - Method in class net.bioclipse.managers.OscarManager

getManagerName() - Method in class net.bioclipse.managers.PubChemManager

getManagerName() - Method in class net.bioclipse.managers.PubmedManager

getManagerName() - Method in class net.bioclipse.managers.QUDTManager

Gives a short one word name of the manager used as variable name when scripting.

getManagerName() - Method in class net.bioclipse.managers.ReportManager

Gives a short one word name of the manager used as variable name when scripting.

getManagerName() - Method in class net.bioclipse.managers.SitemapManager

getManagerName() - Method in class net.bioclipse.managers.UIManager

getManagerName() - Method in class net.bioclipse.managers.WikidataManager

getManagerName() - Method in class net.bioclipse.managers.XMLManager

getManagerName() - Method in class net.bioclipse.managers.ZenodoManager

getMolecule(InChI) - Method in class net.bioclipse.managers.WikidataManager

Return a molecule with the given InChI, or throws an BioclipseException when it does not exist.

getName() - Method in class net.bioclipse.biojava.domain.BiojavaSequence

getNamespaces() - Method in class net.bioclipse.xml.business.NamespaceAggregator

getOAIPMHData(String) - Method in class net.bioclipse.managers.ZenodoManager

getParsedResource() - Method in class net.bioclipse.biojava.domain.BiojavaSequence

Returns the RichSequence

getPlainSequence() - Method in class net.bioclipse.biojava.domain.BiojavaSequence

getResource() - Method in class net.bioclipse.wikidata.domain.WikidataMolecule

getSheet(String, int) - Method in class net.bioclipse.managers.ExcelManager

getSheet(String, int, boolean) - Method in class net.bioclipse.managers.ExcelManager

getSource(String) - Method in class net.bioclipse.managers.BridgedbManager

Looks up the DataSource for the given system code.

getSourceByPrefix(String) - Method in class net.bioclipse.managers.BridgedbManager

Looks up the DataSource for the given Bioregistry.io prefix.

getSourceFromName(String) - Method in class net.bioclipse.managers.BridgedbManager

Looks up the DataSource for the given full name.

getType() - Method in interface net.bioclipse.managers.domain.IMaterial

getType() - Method in class net.bioclipse.managers.domain.Material

guessIdentifierType(String) - Method in class net.bioclipse.managers.BridgedbManager

Based on the given identifier, tries to guess what database that identifier comes from.

H

hasMolecule(InChI) - Method in class net.bioclipse.managers.WikidataManager

Return true if Wikidata contains a molecule with the given InChI.

I

IBactingManager - Interface in io.github.egonw.bacting

Interface for Bacting managers extension the IBioclipseManager with a method to return DOIs relevant to this manager.

IMaterial - Interface in net.bioclipse.managers.domain

An interface to represent a material.

importFile(IRDFStore, String, String) - Method in class net.bioclipse.managers.RDFManager

Reads a RDF file in the given format from the workspace and stores the triples in the given triple store.

importFromStream(IRDFStore, InputStream, String) - Method in class net.bioclipse.managers.RDFManager

Reads RDF triples from an InputStream in the given format and stores the triples in the given triple store.

importFromString(IRDFStore, String, String) - Method in class net.bioclipse.managers.RDFManager

Reads RDF triples from an String in the given format and stores the triples in the given triple store.

importURL(IRDFStore, String) - Method in class net.bioclipse.managers.RDFManager

Reads RDF triples from a URL and stores the triples in the given triple store.

importURL(IRDFStore, String, Map<String, String>) - Method in class net.bioclipse.managers.RDFManager

Reads RDF triples from a URL and stores the triples in the given triple store, with additional HTTP headers.

InChIManager - Class in net.bioclipse.managers

Bioclipse manager that provides functionality to create and validate InChI and InChIKeys.

InChIManager(String) - Constructor for class net.bioclipse.managers.InChIManager

Creates a new InChIManager.

io.github.egonw.bacting - package io.github.egonw.bacting

isAvailable() - Method in class net.bioclipse.managers.InChIManager

Returns true if the InChI library can be used.

isLoaded() - Method in class net.bioclipse.managers.InChIManager

Returns true if the InChI library was properly loaded.

isOnline() - Method in class net.bioclipse.managers.BioclipseManager

Determines if online websites can be reached, reflecting access to the internet.

isValid(String) - Method in class net.bioclipse.managers.XMLManager

isValidCAS(String) - Method in class net.bioclipse.managers.CDKManager

Determines if the given CAS registry number is valid.

isValidQIdentifier(String) - Method in class net.bioclipse.managers.WikidataManager

Determines if an identifier is a valid Wikidata entity identifier, like Q5.

isWellFormed(String) - Method in class net.bioclipse.managers.XMLManager

IWikidataMolecule - Interface in net.bioclipse.wikidata.domain

J

JSoupManager - Class in net.bioclipse.managers

Manager for JSoup functionality to parse HTML content.

JSoupManager(String) - Constructor for class net.bioclipse.managers.JSoupManager

Creates a new JSoupManager.

L

listAllOrganisms() - Method in class net.bioclipse.managers.BridgedbManager

Returns all known organisms as a Java List.

listAllSources() - Method in class net.bioclipse.managers.BridgedbManager

Returns all known sources as a Java List.

listIDMapperProviders() - Method in class net.bioclipse.managers.BridgedbManager

Returns IDMappers supported by Bacting.

listMaterialTypes() - Method in class net.bioclipse.managers.NanoManager

listNamespaces(String) - Method in class net.bioclipse.managers.XMLManager

load() - Method in class net.bioclipse.managers.InChIManager

Loads the InChI library.

loadCompound(int, String) - Method in class net.bioclipse.managers.PubChemManager

loadCompound3d(int, String) - Method in class net.bioclipse.managers.PubChemManager

loadCompoundRDF(int, String) - Method in class net.bioclipse.managers.PubChemManager

loadMolecule(InputStream, IChemFormat) - Method in class net.bioclipse.managers.CDKManager

Creates a new ICDKMolecule from the content of the given InputStream, assuming it is in the format as given by the IChemFormat.

loadMolecule(String) - Method in class net.bioclipse.managers.CDKManager

Loads a molecule from file using CDK.

loadRelationalDatabase(String) - Method in class net.bioclipse.managers.BridgedbManager

Creates a BridgeDb IDMapper for the given Derby database location.

logfileLocation() - Method in class net.bioclipse.managers.BioclipseManager

Returns the location of the current logfile.

M

map(String, String, String) - Method in class net.bioclipse.managers.BridgedbManager

Using the given connection string, it returns mappings for the given identifier.

map(String, String, String, String) - Method in class net.bioclipse.managers.BridgedbManager

Using the given connection string, it returns mappings for the given identifier, but only for the given target data source.

map(String, Xref) - Method in class net.bioclipse.managers.BridgedbManager

Using the given connection string, it returns mappings for the given identifier.

map(String, Xref, String) - Method in class net.bioclipse.managers.BridgedbManager

Using the given connection string, it returns mappings for the given identifier, but only for the given target data source.

map(IDMapper, String, String) - Method in class net.bioclipse.managers.BridgedbManager

Using the given IDMapper string, it returns mappings for the given identifier.

map(IDMapper, String, String, String) - Method in class net.bioclipse.managers.BridgedbManager

Using the given IDMapper string, it returns mappings for the given identifier, but only for the given target data source.

map(IDMapper, Xref) - Method in class net.bioclipse.managers.BridgedbManager

Using the given IDMapper string, it returns mappings for the given identifier.

map(IDMapper, Xref, String) - Method in class net.bioclipse.managers.BridgedbManager

Using the given IDMapper string, it returns mappings for the given identifier, but only for the given target data source.

MarkdownSerializer - Class in net.bioclipse.managers.report.serializer

Serializes the report into Markdown.

MarkdownSerializer() - Constructor for class net.bioclipse.managers.report.serializer.MarkdownSerializer

Material - Class in net.bioclipse.managers.domain

Material() - Constructor for class net.bioclipse.managers.domain.Material

Material(Material) - Constructor for class net.bioclipse.managers.domain.Material

Material(MaterialType) - Constructor for class net.bioclipse.managers.domain.Material

mcss(List<IMolecule>) - Method in class net.bioclipse.managers.CDKManager

Calculates the maximum common substructure (mcss) starting of two or more molecules starting with the mcss of the first two molecules.

molecularFormula(ICDKMolecule) - Method in class net.bioclipse.managers.CDKManager

Calculates the molecular formula for the given molecule.

molecularFormulaObject(ICDKMolecule) - Method in class net.bioclipse.managers.CDKManager

Calculates the molecular formula for the given molecule.

N

NamespaceAggregator - Class in net.bioclipse.xml.business

ContentHandler that extracts XML namespaces.

NamespaceAggregator() - Constructor for class net.bioclipse.xml.business.NamespaceAggregator

NanoManager - Class in net.bioclipse.managers

Bioclipse manager that wraps the CDK-based nanojava library.

NanoManager(String) - Constructor for class net.bioclipse.managers.NanoManager

Creates a new NanoManager.

net.bioclipse.biojava.domain - package net.bioclipse.biojava.domain

net.bioclipse.managers - package net.bioclipse.managers

net.bioclipse.managers.cdkdebug - package net.bioclipse.managers.cdkdebug

net.bioclipse.managers.domain - package net.bioclipse.managers.domain

net.bioclipse.managers.report.serializer - package net.bioclipse.managers.report.serializer

net.bioclipse.wikidata.domain - package net.bioclipse.wikidata.domain

net.bioclipse.xml.business - package net.bioclipse.xml.business

newFile(String) - Method in class net.bioclipse.managers.UIManager

Creates a new file in the Bioclipse workspace.

newFile(String, String) - Method in class net.bioclipse.managers.UIManager

Creates a new file in the Bioclipse workspace with the given content

newMaterial() - Method in class net.bioclipse.managers.NanoManager

newMaterial(Material) - Method in class net.bioclipse.managers.NanoManager

newMaterial(String) - Method in class net.bioclipse.managers.NanoManager

newMaterial(String, String) - Method in class net.bioclipse.managers.NanoManager

newMolecule() - Method in class net.bioclipse.managers.CDKManager

Deprecated.

use CDKManager.newMolecule(IChemObjectBuilder) or CDKManager.newMolecule(IAtomContainer) instead

newMolecule(IAtomContainer) - Method in class net.bioclipse.managers.CDKManager

Creates a new CDKMolecule from the given IAtomContainer.

newMolecule(IChemObjectBuilder) - Method in class net.bioclipse.managers.CDKManager

Creates a new CDKMolecule.

newProject(String) - Method in class net.bioclipse.managers.UIManager

Creates a new project in the Bioclipse workspace.

newQuantity(double, Unit) - Method in class net.bioclipse.managers.QUDTManager

Creates a new jQUDT Quantity for the given input.

newQuantity(double, String) - Method in class net.bioclipse.managers.QUDTManager

Creates a new jQUDT Quantity for the given input.

O

open(Object) - Method in class net.bioclipse.managers.UIManager

Not currently implemented.

OpsinManager - Class in net.bioclipse.managers

Bioclipse manager that wraps OPSIN functionality for processing IUPAC names.

OpsinManager(String) - Constructor for class net.bioclipse.managers.OpsinManager

Creates a new OpsinManager.

options() - Method in class net.bioclipse.managers.InChIManager

OscarManager - Class in net.bioclipse.managers

Bioclipse manager that adds text mining functionality.

OscarManager(String) - Constructor for class net.bioclipse.managers.OscarManager

Creates a new OscarManager.

P

parse(String) - Method in class net.bioclipse.managers.JSoupManager

Parses a file with HTML content from the workspace into the JSoup Document.

parse(String) - Method in class net.bioclipse.managers.SitemapManager

Extracts the URLs in a sitemap, each as a String representation.

parseIUPACName(String) - Method in class net.bioclipse.managers.OpsinManager

Parses a IUPAC name into a molecule.

parseIUPACNameAsCML(String) - Method in class net.bioclipse.managers.OpsinManager

Parses a IUPAC name into a molecule.

parseIUPACNameAsSMILES(String) - Method in class net.bioclipse.managers.OpsinManager

Parses a IUPAC name into a molecule.

parseString(String) - Method in class net.bioclipse.managers.JSoupManager

Parses a string with HTML content into the JSoup Document.

partition(IMolecule) - Method in class net.bioclipse.managers.CDKManager

perceiveCDKAtomTypes(IMolecule) - Method in class net.bioclipse.managers.cdkdebug.CDKDebugManager

Returns a string of atom types as recognized by the CDK.

processSPARQLXML(byte[], String) - Method in class net.bioclipse.managers.RDFManager

Processes XML returned by a remote SPARQL end point.

proteinFromPlainSequence(String) - Method in class net.bioclipse.managers.BiojavaManager

proteinFromPlainSequence(String, String) - Method in class net.bioclipse.managers.BiojavaManager

PubChemManager - Class in net.bioclipse.managers

Bioclipse manager that provides functionality to interact with the PubChem database.

PubChemManager(String) - Constructor for class net.bioclipse.managers.PubChemManager

Creates a new PubChemManager.

PubmedManager - Class in net.bioclipse.managers

PubmedManager(String) - Constructor for class net.bioclipse.managers.PubmedManager

Creates a new PubmedManager.

Q

QUDTManager - Class in net.bioclipse.managers

Bioclipse manager providing unit conversion functionality.

QUDTManager(String) - Constructor for class net.bioclipse.managers.QUDTManager

Creates a new QUDTManager.

R

RDFManager - Class in net.bioclipse.managers

Bioclipse manager that provides functionality around the Resource Description Framework standard.

RDFManager(String) - Constructor for class net.bioclipse.managers.RDFManager

Creates a new RDFManager.

READ_TIME_OUT - Static variable in class net.bioclipse.managers.RDFManager

readFile(String) - Method in class net.bioclipse.managers.UIManager

Read a file content line by line into memory.

readFileIntoArray(String) - Method in class net.bioclipse.managers.UIManager

Read a file line by line into memory.

readString(String) - Method in class net.bioclipse.managers.XMLManager

readValid(String) - Method in class net.bioclipse.managers.XMLManager

readValidString(String) - Method in class net.bioclipse.managers.XMLManager

readWellFormed(String) - Method in class net.bioclipse.managers.XMLManager

registerDataSource(String, String) - Method in class net.bioclipse.managers.BridgedbManager

Creates a new DataSource based on the system code and full name.

remove(String) - Method in class net.bioclipse.managers.UIManager

Deletes the file in the Bioclipse workspace.

removeHTMLTags(String) - Method in class net.bioclipse.managers.JSoupManager

Takes a HTML string and removes all tags.

renewFile(String) - Method in class net.bioclipse.managers.UIManager

Creates a new empty file in the Bioclipse workspace or empties the existing file.

ReportManager - Class in net.bioclipse.managers

Bioclipse manager providing reporting functionality.

ReportManager(String) - Constructor for class net.bioclipse.managers.ReportManager

Creates a new ReportManager.

requireVersion(String) - Method in class net.bioclipse.managers.BioclipseManager

Method to check if Bioclipse has the right version that can be used to ensure it is new enough.

resolve(String) - Method in class net.bioclipse.managers.ChemspiderManager

Looks up ChemSpider identifiers for the given InChIKey.

S

search(String) - Method in class net.bioclipse.managers.DuckDuckGoManager

search(String) - Method in class net.bioclipse.managers.PubChemManager

Searches PubChem for compounds using the given query.

search(String, String, int) - Method in class net.bioclipse.managers.BridgedbManager

Using the given connection string, it returns mappings for the given identifier, but only for the given target data source.

search(IDMapper, String, int) - Method in class net.bioclipse.managers.BridgedbManager

Searches in the given database for hits, with a given maximum.

select(Element, String) - Method in class net.bioclipse.managers.JSoupManager

Selects a subsection of the Document and returns it as an Elements object.

serialize(IReport) - Method in class net.bioclipse.managers.report.serializer.MarkdownSerializer

Converts the IReport into a Markdown String.

setRichSequence(RichSequence) - Method in class net.bioclipse.biojava.domain.BiojavaSequence

SitemapManager - Class in net.bioclipse.managers

Bioclipse manager that helps work with sitemaps.

SitemapManager(String) - Constructor for class net.bioclipse.managers.SitemapManager

Creates a new SitemapManager.

size(IRDFStore) - Method in class net.bioclipse.managers.RDFManager

Returns the number of RDF triples in the triple store.

sparql(IRDFStore, String) - Method in class net.bioclipse.managers.RDFManager

Queries a local RDF triple store.

sparqlRemote(String, String) - Method in class net.bioclipse.managers.BioclipseManager

Queries a remote SPARQL end point without Apache Jena.

sparqlRemote(String, String) - Method in class net.bioclipse.managers.RDFManager

Queries a remote SPARQL end point.

startPrefixMapping(String, String) - Method in class net.bioclipse.xml.business.NamespaceAggregator

T

toCML() - Method in class net.bioclipse.wikidata.domain.WikidataMolecule

toFasta() - Method in class net.bioclipse.biojava.domain.BiojavaSequence

Convert RichSequence to FASTA and return as String.

toSMILES() - Method in class net.bioclipse.wikidata.domain.WikidataMolecule

toString() - Method in class net.bioclipse.biojava.domain.BiojavaDNA

toString() - Method in class net.bioclipse.biojava.domain.BiojavaProtein

totalFormalCharge(IMolecule) - Method in class net.bioclipse.managers.CDKManager

Calculates the total formal charge.

U

UIManager - Class in net.bioclipse.managers

Bioclipse manager providing core functionality, focusing on the Bioclipse workspace and user interface interaction.

UIManager(String) - Constructor for class net.bioclipse.managers.UIManager

Creates a new UIManager.

V

validateAllOfType(IRDFStore, String, String, String) - Method in class net.bioclipse.managers.RDFManager

Validates triples according to some shape expression in ShEx format.

version() - Method in class net.bioclipse.managers.BioclipseManager

Returns the version of the current Bioclipse libraries.

W

warning(SAXParseException) - Method in class net.bioclipse.xml.business.DummyErrorHandler

WikidataManager - Class in net.bioclipse.managers

Bioclipse manager that provides functionality around the Resource Description Framework standard.

WikidataManager(String) - Constructor for class net.bioclipse.managers.WikidataManager

Creates a new WikidataManager.

WikidataMolecule - Class in net.bioclipse.wikidata.domain

WikidataMolecule(String) - Constructor for class net.bioclipse.wikidata.domain.WikidataMolecule

X

XMLManager - Class in net.bioclipse.managers

Bioclipse manager that provides functionality around the eXtensible Markup Language standard.

XMLManager(String) - Constructor for class net.bioclipse.managers.XMLManager

Creates a new XMLManager.

xref(String) - Method in class net.bioclipse.managers.BridgedbManager

Creates a Xref object for the given identifier.

xref(String, String) - Method in class net.bioclipse.managers.BridgedbManager

Creates a Xref object for the given identifier.

Z

ZenodoManager - Class in net.bioclipse.managers

ZenodoManager(String) - Constructor for class net.bioclipse.managers.ZenodoManager

Creates a new ZenodoManager.

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