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cdk.jar.zip
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.mavenResources.target.classes
annotation.javafiles
atomtype.javafiles
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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