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> cdk.jar.zip
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  • >> Package Explorer
  • >>> Java Explorer <2.6.8>
    • .mavenResources.target.classes
    • annotation.javafiles
    • atomtype.javafiles
    • build.props
    • builder3d.javafiles
    • builder3dtools.javafiles
    • charges.javafiles
    • cip.javafiles
    • cmllite-schema
      • pmr
        • attributes
          • attributes.rnc
        • elements
          • elements.rnc
          • elements.rng
        • schematron
          • build.bat
          • clean.bat
          • cml-lite.sch
          • xsl
            • cml-lite.xsl
            • extract-doc.xsl
            • iso_schematron_skeleton.xsl
            • iso_svrl.xsl
            • svrl2html.xsl
        • types
          • cmltypes.rnc
          • XMLFP.rnc
    • com
      • hp
        • hpl
          • jena
            • assembler
              • acceptance
                • AllAccept.java
                • TestDatabaseModes.java
              • Assembler.java
              • AssemblerHelp.java
              • assemblers
                • AssemblerBase.java
                • AssemblerGroup.java
                • ConnectionAssembler.java
                • ContentAssembler.java
                • DefaultModelAssembler.java
                • DocumentManagerAssembler.java
                • FileManagerAssembler.java
                • FileModelAssembler.java
                • InfModelAssembler.java
                • LocationMapperAssembler.java
                • MemoryModelAssembler.java
                • ModelAssembler.java
                • ModelSourceAssembler.java
                • NamedModelAssembler.java
                • OntModelAssembler.java
                • OntModelSpecAssembler.java
                • PrefixMappingAssembler.java
                • RDBModelAssembler.java
                • ReasonerFactoryAssembler.java
                • RuleSetAssembler.java
                • UnionModelAssembler.java
              • BadObjectException.java
              • ConnectionDescription.java
              • Content.java
              • exceptions
                • AmbiguousSpecificTypeException.java
                • AssemblerException.java
                • CannotConstructException.java
                • CannotHaveRulesException.java
                • CannotLoadClassException.java
                • NoImplementationException.java
                • NoSpecificTypeException.java
                • NotExpectedTypeException.java
                • NotUniqueException.java
                • PropertyRequiredException.java
                • ReasonerClashException.java
                • TransactionAbortedException.java
                • UnknownEncodingException.java
                • UnknownReasonerException.java
                • UnknownStyleException.java
              • ImportManager.java
              • JA.java
              • Mode.java
              • ModelExpansion.java
              • RuleSet.java
              • test
              • datatypes
                • BaseDatatype.java
                • DatatypeFormatException.java
                • RDFDatatype.java
                • TypeMapper.java
                • xsd
                  • AbstractDateTime.java
                  • IllegalDateTimeFieldException.java
                  • impl
                    • XMLLiteralType.java
                    • XSDAbstractDateTimeType.java
                    • XSDBaseNumericType.java
                    • XSDBaseStringType.java
                    • XSDByteType.java
                    • XSDDateTimeType.java
                    • XSDDateType.java
                    • XSDDayType.java
                    • XSDDouble.java
                    • XSDDurationType.java
                    • XSDFloat.java
                    • XSDGenericType.java
                    • XSDMonthDayType.java
                    • XSDMonthType.java
                    • XSDTimeType.java
                    • XSDYearMonthType.java
                    • XSDYearType.java
                  • XSDbase64Binary.java
                  • XSDDatatype.java
                  • XSDDateTime.java
                  • XSDDuration.java
                  • XSDhexBinary.java
              • db
                • DBConnection.java
                • GraphRDB.java
                • IDBConnection.java
                • impl
                  • DBBlob.java
                  • DBBulkUpdateHandler.java
                  • DBIDInt.java
                  • DBPattern.java
                  • DBPrefixMappingImpl.java
                  • DBProp.java
                  • DBPropDatabase.java
                  • DBPropGraph.java
                  • DBPropLSet.java
                  • DBPropPrefix.java
                  • DBPropPSet.java
                  • DBQuery.java
                  • DBQueryHandler.java
                  • DBQueryStage.java
                  • DBQueryStageCompiler.java
                  • DBReifier.java
                  • DBReifierGraph.java
                  • DBTransactionHandler.java
                  • DriverMap.java
                  • DriverRDB.java
                  • Driver_Derby.java
                  • Driver_HSQL.java
                  • Driver_HSQLDB.java
                  • Driver_MsSQL.java
                  • Driver_MySQL.java
                  • Driver_Oracle.java
                  • Driver_Oracle_LOB.java
                  • Driver_PostgreSQL.java
                  • Free.java
                  • GraphRDBMaker.java
                  • ICache.java
                  • IDBBlob.java
                  • IDBID.java
                  • IPSet.java
                  • IRDBDriver.java
                  • LRUCache.java
                  • PSet_ReifStore_RDB.java
                  • PSet_TripleStore_RDB.java
                  • ReificationCache.java
                  • ReificationCacheMap.java
                  • ReificationStatementMask.java
                  • ResultSetIterator.java
                  • ResultSetReifIterator.java
                  • ResultSetStringIterator.java
                  • ResultSetTripleIterator.java
                  • SimpleCache.java
                  • SpecializedGraph.java
                  • SpecializedGraphBase.java
                  • SpecializedGraphReifier.java
                  • SpecializedGraphReifier_RDB.java
                  • SpecializedGraph_TripleStore.java
                  • SpecializedGraph_TripleStore_RDB.java
                  • SQLCache.java
                  • VarDesc.java
                • ModelRDB.java
                • RDFRDBException.java
                • test
                • enhanced
                  • AlreadyLinkedViewException.java
                  • BuiltinPersonalities.java
                  • EnhGraph.java
                  • EnhNode.java
                  • GraphPersonality.java
                  • Implementation.java
                  • NodePersonality.java
                  • Personality.java
                  • PersonalityConfigException.java
                  • Polymorphic.java
                  • test
                    • UnsupportedPolymorphismException.java
                  • graph
                    • BulkUpdateHandler.java
                    • Capabilities.java
                    • compose
                      • CompositionBase.java
                      • Delta.java
                      • Difference.java
                      • DisjointUnion.java
                      • Dyadic.java
                      • Intersection.java
                      • MultiUnion.java
                      • Polyadic.java
                      • PolyadicPrefixMappingImpl.java
                      • test
                        • Union.java
                      • Factory.java
                      • FrontsNode.java
                      • FrontsTriple.java
                      • GetTriple.java
                      • Graph.java
                      • GraphAdd.java
                      • GraphEventManager.java
                      • GraphEvents.java
                      • GraphExtract.java
                      • GraphListener.java
                      • GraphMaker.java
                      • GraphStatisticsHandler.java
                      • GraphUtil.java
                      • impl
                        • AllCapabilities.java
                        • BaseGraphMaker.java
                        • FileGraph.java
                        • FileGraphMaker.java
                        • FileGraphTransactionHandler.java
                        • Fragments.java
                        • FragmentTripleIterator.java
                        • GraphAddList.java
                        • GraphBase.java
                        • GraphMatcher.java
                        • GraphWithPerform.java
                        • LiteralLabel.java
                        • ReificationWrapper.java
                        • ReificationWrapperGraph.java
                        • ReifierFragmentHandler.java
                        • ReifierFragmentsMap.java
                        • ReifierTripleMap.java
                        • SimpleBulkUpdateHandler.java
                        • SimpleEventManager.java
                        • SimpleGraphMaker.java
                        • SimpleReifier.java
                        • SimpleReifierFragmentHandler.java
                        • SimpleReifierFragmentsMap.java
                        • SimpleReifierTripleMap.java
                        • SimpleTransactionHandler.java
                        • TransactionHandlerBase.java
                        • TripleStore.java
                        • WrappedBulkUpdateHandler.java
                        • WrappedGraph.java
                        • WrappedReifier.java
                      • Node.java
                      • NodeCache.java
                      • NodeVisitor.java
                      • Node_ANY.java
                      • Node_Blank.java
                      • Node_Concrete.java
                      • Node_Fluid.java
                      • Node_Literal.java
                      • Node_NULL.java
                      • Node_URI.java
                      • Node_Variable.java
                      • query
                        • Applyer.java
                        • Bind.java
                        • BindingQueryPlan.java
                        • Bound.java
                        • BufferPipe.java
                        • ConstraintStage.java
                        • Domain.java
                        • Dyadic.java
                        • Element.java
                        • Expression.java
                        • ExpressionFunctionURIs.java
                        • ExpressionSet.java
                        • Fixed.java
                        • FixedValuator.java
                        • GuardArranger.java
                        • IndexValues.java
                        • InitialStage.java
                        • Mapping.java
                        • Matcher.java
                        • NamedGraphMap.java
                        • NamedTripleBunches.java
                        • Pattern.java
                        • PatternCompiler.java
                        • PatternLiteral.java
                        • PatternStage.java
                        • PatternStageBase.java
                        • PatternStageCompiler.java
                        • Pipe.java
                        • Query.java
                        • QueryHandler.java
                        • QueryNode.java
                        • QueryNodeFactory.java
                        • QueryNodeFactoryBase.java
                        • QueryTriple.java
                        • regexptrees
                          • Alternatives.java
                          • AnyOf.java
                          • AnySingle.java
                          • BackReference.java
                          • EndOfLine.java
                          • MultiOperandTree.java
                          • NoneOf.java
                          • Nothing.java
                          • OneOrMore.java
                          • Optional.java
                          • Paren.java
                          • PerlPatternParser.java
                          • RegexpTree.java
                          • RegexpTreeGenerator.java
                          • Repeated.java
                          • Sequence.java
                          • SimpleGenerator.java
                          • StartOfLine.java
                          • test
                            • Text.java
                            • ZeroOrMore.java
                          • Rewrite.java
                          • SimpleQueryEngine.java
                          • SimpleQueryHandler.java
                          • SimpleQueryPlan.java
                          • SimpleTreeQueryPlan.java
                          • SimpleTripleSorter.java
                          • SlotValuator.java
                          • Stage.java
                          • StageElement.java
                          • test
                            • TreeQueryPlan.java
                            • TripleSorter.java
                            • Util.java
                            • Valuator.java
                            • ValuatorSet.java
                            • VariableIndexes.java
                            • VariableValues.java
                          • Reifier.java
                          • test
                            • TransactionHandler.java
                            • Triple.java
                            • TripleBoundary.java
                            • TripleCache.java
                            • TripleIterator.java
                            • TripleMatch.java
                            • TripleMatchFilter.java
                            • TripleMatchIterator.java
                          • iri
                            • impl
                              • AbsIRIFactoryImpl.java
                              • AbsIRIImpl.java
                              • AbsLexer.java
                              • AFS_Build.java
                              • BuildViolationCodes.java
                              • ComponentPattern.java
                              • ComponentPatternParser.java
                              • ErrorAction.java
                              • Expansion.java
                              • Force.java
                              • GroupAction.java
                              • HostAction.java
                              • IRIExamples.java
                              • IRIFactoryImpl.java
                              • IRIImpl.java
                              • IRIImplException.java
                              • Lexer.java
                              • LexerFragment.java
                              • LexerHost.java
                              • LexerPath.java
                              • LexerPort.java
                              • LexerQuery.java
                              • LexerScheme.java
                              • LexerUserinfo.java
                              • LexerXHost.java
                              • Main.java
                              • Parser.java
                              • PatternCompiler.java
                              • ResolvedRelativeIRI.java
                              • SchemeSpecification.java
                              • SchemeSpecificPart.java
                              • Specification.java
                              • Test.java
                              • VarPattern.java
                              • ViolationCodeInfo.java
                              • ViolationImpl.java
                            • IRI.java
                            • IRIComponents.java
                            • IRIException.java
                            • IRIFactory.java
                            • IRIFactoryI.java
                            • IRIRelativize.java
                            • MalformedIDNException.java
                            • Violation.java
                            • ViolationCodes.java
                          • Jena.java
                          • JenaRuntime.java
                          • mem
                            • ArrayBunch.java
                            • BunchMap.java
                            • faster
                              • FasterPatternStage.java
                              • FasterTripleStore.java
                              • GraphMemFaster.java
                              • GraphMemFasterQueryHandler.java
                              • NodeToTriplesMapFaster.java
                              • ProcessedTriple.java
                              • test
                              • GraphMem.java
                              • GraphMemBase.java
                              • GraphMemBaseQueryHandler.java
                              • GraphMemBulkUpdateHandler.java
                              • GraphTripleStore.java
                              • GraphTripleStoreBase.java
                              • HashCommon.java
                              • HashedBunchMap.java
                              • HashedTripleBunch.java
                              • MatchOrBind.java
                              • MixedGraphMem.java
                              • MixedGraphMemStore.java
                              • NodeToTriplesMap.java
                              • NodeToTriplesMapBase.java
                              • ObjectIterator.java
                              • SetBunch.java
                              • SmallGraphMem.java
                              • StoreTripleIterator.java
                              • test
                                • TrackingTripleIterator.java
                                • TripleBunch.java
                                • WrappedHashMap.java
                              • n3
                                • IRIResolver.java
                                • JenaReaderBase.java
                                • JenaURIException.java
                                • N3IndentedWriter.java
                                • N3JenaWriter.java
                                • N3JenaWriterCommon.java
                                • N3JenaWriterPlain.java
                                • N3JenaWriterPP.java
                                • N3JenaWriterTriples.java
                                • N3TurtleJenaWriter.java
                                • RelativeURIException.java
                                • test
                                  • turtle
                                    • LabelToNodeMap.java
                                    • parser
                                      • JavaCharStream.java
                                      • ParseException.java
                                      • Token.java
                                      • TokenMgrError.java
                                      • TurtleParser.java
                                      • TurtleParserConstants.java
                                      • TurtleParserTokenManager.java
                                    • ParserBase.java
                                    • ParserTurtle.java
                                    • test
                                      • TurtleEventDump.java
                                      • TurtleEventHandler.java
                                      • TurtleEventInserter.java
                                      • TurtleEventNull.java
                                      • TurtleParseException.java
                                      • TurtleReader.java
                                  • ontology
                                    • AllDifferent.java
                                    • AllValuesFromRestriction.java
                                    • AnnotationProperty.java
                                    • BooleanClassDescription.java
                                    • CardinalityQRestriction.java
                                    • CardinalityRestriction.java
                                    • ComplementClass.java
                                    • ConversionException.java
                                    • DataRange.java
                                    • DatatypeProperty.java
                                    • EnumeratedClass.java
                                    • FunctionalProperty.java
                                    • HasValueRestriction.java
                                    • impl
                                      • AbstractProfile.java
                                      • AllDifferentImpl.java
                                      • AllValuesFromRestrictionImpl.java
                                      • AnnotationPropertyImpl.java
                                      • BooleanClassDescriptionImpl.java
                                      • CardinalityQRestrictionImpl.java
                                      • CardinalityRestrictionImpl.java
                                      • ComplementClassImpl.java
                                      • DAML_OILLegacyProfile.java
                                      • DAML_OILProfile.java
                                      • DataRangeImpl.java
                                      • DatatypePropertyImpl.java
                                      • EnumeratedClassImpl.java
                                      • FunctionalPropertyImpl.java
                                      • HasValueRestrictionImpl.java
                                      • IndividualImpl.java
                                      • IntersectionClassImpl.java
                                      • InverseFunctionalPropertyImpl.java
                                      • MaxCardinalityQRestrictionImpl.java
                                      • MaxCardinalityRestrictionImpl.java
                                      • MinCardinalityQRestrictionImpl.java
                                      • MinCardinalityRestrictionImpl.java
                                      • ObjectPropertyImpl.java
                                      • OntClassImpl.java
                                      • OntModelImpl.java
                                      • OntologyImpl.java
                                      • OntPropertyImpl.java
                                      • OntResourceImpl.java
                                      • OWLDLProfile.java
                                      • OWLLiteProfile.java
                                      • OWLProfile.java
                                      • QualifiedRestrictionImpl.java
                                      • RDFSProfile.java
                                      • RestrictionImpl.java
                                      • SomeValuesFromRestrictionImpl.java
                                      • SymmetricPropertyImpl.java
                                      • test
                                        • TransitivePropertyImpl.java
                                        • UnionClassImpl.java
                                      • Individual.java
                                      • IntersectionClass.java
                                      • InverseFunctionalProperty.java
                                      • LanguageConsistencyException.java
                                      • MaxCardinalityQRestriction.java
                                      • MaxCardinalityRestriction.java
                                      • MinCardinalityQRestriction.java
                                      • MinCardinalityRestriction.java
                                      • ObjectProperty.java
                                      • OntClass.java
                                      • OntDocumentManager.java
                                      • OntModel.java
                                      • OntModelSpec.java
                                      • Ontology.java
                                      • OntologyException.java
                                      • OntProperty.java
                                      • OntResource.java
                                      • OntTools.java
                                      • Profile.java
                                      • ProfileException.java
                                      • ProfileRegistry.java
                                      • QualifiedRestriction.java
                                      • Restriction.java
                                      • SomeValuesFromRestriction.java
                                      • SymmetricProperty.java
                                      • TransitiveProperty.java
                                      • UnionClass.java
                                    • rdf
                                      • arp
                                        • ALiteral.java
                                        • AResource.java
                                        • ARP.java
                                        • ARPConfig.java
                                        • ARPErrorNumbers.java
                                        • ARPEventHandler.java
                                        • ARPHandlers.java
                                        • ARPOptions.java
                                        • DOM2Model.java
                                        • ExtendedHandler.java
                                        • FatalParsingErrorException.java
                                        • impl
                                          • AbsXMLContext.java
                                          • ANode.java
                                          • AResourceInternal.java
                                          • ARPDatatypeLiteral.java
                                          • ARPResource.java
                                          • ARPSaxErrorHandler.java
                                          • ARPString.java
                                          • AttributeLexer.java
                                          • CharacterModel.java
                                          • DefaultErrorHandler.java
                                          • ElementLexer.java
                                          • LexicalHandlerImpl.java
                                          • Location.java
                                          • Names.java
                                          • ParserSupport.java
                                          • QNameLexer.java
                                          • RDFXMLParser.java
                                          • SAX2RDFImpl.java
                                          • Taint.java
                                          • TaintImpl.java
                                          • UntaintableURIReference.java
                                          • URIReference.java
                                          • WrappedException.java
                                          • XMLBaselessContext.java
                                          • XMLContext.java
                                          • XMLHandler.java
                                        • JenaHandler.java
                                        • JenaReader.java
                                        • lang
                                          • IanaLanguageTag.java
                                          • Iso3166.java
                                          • Iso639.java
                                          • LanguageTag.java
                                          • LanguageTagCodes.java
                                          • LanguageTagSyntaxException.java
                                        • NamespaceHandler.java
                                        • NTriple.java
                                        • ParseException.java
                                        • SAX2Model.java
                                        • SAX2RDF.java
                                        • StatementHandler.java
                                        • states
                                          • AbsWantLiteralValueOrDescription.java
                                          • AbsXMLLiteral.java
                                          • Collection.java
                                          • DAMLCollection.java
                                          • Frame.java
                                          • FrameI.java
                                          • HasSubjectFrameI.java
                                          • InnerXMLLiteral.java
                                          • LookingForRDF.java
                                          • OuterXMLLiteral.java
                                          • RDFCollection.java
                                          • StartStateRDForDescription.java
                                          • test
                                            • WantDescription.java
                                            • WantEmpty.java
                                            • WantLiteralValueOrDescription.java
                                            • WantPropertyElement.java
                                            • WantsObjectFrameI.java
                                            • WantsObjectI.java
                                            • WantTopLevelDescription.java
                                            • WantTypedLiteral.java
                                          • test
                                          • listeners
                                            • ChangedListener.java
                                            • NullListener.java
                                            • ObjectListener.java
                                            • StatementListener.java
                                          • model
                                            • Alt.java
                                            • AltHasNoDefaultException.java
                                            • AnonId.java
                                            • Bag.java
                                            • Container.java
                                            • DoesNotReifyException.java
                                            • EmptyListException.java
                                            • EmptyListUpdateException.java
                                            • HasNoModelException.java
                                            • impl
                                              • AltImpl.java
                                              • BagImpl.java
                                              • ContainerI.java
                                              • ContainerImpl.java
                                              • ContNodeIteratorFactoryImpl.java
                                              • ContNodeIteratorImpl.java
                                              • InfModelImpl.java
                                              • IStream.java
                                              • IteratorFactory.java
                                              • LiteralImpl.java
                                              • MemoryModelGetter.java
                                              • ModelCom.java
                                              • ModelListenerAdapter.java
                                              • ModelMakerImpl.java
                                              • ModelReifier.java
                                              • NodeIteratorFactory.java
                                              • NodeIteratorImpl.java
                                              • NsIteratorImpl.java
                                              • NTripleReader.java
                                              • NTripleWriter.java
                                              • PropertyImpl.java
                                              • RDFDefaultErrorHandler.java
                                              • RDFListImpl.java
                                              • RDFReaderFImpl.java
                                              • RDFWriterFImpl.java
                                              • ReifiedStatementImpl.java
                                              • ResIteratorImpl.java
                                              • ResourceImpl.java
                                              • RSIteratorImpl.java
                                              • SelectorImpl.java
                                              • SeqImpl.java
                                              • SeqNodeIteratorFactoryImpl.java
                                              • SeqNodeIteratorImpl.java
                                              • StatementBase.java
                                              • StatementImpl.java
                                              • StmtIteratorImpl.java
                                              • Util.java
                                            • InfModel.java
                                            • InvalidListException.java
                                            • ListIndexException.java
                                            • Literal.java
                                            • LiteralRequiredException.java
                                            • Model.java
                                            • ModelChangedListener.java
                                            • ModelCon.java
                                            • ModelExtract.java
                                            • ModelFactory.java
                                            • ModelFactoryBase.java
                                            • ModelGetter.java
                                            • ModelGraphInterface.java
                                            • ModelMaker.java
                                            • ModelReader.java
                                            • ModelSource.java
                                            • NodeIterator.java
                                            • NsIterator.java
                                            • ObjectF.java
                                            • Property.java
                                            • RDFErrorHandler.java
                                            • RDFList.java
                                            • RDFNode.java
                                            • RDFReader.java
                                            • RDFReaderF.java
                                            • RDFVisitor.java
                                            • RDFWriter.java
                                            • RDFWriterF.java
                                            • ReifiedStatement.java
                                            • ResIterator.java
                                            • Resource.java
                                            • ResourceF.java
                                            • ResourceFactory.java
                                            • ResourceRequiredException.java
                                            • RSIterator.java
                                            • Schema.java
                                            • Selector.java
                                            • Seq.java
                                            • SeqIndexBoundsException.java
                                            • SimpleSelector.java
                                            • Statement.java
                                            • StatementBoundary.java
                                            • StatementBoundaryBase.java
                                            • StatementTripleBoundary.java
                                            • StmtIterator.java
                                            • test
                                          • reasoner
                                            • BaseInfGraph.java
                                            • Derivation.java
                                            • FGraph.java
                                            • Finder.java
                                            • FinderUtil.java
                                            • IllegalParameterException.java
                                            • InfGraph.java
                                            • Reasoner.java
                                            • ReasonerException.java
                                            • ReasonerFactory.java
                                            • ReasonerRegistry.java
                                            • rulesys
                                              • BackwardRuleInfGraphI.java
                                              • BasicFBReifier.java
                                              • BasicForwardRuleInfGraph.java
                                              • BasicForwardRuleReasoner.java
                                              • BindingEnvironment.java
                                              • Builtin.java
                                              • BuiltinException.java
                                              • BuiltinRegistry.java
                                              • builtins
                                                • AddOne.java
                                                • AssertDisjointPairs.java
                                                • BaseBuiltin.java
                                                • Bound.java
                                                • CountLiteralValues.java
                                                • Difference.java
                                                • Drop.java
                                                • Equal.java
                                                • GE.java
                                                • GreaterThan.java
                                                • Hide.java
                                                • IsBNode.java
                                                • IsDType.java
                                                • IsFunctor.java
                                                • IsLiteral.java
                                                • LE.java
                                                • LessThan.java
                                                • ListContains.java
                                                • ListEntry.java
                                                • ListEqual.java
                                                • ListLength.java
                                                • ListMapAsObject.java
                                                • ListMapAsSubject.java
                                                • ListNotContains.java
                                                • ListNotEqual.java
                                                • MakeInstance.java
                                                • MakeTemp.java
                                                • Max.java
                                                • Min.java
                                                • NotBNode.java
                                                • NotDType.java
                                                • NotEqual.java
                                                • NotFunctor.java
                                                • NotLiteral.java
                                                • NoValue.java
                                                • Now.java
                                                • Print.java
                                                • Product.java
                                                • Quotient.java
                                                • Regex.java
                                                • Remove.java
                                                • StrConcat.java
                                                • Sum.java
                                                • Table.java
                                                • TableAll.java
                                                • Unbound.java
                                                • UriConcat.java
                                              • ClauseEntry.java
                                              • DAMLMicroReasoner.java
                                              • DAMLMicroReasonerFactory.java
                                              • FBRuleInfGraph.java
                                              • FBRuleReasoner.java
                                              • ForwardRuleInfGraphI.java
                                              • Functor.java
                                              • GenericRuleReasoner.java
                                              • GenericRuleReasonerFactory.java
                                              • impl
                                                • BaseRuleReasonerFactory.java
                                                • BBRuleContext.java
                                                • BFRuleContext.java
                                                • BindingStack.java
                                                • BindingVector.java
                                                • ChoicePointFrame.java
                                                • ConsumerChoicePointFrame.java
                                                • EnvironmentFrame.java
                                                • EnvironmentFrameWithDerivation.java
                                                • FrameObject.java
                                                • FRuleEngine.java
                                                • FRuleEngineI.java
                                                • Generator.java
                                                • GenericChoiceFrame.java
                                                • GenericTripleMatchFrame.java
                                                • LPAgendaEntry.java
                                                • LPBindingEnvironment.java
                                                • LPBRuleEngine.java
                                                • LPInterpreter.java
                                                • LPInterpreterContext.java
                                                • LPInterpreterState.java
                                                • LPRuleStore.java
                                                • LPRuleSyntaxException.java
                                                • LPTopGoalIterator.java
                                                • MutableTriplePattern.java
                                                • OWLExptRuleTranslationHook.java
                                                • OWLRuleTranslationHook.java
                                                • RDFSCMPPreprocessHook.java
                                                • RETEClauseFilter.java
                                                • RETEConflictSet.java
                                                • RETEEngine.java
                                                • RETENode.java
                                                • RETEQueue.java
                                                • RETERuleContext.java
                                                • RETESinkNode.java
                                                • RETESourceNode.java
                                                • RETETerminal.java
                                                • RuleClauseCode.java
                                                • RuleStore.java
                                                • StateFlag.java
                                                • TempNodeCache.java
                                                • TopLevelTripleMatchFrame.java
                                                • TripleMatchFrame.java
                                                • WrappedReasonerFactory.java
                                              • LPBackwardRuleInfGraph.java
                                              • LPBackwardRuleReasoner.java
                                              • Node_RuleVariable.java
                                              • OWLFBRuleReasoner.java
                                              • OWLFBRuleReasonerFactory.java
                                              • OWLMicroReasoner.java
                                              • OWLMicroReasonerFactory.java
                                              • OWLMiniReasoner.java
                                              • OWLMiniReasonerFactory.java
                                              • RDFSFBRuleReasoner.java
                                              • RDFSFBRuleReasonerFactory.java
                                              • RDFSForwardRuleReasoner.java
                                              • RDFSRuleInfGraph.java
                                              • RDFSRuleReasoner.java
                                              • RDFSRuleReasonerFactory.java
                                              • RETERuleInfGraph.java
                                              • Rule.java
                                              • RuleContext.java
                                              • RuleDerivation.java
                                              • RulePreprocessHook.java
                                              • RuleReasoner.java
                                              • RuleReasonerFactory.java
                                              • SilentAddI.java
                                              • test
                                                • Util.java
                                              • StandardValidityReport.java
                                              • test
                                                • transitiveReasoner
                                                  • GraphNode.java
                                                  • TransitiveEngine.java
                                                  • TransitiveGraphCache.java
                                                  • TransitiveInfGraph.java
                                                  • TransitiveReasoner.java
                                                  • TransitiveReasonerFactory.java
                                                • TriplePattern.java
                                                • ValidityReport.java
                                              • regression
                                                • DiHyperCube.java
                                                • GetModel.java
                                                • HyperCube.java
                                                • MegaTestSuite.java
                                                • NewRegression.java
                                                • NewRegressionAddAndContains.java
                                                • NewRegressionAddModel.java
                                                • NewRegressionAltMethods.java
                                                • NewRegressionBagMethods.java
                                                • NewRegressionBase.java
                                                • NewRegressionContainerMethods.java
                                                • NewRegressionContainers.java
                                                • NewRegressionGet.java
                                                • NewRegressionListSubjects.java
                                                • NewRegressionLiterals.java
                                                • NewRegressionObjects.java
                                                • NewRegressionResourceMethods.java
                                                • NewRegressionResources.java
                                                • NewRegressionSelector.java
                                                • NewRegressionSeq.java
                                                • NewRegressionSeqMethods.java
                                                • NewRegressionSet.java
                                                • NewRegressionStatementMethods.java
                                                • NewRegressionStatements.java
                                                • Regression.java
                                                • ResourceReader.java
                                                • TestCaseBasic.java
                                                • testMatch.java
                                                • testNTripleReader.java
                                                • testReaderInterface.java
                                              • shared
                                                • AddDeniedException.java
                                                • AlreadyExistsException.java
                                                • AlreadyReifiedException.java
                                                • AssertionFailureException.java
                                                • BadBooleanException.java
                                                • BadCharLiteralException.java
                                                • BadDescriptionException.java
                                                • BadDescriptionMultipleRootsException.java
                                                • BadDescriptionNoRootException.java
                                                • BadURIException.java
                                                • BrokenException.java
                                                • CannotCreateException.java
                                                • CannotEncodeCharacterException.java
                                                • CannotReifyException.java
                                                • ClosedException.java
                                                • Command.java
                                                • ConfigException.java
                                                • DeleteDeniedException.java
                                                • DoesNotExistException.java
                                                • impl
                                                  • JenaParameters.java
                                                  • PrefixMappingImpl.java
                                                • InvalidPropertyURIException.java
                                                • JenaException.java
                                                • Lock.java
                                                • LockMRSW.java
                                                • LockMutex.java
                                                • LockNone.java
                                                • NamespaceEndsWithNameCharException.java
                                                • NoReaderForLangException.java
                                                • NoReasonerSuppliedException.java
                                                • NoSuchReasonerException.java
                                                • NotFoundException.java
                                                • NoWriterForLangException.java
                                                • PrefixMapping.java
                                                • PropertyNotFoundException.java
                                                • QueryStageException.java
                                                • RandomOrderGraph.java
                                                • ReificationStyle.java
                                                • RulesetNotFoundException.java
                                                • SyntaxError.java
                                                • test
                                                  • UnknownPropertyException.java
                                                  • UpdateDeniedException.java
                                                  • uuid
                                                    • Bits.java
                                                    • JenaUUID.java
                                                    • LibUUID.java
                                                    • test
                                                      • UUIDFactory.java
                                                      • UUID_nil.java
                                                      • UUID_V1.java
                                                      • UUID_V1_Gen.java
                                                      • UUID_V4.java
                                                      • UUID_V4_Gen.java
                                                    • wg
                                                      • LazyFileInputStream.java
                                                      • LazyInputStream.java
                                                      • LazyURLInputStream.java
                                                      • LazyZipEntryInputStream.java
                                                      • TestInputStreamFactory.java
                                                    • WrappedException.java
                                                    • WrappedIOException.java
                                                  • test
                                                    • util
                                                      • cache
                                                        • Cache.java
                                                        • CacheControl.java
                                                        • CacheManager.java
                                                        • EnhancedNodeCache.java
                                                        • RandCache.java
                                                      • CharEncoding.java
                                                      • CollectionFactory.java
                                                      • FileManager.java
                                                      • FileUtils.java
                                                      • iterator
                                                        • ArrayIterator.java
                                                        • ClosableIterator.java
                                                        • ConcatenatedIterator.java
                                                        • EarlyBindingIterator.java
                                                        • ExtendedIterator.java
                                                        • Filter.java
                                                        • FilterDropIterator.java
                                                        • FilterIterator.java
                                                        • FilterKeepIterator.java
                                                        • IteratorIterator.java
                                                        • LateBindingIterator.java
                                                        • LazyIterator.java
                                                        • Map1.java
                                                        • Map1Iterator.java
                                                        • MapFilter.java
                                                        • MapFilterIterator.java
                                                        • NiceIterator.java
                                                        • NullIterator.java
                                                        • RandomOrderIterator.java
                                                        • SingletonIterator.java
                                                        • test
                                                          • UniqueExtendedIterator.java
                                                          • WrappedIterator.java
                                                        • IteratorCollection.java
                                                        • junit
                                                          • Manifest.java
                                                          • ManifestItemHandler.java
                                                          • TestException.java
                                                          • TestFactoryManifest.java
                                                          • TestUtils.java
                                                        • LocationMapper.java
                                                        • Locator.java
                                                        • LocatorClassLoader.java
                                                        • LocatorFile.java
                                                        • LocatorURL.java
                                                        • LocatorZip.java
                                                        • ModelLoader.java
                                                        • ModelQueryUtil.java
                                                        • MonitorGraph.java
                                                        • MonitorModel.java
                                                        • OneToManyMap.java
                                                        • PrintUtil.java
                                                        • QueryMapper.java
                                                        • ResourceUtils.java
                                                        • test
                                                          • Tokenizer.java
                                                          • tuple
                                                            • TupleItem.java
                                                            • TupleSet.java
                                                          • TypedStream.java
                                                          • URIref.java
                                                        • vocabulary
                                                          • DAMLVocabulary.java
                                                          • DAML_OIL.java
                                                          • DB.java
                                                          • DC.java
                                                          • DCTerms.java
                                                          • DCTypes.java
                                                          • DC_10.java
                                                          • DC_11.java
                                                          • LocationMappingVocab.java
                                                          • OntDocManagerVocab.java
                                                          • OntEventsVocab.java
                                                          • OWL.java
                                                          • OWLResults.java
                                                          • OWLTest.java
                                                          • RDF.java
                                                          • RDFS.java
                                                          • RDFSyntax.java
                                                          • RDFTest.java
                                                          • ReasonerVocabulary.java
                                                          • ResultSet.java
                                                          • RSS.java
                                                          • test
                                                            • TestManifest.java
                                                            • TestManifestX.java
                                                            • VCARD.java
                                                            • XSD.java
                                                          • xmloutput
                                                            • impl
                                                              • Abbreviated.java
                                                              • BaseXMLWriter.java
                                                              • Basic.java
                                                              • PairEntry.java
                                                              • Relation.java
                                                              • SimpleLogger.java
                                                              • Unparser.java
                                                            • RDFXMLWriterI.java
                                                            • test
                                                      • ibm
                                                        • icu
                                                          • impl
                                                            • BOCU.java
                                                            • CalendarAstronomer.java
                                                            • CalendarCache.java
                                                            • CalendarData.java
                                                            • CharacterIteratorWrapper.java
                                                            • CharTrie.java
                                                            • data
                                                              • BreakIteratorRules.java
                                                              • BreakIteratorRules_th.java
                                                              • HolidayBundle.java
                                                              • HolidayBundle_da.java
                                                              • HolidayBundle_da_DK.java
                                                              • HolidayBundle_de.java
                                                              • HolidayBundle_de_AT.java
                                                              • HolidayBundle_de_DE.java
                                                              • HolidayBundle_el.java
                                                              • HolidayBundle_el_GR.java
                                                              • HolidayBundle_en.java
                                                              • HolidayBundle_en_CA.java
                                                              • HolidayBundle_en_GB.java
                                                              • HolidayBundle_en_US.java
                                                              • HolidayBundle_es.java
                                                              • HolidayBundle_es_MX.java
                                                              • HolidayBundle_fr.java
                                                              • HolidayBundle_fr_CA.java
                                                              • HolidayBundle_fr_FR.java
                                                              • HolidayBundle_it.java
                                                              • HolidayBundle_it_IT.java
                                                              • HolidayBundle_iw.java
                                                              • HolidayBundle_iw_IL.java
                                                              • HolidayBundle_ja_JP.java
                                                              • icudt34b
                                                                • af.res
                                                                • af_ZA.res
                                                                • am.res
                                                                • am_ET.res
                                                                • ar.res
                                                                • ar_AE.res
                                                                • ar_BH.res
                                                                • ar_DZ.res
                                                                • ar_EG.res
                                                                • ar_IQ.res
                                                                • ar_JO.res
                                                                • ar_KW.res
                                                                • ar_LB.res
                                                                • ar_LY.res
                                                                • ar_MA.res
                                                                • ar_OM.res
                                                                • ar_QA.res
                                                                • ar_SA.res
                                                                • ar_SD.res
                                                                • ar_SY.res
                                                                • ar_TN.res
                                                                • ar_YE.res
                                                                • as.res
                                                                • as_IN.res
                                                                • az.res
                                                                • az_AZ.res
                                                                • az_Cyrl.res
                                                                • az_Cyrl_AZ.res
                                                                • az_Latn.res
                                                                • az_Latn_AZ.res
                                                                • be.res
                                                                • be_BY.res
                                                                • bg.res
                                                                • bg_BG.res
                                                                • bn.res
                                                                • bn_IN.res
                                                                • ca.res
                                                                • ca_ES.res
                                                                • char.brk
                                                                • coll
                                                                  • ar.res
                                                                  • ar_AE.res
                                                                  • ar_BH.res
                                                                  • ar_DZ.res
                                                                  • ar_EG.res
                                                                  • ar_IN.res
                                                                  • ar_IQ.res
                                                                  • ar_JO.res
                                                                  • ar_KW.res
                                                                  • ar_LB.res
                                                                  • ar_LY.res
                                                                  • ar_MA.res
                                                                  • ar_OM.res
                                                                  • ar_QA.res
                                                                  • ar_SA.res
                                                                  • ar_SD.res
                                                                  • ar_SY.res
                                                                  • ar_TN.res
                                                                  • ar_YE.res
                                                                  • be.res
                                                                  • be_BY.res
                                                                  • bg.res
                                                                  • bg_BG.res
                                                                  • ca.res
                                                                  • ca_ES.res
                                                                  • cs.res
                                                                  • cs_CZ.res
                                                                  • da.res
                                                                  • da_DK.res
                                                                  • de.res
                                                                  • de_AT.res
                                                                  • de_BE.res
                                                                  • de_CH.res
                                                                  • de_DE.res
                                                                  • de_LU.res
                                                                  • de__PHONEBOOK.res
                                                                  • el.res
                                                                  • el_GR.res
                                                                  • en.res
                                                                  • en_AU.res
                                                                  • en_BE.res
                                                                  • en_BW.res
                                                                  • en_CA.res
                                                                  • en_GB.res
                                                                  • en_HK.res
                                                                  • en_IE.res
                                                                  • en_IN.res
                                                                  • en_MT.res
                                                                  • en_NZ.res
                                                                  • en_PH.res
                                                                  • en_SG.res
                                                                  • en_US.res
                                                                  • en_US_POSIX.res
                                                                  • en_VI.res
                                                                  • en_ZA.res
                                                                  • en_ZW.res
                                                                  • eo.res
                                                                  • es.res
                                                                  • es_AR.res
                                                                  • es_BO.res
                                                                  • es_CL.res
                                                                  • es_CO.res
                                                                  • es_CR.res
                                                                  • es_DO.res
                                                                  • es_EC.res
                                                                  • es_ES.res
                                                                  • es_GT.res
                                                                  • es_HN.res
                                                                  • es_MX.res
                                                                  • es_NI.res
                                                                  • es_PA.res
                                                                  • es_PE.res
                                                                  • es_PR.res
                                                                  • es_PY.res
                                                                  • es_SV.res
                                                                  • es_US.res
                                                                  • es_UY.res
                                                                  • es_VE.res
                                                                  • es__TRADITIONAL.res
                                                                  • et.res
                                                                  • et_EE.res
                                                                  • fa.res
                                                                  • fa_AF.res
                                                                  • fa_IR.res
                                                                  • fi.res
                                                                  • fi_FI.res
                                                                  • fo.res
                                                                  • fo_FO.res
                                                                  • fr.res
                                                                  • fr_BE.res
                                                                  • fr_CA.res
                                                                  • fr_CH.res
                                                                  • fr_FR.res
                                                                  • fr_LU.res
                                                                  • ga.res
                                                                  • ga_IE.res
                                                                  • gu.res
                                                                  • gu_IN.res
                                                                  • he.res
                                                                  • he_IL.res
                                                                  • hi.res
                                                                  • hi_IN.res
                                                                  • hi__DIRECT.res
                                                                  • hr.res
                                                                  • hr_HR.res
                                                                  • hu.res
                                                                  • hu_HU.res
                                                                  • id.res
                                                                  • id_ID.res
                                                                  • is.res
                                                                  • is_IS.res
                                                                  • it.res
                                                                  • it_CH.res
                                                                  • it_IT.res
                                                                  • ja.res
                                                                  • ja_JP.res
                                                                  • kk.res
                                                                  • kk_KZ.res
                                                                  • kl.res
                                                                  • kl_GL.res
                                                                  • kn.res
                                                                  • kn_IN.res
                                                                  • ko.res
                                                                  • ko_KR.res
                                                                  • lt.res
                                                                  • lt_LT.res
                                                                  • lv.res
                                                                  • lv_LV.res
                                                                  • mk.res
                                                                  • mk_MK.res
                                                                  • ml.res
                                                                  • mr.res
                                                                  • mr_IN.res
                                                                  • ms.res
                                                                  • ms_BN.res
                                                                  • ms_MY.res
                                                                  • mt.res
                                                                  • mt_MT.res
                                                                  • nb.res
                                                                  • nb_NO.res
                                                                  • nl.res
                                                                  • nl_BE.res
                                                                  • nl_NL.res
                                                                  • nn.res
                                                                  • nn_NO.res
                                                                  • om.res
                                                                  • om_ET.res
                                                                  • om_KE.res
                                                                  • or.res
                                                                  • pa.res
                                                                  • pa_IN.res
                                                                  • pl.res
                                                                  • pl_PL.res
                                                                  • ps.res
                                                                  • ps_AF.res
                                                                  • pt.res
                                                                  • pt_BR.res
                                                                  • pt_PT.res
                                                                  • res_index.res
                                                                  • res_index.txt
                                                                  • ro.res
                                                                  • root.res
                                                                  • ro_RO.res
                                                                  • ru.res
                                                                  • ru_RU.res
                                                                  • ru_UA.res
                                                                  • sh.res
                                                                  • sh_BA.res
                                                                  • sh_YU.res
                                                                  • sk.res
                                                                  • sk_SK.res
                                                                  • sl.res
                                                                  • sl_SI.res
                                                                  • sq.res
                                                                  • sq_AL.res
                                                                  • sr.res
                                                                  • sr_BA.res
                                                                  • sr_Cyrl.res
                                                                  • sr_Cyrl_BA.res
                                                                  • sr_Cyrl_YU.res
                                                                  • sr_YU.res
                                                                  • sv.res
                                                                  • sv_FI.res
                                                                  • sv_SE.res
                                                                  • ta.res
                                                                  • ta_IN.res
                                                                  • te.res
                                                                  • te_IN.res
                                                                  • th.res
                                                                  • th_TH.res
                                                                  • tr.res
                                                                  • tr_TR.res
                                                                  • uk.res
                                                                  • uk_UA.res
                                                                  • vi.res
                                                                  • vi_VN.res
                                                                  • zh.res
                                                                  • zh_CN.res
                                                                  • zh_Hant.res
                                                                  • zh_HK.res
                                                                  • zh_MO.res
                                                                  • zh_SG.res
                                                                  • zh_TW.res
                                                                  • zh_TW_STROKE.res
                                                                  • zh__PINYIN.res
                                                                • cs.res
                                                                • cs_CZ.res
                                                                • CurrencyData.res
                                                                • cy.res
                                                                • cy_GB.res
                                                                • da.res
                                                                • da_DK.res
                                                                • de.res
                                                                • de_AT.res
                                                                • de_BE.res
                                                                • de_CH.res
                                                                • de_DE.res
                                                                • de_LU.res
                                                                • el.res
                                                                • el_GR.res
                                                                • en.res
                                                                • en_AU.res
                                                                • en_BE.res
                                                                • en_BW.res
                                                                • en_CA.res
                                                                • en_GB.res
                                                                • en_HK.res
                                                                • en_IE.res
                                                                • en_IN.res
                                                                • en_MT.res
                                                                • en_NZ.res
                                                                • en_PH.res
                                                                • en_PK.res
                                                                • en_SG.res
                                                                • en_US.res
                                                                • en_US_POSIX.res
                                                                • en_VI.res
                                                                • en_ZA.res
                                                                • en_ZW.res
                                                                • eo.res
                                                                • es.res
                                                                • es_AR.res
                                                                • es_BO.res
                                                                • es_CL.res
                                                                • es_CO.res
                                                                • es_CR.res
                                                                • es_DO.res
                                                                • es_EC.res
                                                                • es_ES.res
                                                                • es_GT.res
                                                                • es_HN.res
                                                                • es_MX.res
                                                                • es_NI.res
                                                                • es_PA.res
                                                                • es_PE.res
                                                                • es_PR.res
                                                                • es_PY.res
                                                                • es_SV.res
                                                                • es_US.res
                                                                • es_UY.res
                                                                • es_VE.res
                                                                • et.res
                                                                • et_EE.res
                                                                • eu.res
                                                                • eu_ES.res
                                                                • fa.res
                                                                • fa_AF.res
                                                                • fa_IR.res
                                                                • fi.res
                                                                • fi_FI.res
                                                                • fo.res
                                                                • fo_FO.res
                                                                • fr.res
                                                                • fr_BE.res
                                                                • fr_CA.res
                                                                • fr_CH.res
                                                                • fr_FR.res
                                                                • fr_LU.res
                                                                • ga.res
                                                                • ga_IE.res
                                                                • gl.res
                                                                • gl_ES.res
                                                                • gu.res
                                                                • gu_IN.res
                                                                • gv.res
                                                                • gv_GB.res
                                                                • he.res
                                                                • he_IL.res
                                                                • hi.res
                                                                • hi_IN.res
                                                                • hr.res
                                                                • hr_HR.res
                                                                • hu.res
                                                                • hu_HU.res
                                                                • hy.res
                                                                • hy_AM.res
                                                                • hy_AM_REVISED.res
                                                                • id.res
                                                                • id_ID.res
                                                                • in.res
                                                                • invuca.icu
                                                                • in_ID.res
                                                                • is.res
                                                                • is_IS.res
                                                                • it.res
                                                                • it_CH.res
                                                                • it_IT.res
                                                                • iw.res
                                                                • iw_IL.res
                                                                • ja.res
                                                                • ja_JP.res
                                                                • ja_JP_TRADITIONAL.res
                                                                • kk.res
                                                                • kk_KZ.res
                                                                • kl.res
                                                                • kl_GL.res
                                                                • kn.res
                                                                • kn_IN.res
                                                                • ko.res
                                                                • kok.res
                                                                • kok_IN.res
                                                                • ko_KR.res
                                                                • kw.res
                                                                • kw_GB.res
                                                                • line.brk
                                                                • line_th.brk
                                                                • lt.res
                                                                • lt_LT.res
                                                                • lv.res
                                                                • lv_LV.res
                                                                • mk.res
                                                                • mk_MK.res
                                                                • ml.res
                                                                • ml_IN.res
                                                                • mr.res
                                                                • mr_IN.res
                                                                • ms.res
                                                                • ms_BN.res
                                                                • ms_MY.res
                                                                • mt.res
                                                                • mt_MT.res
                                                                • nb.res
                                                                • nb_NO.res
                                                                • nl.res
                                                                • nl_BE.res
                                                                • nl_NL.res
                                                                • nn.res
                                                                • nn_NO.res
                                                                • no.res
                                                                • no_NO.res
                                                                • no_NO_NY.res
                                                                • om.res
                                                                • om_ET.res
                                                                • om_KE.res
                                                                • or.res
                                                                • or_IN.res
                                                                • pa.res
                                                                • pa_IN.res
                                                                • pl.res
                                                                • pl_PL.res
                                                                • pnames.icu
                                                                • ps.res
                                                                • ps_AF.res
                                                                • pt.res
                                                                • pt_BR.res
                                                                • pt_PT.res
                                                                • rbnf
                                                                  • da.res
                                                                  • de.res
                                                                  • en.res
                                                                  • en_GB.res
                                                                  • eo.res
                                                                  • es.res
                                                                  • fa.res
                                                                  • fa_AF.res
                                                                  • fr.res
                                                                  • fr_BE.res
                                                                  • fr_CH.res
                                                                  • ga.res
                                                                  • he.res
                                                                  • it.res
                                                                  • ja.res
                                                                  • mt.res
                                                                  • nl.res
                                                                  • pl.res
                                                                  • pt.res
                                                                  • res_index.res
                                                                  • res_index.txt
                                                                  • root.res
                                                                  • ru.res
                                                                  • sv.res
                                                                  • th.res
                                                                  • uk.res
                                                                • res_index.res
                                                                • res_index.txt
                                                                • ro.res
                                                                • root.res
                                                                • ro_RO.res
                                                                • ru.res
                                                                • ru_RU.res
                                                                • ru_UA.res
                                                                • sent.brk
                                                                • sh.res
                                                                • sh_CS.res
                                                                • sh_YU.res
                                                                • sk.res
                                                                • sk_SK.res
                                                                • sl.res
                                                                • sl_SI.res
                                                                • so.res
                                                                • so_DJ.res
                                                                • so_ET.res
                                                                • so_KE.res
                                                                • so_SO.res
                                                                • sq.res
                                                                • sq_AL.res
                                                                • sr.res
                                                                • sr_CS.res
                                                                • sr_Cyrl.res
                                                                • sr_Cyrl_CS.res
                                                                • sr_Cyrl_YU.res
                                                                • sr_Latn.res
                                                                • sr_Latn_CS.res
                                                                • sr_Latn_YU.res
                                                                • sr_YU.res
                                                                • sv.res
                                                                • sv_FI.res
                                                                • sv_SE.res
                                                                • sw.res
                                                                • sw_KE.res
                                                                • sw_TZ.res
                                                                • ta.res
                                                                • ta_IN.res
                                                                • te.res
                                                                • te_IN.res
                                                                • th.res
                                                                • th_TH.res
                                                                • th_TH_TRADITIONAL.res
                                                                • ti.res
                                                                • title.brk
                                                                • ti_ER.res
                                                                • ti_ET.res
                                                                • tr.res
                                                                • translit
                                                                  • el.res
                                                                  • en.res
                                                                  • res_index.txt
                                                                  • root.res
                                                                • tr_TR.res
                                                                • ubidi.icu
                                                                • ucadata.icu
                                                                • ucase.icu
                                                                • uidna.spp
                                                                • uk.res
                                                                • uk_UA.res
                                                                • unames.icu
                                                                • unorm.icu
                                                                • uprops.icu
                                                                • ur.res
                                                                • ur_PK.res
                                                                • uz.res
                                                                • uz_Cyrl.res
                                                                • uz_Cyrl_UZ.res
                                                                • uz_Latn.res
                                                                • uz_Latn_UZ.res
                                                                • uz_UZ.res
                                                                • vi.res
                                                                • vi_VN.res
                                                                • word.brk
                                                                • word_ja.brk
                                                                • word_POSIX.brk
                                                                • word_th.brk
                                                                • zh.res
                                                                • zh_CN.res
                                                                • zh_Hans.res
                                                                • zh_Hans_CN.res
                                                                • zh_Hans_SG.res
                                                                • zh_Hant.res
                                                                • zh_Hant_HK.res
                                                                • zh_Hant_MO.res
                                                                • zh_Hant_TW.res
                                                                • zh_HK.res
                                                                • zh_MO.res
                                                                • zh_SG.res
                                                                • zh_TW.res
                                                              • ResourceReader.java
                                                              • th.brk
                                                              • TokenIterator.java
                                                            • ICUBinary.java
                                                            • ICUBinaryStream.java
                                                            • ICUData.java
                                                            • ICUDebug.java
                                                            • ICUListResourceBundle.java
                                                            • ICULocaleData.java
                                                            • ICULocaleService.java
                                                            • ICUNotifier.java
                                                            • ICUResourceBundle.java
                                                            • ICUResourceBundleImpl.java
                                                            • ICUResourceBundleIterator.java
                                                            • ICUResourceBundleReader.java
                                                            • ICURWLock.java
                                                            • ICUService.java
                                                            • ImplicitCEGenerator.java
                                                            • IntTrie.java
                                                            • IntTrieBuilder.java
                                                            • JDKTimeZone.java
                                                            • LocaleUtility.java
                                                            • NormalizerDataReader.java
                                                            • NormalizerImpl.java
                                                            • ReplaceableUCharacterIterator.java
                                                            • ResourceBundleWrapper.java
                                                            • RuleCharacterIterator.java
                                                            • SortedSetRelation.java
                                                            • StringPrepDataReader.java
                                                            • StringUCharacterIterator.java
                                                            • TimeZoneAdapter.java
                                                            • Trie.java
                                                            • TrieBuilder.java
                                                            • TrieIterator.java
                                                            • UBiDiProps.java
                                                            • UCaseProps.java
                                                            • UCharacterIteratorWrapper.java
                                                            • UCharacterName.java
                                                            • UCharacterNameChoice.java
                                                            • UCharacterNameReader.java
                                                            • UCharacterProperty.java
                                                            • UCharacterPropertyReader.java
                                                            • UCharacterUtility.java
                                                            • UCharArrayIterator.java
                                                            • UPropertyAliases.java
                                                            • URLHandler.java
                                                            • USerializedSet.java
                                                            • UTF32.java
                                                            • Utility.java
                                                            • UtilityExtensions.java
                                                            • ZoneInfoExt.java
                                                            • ZoneMeta.java
                                                            • ZoneMetaData.java
                                                          • lang
                                                            • UCharacter.java
                                                            • UCharacterCategory.java
                                                            • UCharacterDirection.java
                                                            • UCharacterEnums.java
                                                            • UCharacterNameIterator.java
                                                            • UCharacterTypeIterator.java
                                                            • UProperty.java
                                                            • UScript.java
                                                            • UScriptRun.java
                                                          • math
                                                            • BigDecimal.java
                                                            • MathContext.java
                                                          • text
                                                            • AbsoluteValueSubstitution.java
                                                            • AnyTransliterator.java
                                                            • ArabicShaping.java
                                                            • ArabicShapingException.java
                                                            • BreakDictionary.java
                                                            • BreakIterator.java
                                                            • BreakIteratorFactory.java
                                                            • BreakTransliterator.java
                                                            • CanonicalIterator.java
                                                            • CharsetDetector.java
                                                            • CharsetMatch.java
                                                            • CharsetRecognizer.java
                                                            • CharsetRecog_2022.java
                                                            • CharsetRecog_mbcs.java
                                                            • CharsetRecog_sbcs.java
                                                            • CharsetRecog_Unicode.java
                                                            • CharsetRecog_UTF8.java
                                                            • ChineseDateFormat.java
                                                            • ChineseDateFormatSymbols.java
                                                            • CollationElementIterator.java
                                                            • CollationKey.java
                                                            • CollationParsedRuleBuilder.java
                                                            • CollationRuleParser.java
                                                            • Collator.java
                                                            • CollatorReader.java
                                                            • CollatorServiceShim.java
                                                            • ComposedCharIter.java
                                                            • CompoundTransliterator.java
                                                            • CurrencyFormat.java
                                                            • DateFormat.java
                                                            • DateFormatSymbols.java
                                                            • DecimalFormat.java
                                                            • DecimalFormatSymbols.java
                                                            • DecompData.java
                                                            • DictionaryBasedBreakIterator.java
                                                            • DigitList.java
                                                            • EscapeTransliterator.java
                                                            • FractionalPartSubstitution.java
                                                            • FunctionReplacer.java
                                                            • IDNA.java
                                                            • IntegralPartSubstitution.java
                                                            • LowercaseTransliterator.java
                                                            • MeasureFormat.java
                                                            • MessageFormat.java
                                                            • ModulusSubstitution.java
                                                            • MultiplierSubstitution.java
                                                            • NameUnicodeTransliterator.java
                                                            • NFRule.java
                                                            • NFRuleSet.java
                                                            • NFSubstitution.java
                                                            • NormalizationTransliterator.java
                                                            • Normalizer.java
                                                            • NullSubstitution.java
                                                            • NullTransliterator.java
                                                            • NumberFormat.java
                                                            • NumberFormatServiceShim.java
                                                            • NumeratorSubstitution.java
                                                            • Punycode.java
                                                            • Quantifier.java
                                                            • RawCollationKey.java
                                                            • RBBIDataWrapper.java
                                                            • RBNFChinesePostProcessor.java
                                                            • RBNFPostProcessor.java
                                                            • RemoveTransliterator.java
                                                            • Replaceable.java
                                                            • ReplaceableContextIterator.java
                                                            • ReplaceableString.java
                                                            • RuleBasedBreakIterator.java
                                                            • RuleBasedBreakIterator_New.java
                                                            • RuleBasedBreakIterator_Old.java
                                                            • RuleBasedCollator.java
                                                            • RuleBasedNumberFormat.java
                                                            • RuleBasedTransliterator.java
                                                            • SameValueSubstitution.java
                                                            • SCSU.java
                                                            • SearchIterator.java
                                                            • SimpleDateFormat.java
                                                            • StringCharacterIterator.java
                                                            • StringMatcher.java
                                                            • StringPrep.java
                                                            • StringPrepParseException.java
                                                            • StringReplacer.java
                                                            • StringSearch.java
                                                            • SymbolTable.java
                                                            • TitlecaseTransliterator.java
                                                            • TransformTransliterator.java
                                                            • TransliterationRule.java
                                                            • TransliterationRuleSet.java
                                                            • Transliterator.java
                                                            • TransliteratorIDParser.java
                                                            • TransliteratorParser.java
                                                            • TransliteratorRegistry.java
                                                            • UCharacterIterator.java
                                                            • UFormat.java
                                                            • UForwardCharacterIterator.java
                                                            • UnescapeTransliterator.java
                                                            • UnicodeCompressor.java
                                                            • UnicodeDecompressor.java
                                                            • UnicodeFilter.java
                                                            • UnicodeMatcher.java
                                                            • UnicodeNameTransliterator.java
                                                            • UnicodeReplacer.java
                                                            • UnicodeSet.java
                                                            • UnicodeSetIterator.java
                                                            • UppercaseTransliterator.java
                                                            • UTF16.java
                                                          • util
                                                            • BuddhistCalendar.java
                                                            • ByteArrayWrapper.java
                                                            • Calendar.java
                                                            • CalendarFactory.java
                                                            • CaseInsensitiveString.java
                                                            • CECalendar.java
                                                            • ChineseCalendar.java
                                                            • CompactByteArray.java
                                                            • CompactCharArray.java
                                                            • CopticCalendar.java
                                                            • Currency.java
                                                            • CurrencyAmount.java
                                                            • CurrencyServiceShim.java
                                                            • DateRule.java
                                                            • EasterHoliday.java
                                                            • EasterRule.java
                                                            • EthiopicCalendar.java
                                                            • GregorianCalendar.java
                                                            • HebrewCalendar.java
                                                            • HebrewHoliday.java
                                                            • Holiday.java
                                                            • IslamicCalendar.java
                                                            • JapaneseCalendar.java
                                                            • LocaleData.java
                                                            • Measure.java
                                                            • MeasureUnit.java
                                                            • OverlayBundle.java
                                                            • Range.java
                                                            • RangeDateRule.java
                                                            • RangeValueIterator.java
                                                            • SimpleDateRule.java
                                                            • SimpleHoliday.java
                                                            • SimpleTimeZone.java
                                                            • StringTokenizer.java
                                                            • STZInfo.java
                                                            • TimeZone.java
                                                            • ULocale.java
                                                            • UniversalTimeScale.java
                                                            • UResourceBundle.java
                                                            • UResourceTypeMismatchException.java
                                                            • ValueIterator.java
                                                            • VersionInfo.java
                                                    • control.javafiles
                                                    • core.javafiles
                                                    • data.javafiles
                                                    • datadebug.javafiles
                                                    • dict.javafiles
                                                    • diff.javafiles
                                                    • etc
                                                      • daml-micro.rules
                                                      • db-default-drivers.n3
                                                      • derby.sql
                                                      • dig-daml-axioms.rdf
                                                      • dig-owl-axioms.rdf
                                                      • generic_generic.sql
                                                      • hsql.sql
                                                      • location-mapping.ex
                                                      • mssql.sql
                                                      • mysql.sql
                                                      • ont-policy-test.rdf
                                                      • ont-policy.rdf
                                                      • oracle.sql
                                                      • owl-b.rules
                                                      • owl-fb-micro.rules
                                                      • owl-fb-mini.rules
                                                      • owl-fb-old.rules
                                                      • owl-fb.rules
                                                      • owl.rules
                                                      • postgresql.sql
                                                      • rdfs-b-tuned.rules
                                                      • rdfs-b.rules
                                                      • rdfs-fb-lp-expt.rules
                                                      • rdfs-fb-tgc-noresource.rules
                                                      • rdfs-fb-tgc-simple.rules
                                                      • rdfs-fb-tgc.rules
                                                      • rdfs-fb.rules
                                                      • rdfs-noresource.rules
                                                      • rdfs.rules
                                                      • schemagen.rdf
                                                      • test.sql
                                                    • extra.javafiles
                                                    • fingerprint.javafiles
                                                    • forcefield.javafiles
                                                    • formula.javafiles
                                                    • inchi.javafiles
                                                    • interfaces.javafiles
                                                    • io-formats.set
                                                    • io.javafiles
                                                    • ioformats.javafiles
                                                    • ionpot.javafiles
                                                    • iordf.javafiles
                                                    • isomorphism.javafiles
                                                    • Jama
                                                      • CholeskyDecomposition.java
                                                      • EigenvalueDecomposition.java
                                                      • LUDecomposition.java
                                                      • Matrix.java
                                                      • QRDecomposition.java
                                                      • SingularValueDecomposition.java
                                                      • util
                                                        • Maths.java
                                                    • javax
                                                      • vecmath
                                                        • AxisAngle4d.java
                                                        • AxisAngle4f.java
                                                        • Color3b.java
                                                        • Color3f.java
                                                        • Color4b.java
                                                        • Color4f.java
                                                        • GMatrix.java
                                                        • GVector.java
                                                        • Matrix3d.java
                                                        • Matrix3f.java
                                                        • Matrix4d.java
                                                        • Matrix4f.java
                                                        • MismatchedSizeException.java
                                                        • Point2d.java
                                                        • Point2f.java
                                                        • Point3d.java
                                                        • Point3f.java
                                                        • Point3i.java
                                                        • Point4d.java
                                                        • Point4f.java
                                                        • Point4i.java
                                                        • Quat4d.java
                                                        • Quat4f.java
                                                        • SingularMatrixException.java
                                                        • TexCoord2f.java
                                                        • TexCoord3f.java
                                                        • Tuple2d.java
                                                        • Tuple2f.java
                                                        • Tuple3b.java
                                                        • Tuple3d.java
                                                        • Tuple3f.java
                                                        • Tuple3i.java
                                                        • Tuple4b.java
                                                        • Tuple4d.java
                                                        • Tuple4f.java
                                                        • Tuple4i.java
                                                        • VecmathTest.java
                                                        • Vector2d.java
                                                        • Vector2f.java
                                                        • Vector3d.java
                                                        • Vector3f.java
                                                        • Vector4d.java
                                                        • Vector4f.java
                                                      • xml
                                                        • namespace
                                                          • QName.java
                                                    • jena
                                                      • cmdline
                                                        • Arg.java
                                                        • ArgDecl.java
                                                        • ArgHandler.java
                                                        • CmdLineUtils.java
                                                        • CommandLine.java
                                                      • dbcreate.java
                                                      • dbdump.java
                                                      • dblist.java
                                                      • dbload.java
                                                      • dbquery.java
                                                      • dbremove.java
                                                      • juuid.java
                                                      • qtest.java
                                                      • query.java
                                                      • rdfcat.java
                                                      • rdfcompare.java
                                                      • rdfcopy.java
                                                      • rdfparse.java
                                                      • rset.java
                                                      • RuleMap.java
                                                      • schemagen.java
                                                      • sparql.java
                                                      • test
                                                        • turtle.java
                                                        • util
                                                          • DBcmd.java
                                                        • version.java
                                                      • libio-cml-customizers.set
                                                      • libiocml.javafiles
                                                      • libiomd.javafiles
                                                      • log4j.javafiles
                                                      • log4j.properties
                                                      • META-INF
                                                        • INDEX.LIST
                                                        • jnati
                                                          • jnati.default-properties
                                                          • jnati.instance.default-properties
                                                          • system.txt
                                                        • jniinchi
                                                          • 1.03_1
                                                            • FREEBSD-AMD64
                                                              • libJniInchi-1.03_1-FREEBSD-AMD64.so
                                                              • MANIFEST.xml
                                                            • LINUX-AMD64
                                                              • libJniInchi-1.03_1-LINUX-AMD64.so
                                                              • MANIFEST.xml
                                                            • LINUX-X86
                                                              • libJniInchi-1.03_1-LINUX-X86.so
                                                              • MANIFEST.xml
                                                            • MAC-X86_64
                                                              • JniInchi-1.03_1-MAC-X86_64
                                                              • MANIFEST.xml
                                                            • WINDOWS-AMD64
                                                              • JniInchi-1.03_1-WINDOWS-AMD64.dll
                                                              • MANIFEST.xml
                                                            • WINDOWS-X86
                                                              • JniInchi-1.03_1-WINDOWS-X86.dll
                                                              • MANIFEST.xml
                                                        • LICENSE
                                                        • LICENSE.txt
                                                        • MANIFEST.MF
                                                        • maven
                                                          • cml
                                                            • cmlxom
                                                              • pom.properties
                                                              • pom.xml
                                                          • commons-logging
                                                            • commons-logging
                                                              • pom.properties
                                                              • pom.xml
                                                          • log4j
                                                            • log4j
                                                              • pom.properties
                                                              • pom.xml
                                                          • net.sf.jnati
                                                            • jnati-core
                                                              • pom.properties
                                                              • pom.xml
                                                            • jnati-deploy
                                                              • pom.properties
                                                              • pom.xml
                                                          • org.slf4j
                                                            • slf4j-api
                                                              • pom.properties
                                                              • pom.xml
                                                            • slf4j-simple
                                                              • pom.properties
                                                              • pom.xml
                                                          • signatures
                                                            • signatures
                                                              • pom.properties
                                                              • pom.xml
                                                        • NOTICE
                                                        • services
                                                          • org.xmlpull.v1.XmlPullParserFactory
                                                      • net
                                                        • sf
                                                          • jnati
                                                            • ArtefactDescriptor.java
                                                            • config
                                                              • Configuration.java
                                                              • ResolvingProperties.java
                                                            • deploy
                                                              • artefact
                                                                • Artefact.java
                                                                • ArtefactFile.java
                                                                • ConfigManager.java
                                                                • ManifestReader.java
                                                              • NativeArtefactLocator.java
                                                              • NativeLibraryLoader.java
                                                              • repository
                                                                • ArtefactRepository.java
                                                                • ClasspathRepository.java
                                                                • LocalRepository.java
                                                                • RemoteRepository.java
                                                              • resolver
                                                                • ArtefactNotFoundException.java
                                                                • ArtefactResolver.java
                                                                • ConfigurationException.java
                                                              • source
                                                                • ArtefactSource.java
                                                                • FileSource.java
                                                                • JarSource.java
                                                                • TempJarSource.java
                                                                • UrlSource.java
                                                            • FileUtils.java
                                                            • NativeCodeException.java
                                                            • SystemType.java
                                                            • SystemTyper.java
                                                          • jniinchi
                                                            • INCHI_BOND_STEREO.java
                                                            • INCHI_BOND_TYPE.java
                                                            • INCHI_KEY.java
                                                            • INCHI_KEY_STATUS.java
                                                            • INCHI_OPTION.java
                                                            • INCHI_PARITY.java
                                                            • INCHI_RADICAL.java
                                                            • INCHI_RET.java
                                                            • INCHI_STATUS.java
                                                            • INCHI_STEREOTYPE.java
                                                            • JniInchiAtom.java
                                                            • JniInchiBond.java
                                                            • JniInchiException.java
                                                            • JniInchiInput.java
                                                            • JniInchiInputData.java
                                                            • JniInchiInputInchi.java
                                                            • JniInchiOutput.java
                                                            • JniInchiOutputKey.java
                                                            • JniInchiOutputStructure.java
                                                            • JniInchiStereo0D.java
                                                            • JniInchiStructure.java
                                                            • JniInchiWrapper.java
                                                            • LoadNativeLibraryException.java
                                                            • Main.java
                                                      • nonotify.javafiles
                                                      • nu
                                                        • xom
                                                          • ASCIIWriter.java
                                                          • Attribute.java
                                                          • benchmarks
                                                            • Builder.java
                                                            • canonical
                                                              • CanonicalizationException.java
                                                              • Canonicalizer.java
                                                            • CDATASection.java
                                                            • characters.dat
                                                            • Comment.java
                                                            • compositions.dat
                                                            • converters
                                                              • DOMConverter.java
                                                              • SAXConverter.java
                                                            • CycleException.java
                                                            • DocType.java
                                                            • Document.java
                                                            • DocumentFragment.java
                                                            • EBCDICWriter.java
                                                            • Element.java
                                                            • Elements.java
                                                            • GenericWriter.java
                                                            • IllegalAddException.java
                                                            • IllegalCharacterDataException.java
                                                            • IllegalDataException.java
                                                            • IllegalNameException.java
                                                            • IllegalTargetException.java
                                                            • Info.java
                                                            • ISOArabicWriter.java
                                                            • ISOCyrillicWriter.java
                                                            • ISOGreekWriter.java
                                                            • ISOHebrewWriter.java
                                                            • ISOThaiWriter.java
                                                            • JaxenConnector.java
                                                            • JaxenNavigator.java
                                                            • JDK15XML1_0Parser.java
                                                            • Latin10Writer.java
                                                            • Latin1Writer.java
                                                            • Latin2Writer.java
                                                            • Latin3Writer.java
                                                            • Latin4Writer.java
                                                            • Latin5Writer.java
                                                            • Latin6Writer.java
                                                            • Latin7Writer.java
                                                            • Latin8Writer.java
                                                            • Latin9Writer.java
                                                            • MalformedURIException.java
                                                            • MultipleParentException.java
                                                            • Namespace.java
                                                            • NamespaceConflictException.java
                                                            • Namespaces.java
                                                            • Node.java
                                                            • NodeFactory.java
                                                            • Nodes.java
                                                            • NonVerifyingHandler.java
                                                            • NoSuchAttributeException.java
                                                            • NoSuchChildException.java
                                                            • ParentNode.java
                                                            • ParsingException.java
                                                            • ProcessingInstruction.java
                                                            • samples
                                                              • Serializer.java
                                                              • tests
                                                                • XOMTestCase.java
                                                              • Text.java
                                                              • TextWriter.java
                                                              • TextWriterFactory.java
                                                              • UCSWriter.java
                                                              • UnavailableCharacterException.java
                                                              • UnicodeUtil.java
                                                              • UnicodeWriter.java
                                                              • UnsynchronizedBufferedWriter.java
                                                              • URIUtil.java
                                                              • ValidityException.java
                                                              • Verifier.java
                                                              • WellformednessException.java
                                                              • xinclude
                                                                • BadEncodingAttributeException.java
                                                                • BadHrefAttributeException.java
                                                                • BadHTTPHeaderException.java
                                                                • BadParseAttributeException.java
                                                                • EncodingHeuristics.java
                                                                • InclusionLoopException.java
                                                                • MisplacedFallbackException.java
                                                                • NoIncludeLocationException.java
                                                                • XIncludeException.java
                                                                • XIncluder.java
                                                                • XPointer.java
                                                                • XPointerException.java
                                                                • XPointerResourceException.java
                                                                • XPointerSyntaxException.java
                                                              • XML1_0Parser.java
                                                              • XMLException.java
                                                              • XOMHandler.java
                                                              • XPathContext.java
                                                              • XPathException.java
                                                              • XPathTypeException.java
                                                              • xslt
                                                                • XOMInputSource.java
                                                                • XOMReader.java
                                                                • XOMResult.java
                                                                • XOMSource.java
                                                                • XSLException.java
                                                                • XSLTHandler.java
                                                                • XSLTransform.java
                                                          • org
                                                            • apache
                                                              • commons
                                                                • cli
                                                                  • AlreadySelectedException.java
                                                                  • BasicParser.java
                                                                  • CommandLine.java
                                                                  • CommandLineParser.java
                                                                  • GnuParser.java
                                                                  • HelpFormatter.java
                                                                  • MissingArgumentException.java
                                                                  • MissingOptionException.java
                                                                  • Option.java
                                                                  • OptionBuilder.java
                                                                  • OptionGroup.java
                                                                  • Options.java
                                                                  • ParseException.java
                                                                  • Parser.java
                                                                  • PatternOptionBuilder.java
                                                                  • PosixParser.java
                                                                  • TypeHandler.java
                                                                  • UnrecognizedOptionException.java
                                                                • logging
                                                                  • impl
                                                                    • AvalonLogger.java
                                                                    • Jdk13LumberjackLogger.java
                                                                    • Jdk14Logger.java
                                                                    • Log4JLogger.java
                                                                    • LogFactoryImpl.java
                                                                    • LogKitLogger.java
                                                                    • NoOpLog.java
                                                                    • ServletContextCleaner.java
                                                                    • SimpleLog.java
                                                                    • WeakHashtable.java
                                                                  • Log.java
                                                                  • LogConfigurationException.java
                                                                  • LogFactory.java
                                                                  • LogSource.java
                                                              • log4j
                                                                • Appender.java
                                                                • AppenderSkeleton.java
                                                                • AsyncAppender.java
                                                                • BasicConfigurator.java
                                                                • Category.java
                                                                • CategoryKey.java
                                                                • chainsaw
                                                                  • ControlPanel.java
                                                                  • DetailPanel.java
                                                                  • EventDetails.java
                                                                  • ExitAction.java
                                                                  • LoadXMLAction.java
                                                                  • LoggingReceiver.java
                                                                  • Main.java
                                                                  • MyTableModel.java
                                                                  • XMLFileHandler.java
                                                                • config
                                                                  • PropertyGetter.java
                                                                  • PropertyPrinter.java
                                                                  • PropertySetter.java
                                                                  • PropertySetterException.java
                                                                • ConsoleAppender.java
                                                                • DailyRollingFileAppender.java
                                                                • DefaultCategoryFactory.java
                                                                • Dispatcher.java
                                                                • FileAppender.java
                                                                • helpers
                                                                  • AbsoluteTimeDateFormat.java
                                                                  • AppenderAttachableImpl.java
                                                                  • BoundedFIFO.java
                                                                  • CountingQuietWriter.java
                                                                  • CyclicBuffer.java
                                                                  • DateLayout.java
                                                                  • DateTimeDateFormat.java
                                                                  • FileWatchdog.java
                                                                  • FormattingInfo.java
                                                                  • ISO8601DateFormat.java
                                                                  • Loader.java
                                                                  • LogLog.java
                                                                  • NullEnumeration.java
                                                                  • OnlyOnceErrorHandler.java
                                                                  • OptionConverter.java
                                                                  • PatternConverter.java
                                                                  • PatternParser.java
                                                                  • QuietWriter.java
                                                                  • RelativeTimeDateFormat.java
                                                                  • SyslogQuietWriter.java
                                                                  • SyslogWriter.java
                                                                  • ThreadLocalMap.java
                                                                  • Transform.java
                                                                • Hierarchy.java
                                                                • HTMLLayout.java
                                                                • jdbc
                                                                  • JDBCAppender.java
                                                                • jmx
                                                                  • AbstractDynamicMBean.java
                                                                  • Agent.java
                                                                  • AppenderDynamicMBean.java
                                                                  • HierarchyDynamicMBean.java
                                                                  • LayoutDynamicMBean.java
                                                                  • LoggerDynamicMBean.java
                                                                  • MethodUnion.java
                                                                • Layout.java
                                                                • Level.java
                                                                • lf5
                                                                  • AppenderFinalizer.java
                                                                  • config
                                                                    • defaultconfig.properties
                                                                  • DefaultLF5Configurator.java
                                                                  • LF5Appender.java
                                                                  • Log4JLogRecord.java
                                                                  • LogLevel.java
                                                                  • LogLevelFormatException.java
                                                                  • LogRecord.java
                                                                  • LogRecordFilter.java
                                                                  • PassingLogRecordFilter.java
                                                                  • StartLogFactor5.java
                                                                  • util
                                                                    • AdapterLogRecord.java
                                                                    • DateFormatManager.java
                                                                    • LogFileParser.java
                                                                    • LogMonitorAdapter.java
                                                                    • Resource.java
                                                                    • ResourceUtils.java
                                                                    • StreamUtils.java
                                                                  • viewer
                                                                    • categoryexplorer
                                                                      • CategoryAbstractCellEditor.java
                                                                      • CategoryElement.java
                                                                      • CategoryExplorerLogRecordFilter.java
                                                                      • CategoryExplorerModel.java
                                                                      • CategoryExplorerTree.java
                                                                      • CategoryImmediateEditor.java
                                                                      • CategoryNode.java
                                                                      • CategoryNodeEditor.java
                                                                      • CategoryNodeEditorRenderer.java
                                                                      • CategoryNodeRenderer.java
                                                                      • CategoryPath.java
                                                                      • TreeModelAdapter.java
                                                                    • configure
                                                                      • ConfigurationManager.java
                                                                      • MRUFileManager.java
                                                                    • FilteredLogTableModel.java
                                                                    • images
                                                                      • channelexplorer_new.gif
                                                                      • channelexplorer_satellite.gif
                                                                      • lf5_small_icon.gif
                                                                    • LF5SwingUtils.java
                                                                    • LogBrokerMonitor.java
                                                                    • LogFactor5Dialog.java
                                                                    • LogFactor5ErrorDialog.java
                                                                    • LogFactor5InputDialog.java
                                                                    • LogFactor5LoadingDialog.java
                                                                    • LogTable.java
                                                                    • LogTableColumn.java
                                                                    • LogTableColumnFormatException.java
                                                                    • LogTableModel.java
                                                                    • LogTableRowRenderer.java
                                                                    • TrackingAdjustmentListener.java
                                                                • Logger.java
                                                                • LogManager.java
                                                                • MDC.java
                                                                • NDC.java
                                                                • net
                                                                  • DefaultEvaluator.java
                                                                  • JMSAppender.java
                                                                  • JMSSink.java
                                                                  • SimpleSocketServer.java
                                                                  • SMTPAppender.java
                                                                  • SocketAppender.java
                                                                  • SocketHubAppender.java
                                                                  • SocketNode.java
                                                                  • SocketServer.java
                                                                  • SyslogAppender.java
                                                                  • TelnetAppender.java
                                                                • nt
                                                                  • NTEventLogAppender.java
                                                                • or
                                                                  • DefaultRenderer.java
                                                                  • jms
                                                                    • MessageRenderer.java
                                                                  • ObjectRenderer.java
                                                                  • RendererMap.java
                                                                  • sax
                                                                    • AttributesRenderer.java
                                                                  • ThreadGroupRenderer.java
                                                                • PatternLayout.java
                                                                • Priority.java
                                                                • PropertyConfigurator.java
                                                                • PropertyWatchdog.java
                                                                • ProvisionNode.java
                                                                • RollingCalendar.java
                                                                • RollingFileAppender.java
                                                                • SimpleLayout.java
                                                                • spi
                                                                  • AppenderAttachable.java
                                                                  • Configurator.java
                                                                  • DefaultRepositorySelector.java
                                                                  • ErrorCode.java
                                                                  • ErrorHandler.java
                                                                  • Filter.java
                                                                  • HierarchyEventListener.java
                                                                  • LocationInfo.java
                                                                  • LoggerFactory.java
                                                                  • LoggerRepository.java
                                                                  • LoggingEvent.java
                                                                  • NOPLogger.java
                                                                  • NOPLoggerRepository.java
                                                                  • NullWriter.java
                                                                  • OptionHandler.java
                                                                  • RendererSupport.java
                                                                  • RepositorySelector.java
                                                                  • RootCategory.java
                                                                  • RootLogger.java
                                                                  • ThrowableInformation.java
                                                                  • TriggeringEventEvaluator.java
                                                                  • VectorWriter.java
                                                                • TTCCLayout.java
                                                                • varia
                                                                  • DenyAllFilter.java
                                                                  • ExternallyRolledFileAppender.java
                                                                  • FallbackErrorHandler.java
                                                                  • HUP.java
                                                                  • HUPNode.java
                                                                  • LevelMatchFilter.java
                                                                  • LevelRangeFilter.java
                                                                  • NullAppender.java
                                                                  • ReloadingPropertyConfigurator.java
                                                                  • Roller.java
                                                                  • StringMatchFilter.java
                                                                • WriterAppender.java
                                                                • xml
                                                                  • DOMConfigurator.java
                                                                  • log4j.dtd
                                                                  • Log4jEntityResolver.java
                                                                  • SAXErrorHandler.java
                                                                  • UnrecognizedElementHandler.java
                                                                  • XMLLayout.java
                                                                  • XMLWatchdog.java
                                                            • jaxen
                                                              • BaseXPath.java
                                                              • Context.java
                                                              • ContextSupport.java
                                                              • DefaultNavigator.java
                                                              • expr
                                                                • AdditiveExpr.java
                                                                • AllNodeStep.java
                                                                • BinaryExpr.java
                                                                • CommentNodeStep.java
                                                                • DefaultAbsoluteLocationPath.java
                                                                • DefaultAdditiveExpr.java
                                                                • DefaultAllNodeStep.java
                                                                • DefaultAndExpr.java
                                                                • DefaultArithExpr.java
                                                                • DefaultBinaryExpr.java
                                                                • DefaultCommentNodeStep.java
                                                                • DefaultDivExpr.java
                                                                • DefaultEqualityExpr.java
                                                                • DefaultEqualsExpr.java
                                                                • DefaultExpr.java
                                                                • DefaultFilterExpr.java
                                                                • DefaultFunctionCallExpr.java
                                                                • DefaultGreaterThanEqualExpr.java
                                                                • DefaultGreaterThanExpr.java
                                                                • DefaultLessThanEqualExpr.java
                                                                • DefaultLessThanExpr.java
                                                                • DefaultLiteralExpr.java
                                                                • DefaultLocationPath.java
                                                                • DefaultLogicalExpr.java
                                                                • DefaultMinusExpr.java
                                                                • DefaultModExpr.java
                                                                • DefaultMultiplicativeExpr.java
                                                                • DefaultMultiplyExpr.java
                                                                • DefaultNameStep.java
                                                                • DefaultNotEqualsExpr.java
                                                                • DefaultNumberExpr.java
                                                                • DefaultOrExpr.java
                                                                • DefaultPathExpr.java
                                                                • DefaultPlusExpr.java
                                                                • DefaultPredicate.java
                                                                • DefaultProcessingInstructionNodeStep.java
                                                                • DefaultRelationalExpr.java
                                                                • DefaultRelativeLocationPath.java
                                                                • DefaultStep.java
                                                                • DefaultTextNodeStep.java
                                                                • DefaultTruthExpr.java
                                                                • DefaultUnaryExpr.java
                                                                • DefaultUnionExpr.java
                                                                • DefaultVariableReferenceExpr.java
                                                                • DefaultXPathExpr.java
                                                                • DefaultXPathFactory.java
                                                                • EqualityExpr.java
                                                                • Expr.java
                                                                • FilterExpr.java
                                                                • FunctionCallExpr.java
                                                                • IdentitySet.java
                                                                • iter
                                                                  • IterableAncestorAxis.java
                                                                  • IterableAncestorOrSelfAxis.java
                                                                  • IterableAttributeAxis.java
                                                                  • IterableAxis.java
                                                                  • IterableChildAxis.java
                                                                  • IterableDescendantAxis.java
                                                                  • IterableDescendantOrSelfAxis.java
                                                                  • IterableFollowingAxis.java
                                                                  • IterableFollowingSiblingAxis.java
                                                                  • IterableNamespaceAxis.java
                                                                  • IterableParentAxis.java
                                                                  • IterablePrecedingAxis.java
                                                                  • IterablePrecedingSiblingAxis.java
                                                                  • IterableSelfAxis.java
                                                                • LiteralExpr.java
                                                                • LocationPath.java
                                                                • LogicalExpr.java
                                                                • MultiplicativeExpr.java
                                                                • NameStep.java
                                                                • NodeComparator.java
                                                                • NumberExpr.java
                                                                • PathExpr.java
                                                                • Predicate.java
                                                                • Predicated.java
                                                                • PredicateSet.java
                                                                • ProcessingInstructionNodeStep.java
                                                                • RelationalExpr.java
                                                                • Step.java
                                                                • TextNodeStep.java
                                                                • UnaryExpr.java
                                                                • UnionExpr.java
                                                                • VariableReferenceExpr.java
                                                                • Visitable.java
                                                                • Visitor.java
                                                                • VisitorSupport.java
                                                                • XPathExpr.java
                                                                • XPathFactory.java
                                                              • function
                                                                • BooleanFunction.java
                                                                • CeilingFunction.java
                                                                • ConcatFunction.java
                                                                • ContainsFunction.java
                                                                • CountFunction.java
                                                                • ext
                                                                  • EndsWithFunction.java
                                                                  • EvaluateFunction.java
                                                                  • LocaleFunctionSupport.java
                                                                  • LowerFunction.java
                                                                  • MatrixConcatFunction.java
                                                                  • UpperFunction.java
                                                                • FalseFunction.java
                                                                • FloorFunction.java
                                                                • IdFunction.java
                                                                • LangFunction.java
                                                                • LastFunction.java
                                                                • LocalNameFunction.java
                                                                • NameFunction.java
                                                                • NamespaceUriFunction.java
                                                                • NormalizeSpaceFunction.java
                                                                • NotFunction.java
                                                                • NumberFunction.java
                                                                • PositionFunction.java
                                                                • RoundFunction.java
                                                                • StartsWithFunction.java
                                                                • StringFunction.java
                                                                • StringLengthFunction.java
                                                                • SubstringAfterFunction.java
                                                                • SubstringBeforeFunction.java
                                                                • SubstringFunction.java
                                                                • SumFunction.java
                                                                • TranslateFunction.java
                                                                • TrueFunction.java
                                                                • xslt
                                                                  • DocumentFunction.java
                                                              • Function.java
                                                              • FunctionCallException.java
                                                              • FunctionContext.java
                                                              • JaxenConstants.java
                                                              • JaxenException.java
                                                              • JaxenHandler.java
                                                              • JaxenRuntimeException.java
                                                              • NamedAccessNavigator.java
                                                              • NamespaceContext.java
                                                              • Navigator.java
                                                              • QualifiedName.java
                                                              • saxpath
                                                                • Axis.java
                                                                • base
                                                                  • Token.java
                                                                  • TokenTypes.java
                                                                  • Verifier.java
                                                                  • XPathLexer.java
                                                                  • XPathReader.java
                                                                • helpers
                                                                  • DefaultXPathHandler.java
                                                                  • XPathReaderFactory.java
                                                                • Operator.java
                                                                • SAXPathEventSource.java
                                                                • SAXPathException.java
                                                                • XPathHandler.java
                                                                • XPathReader.java
                                                                • XPathSyntaxException.java
                                                              • SimpleFunctionContext.java
                                                              • SimpleNamespaceContext.java
                                                              • SimpleVariableContext.java
                                                              • UnresolvableException.java
                                                              • UnsupportedAxisException.java
                                                              • util
                                                                • AncestorAxisIterator.java
                                                                • AncestorOrSelfAxisIterator.java
                                                                • DescendantAxisIterator.java
                                                                • DescendantOrSelfAxisIterator.java
                                                                • FollowingAxisIterator.java
                                                                • FollowingSiblingAxisIterator.java
                                                                • PrecedingAxisIterator.java
                                                                • PrecedingSiblingAxisIterator.java
                                                                • SelfAxisIterator.java
                                                                • SingleObjectIterator.java
                                                                • SingletonList.java
                                                              • VariableContext.java
                                                              • XPath.java
                                                              • XPathFunctionContext.java
                                                              • XPathSyntaxException.java
                                                            • openscience
                                                              • cdk
                                                                • AminoAcid.java
                                                                • annotations
                                                                  • TestClass.java
                                                                  • TestMethod.java
                                                                • aromaticity
                                                                  • AromaticityCalculator.java
                                                                  • CDKHueckelAromaticityDetector.java
                                                                • Association.java
                                                                • Atom.java
                                                                • AtomContainer.java
                                                                • AtomContainerSet.java
                                                                • AtomParity.java
                                                                • atomtype
                                                                  • CDKAtomTypeMatcher.java
                                                                  • EStateAtomTypeMatcher.java
                                                                  • IAtomTypeGuesser.java
                                                                  • IAtomTypeMatcher.java
                                                                  • mapper
                                                                    • AtomTypeMapper.java
                                                                  • MM2AtomTypeMatcher.java
                                                                  • MMFF94AtomTypeMatcher.java
                                                                  • StructGenAtomTypeGuesser.java
                                                                  • StructGenMatcher.java
                                                                  • SybylAtomTypeMatcher.java
                                                                • AtomType.java
                                                                • BioPolymer.java
                                                                • Bond.java
                                                                • CDK.java
                                                                • CDKConstants.java
                                                                • charges
                                                                  • AtomTypeCharges.java
                                                                  • Electronegativity.java
                                                                  • GasteigerMarsiliPartialCharges.java
                                                                  • GasteigerPEPEPartialCharges.java
                                                                  • IChargeCalculator.java
                                                                  • IElectronicPropertyCalculator.java
                                                                  • InductivePartialCharges.java
                                                                  • MMFF94PartialCharges.java
                                                                  • PiElectronegativity.java
                                                                  • Polarizability.java
                                                                  • StabilizationCharges.java
                                                                • ChemFile.java
                                                                • ChemModel.java
                                                                • ChemObject.java
                                                                • ChemSequence.java
                                                                • config
                                                                  • AtomTypeFactory.java
                                                                  • atomtypes
                                                                    • AtomTypeHandler.java
                                                                    • AtomTypeReader.java
                                                                    • OWLAtomTypeHandler.java
                                                                    • OWLAtomTypeMappingHandler.java
                                                                    • OWLAtomTypeMappingReader.java
                                                                    • OWLAtomTypeReader.java
                                                                  • CDKBasedAtomTypeConfigurator.java
                                                                  • data
                                                                    • chemicalElements.xml
                                                                    • electroneg-pauling.txt
                                                                    • isotopes.xml
                                                                    • jmol_atomtypes.txt
                                                                    • log4j.properties
                                                                    • mm2_atomtypes.xml
                                                                    • mmff94_atomtypes.xml
                                                                    • mol2_atomtypes.xml
                                                                    • pdb_atomtypes.xml
                                                                    • radii-covalent.txt
                                                                    • radii-vdw.txt
                                                                    • structgen_atomtypes.xml
                                                                    • whim_weights.txt
                                                                  • Elements.java
                                                                  • fragments
                                                                    • EStateFragments.java
                                                                  • IAtomTypeConfigurator.java
                                                                  • IsotopeFactory.java
                                                                  • isotopes
                                                                    • IsotopeHandler.java
                                                                    • IsotopeReader.java
                                                                  • OWLBasedAtomTypeConfigurator.java
                                                                  • TXTBasedAtomTypeConfigurator.java
                                                                • ConformerContainer.java
                                                                • controller
                                                                  • IMouseEventRelay.java
                                                                  • IViewEventRelay.java
                                                                  • SwingEventRelay.java
                                                                  • SwingMouseEventRelay.java
                                                                  • UndoAdapter.java
                                                                • Crystal.java
                                                                • debug
                                                                  • DebugAdductFormula.java
                                                                  • DebugAminoAcid.java
                                                                  • DebugAtom.java
                                                                  • DebugAtomContainer.java
                                                                  • DebugAtomContainerSet.java
                                                                  • DebugAtomParity.java
                                                                  • DebugAtomType.java
                                                                  • DebugBioPolymer.java
                                                                  • DebugBond.java
                                                                  • DebugChemFile.java
                                                                  • DebugChemModel.java
                                                                  • DebugChemObject.java
                                                                  • DebugChemObjectBuilder.java
                                                                  • DebugChemSequence.java
                                                                  • DebugCrystal.java
                                                                  • DebugElectronContainer.java
                                                                  • DebugElement.java
                                                                  • DebugFragmentAtom.java
                                                                  • DebugIsotope.java
                                                                  • DebugLonePair.java
                                                                  • DebugMapping.java
                                                                  • DebugMolecularFormula.java
                                                                  • DebugMolecularFormulaSet.java
                                                                  • DebugMolecule.java
                                                                  • DebugMoleculeSet.java
                                                                  • DebugMonomer.java
                                                                  • DebugPDBAtom.java
                                                                  • DebugPDBMonomer.java
                                                                  • DebugPDBPolymer.java
                                                                  • DebugPDBStructure.java
                                                                  • DebugPolymer.java
                                                                  • DebugPseudoAtom.java
                                                                  • DebugReaction.java
                                                                  • DebugReactionScheme.java
                                                                  • DebugReactionSet.java
                                                                  • DebugRing.java
                                                                  • DebugRingSet.java
                                                                  • DebugSingleElectron.java
                                                                  • DebugStrand.java
                                                                • DefaultChemObjectBuilder.java
                                                                • dict
                                                                  • CDKDictionaryReferences.java
                                                                  • data
                                                                    • atom-type-mappings.owl
                                                                    • atom-types.owl
                                                                    • cdk-atom-types.owl
                                                                    • cdk-sybyl-mappings.owl
                                                                    • cdk.xml
                                                                    • chemical.xml
                                                                    • descriptor-algorithms.owl
                                                                    • elements.owl
                                                                    • emboss.xml
                                                                    • reaction-processes.owl
                                                                    • sybyl-atom-types.owl
                                                                  • Dictionary.java
                                                                  • DictionaryDatabase.java
                                                                  • DictionaryHandler.java
                                                                  • DictRef.java
                                                                  • Entry.java
                                                                  • EntryReact.java
                                                                  • OWLFile.java
                                                                  • OWLReact.java
                                                                • ElectronContainer.java
                                                                • Element.java
                                                                • EnzymeResidueLocator.java
                                                                • event
                                                                  • ChemObjectChangeEvent.java
                                                                  • ICDKChangeListener.java
                                                                  • ICDKSelectionChangeListener.java
                                                                • exception
                                                                  • CDKException.java
                                                                  • IncorrectUseOfCDKCoreClassError.java
                                                                  • InvalidSmilesException.java
                                                                  • NoSuchAtomException.java
                                                                  • NoSuchAtomTypeException.java
                                                                  • UnsupportedChemObjectException.java
                                                                • fingerprint
                                                                  • data
                                                                    • maccs.txt
                                                                    • SMARTS_InteLigand.txt
                                                                  • EStateFingerprinter.java
                                                                  • ExtendedFingerprinter.java
                                                                  • Fingerprinter.java
                                                                  • FingerprinterTool.java
                                                                  • GraphOnlyFingerprinter.java
                                                                  • HybridizationFingerprinter.java
                                                                  • IFingerprinter.java
                                                                  • MACCSFingerprinter.java
                                                                  • PubchemFingerprinter.java
                                                                  • StandardSubstructureSets.java
                                                                  • SubstructureFingerprinter.java
                                                                • formula
                                                                  • AdductFormula.java
                                                                  • IsotopeContainer.java
                                                                  • IsotopePattern.java
                                                                  • IsotopePatternGenerator.java
                                                                  • IsotopePatternManipulator.java
                                                                  • IsotopePatternSimilarity.java
                                                                  • MassToFormulaTool.java
                                                                  • MolecularFormula.java
                                                                  • MolecularFormulaChecker.java
                                                                  • MolecularFormulaRange.java
                                                                  • MolecularFormulaSet.java
                                                                  • rules
                                                                    • ChargeRule.java
                                                                    • ElementRule.java
                                                                    • IRule.java
                                                                    • IsotopePatternRule.java
                                                                    • MMElementRule.java
                                                                    • NitrogenRule.java
                                                                    • RDBERule.java
                                                                    • ToleranceRangeRule.java
                                                                • fragment
                                                                  • ExhaustiveFragmenter.java
                                                                  • FragmentUtils.java
                                                                  • IFragmenter.java
                                                                  • MurckoFragmenter.java
                                                                • FragmentAtom.java
                                                                • geometry
                                                                  • alignment
                                                                    • KabschAlignment.java
                                                                  • AtomTools.java
                                                                  • BondTools.java
                                                                  • cip
                                                                    • CIPTool.java
                                                                    • ILigand.java
                                                                    • ImmutableHydrogen.java
                                                                    • ImplicitHydrogenLigand.java
                                                                    • LigancyFourChirality.java
                                                                    • Ligand.java
                                                                    • rules
                                                                      • AtomicNumberRule.java
                                                                      • CIPLigandRule.java
                                                                      • CombinedAtomicMassNumberRule.java
                                                                      • ISequenceSubRule.java
                                                                      • MassNumberRule.java
                                                                    • TerminalLigand.java
                                                                    • VisitedAtoms.java
                                                                  • CrystalGeometryTools.java
                                                                  • GeometryTools.java
                                                                  • IRDFWeightFunction.java
                                                                  • Projector.java
                                                                  • RDFCalculator.java
                                                                  • surface
                                                                    • NeighborList.java
                                                                    • NumericalSurface.java
                                                                    • Tessellate.java
                                                                    • Triangle.java
                                                                  • volume
                                                                    • VABCVolume.java
                                                                  • ZMatrixTools.java
                                                                • graph
                                                                  • AtomContainerAtomPermutor.java
                                                                  • AtomContainerBondPermutor.java
                                                                  • AtomContainerPermutor.java
                                                                  • BFSShortestPath.java
                                                                  • BiconnectivityInspector.java
                                                                  • ConnectivityChecker.java
                                                                  • invariant
                                                                    • CanonicalLabeler.java
                                                                    • ConjugatedPiSystemsDetector.java
                                                                    • EquivalentClassPartitioner.java
                                                                    • exception
                                                                      • BadMatrixFormatException.java
                                                                      • IndexOutOfBoundsException.java
                                                                      • MatrixNotInvertibleException.java
                                                                    • GIMatrix.java
                                                                    • HuLuIndexTool.java
                                                                    • MorganNumbersTools.java
                                                                  • matrix
                                                                    • AdjacencyMatrix.java
                                                                    • ConnectionMatrix.java
                                                                    • IGraphMatrix.java
                                                                    • TopologicalMatrix.java
                                                                  • MinimalPathIterator.java
                                                                  • MoleculeGraphs.java
                                                                  • PathTools.java
                                                                  • rebond
                                                                    • Bspt.java
                                                                    • Point.java
                                                                    • RebondTool.java
                                                                  • SpanningTree.java
                                                                • IImplementationSpecification.java
                                                                • inchi
                                                                  • InChIGenerator.java
                                                                  • InChIGeneratorFactory.java
                                                                  • InChIToStructure.java
                                                                • index
                                                                  • CASNumber.java
                                                                • interfaces
                                                                  • IAdductFormula.java
                                                                  • IAminoAcid.java
                                                                  • IAtom.java
                                                                  • IAtomContainer.java
                                                                  • IAtomContainerSet.java
                                                                  • IAtomParity.java
                                                                  • IAtomType.java
                                                                  • IBioPolymer.java
                                                                  • IBond.java
                                                                  • ICDKObject.java
                                                                  • IChemFile.java
                                                                  • IChemModel.java
                                                                  • IChemObject.java
                                                                  • IChemObjectBuilder.java
                                                                  • IChemObjectChangeEvent.java
                                                                  • IChemObjectListener.java
                                                                  • IChemSequence.java
                                                                  • ICrystal.java
                                                                  • IElectronContainer.java
                                                                  • IElement.java
                                                                  • IFragmentAtom.java
                                                                  • IIsotope.java
                                                                  • ILonePair.java
                                                                  • IMapping.java
                                                                  • IMolecularFormula.java
                                                                  • IMolecularFormulaSet.java
                                                                  • IMolecule.java
                                                                  • IMoleculeSet.java
                                                                  • IMonomer.java
                                                                  • IPDBAtom.java
                                                                  • IPDBMonomer.java
                                                                  • IPDBPolymer.java
                                                                  • IPDBStructure.java
                                                                  • IPolymer.java
                                                                  • IPseudoAtom.java
                                                                  • IReaction.java
                                                                  • IReactionScheme.java
                                                                  • IReactionSet.java
                                                                  • IRing.java
                                                                  • IRingSet.java
                                                                  • ISingleElectron.java
                                                                  • IStereoElement.java
                                                                  • IStrand.java
                                                                  • ITetrahedralChirality.java
                                                                • io
                                                                  • CDKSourceCodeWriter.java
                                                                  • CIFReader.java
                                                                  • cml
                                                                    • CDKConvention.java
                                                                    • CMLCoreModule.java
                                                                    • CMLErrorHandler.java
                                                                    • CMLHandler.java
                                                                    • CMLReactionModule.java
                                                                    • CMLResolver.java
                                                                    • CMLStack.java
                                                                    • CustomSerializer.java
                                                                    • data
                                                                      • cml1_0.dtd
                                                                      • cml1_0_1.dtd
                                                                      • cml1_0_1.xsd
                                                                      • cml23.xsd
                                                                      • cml25b1.xsd
                                                                      • cmlAll.xsd
                                                                      • cmlCore.xsd
                                                                    • ICMLConvention.java
                                                                    • ICMLModule.java
                                                                    • JMOLANIMATIONConvention.java
                                                                    • MDLMolConvention.java
                                                                    • MDMoleculeConvention.java
                                                                    • PDBConvention.java
                                                                    • PMPConvention.java
                                                                    • QSARConvention.java
                                                                  • CMLReader.java
                                                                  • CMLWriter.java
                                                                  • CrystClustReader.java
                                                                  • CrystClustWriter.java
                                                                  • CTXReader.java
                                                                  • DefaultChemObjectReader.java
                                                                  • DefaultChemObjectWriter.java
                                                                  • FormatFactory.java
                                                                  • formats
                                                                    • ABINITFormat.java
                                                                    • Aces2Format.java
                                                                    • ADFFormat.java
                                                                    • AlchemyFormat.java
                                                                    • BGFFormat.java
                                                                    • BSFormat.java
                                                                    • CacaoCartesianFormat.java
                                                                    • CacaoInternalFormat.java
                                                                    • CACheFormat.java
                                                                    • CDKOWLFormat.java
                                                                    • CDKSourceCodeFormat.java
                                                                    • Chem3D_Cartesian_1Format.java
                                                                    • Chem3D_Cartesian_2Format.java
                                                                    • ChemDrawFormat.java
                                                                    • ChemtoolFormat.java
                                                                    • CIFFormat.java
                                                                    • CMLFormat.java
                                                                    • CMLRSSFormat.java
                                                                    • CRK2DFormat.java
                                                                    • CRK3DFormat.java
                                                                    • CrystClustFormat.java
                                                                    • CTXFormat.java
                                                                    • DaltonFormat.java
                                                                    • DMol3Format.java
                                                                    • DOCK5Format.java
                                                                    • FenskeHall_ZMatrixFormat.java
                                                                    • FingerprintFormat.java
                                                                    • GamessFormat.java
                                                                    • Gaussian03Format.java
                                                                    • Gaussian90Format.java
                                                                    • Gaussian92Format.java
                                                                    • Gaussian94Format.java
                                                                    • Gaussian95Format.java
                                                                    • Gaussian98Format.java
                                                                    • GaussianInputFormat.java
                                                                    • GhemicalMMFormat.java
                                                                    • GhemicalSPMFormat.java
                                                                    • GROMOS96Format.java
                                                                    • HINFormat.java
                                                                    • IChemFormat.java
                                                                    • IChemFormatMatcher.java
                                                                    • INChIFormat.java
                                                                    • INChIPlainTextFormat.java
                                                                    • IResourceFormat.java
                                                                    • JaguarFormat.java
                                                                    • JMEFormat.java
                                                                    • MacroModelFormat.java
                                                                    • MDLFormat.java
                                                                    • MDLRXNFormat.java
                                                                    • MDLRXNV3000Format.java
                                                                    • MDLV2000Format.java
                                                                    • MDLV3000Format.java
                                                                    • MMODFormat.java
                                                                    • Mol2Format.java
                                                                    • MOPAC2002Format.java
                                                                    • MOPAC7Format.java
                                                                    • MOPAC93Format.java
                                                                    • MOPAC97Format.java
                                                                    • MoSSOutputFormat.java
                                                                    • MPQCFormat.java
                                                                    • NWChemFormat.java
                                                                    • PCModelFormat.java
                                                                    • PDBFormat.java
                                                                    • PDBMLFormat.java
                                                                    • PMPFormat.java
                                                                    • POVRayFormat.java
                                                                    • PQSChemFormat.java
                                                                    • PubChemASNFormat.java
                                                                    • PubChemCompoundsXMLFormat.java
                                                                    • PubChemCompoundXMLFormat.java
                                                                    • PubChemFormat.java
                                                                    • PubChemSubstancesASNFormat.java
                                                                    • PubChemSubstancesXMLFormat.java
                                                                    • PubChemSubstanceXMLFormat.java
                                                                    • QChemFormat.java
                                                                    • RawCopyFormat.java
                                                                    • RGroupQueryFormat.java
                                                                    • SDFFormat.java
                                                                    • ShelXFormat.java
                                                                    • SMARTSFormat.java
                                                                    • SMILESFIXFormat.java
                                                                    • SMILESFormat.java
                                                                    • SpartanFormat.java
                                                                    • SVGFormat.java
                                                                    • SybylDescriptorFormat.java
                                                                    • TinkerMM2Format.java
                                                                    • TinkerXYZFormat.java
                                                                    • TurboMoleFormat.java
                                                                    • UniChemXYZFormat.java
                                                                    • VASPFormat.java
                                                                    • ViewmolFormat.java
                                                                    • XEDFormat.java
                                                                    • XYZFormat.java
                                                                    • YasaraFormat.java
                                                                    • ZindoFormat.java
                                                                    • ZMatrixFormat.java
                                                                  • GamessReader.java
                                                                  • Gaussian03Reader.java
                                                                  • Gaussian98Reader.java
                                                                  • GhemicalMMReader.java
                                                                  • HINReader.java
                                                                  • HINWriter.java
                                                                  • IChemObjectIO.java
                                                                  • IChemObjectReader.java
                                                                  • IChemObjectReaderErrorHandler.java
                                                                  • IChemObjectWriter.java
                                                                  • inchi
                                                                    • INChIContentProcessorTool.java
                                                                    • INChIHandler.java
                                                                  • INChIPlainTextReader.java
                                                                  • INChIReader.java
                                                                  • ISimpleChemObjectReader.java
                                                                  • iterator
                                                                    • DefaultIteratingChemObjectReader.java
                                                                    • event
                                                                      • DefaultEventChemObjectReader.java
                                                                      • EventCMLHandler.java
                                                                      • EventCMLReader.java
                                                                      • IEventChemObjectReader.java
                                                                    • IIteratingChemObjectReader.java
                                                                    • IteratingMDLConformerReader.java
                                                                    • IteratingMDLReader.java
                                                                    • IteratingPCCompoundASNReader.java
                                                                    • IteratingPCCompoundXMLReader.java
                                                                    • IteratingPCSubstancesXMLReader.java
                                                                    • IteratingSMILESReader.java
                                                                  • listener
                                                                    • IChemObjectIOListener.java
                                                                    • IReaderListener.java
                                                                    • IWriterListener.java
                                                                    • PropertiesListener.java
                                                                    • SwingGUIListener.java
                                                                    • TextGUIListener.java
                                                                  • MDLReader.java
                                                                  • MDLRXNReader.java
                                                                  • MDLRXNV2000Reader.java
                                                                  • MDLRXNV3000Reader.java
                                                                  • MDLRXNWriter.java
                                                                  • MDLV2000Reader.java
                                                                  • MDLV2000Writer.java
                                                                  • MDLV3000Reader.java
                                                                  • Mol2Reader.java
                                                                  • Mol2Writer.java
                                                                  • MoSSOutputReader.java
                                                                  • PCCompoundASNReader.java
                                                                  • PCCompoundXMLReader.java
                                                                  • PCSubstanceXMLReader.java
                                                                  • PDBReader.java
                                                                  • PDBWriter.java
                                                                  • PMPReader.java
                                                                  • program
                                                                    • GaussianInputWriter.java
                                                                  • pubchemxml
                                                                    • PubChemXMLHelper.java
                                                                  • random
                                                                    • DefaultRandomAccessChemObjectReader.java
                                                                    • IRandomAccessChemObjectReader.java
                                                                    • RandomAccessReader.java
                                                                    • RandomAccessSDFReader.java
                                                                  • rdf
                                                                    • CDKOWLReader.java
                                                                    • CDKOWLWriter.java
                                                                  • ReaderEvent.java
                                                                  • ReaderFactory.java
                                                                  • RGroupQueryReader.java
                                                                  • RGroupQueryWriter.java
                                                                  • RssWriter.java
                                                                  • SDFWriter.java
                                                                  • setting
                                                                    • BooleanIOSetting.java
                                                                    • IntegerIOSetting.java
                                                                    • IOSetting.java
                                                                    • OptionIOSetting.java
                                                                    • StringIOSetting.java
                                                                  • ShelXReader.java
                                                                  • ShelXWriter.java
                                                                  • SMILESReader.java
                                                                  • SMILESWriter.java
                                                                  • VASPReader.java
                                                                  • WriterFactory.java
                                                                  • XYZReader.java
                                                                  • XYZWriter.java
                                                                  • ZMatrixReader.java
                                                                • isomorphism
                                                                  • AtomMappingTools.java
                                                                  • IsomorphismTester.java
                                                                  • matchers
                                                                    • InverseSymbolSetQueryAtom.java
                                                                    • IQueryAtom.java
                                                                    • IQueryAtomContainer.java
                                                                    • IQueryBond.java
                                                                    • IRGroupQuery.java
                                                                    • OrderQueryBond.java
                                                                    • OrderQueryBondOrderOnly.java
                                                                    • QueryAtomContainer.java
                                                                    • QueryAtomContainerCreator.java
                                                                    • RGroup.java
                                                                    • RGroupList.java
                                                                    • RGroupQuery.java
                                                                    • smarts
                                                                      • AliphaticAtom.java
                                                                      • AliphaticSymbolAtom.java
                                                                      • AnyAtom.java
                                                                      • AnyOrderQueryBond.java
                                                                      • AromaticAtom.java
                                                                      • AromaticOrSingleQueryBond.java
                                                                      • AromaticQueryBond.java
                                                                      • AromaticSymbolAtom.java
                                                                      • AtomicNumberAtom.java
                                                                      • ChiralityAtom.java
                                                                      • ConnectionCountAtom.java
                                                                      • DegreeAtom.java
                                                                      • ExplicitConnectionAtom.java
                                                                      • FormalChargeAtom.java
                                                                      • HybridizationNumberAtom.java
                                                                      • HydrogenAtom.java
                                                                      • ImplicitHCountAtom.java
                                                                      • LogicalOperatorAtom.java
                                                                      • LogicalOperatorBond.java
                                                                      • MassAtom.java
                                                                      • NonCHHeavyAtom.java
                                                                      • OrderQueryBond.java
                                                                      • PeriodicGroupNumberAtom.java
                                                                      • RecursiveSmartsAtom.java
                                                                      • RingAtom.java
                                                                      • RingBond.java
                                                                      • RingIdentifierAtom.java
                                                                      • RingMembershipAtom.java
                                                                      • SmallestRingAtom.java
                                                                      • SMARTSAtom.java
                                                                      • SMARTSBond.java
                                                                      • StereoBond.java
                                                                      • TotalConnectionAtom.java
                                                                      • TotalHCountAtom.java
                                                                      • TotalRingConnectionAtom.java
                                                                      • TotalValencyAtom.java
                                                                    • SymbolAndChargeQueryAtom.java
                                                                    • SymbolChargeIDQueryAtom.java
                                                                    • SymbolQueryAtom.java
                                                                    • SymbolSetQueryAtom.java
                                                                  • mcss
                                                                    • RGraph.java
                                                                    • RMap.java
                                                                    • RNode.java
                                                                  • UniversalIsomorphismTester.java
                                                                • Isotope.java
                                                                • iupac
                                                                  • parser
                                                                    • AttachedGroup.java
                                                                    • MoleculeBuilder.java
                                                                    • NomParser.java
                                                                    • NomParserConstants.java
                                                                    • NomParserTokenManager.java
                                                                    • ParseException.java
                                                                    • SimpleCharStream.java
                                                                    • Token.java
                                                                    • TokenMgrError.java
                                                                • layout
                                                                  • AtomPlacer.java
                                                                  • HydrogenPlacer.java
                                                                  • OverlapResolver.java
                                                                  • RingPlacer.java
                                                                  • StructureDiagramGenerator.java
                                                                  • TemplateHandler.java
                                                                  • templates
                                                                    • adamantane.cml
                                                                    • cubane.cml
                                                                    • diamantane.cml
                                                                    • ring1.cml
                                                                    • sterane.cml
                                                                    • templates.list
                                                                • libio
                                                                  • cml
                                                                    • Convertor.java
                                                                    • ICMLCustomizer.java
                                                                    • MDMoleculeCustomizer.java
                                                                    • PDBAtomCustomizer.java
                                                                    • QSARCustomizer.java
                                                                  • jena
                                                                    • CDK.java
                                                                    • Convertor.java
                                                                  • md
                                                                    • ChargeGroup.java
                                                                    • MDMolecule.java
                                                                    • Residue.java
                                                                • LonePair.java
                                                                • Mapping.java
                                                                • math
                                                                  • Complex.java
                                                                  • FortranFormat.java
                                                                  • IFunction.java
                                                                  • IMatrix.java
                                                                  • IVector.java
                                                                  • MathTools.java
                                                                  • Matrix.java
                                                                  • Primes.java
                                                                  • qm
                                                                    • AngularMomentum.java
                                                                    • ClosedShellJob.java
                                                                    • FourierGridBasis.java
                                                                    • GaussiansBasis.java
                                                                    • IBasis.java
                                                                    • OneElectronJob.java
                                                                    • Orbitals.java
                                                                    • SimpleBasisSet.java
                                                                  • Quaternion.java
                                                                  • RandomNumbersTool.java
                                                                  • Vector.java
                                                                • modeling
                                                                  • builder3d
                                                                    • AtomPlacer3D.java
                                                                    • AtomTetrahedralLigandPlacer3D.java
                                                                    • data
                                                                      • ringTemplateFingerprints.txt.gz
                                                                      • ringTemplateStructures.sdf.gz
                                                                    • ForceFieldConfigurator.java
                                                                    • MM2BasedAtomTypePattern.java
                                                                    • MM2BasedParameterSetReader.java
                                                                    • MMFF94BasedAtomTypePattern.java
                                                                    • MMFF94BasedParameterSetReader.java
                                                                    • MMFF94ParametersCall.java
                                                                    • ModelBuilder3D.java
                                                                    • TemplateExtractor.java
                                                                    • TemplateHandler3D.java
                                                                  • forcefield
                                                                    • data
                                                                      • mm2.prm
                                                                      • mmff94.prm
                                                                      • mmffdfsb.par
                                                                      • mmffvdw.prm
                                                                • Molecule.java
                                                                • MoleculeSet.java
                                                                • Monomer.java
                                                                • nonotify
                                                                  • NNAdductFormula.java
                                                                  • NNAminoAcid.java
                                                                  • NNAtom.java
                                                                  • NNAtomContainer.java
                                                                  • NNAtomContainerSet.java
                                                                  • NNAtomParity.java
                                                                  • NNAtomType.java
                                                                  • NNBioPolymer.java
                                                                  • NNBond.java
                                                                  • NNChemFile.java
                                                                  • NNChemModel.java
                                                                  • NNChemObject.java
                                                                  • NNChemSequence.java
                                                                  • NNCrystal.java
                                                                  • NNElectronContainer.java
                                                                  • NNElement.java
                                                                  • NNFragmentAtom.java
                                                                  • NNIsotope.java
                                                                  • NNLonePair.java
                                                                  • NNMapping.java
                                                                  • NNMolecularFormula.java
                                                                  • NNMolecularFormulaSet.java
                                                                  • NNMolecule.java
                                                                  • NNMoleculeSet.java
                                                                  • NNMonomer.java
                                                                  • NNPDBAtom.java
                                                                  • NNPDBMonomer.java
                                                                  • NNPDBPolymer.java
                                                                  • NNPDBStructure.java
                                                                  • NNPolymer.java
                                                                  • NNPseudoAtom.java
                                                                  • NNReaction.java
                                                                  • NNReactionScheme.java
                                                                  • NNReactionSet.java
                                                                  • NNRing.java
                                                                  • NNRingSet.java
                                                                  • NNSingleElectron.java
                                                                  • NNStrand.java
                                                                  • NoNotificationChemObjectBuilder.java
                                                                • normalize
                                                                  • Normalizer.java
                                                                  • SMSDNormalizer.java
                                                                • pharmacophore
                                                                  • PharmacophoreAngleBond.java
                                                                  • PharmacophoreAtom.java
                                                                  • PharmacophoreBond.java
                                                                  • PharmacophoreMatcher.java
                                                                  • PharmacophoreQuery.java
                                                                  • PharmacophoreQueryAngleBond.java
                                                                  • PharmacophoreQueryAtom.java
                                                                  • PharmacophoreQueryBond.java
                                                                  • PharmacophoreUtils.java
                                                                • PhysicalConstants.java
                                                                • Polymer.java
                                                                • protein
                                                                  • data
                                                                    • PDBAtom.java
                                                                    • PDBMonomer.java
                                                                    • PDBPolymer.java
                                                                    • PDBStrand.java
                                                                    • PDBStructure.java
                                                                  • ProteinPocketFinder.java
                                                                • PseudoAtom.java
                                                                • qsar
                                                                  • AbstractAtomicDescriptor.java
                                                                  • AbstractBondDescriptor.java
                                                                  • AtomValenceTool.java
                                                                  • DescriptorEngine.java
                                                                  • DescriptorException.java
                                                                  • descriptors
                                                                    • atomic
                                                                      • AtomDegreeDescriptor.java
                                                                      • AtomHybridizationDescriptor.java
                                                                      • AtomHybridizationVSEPRDescriptor.java
                                                                      • AtomValenceDescriptor.java
                                                                      • BondsToAtomDescriptor.java
                                                                      • CovalentRadiusDescriptor.java
                                                                      • data
                                                                        • X_AffiProton_HOSE.db
                                                                        • X_AffiProton_HOSE_S.db
                                                                        • X_IP_HOSE.db
                                                                        • X_IP_HOSE_S.db
                                                                      • DistanceToAtomDescriptor.java
                                                                      • EffectiveAtomPolarizabilityDescriptor.java
                                                                      • InductiveAtomicHardnessDescriptor.java
                                                                      • InductiveAtomicSoftnessDescriptor.java
                                                                      • IPAtomicHOSEDescriptor.java
                                                                      • IPAtomicLearningDescriptor.java
                                                                      • IsProtonInAromaticSystemDescriptor.java
                                                                      • IsProtonInConjugatedPiSystemDescriptor.java
                                                                      • PartialPiChargeDescriptor.java
                                                                      • PartialSigmaChargeDescriptor.java
                                                                      • PartialTChargeMMFF94Descriptor.java
                                                                      • PartialTChargePEOEDescriptor.java
                                                                      • PeriodicTablePositionDescriptor.java
                                                                      • PiElectronegativityDescriptor.java
                                                                      • ProtonAffinityHOSEDescriptor.java
                                                                      • ProtonTotalPartialChargeDescriptor.java
                                                                      • RDFProtonDescriptor_G3R.java
                                                                      • RDFProtonDescriptor_GDR.java
                                                                      • RDFProtonDescriptor_GHR.java
                                                                      • RDFProtonDescriptor_GHR_topol.java
                                                                      • RDFProtonDescriptor_GSR.java
                                                                      • SigmaElectronegativityDescriptor.java
                                                                      • StabilizationPlusChargeDescriptor.java
                                                                      • VdWRadiusDescriptor.java
                                                                    • atompair
                                                                      • PiContactDetectionDescriptor.java
                                                                    • bond
                                                                      • AtomicNumberDifferenceDescriptor.java
                                                                      • BondPartialPiChargeDescriptor.java
                                                                      • BondPartialSigmaChargeDescriptor.java
                                                                      • BondPartialTChargeDescriptor.java
                                                                      • BondSigmaElectronegativityDescriptor.java
                                                                      • IPBondLearningDescriptor.java
                                                                    • data
                                                                      • taepeptides.txt
                                                                    • molecular
                                                                      • AcidicGroupCountDescriptor.java
                                                                      • ALOGPDescriptor.java
                                                                      • AminoAcidCountDescriptor.java
                                                                      • APolDescriptor.java
                                                                      • AromaticAtomsCountDescriptor.java
                                                                      • AromaticBondsCountDescriptor.java
                                                                      • AtomCountDescriptor.java
                                                                      • AutocorrelationDescriptorCharge.java
                                                                      • AutocorrelationDescriptorMass.java
                                                                      • AutocorrelationDescriptorPolarizability.java
                                                                      • BasicGroupCountDescriptor.java
                                                                      • BCUTDescriptor.java
                                                                      • BondCountDescriptor.java
                                                                      • BPolDescriptor.java
                                                                      • CarbonTypesDescriptor.java
                                                                      • ChiChainDescriptor.java
                                                                      • ChiClusterDescriptor.java
                                                                      • ChiIndexUtils.java
                                                                      • ChiPathClusterDescriptor.java
                                                                      • ChiPathDescriptor.java
                                                                      • CPSADescriptor.java
                                                                      • EccentricConnectivityIndexDescriptor.java
                                                                      • FMFDescriptor.java
                                                                      • FragmentComplexityDescriptor.java
                                                                      • GravitationalIndexDescriptor.java
                                                                      • HBondAcceptorCountDescriptor.java
                                                                      • HBondDonorCountDescriptor.java
                                                                      • HybridizationRatioDescriptor.java
                                                                      • IPMolecularLearningDescriptor.java
                                                                      • KappaShapeIndicesDescriptor.java
                                                                      • KierHallSmartsDescriptor.java
                                                                      • LargestChainDescriptor.java
                                                                      • LargestPiSystemDescriptor.java
                                                                      • LengthOverBreadthDescriptor.java
                                                                      • LongestAliphaticChainDescriptor.java
                                                                      • MannholdLogPDescriptor.java
                                                                      • MDEDescriptor.java
                                                                      • MomentOfInertiaDescriptor.java
                                                                      • PetitjeanNumberDescriptor.java
                                                                      • PetitjeanShapeIndexDescriptor.java
                                                                      • RotatableBondsCountDescriptor.java
                                                                      • RuleOfFiveDescriptor.java
                                                                      • TPSADescriptor.java
                                                                      • VABCDescriptor.java
                                                                      • VAdjMaDescriptor.java
                                                                      • WeightDescriptor.java
                                                                      • WeightedPathDescriptor.java
                                                                      • WHIMDescriptor.java
                                                                      • WienerNumbersDescriptor.java
                                                                      • XLogPDescriptor.java
                                                                      • ZagrebIndexDescriptor.java
                                                                    • protein
                                                                      • TaeAminoAcidDescriptor.java
                                                                  • DescriptorSpecification.java
                                                                  • DescriptorValue.java
                                                                  • IAtomicDescriptor.java
                                                                  • IAtomPairDescriptor.java
                                                                  • IBondDescriptor.java
                                                                  • IDescriptor.java
                                                                  • IMolecularDescriptor.java
                                                                  • result
                                                                    • BooleanResult.java
                                                                    • BooleanResultType.java
                                                                    • DoubleArrayResult.java
                                                                    • DoubleArrayResultType.java
                                                                    • DoubleResult.java
                                                                    • DoubleResultType.java
                                                                    • IDescriptorResult.java
                                                                    • IntegerArrayResult.java
                                                                    • IntegerArrayResultType.java
                                                                    • IntegerResult.java
                                                                    • IntegerResultType.java
                                                                • reaction
                                                                  • IReactionMechanism.java
                                                                  • IReactionProcess.java
                                                                  • mechanism
                                                                    • AdductionLPMechanism.java
                                                                    • AdductionPBMechanism.java
                                                                    • HeterolyticCleavageMechanism.java
                                                                    • HomolyticCleavageMechanism.java
                                                                    • RadicalSiteIonizationMechanism.java
                                                                    • RadicalSiteRearrangementMechanism.java
                                                                    • RearrangementChargeMechanism.java
                                                                    • RemovingSEofBMechanism.java
                                                                    • RemovingSEofNBMechanism.java
                                                                    • SharingElectronMechanism.java
                                                                    • TautomerizationMechanism.java
                                                                  • ReactionChain.java
                                                                  • ReactionEngine.java
                                                                  • ReactionSpecification.java
                                                                  • type
                                                                    • AdductionProtonLPReaction.java
                                                                    • AdductionProtonPBReaction.java
                                                                    • AdductionSodiumLPReaction.java
                                                                    • CarbonylEliminationReaction.java
                                                                    • ElectronImpactNBEReaction.java
                                                                    • ElectronImpactPDBReaction.java
                                                                    • ElectronImpactSDBReaction.java
                                                                    • HeterolyticCleavagePBReaction.java
                                                                    • HeterolyticCleavageSBReaction.java
                                                                    • HomolyticCleavageReaction.java
                                                                    • HyperconjugationReaction.java
                                                                    • parameters
                                                                      • IParameterReact.java
                                                                      • ParameterReact.java
                                                                      • SetReactionCenter.java
                                                                    • PiBondingMovementReaction.java
                                                                    • RadicalChargeSiteInitiationHReaction.java
                                                                    • RadicalChargeSiteInitiationReaction.java
                                                                    • RadicalSiteHrAlphaReaction.java
                                                                    • RadicalSiteHrBetaReaction.java
                                                                    • RadicalSiteHrDeltaReaction.java
                                                                    • RadicalSiteHrGammaReaction.java
                                                                    • RadicalSiteInitiationHReaction.java
                                                                    • RadicalSiteInitiationReaction.java
                                                                    • RadicalSiteRrAlphaReaction.java
                                                                    • RadicalSiteRrBetaReaction.java
                                                                    • RadicalSiteRrDeltaReaction.java
                                                                    • RadicalSiteRrGammaReaction.java
                                                                    • RearrangementAnionReaction.java
                                                                    • RearrangementCationReaction.java
                                                                    • RearrangementLonePairReaction.java
                                                                    • RearrangementRadicalReaction.java
                                                                    • SharingAnionReaction.java
                                                                    • SharingChargeDBReaction.java
                                                                    • SharingChargeSBReaction.java
                                                                    • SharingLonePairReaction.java
                                                                    • TautomerizationReaction.java
                                                                • Reaction.java
                                                                • ReactionScheme.java
                                                                • ReactionSet.java
                                                                • renderer
                                                                  • AbstractRenderer.java
                                                                  • AtomContainerRenderer.java
                                                                  • AverageBondLengthCalculator.java
                                                                  • BoundsCalculator.java
                                                                  • color
                                                                    • CDK2DAtomColors.java
                                                                    • CDKAtomColors.java
                                                                    • CPKAtomColors.java
                                                                    • IAtomColorer.java
                                                                    • PartialAtomicChargeColors.java
                                                                    • RasmolColors.java
                                                                  • elements
                                                                    • AtomSymbolElement.java
                                                                    • ElementGroup.java
                                                                    • GeneralPath.java
                                                                    • IRenderingElement.java
                                                                    • IRenderingVisitor.java
                                                                    • LineElement.java
                                                                    • OvalElement.java
                                                                    • path
                                                                      • Close.java
                                                                      • CubicTo.java
                                                                      • LineTo.java
                                                                      • MoveTo.java
                                                                      • PathBuilder.java
                                                                      • PathElement.java
                                                                      • QuadTo.java
                                                                      • Type.java
                                                                    • PathElement.java
                                                                    • RectangleElement.java
                                                                    • RingElement.java
                                                                    • TextElement.java
                                                                    • TextGroupElement.java
                                                                    • WedgeLineElement.java
                                                                  • font
                                                                    • AbstractFontManager.java
                                                                    • AWTFontManager.java
                                                                    • IFontManager.java
                                                                  • generators
                                                                    • BasicAtomGenerator.java
                                                                    • BasicBondGenerator.java
                                                                    • BasicGenerator.java
                                                                    • BasicSceneGenerator.java
                                                                    • IGenerator.java
                                                                    • IGeneratorParameter.java
                                                                    • parameter
                                                                      • AbstractGeneratorParameter.java
                                                                    • RingGenerator.java
                                                                  • GraphRendererModel.java
                                                                  • IRenderer.java
                                                                  • RendererModel.java
                                                                  • selection
                                                                    • AbstractSelection.java
                                                                    • IChemObjectSelection.java
                                                                  • visitor
                                                                    • IDrawVisitor.java
                                                                • Ring.java
                                                                • ringsearch
                                                                  • AllRingsFinder.java
                                                                  • cyclebasis
                                                                    • CycleBasis.java
                                                                    • SimpleCycle.java
                                                                    • SimpleCycleBasis.java
                                                                  • FiguerasSSSRFinder.java
                                                                  • Path.java
                                                                  • Queue.java
                                                                  • RingPartitioner.java
                                                                  • SSSRFinder.java
                                                                • RingSet.java
                                                                • signature
                                                                  • AtomSignature.java
                                                                  • MoleculeFromSignatureBuilder.java
                                                                  • MoleculeSignature.java
                                                                  • Orbit.java
                                                                  • SignatureQuotientGraph.java
                                                                • similarity
                                                                  • DistanceMoment.java
                                                                  • Tanimoto.java
                                                                • SingleElectron.java
                                                                • smiles
                                                                  • DeduceBondSystemTool.java
                                                                  • InvPair.java
                                                                  • smarts
                                                                    • parser
                                                                      • ASTAliphatic.java
                                                                      • ASTAnyAtom.java
                                                                      • ASTAromatic.java
                                                                      • ASTAtom.java
                                                                      • ASTAtomicMass.java
                                                                      • ASTAtomicNumber.java
                                                                      • ASTCharge.java
                                                                      • ASTChirality.java
                                                                      • ASTElement.java
                                                                      • ASTExplicitAtom.java
                                                                      • ASTExplicitConnectivity.java
                                                                      • ASTExplicitHighAndBond.java
                                                                      • ASTExplicitHighAndExpression.java
                                                                      • ASTGroup.java
                                                                      • ASTHybrdizationNumber.java
                                                                      • ASTImplicitHCount.java
                                                                      • ASTImplicitHighAndBond.java
                                                                      • ASTImplicitHighAndExpression.java
                                                                      • ASTLowAndBond.java
                                                                      • ASTLowAndExpression.java
                                                                      • ASTNonCHHeavyAtom.java
                                                                      • ASTNotBond.java
                                                                      • ASTNotExpression.java
                                                                      • ASTOrBond.java
                                                                      • ASTOrExpression.java
                                                                      • ASTPeriodicGroupNumber.java
                                                                      • ASTPrimitiveAtomExpression.java
                                                                      • ASTReaction.java
                                                                      • ASTRecursiveSmartsExpression.java
                                                                      • ASTRingConnectivity.java
                                                                      • ASTRingIdentifier.java
                                                                      • ASTRingMembership.java
                                                                      • ASTSimpleBond.java
                                                                      • ASTSmallestRingSize.java
                                                                      • ASTSmarts.java
                                                                      • ASTStart.java
                                                                      • ASTTotalConnectivity.java
                                                                      • ASTTotalHCount.java
                                                                      • ASTValence.java
                                                                      • JJTSMARTSParserState.java
                                                                      • Node.java
                                                                      • ParseException.java
                                                                      • SimpleCharStream.java
                                                                      • SimpleNode.java
                                                                      • SMARTSParser.java
                                                                      • SMARTSParserConstants.java
                                                                      • SMARTSParserTokenManager.java
                                                                      • SMARTSParserTreeConstants.java
                                                                      • SMARTSParserVisitor.java
                                                                      • Token.java
                                                                      • TokenMgrError.java
                                                                      • visitor
                                                                        • Smarts2MQLVisitor.java
                                                                        • SmartsDumpVisitor.java
                                                                        • SmartsQueryVisitor.java
                                                                    • SMARTSQueryTool.java
                                                                  • SmilesGenerator.java
                                                                  • SmilesParser.java
                                                                • smsd
                                                                  • algorithm
                                                                    • matchers
                                                                      • AtomMatcher.java
                                                                      • BondMatcher.java
                                                                      • DefaultBondMatcher.java
                                                                      • DefaultMatcher.java
                                                                      • DefaultMCSPlusAtomMatcher.java
                                                                      • DefaultRGraphAtomMatcher.java
                                                                      • DefaultVFAtomMatcher.java
                                                                      • DefaultVFBondMatcher.java
                                                                      • VFAtomMatcher.java
                                                                      • VFBondMatcher.java
                                                                    • mcgregor
                                                                      • McGregor.java
                                                                      • McGregorChecks.java
                                                                      • McgregorHelper.java
                                                                      • QueryProcessor.java
                                                                      • TargetProcessor.java
                                                                    • mcsplus
                                                                      • BKKCKCF.java
                                                                      • ExactMapping.java
                                                                      • GenerateCompatibilityGraph.java
                                                                      • MCSPlus.java
                                                                      • MCSPlusHandler.java
                                                                    • rgraph
                                                                      • CDKMCS.java
                                                                      • CDKMCSHandler.java
                                                                      • CDKRGraph.java
                                                                      • CDKRMap.java
                                                                      • CDKRMapHandler.java
                                                                      • CDKRNode.java
                                                                      • CDKSubGraphHandler.java
                                                                    • single
                                                                      • SingleMapping.java
                                                                      • SingleMappingHandler.java
                                                                    • vflib
                                                                      • builder
                                                                        • EdgeBuilder.java
                                                                        • NodeBuilder.java
                                                                        • TargetProperties.java
                                                                        • VFQueryBuilder.java
                                                                      • interfaces
                                                                        • IEdge.java
                                                                        • IMapper.java
                                                                        • INode.java
                                                                        • IQuery.java
                                                                        • IQueryCompiler.java
                                                                        • IState.java
                                                                      • map
                                                                        • Match.java
                                                                        • VFMapper.java
                                                                        • VFMCSMapper.java
                                                                        • VFState.java
                                                                      • query
                                                                        • QueryCompiler.java
                                                                      • VFlibMCSHandler.java
                                                                      • VFlibSubStructureHandler.java
                                                                      • VFlibTurboHandler.java
                                                                  • filters
                                                                    • ChemicalFilters.java
                                                                    • PostFilter.java
                                                                  • global
                                                                    • TimeOut.java
                                                                  • helper
                                                                    • BinaryTree.java
                                                                    • BondEnergy.java
                                                                    • FinalMappings.java
                                                                    • LabelContainer.java
                                                                  • interfaces
                                                                    • AbstractMCS.java
                                                                    • AbstractMCSAlgorithm.java
                                                                    • AbstractSubGraph.java
                                                                    • Algorithm.java
                                                                    • IFinalMapping.java
                                                                    • IMCSBase.java
                                                                  • Isomorphism.java
                                                                  • labelling
                                                                    • AbstractReactionLabeller.java
                                                                    • AtomContainerAtomPermutor.java
                                                                    • AtomContainerPrinter.java
                                                                    • CanonicalLabellingAdaptor.java
                                                                    • ICanonicalMoleculeLabeller.java
                                                                    • ICanonicalReactionLabeller.java
                                                                    • MoleculeSignatureLabellingAdaptor.java
                                                                    • Permutor.java
                                                                    • SignatureReactionCanoniser.java
                                                                    • SmilesReactionCanoniser.java
                                                                  • ring
                                                                    • HanserRingFinder.java
                                                                    • PathEdge.java
                                                                    • PathGraph.java
                                                                    • RingFilter.java
                                                                    • RingFinder.java
                                                                  • tools
                                                                    • BondEnergies.java
                                                                    • ExtAtomContainerManipulator.java
                                                                    • MoleculeSanityCheck.java
                                                                    • MolHandler.java
                                                                    • TimeManager.java
                                                                • stereo
                                                                  • StereoTool.java
                                                                  • TetrahedralChirality.java
                                                                • Strand.java
                                                                • structgen
                                                                  • IStructureGenerationListener.java
                                                                  • RandomGenerator.java
                                                                  • SingleStructureRandomGenerator.java
                                                                  • stochastic
                                                                    • operator
                                                                      • ChemGraph.java
                                                                      • CrossoverMachine.java
                                                                    • PartialFilledStructureMerger.java
                                                                  • VicinitySampler.java
                                                                • tautomers
                                                                  • InChITautomerGenerator.java
                                                                • templates
                                                                  • AminoAcids.java
                                                                  • data
                                                                    • list_aminoacids.cml
                                                                  • MoleculeFactory.java
                                                                  • saturatedhydrocarbons
                                                                    • IsoAlkanes.java
                                                                • tools
                                                                  • AtomicProperties.java
                                                                  • AtomTypeTools.java
                                                                  • BremserOneSphereHOSECodePredictor.java
                                                                  • CDKHydrogenAdder.java
                                                                  • CDKUtilities.java
                                                                  • CDKValencyChecker.java
                                                                  • DataFeatures.java
                                                                  • DataFeaturesTool.java
                                                                  • DeAromatizationTool.java
                                                                  • diff
                                                                    • AtomContainerDiff.java
                                                                    • AtomDiff.java
                                                                    • AtomTypeDiff.java
                                                                    • BondDiff.java
                                                                    • ChemObjectDiff.java
                                                                    • ElectronContainerDiff.java
                                                                    • ElementDiff.java
                                                                    • IsotopeDiff.java
                                                                    • LonePairDiff.java
                                                                    • SingleElectronDiff.java
                                                                    • tree
                                                                      • AbstractDifference.java
                                                                      • AbstractDifferenceList.java
                                                                      • AtomTypeHybridizationDifference.java
                                                                      • BondOrderDifference.java
                                                                      • BooleanArrayDifference.java
                                                                      • BooleanDifference.java
                                                                      • ChemObjectDifference.java
                                                                      • DoubleDifference.java
                                                                      • IDifference.java
                                                                      • IDifferenceList.java
                                                                      • IntegerDifference.java
                                                                      • Point2dDifference.java
                                                                      • Point3dDifference.java
                                                                      • StringDifference.java
                                                                  • ElementComparator.java
                                                                  • features
                                                                    • MoleculeFeaturesTool.java
                                                                  • FixedSizeStack.java
                                                                  • FormatStringBuffer.java
                                                                  • GridGenerator.java
                                                                  • HOSECodeAnalyser.java
                                                                  • HOSECodeGenerator.java
                                                                  • IDCreator.java
                                                                  • IDeduceBondOrderTool.java
                                                                  • ILoggingTool.java
                                                                  • IonizationPotentialTool.java
                                                                  • IValencyChecker.java
                                                                  • LoggingTool.java
                                                                  • LoggingToolFactory.java
                                                                  • LonePairElectronChecker.java
                                                                  • manipulator
                                                                    • AminoAcidManipulator.java
                                                                    • AtomContainerComparator.java
                                                                    • AtomContainerComparatorBy2DCenter.java
                                                                    • AtomContainerManipulator.java
                                                                    • AtomContainerSetManipulator.java
                                                                    • AtomTypeManipulator.java
                                                                    • BondManipulator.java
                                                                    • ChemFileManipulator.java
                                                                    • ChemModelManipulator.java
                                                                    • ChemSequenceManipulator.java
                                                                    • MolecularFormulaManipulator.java
                                                                    • MolecularFormulaRangeManipulator.java
                                                                    • MolecularFormulaSetManipulator.java
                                                                    • MoleculeSetManipulator.java
                                                                    • ReactionManipulator.java
                                                                    • ReactionSchemeManipulator.java
                                                                    • ReactionSetManipulator.java
                                                                    • RingManipulator.java
                                                                    • RingSetManipulator.java
                                                                    • RingSizeComparator.java
                                                                  • periodictable
                                                                    • ElementPTFactory.java
                                                                    • ElementPTHandler.java
                                                                    • ElementPTReader.java
                                                                    • PeriodicTable.java
                                                                    • PeriodicTableElement.java
                                                                  • ProteinBuilderTool.java
                                                                  • SaturationChecker.java
                                                                  • SmilesValencyChecker.java
                                                                  • StructureResonanceGenerator.java
                                                                  • SwissArmyKnife.java
                                                                  • SystemOutLoggingTool.java
                                                                • validate
                                                                  • AbstractValidator.java
                                                                  • BasicValidator.java
                                                                  • CDKValidator.java
                                                                  • DictionaryValidator.java
                                                                  • Geometry3DValidator.java
                                                                  • IValidator.java
                                                                  • ProblemMarker.java
                                                                  • ValidationReport.java
                                                                  • ValidationTest.java
                                                                  • ValidatorEngine.java
                                                                • Vibration.java
                                                            • slf4j
                                                              • helpers
                                                                • BasicMarker.java
                                                                • BasicMarkerFactory.java
                                                                • BasicMDCAdapter.java
                                                                • MarkerIgnoringBase.java
                                                                • MessageFormatter.java
                                                                • NamedLoggerBase.java
                                                                • NOPLogger.java
                                                                • NOPMakerAdapter.java
                                                                • SubstituteLoggerFactory.java
                                                                • Util.java
                                                              • ILoggerFactory.java
                                                              • IMarkerFactory.java
                                                              • impl
                                                                • SimpleLogger.java
                                                                • SimpleLoggerFactory.java
                                                                • StaticLoggerBinder.java
                                                                • StaticMarkerBinder.java
                                                                • StaticMDCBinder.java
                                                              • Logger.java
                                                              • LoggerFactory.java
                                                              • Marker.java
                                                              • MarkerFactory.java
                                                              • MDC.java
                                                              • spi
                                                                • LocationAwareLogger.java
                                                                • LoggerFactoryBinder.java
                                                                • MarkerFactoryBinder.java
                                                                • MDCAdapter.java
                                                            • w3c
                                                              • dom
                                                                • UserDataHandler.java
                                                            • xmlcml
                                                              • cml
                                                                • attribute
                                                                  • CountExpressionAttribute.java
                                                                  • DelimiterAttribute.java
                                                                  • DictRefAttribute.java
                                                                  • IdAttribute.java
                                                                  • main
                                                                    • CountExpressionAttribute.java
                                                                  • MetadataNameAttribute.java
                                                                  • NamespaceRefAttribute.java
                                                                  • RefAttribute.java
                                                                  • UnitsAttribute.java
                                                                • base
                                                                  • AbstractGenerator.java
                                                                  • AbstractTool.java
                                                                  • AttributeFactory.java
                                                                  • AttributeGenerator.java
                                                                  • attributes.xsd
                                                                  • BooleanArraySTAttribute.java
                                                                  • BooleanSTAttribute.java
                                                                  • CMLAttribute.java
                                                                  • CMLBuilder.java
                                                                  • CMLConstants.java
                                                                  • CMLElement.java
                                                                  • CMLElements.java
                                                                  • CMLElementType.java
                                                                  • CMLLog.java
                                                                  • CMLNamespace.java
                                                                  • CMLNodeFactory.java
                                                                  • CMLSchemaValidator.java
                                                                  • CMLSerializer.java
                                                                  • CMLSimpleType.java
                                                                  • CMLType.java
                                                                  • CMLUtil.java
                                                                  • DoubleArraySTAttribute.java
                                                                  • DoubleSTAttribute.java
                                                                  • ElementGenerator.java
                                                                  • elements.xsd
                                                                  • HasId.java
                                                                  • IntArraySTAttribute.java
                                                                  • IntSTAttribute.java
                                                                  • Message.java
                                                                  • schema.xsd
                                                                  • SchemaManager.java
                                                                  • StringArraySTAttribute.java
                                                                  • StringSTAttribute.java
                                                                  • TypeGenerator.java
                                                                  • types.xsd
                                                                • element
                                                                  • AbstractAbundance.java
                                                                  • AbstractAction.java
                                                                  • AbstractActionList.java
                                                                  • AbstractAmount.java
                                                                  • AbstractAngle.java
                                                                  • AbstractArg.java
                                                                  • AbstractArray.java
                                                                  • AbstractArrayList.java
                                                                  • AbstractAtom.java
                                                                  • AbstractAtomArray.java
                                                                  • AbstractAtomicBasisFunction.java
                                                                  • AbstractAtomParity.java
                                                                  • AbstractAtomSet.java
                                                                  • AbstractAtomType.java
                                                                  • AbstractAtomTypeList.java
                                                                  • AbstractBand.java
                                                                  • AbstractBandList.java
                                                                  • AbstractBasisSet.java
                                                                  • AbstractBond.java
                                                                  • AbstractBondArray.java
                                                                  • AbstractBondSet.java
                                                                  • AbstractBondStereo.java
                                                                  • AbstractBondType.java
                                                                  • AbstractBondTypeList.java
                                                                  • AbstractCellParameter.java
                                                                  • AbstractCml.java
                                                                  • AbstractComplexObject.java
                                                                  • AbstractConditionList.java
                                                                  • AbstractCrystal.java
                                                                  • AbstractDictionary.java
                                                                  • AbstractEigen.java
                                                                  • AbstractElectron.java
                                                                  • AbstractEntry.java
                                                                  • AbstractExpression.java
                                                                  • AbstractFormula.java
                                                                  • AbstractFragment.java
                                                                  • AbstractFragmentList.java
                                                                  • AbstractGradient.java
                                                                  • AbstractIdentifier.java
                                                                  • AbstractIsotope.java
                                                                  • AbstractIsotopeList.java
                                                                  • AbstractJoin.java
                                                                  • AbstractKpoint.java
                                                                  • AbstractKpointList.java
                                                                  • AbstractLabel.java
                                                                  • AbstractLattice.java
                                                                  • AbstractLatticeVector.java
                                                                  • AbstractLength.java
                                                                  • AbstractLine3.java
                                                                  • AbstractLink.java
                                                                  • AbstractList.java
                                                                  • AbstractMap.java
                                                                  • AbstractMatrix.java
                                                                  • AbstractMechanism.java
                                                                  • AbstractMechanismComponent.java
                                                                  • AbstractMetadata.java
                                                                  • AbstractMetadataList.java
                                                                  • AbstractModule.java
                                                                  • AbstractMolecule.java
                                                                  • AbstractMoleculeList.java
                                                                  • AbstractName.java
                                                                  • AbstractObject.java
                                                                  • AbstractObservation.java
                                                                  • AbstractOperator.java
                                                                  • AbstractParameter.java
                                                                  • AbstractParameterList.java
                                                                  • AbstractParticle.java
                                                                  • AbstractPeak.java
                                                                  • AbstractPeakGroup.java
                                                                  • AbstractPeakList.java
                                                                  • AbstractPeakStructure.java
                                                                  • AbstractPlane3.java
                                                                  • AbstractPoint3.java
                                                                  • AbstractPotential.java
                                                                  • AbstractPotentialForm.java
                                                                  • AbstractPotentialList.java
                                                                  • AbstractProduct.java
                                                                  • AbstractProductList.java
                                                                  • AbstractProperty.java
                                                                  • AbstractPropertyList.java
                                                                  • AbstractReactant.java
                                                                  • AbstractReactantList.java
                                                                  • AbstractReaction.java
                                                                  • AbstractReactionList.java
                                                                  • AbstractReactionScheme.java
                                                                  • AbstractReactionStep.java
                                                                  • AbstractReactionStepList.java
                                                                  • AbstractReactiveCentre.java
                                                                  • AbstractRegion.java
                                                                  • AbstractRelatedEntry.java
                                                                  • AbstractSample.java
                                                                  • AbstractScalar.java
                                                                  • AbstractSpectator.java
                                                                  • AbstractSpectatorList.java
                                                                  • AbstractSpectrum.java
                                                                  • AbstractSpectrumData.java
                                                                  • AbstractSpectrumList.java
                                                                  • AbstractSphere3.java
                                                                  • AbstractSubstance.java
                                                                  • AbstractSubstanceList.java
                                                                  • AbstractSymmetry.java
                                                                  • AbstractSystem.java
                                                                  • AbstractTable.java
                                                                  • AbstractTableCell.java
                                                                  • AbstractTableContent.java
                                                                  • AbstractTableHeader.java
                                                                  • AbstractTableHeaderCell.java
                                                                  • AbstractTableRow.java
                                                                  • AbstractTableRowList.java
                                                                  • AbstractTorsion.java
                                                                  • AbstractTransform3.java
                                                                  • AbstractTransitionState.java
                                                                  • AbstractVector3.java
                                                                  • AbstractXaxis.java
                                                                  • AbstractYaxis.java
                                                                  • AbstractZMatrix.java
                                                                  • CMLAbundance.java
                                                                  • CMLAction.java
                                                                  • CMLActionList.java
                                                                  • CMLAmount.java
                                                                  • CMLAngle.java
                                                                  • CMLArg.java
                                                                  • CMLArray.java
                                                                  • CMLArrayList.java
                                                                  • CMLAtom.java
                                                                  • CMLAtomArray.java
                                                                  • CMLAtomicBasisFunction.java
                                                                  • CMLAtomParity.java
                                                                  • CMLAtomSet.java
                                                                  • CMLAtomType.java
                                                                  • CMLAtomTypeList.java
                                                                  • CMLBand.java
                                                                  • CMLBandList.java
                                                                  • CMLBasisSet.java
                                                                  • CMLBond.java
                                                                  • CMLBondArray.java
                                                                  • CMLBondSet.java
                                                                  • CMLBondStereo.java
                                                                  • CMLBondType.java
                                                                  • CMLBondTypeList.java
                                                                  • CMLCellParameter.java
                                                                  • CMLCml.java
                                                                  • CMLComplexObject.java
                                                                  • CMLConditionList.java
                                                                  • CMLCrystal.java
                                                                  • CMLDictionary.java
                                                                  • CMLEigen.java
                                                                  • CMLElectron.java
                                                                  • CMLElementConstants.java
                                                                  • CMLEntry.java
                                                                  • CMLExpression.java
                                                                  • CMLFormula.java
                                                                  • CMLFragment.java
                                                                  • CMLFragmentList.java
                                                                  • CMLGradient.java
                                                                  • CMLIdentifier.java
                                                                  • CMLIsotope.java
                                                                  • CMLIsotopeList.java
                                                                  • CMLJoin.java
                                                                  • CMLKpoint.java
                                                                  • CMLKpointList.java
                                                                  • CMLLabel.java
                                                                  • CMLLattice.java
                                                                  • CMLLatticeVector.java
                                                                  • CMLLength.java
                                                                  • CMLLine3.java
                                                                  • CMLLink.java
                                                                  • CMLList.java
                                                                  • CMLMap.java
                                                                  • CMLMatrix.java
                                                                  • CMLMechanism.java
                                                                  • CMLMechanismComponent.java
                                                                  • CMLMetadata.java
                                                                  • CMLMetadataList.java
                                                                  • CMLModule.java
                                                                  • CMLMolecule.java
                                                                  • CMLMoleculeList.java
                                                                  • CMLName.java
                                                                  • CMLObject.java
                                                                  • CMLObservation.java
                                                                  • CMLOperator.java
                                                                  • CMLParameter.java
                                                                  • CMLParameterList.java
                                                                  • CMLParticle.java
                                                                  • CMLPeak.java
                                                                  • CMLPeakGroup.java
                                                                  • CMLPeakList.java
                                                                  • CMLPeakStructure.java
                                                                  • CMLPlane3.java
                                                                  • CMLPoint3.java
                                                                  • CMLPotential.java
                                                                  • CMLPotentialForm.java
                                                                  • CMLPotentialList.java
                                                                  • CMLProduct.java
                                                                  • CMLProductList.java
                                                                  • CMLProperty.java
                                                                  • CMLPropertyList.java
                                                                  • CMLReactant.java
                                                                  • CMLReactantList.java
                                                                  • CMLReaction.java
                                                                  • CMLReactionConstants.java
                                                                  • CMLReactionList.java
                                                                  • CMLReactionScheme.java
                                                                  • CMLReactionStep.java
                                                                  • CMLReactionStepList.java
                                                                  • CMLReactiveCentre.java
                                                                  • CMLRegion.java
                                                                  • CMLRelatedEntry.java
                                                                  • CMLSample.java
                                                                  • CMLScalar.java
                                                                  • CMLSpectator.java
                                                                  • CMLSpectatorList.java
                                                                  • CMLSpectrum.java
                                                                  • CMLSpectrumData.java
                                                                  • CMLSpectrumList.java
                                                                  • CMLSphere3.java
                                                                  • CMLSubstance.java
                                                                  • CMLSubstanceList.java
                                                                  • CMLSymmetry.java
                                                                  • CMLSystem.java
                                                                  • CMLTable.java
                                                                  • CMLTableCell.java
                                                                  • CMLTableContent.java
                                                                  • CMLTableHeader.java
                                                                  • CMLTableHeaderCell.java
                                                                  • CMLTableRow.java
                                                                  • CMLTableRowList.java
                                                                  • CMLTorsion.java
                                                                  • CMLTransform3.java
                                                                  • CMLTransitionState.java
                                                                  • CMLVector3.java
                                                                  • CMLXaxis.java
                                                                  • CMLYaxis.java
                                                                  • CMLZMatrix.java
                                                                  • FullTorsion.java
                                                                  • ReactionComponent.java
                                                                  • Sprout.java
                                                                • interfacex
                                                                  • HasArraySize.java
                                                                  • HasDataType.java
                                                                  • HasDictRef.java
                                                                  • HasScalar.java
                                                                  • HasUnits.java
                                                                  • PeakOrGroup.java
                                                              • euclid
                                                                • Angle.java
                                                                • ArrayBase.java
                                                                • Axis.java
                                                                • Complex.java
                                                                • Diagonalise.java
                                                                • DoubleTool.java
                                                                • Euclid.java
                                                                • EuclidConstants.java
                                                                • EuclidException.java
                                                                • EuclidRuntimeException.java
                                                                • Int.java
                                                                • Int2.java
                                                                • Int2Array.java
                                                                • Int2Range.java
                                                                • IntArray.java
                                                                • IntMatrix.java
                                                                • IntRange.java
                                                                • IntSet.java
                                                                • IntSquareMatrix.java
                                                                • Line2.java
                                                                • Line3.java
                                                                • Plane3.java
                                                                • Point2.java
                                                                • Point3.java
                                                                • Point3Vector.java
                                                                • Polar.java
                                                                • RandomNumberGenerator.java
                                                                • Real.java
                                                                • Real2.java
                                                                • Real2Array.java
                                                                • Real2Interval.java
                                                                • Real2Range.java
                                                                • Real2Vector.java
                                                                • Real3Range.java
                                                                • RealArray.java
                                                                • RealInterval.java
                                                                • RealMatrix.java
                                                                • RealRange.java
                                                                • RealSquareMatrix.java
                                                                • StringIntegerComparator.java
                                                                • Transform2.java
                                                                • Transform3.java
                                                                • Univariate.java
                                                                • Util.java
                                                                • Vector2.java
                                                                • Vector3.java
                                                                • Window2.java
                                                              • molutil
                                                                • ChemicalElement.java
                                                                • elementdata.xml
                                                                • Molutils.java
                                                            • xmlpull
                                                              • mxp1
                                                                • MXParser.java
                                                                • MXParserCachingStrings.java
                                                                • MXParserFactory.java
                                                                • MXParserNonValidating.java
                                                              • mxp1_serializer
                                                                • MXSerializer.java
                                                              • v1
                                                                • builder
                                                                  • adapter
                                                                    • XmlAttributeAdapter.java
                                                                    • XmlDocumentAdapter.java
                                                                    • XmlElementAdapter.java
                                                                  • impl
                                                                    • XmlAttributeImpl.java
                                                                    • XmlCommentImpl.java
                                                                    • XmlDocumentImpl.java
                                                                    • XmlElementImpl.java
                                                                    • XmlInfosetBuilderImpl.java
                                                                    • XmlNamespaceImpl.java
                                                                  • Iterable.java
                                                                  • XmlAttribute.java
                                                                  • XmlBuilderException.java
                                                                  • XmlCharacters.java
                                                                  • XmlComment.java
                                                                  • XmlContained.java
                                                                  • XmlContainer.java
                                                                  • XmlDoctype.java
                                                                  • XmlDocument.java
                                                                  • XmlElement.java
                                                                  • XmlInfosetBuilder.java
                                                                  • XmlNamespace.java
                                                                  • XmlNotation.java
                                                                  • XmlProcessingInstruction.java
                                                                  • XmlSerializable.java
                                                                  • XmlUnexpandedEntityReference.java
                                                                  • XmlUnparsedEntity.java
                                                                • dom2_builder
                                                                  • DOM2XmlPullBuilder.java
                                                                • parser_pool
                                                                  • XmlPullParserPool.java
                                                                • sax2
                                                                  • Driver.java
                                                                • util
                                                                  • XmlPullUtil.java
                                                                • wrapper
                                                                  • classic
                                                                    • StaticXmlPullParserWrapper.java
                                                                    • StaticXmlSerializerWrapper.java
                                                                    • XmlPullParserDelegate.java
                                                                    • XmlSerializerDelegate.java
                                                                  • XmlPullParserWrapper.java
                                                                  • XmlPullWrapperFactory.java
                                                                  • XmlSerializerWrapper.java
                                                                • XmlPullParser.java
                                                                • XmlPullParserException.java
                                                                • XmlPullParserFactory.java
                                                                • XmlSerializer.java
                                                            • _3pq
                                                              • jgrapht
                                                                • alg
                                                                  • ConnectivityInspector.java
                                                                  • CycleDetector.java
                                                                  • DijkstraShortestPath.java
                                                                  • StrongConnectivityInspector.java
                                                                  • util
                                                                    • VertexDegreeComparator.java
                                                                  • VertexCovers.java
                                                                • demo
                                                                  • HelloJGraphT.java
                                                                  • JGraphAdapterDemo.java
                                                                  • PerformanceDemo.java
                                                                • DirectedGraph.java
                                                                • edge
                                                                  • DefaultEdge.java
                                                                  • DirectedEdge.java
                                                                  • DirectedWeightedEdge.java
                                                                  • EdgeFactories.java
                                                                  • UndirectedEdge.java
                                                                  • UndirectedWeightedEdge.java
                                                                • Edge.java
                                                                • EdgeFactory.java
                                                                • event
                                                                  • ConnectedComponentTraversalEvent.java
                                                                  • EdgeTraversalEvent.java
                                                                  • GraphChangeEvent.java
                                                                  • GraphEdgeChangeEvent.java
                                                                  • GraphListener.java
                                                                  • GraphVertexChangeEvent.java
                                                                  • TraversalListener.java
                                                                  • TraversalListenerAdapter.java
                                                                  • VertexSetListener.java
                                                                  • VertexTraversalEvent.java
                                                                • ext
                                                                  • JGraphModelAdapter.java
                                                                  • VisioExporter.java
                                                                • generate
                                                                  • EmptyGraphGenerator.java
                                                                  • GraphGenerator.java
                                                                  • LinearGraphGenerator.java
                                                                  • RingGraphGenerator.java
                                                                  • WheelGraphGenerator.java
                                                                • graph
                                                                  • AbstractBaseGraph.java
                                                                  • AbstractGraph.java
                                                                  • AsUndirectedGraph.java
                                                                  • DefaultDirectedGraph.java
                                                                  • DefaultDirectedWeightedGraph.java
                                                                  • DefaultListenableGraph.java
                                                                  • DirectedMultigraph.java
                                                                  • DirectedSubgraph.java
                                                                  • DirectedWeightedMultigraph.java
                                                                  • DirectedWeightedSubgraph.java
                                                                  • EdgeListFactory.java
                                                                  • GraphDelegator.java
                                                                  • ListenableDirectedGraph.java
                                                                  • ListenableDirectedWeightedGraph.java
                                                                  • ListenableUndirectedGraph.java
                                                                  • ListenableUndirectedWeightedGraph.java
                                                                  • Multigraph.java
                                                                  • Pseudograph.java
                                                                  • SimpleDirectedGraph.java
                                                                  • SimpleDirectedWeightedGraph.java
                                                                  • SimpleGraph.java
                                                                  • SimpleWeightedGraph.java
                                                                  • Subgraph.java
                                                                  • UndirectedSubgraph.java
                                                                  • UndirectedWeightedSubgraph.java
                                                                  • UnmodifiableDirectedGraph.java
                                                                  • UnmodifiableGraph.java
                                                                  • UnmodifiableUndirectedGraph.java
                                                                  • WeightedMultigraph.java
                                                                  • WeightedPseudograph.java
                                                                • Graph.java
                                                                • GraphHelper.java
                                                                • LabeledElement.java
                                                                • ListenableGraph.java
                                                                • traverse
                                                                  • AbstractGraphIterator.java
                                                                  • BreadthFirstIterator.java
                                                                  • ClosestFirstIterator.java
                                                                  • CrossComponentIterator.java
                                                                  • DepthFirstIterator.java
                                                                  • GraphIterator.java
                                                                  • TopologicalOrderIterator.java
                                                                • UndirectedGraph.java
                                                                • util
                                                                  • FibonacciHeap.java
                                                                  • ModifiableInteger.java
                                                                • VertexFactory.java
                                                                • WeightedGraph.java
                                                          • pcore.javafiles
                                                          • pdb.javafiles
                                                          • pdbcml.javafiles
                                                          • qm.javafiles
                                                          • qsar-descriptors.set
                                                          • qsar.javafiles
                                                          • qsaratomic.javafiles
                                                          • qsarbond.javafiles
                                                          • qsarcml.javafiles
                                                          • qsarionpot.javafiles
                                                          • qsarmolecular.javafiles
                                                          • qsarprotein.javafiles
                                                          • reaction-types.set
                                                          • reaction.javafiles
                                                          • render.javafiles
                                                          • renderbasic.javafiles
                                                          • sdg.javafiles
                                                          • signature
                                                            • AbstractGraphBuilder.java
                                                            • AbstractGraphSignature.java
                                                            • AbstractQuotientGraph.java
                                                            • AbstractVertexSignature.java
                                                            • CanonicalLabellingVisitor.java
                                                            • chemistry
                                                              • AtomPermutor.java
                                                              • AtomSignature.java
                                                              • ChiralCenterFinder.java
                                                              • ChiralityTest.java
                                                              • LargeMoleculeTest.java
                                                              • Molecule.java
                                                              • MoleculeBuilder.java
                                                              • MoleculeFactory.java
                                                              • MoleculeQuotientGraph.java
                                                              • MoleculeReader.java
                                                              • MoleculeSignature.java
                                                              • MoleculeSignatureTest.java
                                                              • MoleculeWriter.java
                                                              • MultipleBondTest.java
                                                              • NumberLabelsTest.java
                                                              • SDFToSignatures.java
                                                              • WriterTest.java
                                                            • ColoredTree.java
                                                            • ColoredTreeVisitor.java
                                                            • DAG.java
                                                            • DAGVisitor.java
                                                            • display
                                                              • ColoredTreePanel.java
                                                              • DisplayableColoredTree.java
                                                              • SignatureViewer.java
                                                              • TestColoredTreePanel.java
                                                              • TestMultipleTrees.java
                                                              • TreeDrawer.java
                                                            • HeightTest.java
                                                            • InvariantArray.java
                                                            • InvariantInt.java
                                                            • InvariantIntIntPair.java
                                                            • InvariantIntStringPair.java
                                                            • InvariantList.java
                                                            • Invariants.java
                                                            • ParsingTest.java
                                                            • PermutationTest.java
                                                            • Permutor.java
                                                            • simple
                                                              • CanonicalLabellingTest.java
                                                              • ReconstructionTest.java
                                                              • SimpleGraph.java
                                                              • SimpleGraphBuilder.java
                                                              • SimpleGraphFactory.java
                                                              • SimpleGraphPermutor.java
                                                              • SimpleGraphSignature.java
                                                              • SimpleGraphTest.java
                                                              • SimpleQuotientGraph.java
                                                              • SimpleQuotientGraphTest.java
                                                              • SimpleVertexSignature.java
                                                            • SymmetryClass.java
                                                            • VirtualGraphBuilder.java
                                                            • VisitableColoredTree.java
                                                            • VisitableDAG.java
                                                          • signature.javafiles
                                                          • smarts.javafiles
                                                          • smiles.javafiles
                                                          • smsd.javafiles
                                                          • standard.javafiles
                                                          • structgen.javafiles
                                                          • tautomer.javafiles
                                                          • valencycheck.javafiles
                                                          • vocabularies
                                                            • assembler.n3
                                                            • daml+oil-2000-12.daml
                                                            • daml+oil.daml
                                                            • dublin-core_11.xml
                                                            • dublin-core_terms.xml
                                                            • dublin-core_types.xml
                                                            • jena-model-spec.n3
                                                            • jenavocab.rdf
                                                            • location-mapping-rdfs.n3
                                                            • ont-event.rdf
                                                            • ont-manager.rdf
                                                            • owl.owl
                                                            • rdf-schema.rdf
                                                            • result-set.n3
                                                            • test-manifest-x.n3
                                                            • test-manifest.n3
                                                            • test-query.n3
                                                          • XPP3_1.1.4c_VERSION