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Hierarchy For All Packages
Package Hierarchies:
aamtool.rgroup
,
aamtool.rxndecoder
,
org.openscience.cdk.smiles
,
org.openscience.smsd
,
org.openscience.smsd.algorithm.matchers
,
org.openscience.smsd.algorithm.mcgregor
,
org.openscience.smsd.algorithm.mcsplus
,
org.openscience.smsd.algorithm.rgraph
,
org.openscience.smsd.algorithm.single
,
org.openscience.smsd.algorithm.vflib
,
org.openscience.smsd.algorithm.vflib.builder
,
org.openscience.smsd.algorithm.vflib.interfaces
,
org.openscience.smsd.algorithm.vflib.map
,
org.openscience.smsd.algorithm.vflib.query
,
org.openscience.smsd.algorithm.vflib.seeds
,
org.openscience.smsd.algorithm.vflib.substructure
,
org.openscience.smsd.filters
,
org.openscience.smsd.helper
,
org.openscience.smsd.interfaces
,
org.openscience.smsd.mcss
,
org.openscience.smsd.ring
,
org.openscience.smsd.tools
,
uk.ac.ebi.aamtool
,
uk.ac.ebi.centres
,
uk.ac.ebi.centres.calculator
,
uk.ac.ebi.centres.cdk
,
uk.ac.ebi.centres.descriptor
,
uk.ac.ebi.centres.exception
,
uk.ac.ebi.centres.graph
,
uk.ac.ebi.centres.io
,
uk.ac.ebi.centres.ligand
,
uk.ac.ebi.centres.priority
,
uk.ac.ebi.centres.priority.access
,
uk.ac.ebi.centres.priority.access.descriptor
,
uk.ac.ebi.centres.priority.descriptor
,
uk.ac.ebi.reactionblast.containers
,
uk.ac.ebi.reactionblast.fingerprints
,
uk.ac.ebi.reactionblast.fingerprints.interfaces
,
uk.ac.ebi.reactionblast.fingerprints.tools
,
uk.ac.ebi.reactionblast.graphics.direct
,
uk.ac.ebi.reactionblast.graphics.direct.awtlayout
,
uk.ac.ebi.reactionblast.graphics.direct.layout
,
uk.ac.ebi.reactionblast.interfaces
,
uk.ac.ebi.reactionblast.io.filesystem
,
uk.ac.ebi.reactionblast.mapping
,
uk.ac.ebi.reactionblast.mapping.algorithm
,
uk.ac.ebi.reactionblast.mapping.algorithm.checks
,
uk.ac.ebi.reactionblast.mapping.blocks
,
uk.ac.ebi.reactionblast.mapping.container
,
uk.ac.ebi.reactionblast.mapping.container.helper
,
uk.ac.ebi.reactionblast.mapping.fixer
,
uk.ac.ebi.reactionblast.mapping.graph
,
uk.ac.ebi.reactionblast.mapping.helper
,
uk.ac.ebi.reactionblast.mapping.interfaces
,
uk.ac.ebi.reactionblast.mechanism
,
uk.ac.ebi.reactionblast.mechanism.helper
,
uk.ac.ebi.reactionblast.mechanism.interfaces
,
uk.ac.ebi.reactionblast.signature
,
uk.ac.ebi.reactionblast.stereo
,
uk.ac.ebi.reactionblast.stereo.compare
,
uk.ac.ebi.reactionblast.stereo.ebi
,
uk.ac.ebi.reactionblast.stereo.inchi
,
uk.ac.ebi.reactionblast.stereo.tools
,
uk.ac.ebi.reactionblast.stereo.wedge
,
uk.ac.ebi.reactionblast.tools
,
uk.ac.ebi.reactionblast.tools.bulk
,
uk.ac.ebi.reactionblast.tools.descriptors
,
uk.ac.ebi.reactionblast.tools.inchi
,
uk.ac.ebi.reactionblast.tools.labelling
,
uk.ac.ebi.reactionblast.tools.matrix
,
uk.ac.ebi.reactionblast.tools.rxnfile
,
uk.ac.ebi.reactionblast.tools.utility
Class Hierarchy
java.lang.Object
uk.ac.ebi.centres.
Abstract2DSignCalculator
<A> (implements uk.ac.ebi.centres.
SignCalculator
<A>)
uk.ac.ebi.reactionblast.graphics.direct.awtlayout.
AbstractAWTLayout
<T>
uk.ac.ebi.reactionblast.graphics.direct.awtlayout.
AbstractAWTReactionLayout
uk.ac.ebi.reactionblast.graphics.direct.awtlayout.
LeftToRightAWTReactionLayout
uk.ac.ebi.reactionblast.graphics.direct.awtlayout.
TopToBottomAWTReactionLayout
uk.ac.ebi.reactionblast.graphics.direct.awtlayout.
AtomLayout
uk.ac.ebi.reactionblast.graphics.direct.awtlayout.
LinearAtomContainerSetLayout
uk.ac.ebi.reactionblast.graphics.direct.awtlayout.
MoleculeLayout
uk.ac.ebi.reactionblast.graphics.direct.layout.
AbstractCanvasGenerator
(implements uk.ac.ebi.reactionblast.graphics.direct.layout.
CanvasGenerator
)
uk.ac.ebi.reactionblast.graphics.direct.layout.
CircularCanvasGenerator
(implements uk.ac.ebi.reactionblast.graphics.direct.layout.
CanvasGenerator
)
uk.ac.ebi.reactionblast.graphics.direct.layout.
GridCanvasGenerator
(implements uk.ac.ebi.reactionblast.graphics.direct.layout.
CanvasGenerator
)
java.util.AbstractCollection<E> (implements java.util.Collection<E>)
java.util.AbstractList<E> (implements java.util.List<E>)
java.util.ArrayList<E> (implements java.lang.Cloneable, java.util.List<E>, java.util.RandomAccess, java.io.Serializable)
uk.ac.ebi.reactionblast.tools.utility.
EBIArrayList
<E>
uk.ac.ebi.centres.graph.
AbstractDigraph
<A> (implements uk.ac.ebi.centres.
ConnectionProvider
<A>, uk.ac.ebi.centres.
Digraph
<A>)
uk.ac.ebi.centres.graph.
ConnectionTableDigraph
<A>
uk.ac.ebi.reactionblast.graphics.direct.
AbstractDirectDrawer
uk.ac.ebi.reactionblast.graphics.direct.
AbstractHighlightDrawer
uk.ac.ebi.reactionblast.graphics.direct.
OutlineHighlighter
(implements uk.ac.ebi.reactionblast.graphics.direct.
Highlighter
)
uk.ac.ebi.reactionblast.graphics.direct.
SimpleHighlighter
(implements uk.ac.ebi.reactionblast.graphics.direct.
Highlighter
)
uk.ac.ebi.reactionblast.graphics.direct.
DirectArrowDrawer
uk.ac.ebi.reactionblast.graphics.direct.
DirectAtomDrawer
uk.ac.ebi.reactionblast.graphics.direct.
DirectBondDrawer
uk.ac.ebi.reactionblast.graphics.direct.
DirectHullDrawer
uk.ac.ebi.reactionblast.graphics.direct.
DirectMoleculeDrawer
uk.ac.ebi.reactionblast.graphics.direct.
DirectRBLastReactionDrawer
uk.ac.ebi.reactionblast.graphics.direct.
DirectReactionDrawer
uk.ac.ebi.reactionblast.graphics.direct.
MoleculeLabelDrawer
uk.ac.ebi.reactionblast.graphics.direct.layout.
AbstractDirectLayout
<T>
uk.ac.ebi.reactionblast.graphics.direct.layout.
AbstractDirectReactionLayout
uk.ac.ebi.reactionblast.graphics.direct.layout.
LeftToRightReactionLayout
uk.ac.ebi.reactionblast.graphics.direct.layout.
TopToBottomReactionLayout
uk.ac.ebi.reactionblast.graphics.direct.layout.
LinearMoleculeSetLayout
uk.ac.ebi.reactionblast.graphics.direct.layout.
SingleMoleculeLayout
uk.ac.ebi.reactionblast.graphics.direct.awtlayout.
ZoomToFitAWTLayout
uk.ac.ebi.reactionblast.graphics.direct.layout.
ZoomToFitLayout
signature.AbstractGraphBuilder
uk.ac.ebi.reactionblast.signature.
RBlastMoleculeFromSignatureBuilder
signature.AbstractGraphSignature
uk.ac.ebi.reactionblast.signature.
BaseMoleculeSignature
uk.ac.ebi.reactionblast.signature.
RBlastMoleculeSignature
uk.ac.ebi.reactionblast.mapping.blocks.
SubgraphMoleculeSignature
uk.ac.ebi.centres.ligand.
AbstractLigand
<A> (implements uk.ac.ebi.centres.
Ligand
<A>)
uk.ac.ebi.centres.ligand.
NonterminalLigand
<A>
uk.ac.ebi.centres.ligand.
TerminalLigand
<A>
uk.ac.ebi.centres.ligand.
PlanarCentre
<A> (implements uk.ac.ebi.centres.
Centre
<A>)
uk.ac.ebi.centres.ligand.
TetrahedralCentre
<A> (implements uk.ac.ebi.centres.
Centre
<A>)
uk.ac.ebi.centres.priority.
AbstractPriorityRule
<A> (implements uk.ac.ebi.centres.
PriorityRule
<A>)
uk.ac.ebi.centres.priority.
AtomicNumberRule
<A>
uk.ac.ebi.centres.priority.
CombinedRule
<A>
uk.ac.ebi.centres.priority.descriptor.
DescriptorRule
<A>
uk.ac.ebi.centres.priority.descriptor.
RSRule
<A>
uk.ac.ebi.centres.priority.descriptor.
ZERule
<A>
uk.ac.ebi.centres.priority.
DuplicateAtomRule
<A>
uk.ac.ebi.centres.priority.
MassNumberRule
<A>
uk.ac.ebi.centres.priority.descriptor.
PairRule
<A>
uk.ac.ebi.reactionblast.tools.labelling.
AbstractReactionLabeller
uk.ac.ebi.reactionblast.signature.
RBlastSignatureReactionCanoniser
(implements uk.ac.ebi.reactionblast.tools.labelling.
ICanonicalReactionLabeller
)
uk.ac.ebi.reactionblast.tools.labelling.
SignatureReactionCanoniser
(implements uk.ac.ebi.reactionblast.tools.labelling.
ICanonicalReactionLabeller
)
uk.ac.ebi.reactionblast.tools.labelling.
SmilesReactionCanoniser
(implements uk.ac.ebi.reactionblast.tools.labelling.
ICanonicalReactionLabeller
)
uk.ac.ebi.centres.calculator.
AbstractSignCalculator
<A> (implements uk.ac.ebi.centres.
SignCalculator
<A>)
uk.ac.ebi.centres.calculator.
ThreeDimensionalSignCalculator
<A>
uk.ac.ebi.centres.cdk.
CDK3DSignCalculator
uk.ac.ebi.centres.calculator.
TwoDimensionalSignCalculator
<A>
uk.ac.ebi.centres.cdk.
CDK2DSignCalculator
signature.AbstractVertexSignature
uk.ac.ebi.reactionblast.signature.
RBlastAtomSignature
uk.ac.ebi.reactionblast.mapping.blocks.
SubgraphAtomSignature
uk.ac.ebi.aamtool.
Annotator
uk.ac.ebi.aamtool.
ReactionDecoder
uk.ac.ebi.centres.graph.
Arc
<A>
uk.ac.ebi.centres.priority.access.descriptor.
ArcPrimaryDescriptor
<A> (implements uk.ac.ebi.centres.priority.access.
DescriptorAccessor
<A>)
uk.ac.ebi.reactionblast.graphics.direct.layout.
ArrowWheel
org.openscience.smsd.
AtomAtomMapping
(implements java.io.Serializable)
uk.ac.ebi.reactionblast.mechanism.helper.
AtomAtomMappingContainer
(implements java.io.Serializable)
org.openscience.smsd.tools.
AtomContainerComparator
(implements java.util.Comparator<T>)
uk.ac.ebi.reactionblast.graphics.direct.
AtomContainerComparatorBy2DCenter
(implements java.util.Comparator<T>)
org.openscience.cdk.tools.manipulator.AtomContainerManipulator
uk.ac.ebi.reactionblast.tools.
ExtAtomContainerManipulator
(implements java.io.Serializable)
uk.ac.ebi.reactionblast.tools.labelling.
AtomContainerPrinter
uk.ac.ebi.reactionblast.tools.
AtomContainerSetComparator
(implements java.util.Comparator<T>)
uk.ac.ebi.reactionblast.mechanism.helper.
AtomStereoChangeInformation
(implements java.io.Serializable)
uk.ac.ebi.centres.priority.access.descriptor.
AuxiliaryDescriptor
<A> (implements uk.ac.ebi.centres.priority.access.
DescriptorAccessor
<A>)
org.openscience.smsd.filters.
BaseFilter
org.openscience.smsd.filters.
ChemicalFilters
org.openscience.smsd.
BaseMapping
(implements org.openscience.smsd.interfaces.
IAtomMapping
)
org.openscience.smsd.
Isomorphism
(implements java.io.Serializable)
org.openscience.smsd.
Substructure
org.openscience.smsd.algorithm.vflib.
BaseMCS
org.openscience.smsd.algorithm.vflib.
VF2MCS
(implements org.openscience.smsd.interfaces.
IResults
)
uk.ac.ebi.centres.graph.
BasicConnectionTable
<A> (implements uk.ac.ebi.centres.
ConnectionTable
<A>)
uk.ac.ebi.centres.cdk.
CDKConnectionTable
uk.ac.ebi.reactionblast.tools.
BasicDebugger
uk.ac.ebi.reactionblast.mapping.container.
CDKReactionBuilder
(implements java.io.Serializable)
uk.ac.ebi.reactionblast.mapping.helper.
Debugger
uk.ac.ebi.reactionblast.mapping.algorithm.
BaseGameTheory
(implements uk.ac.ebi.reactionblast.mapping.interfaces.
IGameTheory
, java.io.Serializable)
uk.ac.ebi.reactionblast.mapping.algorithm.
GameTheoryMatrix
(implements uk.ac.ebi.reactionblast.mapping.interfaces.
IGraphTheoryMatrix
)
uk.ac.ebi.reactionblast.mapping.graph.
GraphMatcher
uk.ac.ebi.reactionblast.mapping.algorithm.
Holder
(implements java.lang.Cloneable, java.io.Serializable)
uk.ac.ebi.reactionblast.mapping.helper.
MappingHandler
uk.ac.ebi.reactionblast.mapping.helper.
AbstractReactor
uk.ac.ebi.reactionblast.mapping.
Reactor
(implements java.io.Serializable)
uk.ac.ebi.reactionblast.tools.rxnfile.
RXNFileManipulator
uk.ac.ebi.reactionblast.mapping.interfaces.
BestMatch
uk.ac.ebi.reactionblast.mapping.container.
BestMatchContainer
(implements java.io.Serializable)
org.openscience.smsd.helper.
BinaryTree
java.util.BitSet (implements java.lang.Cloneable, java.io.Serializable)
uk.ac.ebi.reactionblast.tools.utility.
EBIBitSet
org.openscience.smsd.algorithm.mcsplus.
BKKCKCF
uk.ac.ebi.reactionblast.mapping.blocks.
Block
(implements java.lang.Comparable<T>)
uk.ac.ebi.reactionblast.mapping.blocks.
BlockList
(implements java.lang.Comparable<T>)
uk.ac.ebi.reactionblast.mapping.blocks.
BlockMapper
uk.ac.ebi.reactionblast.mapping.blocks.
BlockMapping
uk.ac.ebi.reactionblast.mapping.blocks.
BlockPair
uk.ac.ebi.reactionblast.mapping.blocks.
BlockReactionCanoniser
(implements uk.ac.ebi.reactionblast.tools.labelling.
ICanonicalReactionLabeller
)
uk.ac.ebi.reactionblast.mechanism.helper.
BondChange
(implements java.io.Serializable)
uk.ac.ebi.reactionblast.tools.bulk.
BondChangeCalculationTransformation
(implements uk.ac.ebi.reactionblast.interfaces.
ITransformation
<T>)
org.openscience.smsd.tools.
BondEnergies
org.openscience.smsd.helper.
BondEnergy
uk.ac.ebi.reactionblast.graphics.direct.layout.
BoundsPrinter
uk.ac.ebi.reactionblast.graphics.direct.layout.
BoundsTree
(implements java.lang.Iterable<T>)
uk.ac.ebi.reactionblast.tools.bulk.
BulkTransformer
uk.ac.ebi.reactionblast.mapping.algorithm.
CalculationProcess
(implements java.io.Serializable)
uk.ac.ebi.reactionblast.mapping.
CallableAtomMappingTool
(implements java.io.Serializable)
uk.ac.ebi.reactionblast.mapping.
CanonicalNumberingGenerator
org.openscience.cdk.smiles.
CanonSmiAdapter
uk.ac.ebi.centres.cdk.
CDKCentreProvider
(implements uk.ac.ebi.centres.
CentreProvider
<A>)
uk.ac.ebi.reactionblast.tools.inchi.
CDKInChI
uk.ac.ebi.centres.cdk.
CDKManager
(implements uk.ac.ebi.centres.
DescriptorManager
<A>)
org.openscience.smsd.algorithm.rgraph.
CDKMCS
org.openscience.smsd.algorithm.rgraph.
CDKMCSHandler
(implements org.openscience.smsd.interfaces.
IResults
)
org.openscience.smsd.algorithm.rgraph.
CDKRGraph
org.openscience.smsd.algorithm.rgraph.
CDKRMapHandler
org.openscience.smsd.algorithm.rgraph.
CDKRNode
uk.ac.ebi.reactionblast.tools.
CDKSMILES
org.openscience.smsd.algorithm.rgraph.
CDKSubGraphHandler
(implements org.openscience.smsd.interfaces.
IResults
)
org.openscience.cdk.io.ChemObjectIO (implements org.openscience.cdk.io.IChemObjectIO)
org.openscience.cdk.io.DefaultChemObjectReader (implements org.openscience.cdk.io.ISimpleChemObjectReader)
uk.ac.ebi.reactionblast.tools.rxnfile.
MDLReaderBase
uk.ac.ebi.reactionblast.tools.rxnfile.
MDLRXNV2000Reader
uk.ac.ebi.reactionblast.tools.rxnfile.
MDLV2000Reader
org.openscience.cdk.io.DefaultChemObjectWriter (implements org.openscience.cdk.io.IChemObjectWriter)
uk.ac.ebi.reactionblast.tools.rxnfile.
MDLV2000RXNWriter
uk.ac.ebi.reactionblast.tools.rxnfile.
MDLV2000Writer
uk.ac.ebi.reactionblast.tools.rxnfile.
MDLWriterBase
uk.ac.ebi.reactionblast.stereo.tools.
Chirality2DTool
(implements uk.ac.ebi.reactionblast.stereo.compare.
ChiralityTool
)
uk.ac.ebi.reactionblast.stereo.tools.
Chirality3DTool
(implements uk.ac.ebi.reactionblast.stereo.compare.
ChiralityTool
)
uk.ac.ebi.reactionblast.stereo.compare.
ChiralityComparisonTool
uk.ac.ebi.reactionblast.tools.matrix.
CholeskyDecomposition
(implements java.io.Serializable)
uk.ac.ebi.centres.cdk.
CMLLoader
uk.ac.ebi.reactionblast.graphics.direct.
ColorRamp
uk.ac.ebi.reactionblast.mapping.graph.
Combination
(implements java.lang.Comparable<T>, java.util.Comparator<T>, java.io.Serializable)
aamtool.rxndecoder.
CommandLineOptions
uk.ac.ebi.aamtool.
CommandLineOptions
uk.ac.ebi.reactionblast.graphics.direct.
ConvexHull
(implements java.lang.Iterable<T>)
uk.ac.ebi.reactionblast.graphics.direct.
ConvexHull.Rectangle
uk.ac.ebi.reactionblast.graphics.direct.layout.
CoordinateFixer
uk.ac.ebi.reactionblast.tools.
CreateDirectory
uk.ac.ebi.reactionblast.tools.descriptors.
CXlogP
uk.ac.ebi.centres.io.
CytoscapeWriter
<A> (implements java.io.Closeable)
org.openscience.smsd.algorithm.matchers.
DefaultAtomMatcher
(implements org.openscience.smsd.algorithm.matchers.
AtomMatcher
)
org.openscience.smsd.algorithm.matchers.
DefaultAtomTypeMatcher
(implements org.openscience.smsd.algorithm.matchers.
AtomMatcher
)
org.openscience.smsd.algorithm.matchers.
DefaultBondMatcher
(implements org.openscience.smsd.algorithm.matchers.
BondMatcher
)
uk.ac.ebi.centres.graph.
DefaultDescriptorManager
<A> (implements uk.ac.ebi.centres.
DescriptorManager
<A>)
org.openscience.smsd.algorithm.matchers.
DefaultMatcher
uk.ac.ebi.centres.
DefaultPerceptor
<A> (implements uk.ac.ebi.centres.
Perceptor
<A>)
uk.ac.ebi.centres.cdk.
CDKPerceptor
uk.ac.ebi.reactionblast.mapping.blocks.
DefinedMapping
uk.ac.ebi.centres.priority.descriptor.
DescriptorList
(implements java.lang.Comparable<T>)
uk.ac.ebi.reactionblast.tools.
Distance
uk.ac.ebi.reactionblast.tools.utility.
EBIDoubleUtility
uk.ac.ebi.reactionblast.tools.
EBIMatrix
(implements java.lang.Cloneable, java.io.Serializable)
uk.ac.ebi.reactionblast.mechanism.
BEMatrix
(implements java.io.Serializable)
uk.ac.ebi.reactionblast.mechanism.
RMatrix
(implements java.io.Serializable)
uk.ac.ebi.reactionblast.tools.
EBIMolSplitter
aamtool.rgroup.
ECRgroupFrequency
org.openscience.smsd.algorithm.mcsplus.
Edge
(implements java.lang.Comparable<T>, java.util.Comparator<T>, java.io.Serializable)
org.openscience.smsd.algorithm.vflib.builder.
EdgeBuilder
(implements org.openscience.smsd.algorithm.vflib.interfaces.
IEdge
)
uk.ac.ebi.reactionblast.tools.matrix.
EigenvalueDecomposition
(implements java.io.Serializable)
org.openscience.smsd.algorithm.mcsplus.
ExactMapping
uk.ac.ebi.reactionblast.fingerprints.
Feature
(implements java.lang.Comparable<T>, java.util.Comparator<T>, uk.ac.ebi.reactionblast.fingerprints.interfaces.
IFeature
, java.io.Serializable)
uk.ac.ebi.reactionblast.io.filesystem.
FilesystemMoleculeDataSource
(implements uk.ac.ebi.reactionblast.interfaces.
IDataSource
<T>)
uk.ac.ebi.reactionblast.io.filesystem.
FilesystemMoleculeDataStore
(implements uk.ac.ebi.reactionblast.interfaces.
IDataStore
<T>)
uk.ac.ebi.reactionblast.io.filesystem.
FilesystemReactionDataSource
(implements uk.ac.ebi.reactionblast.interfaces.
IDataSource
<T>)
uk.ac.ebi.reactionblast.io.filesystem.
FilesystemReactionDataStore
(implements uk.ac.ebi.reactionblast.interfaces.
IDataStore
<T>)
uk.ac.ebi.reactionblast.containers.
FingerPrintContainer
(implements uk.ac.ebi.reactionblast.interfaces.
IFingerPrintContainer
)
uk.ac.ebi.reactionblast.fingerprints.
FingerprintGenerator
(implements uk.ac.ebi.reactionblast.fingerprints.interfaces.
IFingerprintGenerator
)
uk.ac.ebi.reactionblast.fingerprints.tools.
FingerprintSubset
(implements java.io.Serializable)
aamtool.rgroup.
FingerprintType
uk.ac.ebi.reactionblast.signature.
FixedLabeller
(implements uk.ac.ebi.reactionblast.tools.labelling.
ICanonicalMoleculeLabeller
)
org.openscience.smsd.mcss.
Fragment
(implements java.lang.Comparable<T>, java.io.Serializable)
uk.ac.ebi.reactionblast.mapping.algorithm.
GameTheoryFactory
(implements java.io.Serializable)
org.openscience.smsd.algorithm.mcsplus.
GenerateCompatibilityGraph
(implements java.io.Serializable)
uk.ac.ebi.reactionblast.mechanism.
GlobalEntropyCalculator
(implements java.io.Serializable)
org.openscience.smsd.ring.
HanserRingFinder
uk.ac.ebi.reactionblast.mapping.container.
HydrogenFreeFingerPrintContainer
(implements uk.ac.ebi.reactionblast.interfaces.
IFingerPrintContainer
, java.io.Serializable)
uk.ac.ebi.reactionblast.signature.
IdentityLabellingAdaptor
(implements uk.ac.ebi.reactionblast.tools.labelling.
ICanonicalMoleculeLabeller
)
uk.ac.ebi.reactionblast.mapping.interfaces.
IGraphMatching
uk.ac.ebi.reactionblast.mapping.graph.
GraphMatching
(implements java.io.Serializable)
uk.ac.ebi.reactionblast.tools.
ImageGenerator
uk.ac.ebi.reactionblast.containers.
InChIContainer
(implements java.lang.Cloneable, uk.ac.ebi.reactionblast.interfaces.
IInChIContainer
)
uk.ac.ebi.reactionblast.tools.labelling.
InChiMoleculeLabeller
(implements uk.ac.ebi.reactionblast.tools.labelling.
ICanonicalMoleculeLabeller
)
uk.ac.ebi.centres.priority.
InsertionSorter
<A> (implements uk.ac.ebi.centres.
LigandSorter
<A>)
uk.ac.ebi.reactionblast.mapping.helper.
IOReaction
org.openscience.smsd.tools.
IterationManager
(implements java.io.Serializable)
uk.ac.ebi.reactionblast.mapping.container.
KeggReactionFileContainer
(implements java.io.Serializable)
uk.ac.ebi.reactionblast.mapping.container.helper.
Key
(implements uk.ac.ebi.reactionblast.mapping.interfaces.
IKey
, java.io.Serializable)
org.openscience.smsd.helper.
LabelContainer
uk.ac.ebi.reactionblast.graphics.direct.
LabelManager
uk.ac.ebi.reactionblast.tools.
LayoutCheck
uk.ac.ebi.centres.
LigandComparison
(implements uk.ac.ebi.centres.
Comparison
)
uk.ac.ebi.reactionblast.tools.descriptors.
LipinskiRuleOfFiveDescriptor
uk.ac.ebi.reactionblast.tools.matrix.
LUDecomposition
(implements java.io.Serializable)
org.openscience.smsd.algorithm.vflib.
Map1ValueComparator
(implements java.util.Comparator<T>)
org.openscience.smsd.algorithm.vflib.
Map2ValueComparator
(implements java.util.Comparator<T>)
uk.ac.ebi.reactionblast.mapping.blocks.
MappingGraph
uk.ac.ebi.reactionblast.mapping.fixer.
MappingReferenceResolver
uk.ac.ebi.reactionblast.mechanism.
MappingSolution
(implements java.io.Serializable)
uk.ac.ebi.reactionblast.tools.bulk.
MappingTransformation
(implements uk.ac.ebi.reactionblast.interfaces.
ITransformation
<T>)
org.openscience.smsd.algorithm.vflib.map.
Match
uk.ac.ebi.reactionblast.tools.matrix.
Maths
uk.ac.ebi.reactionblast.mechanism.helper.
MatrixPrinter
uk.ac.ebi.reactionblast.mechanism.helper.
Utility
(implements java.io.Serializable)
uk.ac.ebi.reactionblast.mechanism.interfaces.
AbstractChangeCalculator
uk.ac.ebi.reactionblast.mechanism.
BondChangeCalculator
(implements uk.ac.ebi.reactionblast.mechanism.interfaces.
IChangeCalculator
)
uk.ac.ebi.reactionblast.stereo.ebi.
StereoCenteralityTool
uk.ac.ebi.reactionblast.mechanism.
BondChangeAnnotator
org.openscience.smsd.algorithm.mcgregor.
McGregor
org.openscience.smsd.algorithm.mcgregor.
McGregorChecks
org.openscience.smsd.algorithm.mcgregor.
McgregorHelper
org.openscience.smsd.algorithm.mcsplus.
MCSPlus
org.openscience.smsd.algorithm.mcsplus.
MCSPlusHandler
(implements org.openscience.smsd.interfaces.
IResults
)
org.openscience.smsd.mcss.
MCSS
org.openscience.smsd.algorithm.vflib.seeds.
MCSSeedGenerator
(implements java.util.concurrent.Callable<V>)
uk.ac.ebi.reactionblast.mapping.graph.
MCSSolution
(implements java.io.Serializable)
org.openscience.smsd.mcss.
MCSSThread
(implements java.util.concurrent.Callable<V>)
uk.ac.ebi.reactionblast.mapping.graph.
MCSThread
(implements java.util.concurrent.Callable<V>)
uk.ac.ebi.reactionblast.tools.rxnfile.
MDLFileReader
uk.ac.ebi.reactionblast.containers.
MolContainer
(implements uk.ac.ebi.reactionblast.interfaces.
IMolContainer
)
uk.ac.ebi.reactionblast.graphics.direct.layout.
MoleculeAligner
uk.ac.ebi.reactionblast.tools.bulk.
MoleculeCanonicalizationTransformation
(implements uk.ac.ebi.reactionblast.interfaces.
ITransformation
<T>)
org.openscience.smsd.helper.
MoleculeInitializer
uk.ac.ebi.reactionblast.tools.descriptors.
CDKMolecularDescriptor
(implements uk.ac.ebi.reactionblast.interfaces.
IMolDescriptors
)
uk.ac.ebi.reactionblast.mapping.container.
MoleculeMoleculeMapping
(implements java.io.Serializable)
uk.ac.ebi.reactionblast.mechanism.helper.
MoleculeMoleculePair
(implements java.lang.Comparable<T>, java.util.Comparator<T>, java.io.Serializable)
uk.ac.ebi.reactionblast.fingerprints.
MolFingerprint
(implements java.lang.Comparable<T>, java.util.Comparator<T>)
uk.ac.ebi.reactionblast.mapping.container.helper.
MolMapping
(implements java.io.Serializable)
uk.ac.ebi.centres.
MutableDescriptor
org.openscience.smsd.algorithm.vflib.builder.
NodeBuilder
(implements org.openscience.smsd.algorithm.vflib.interfaces.
INode
)
org.openscience.smsd.algorithm.vflib.substructure.
Pair
<T,S>
uk.ac.ebi.reactionblast.graphics.direct.
Params
org.openscience.smsd.ring.
PathEdge
org.openscience.smsd.ring.
PathGraph
uk.ac.ebi.reactionblast.fingerprints.
PatternFingerprinter
(implements java.lang.Cloneable, java.lang.Comparable<T>, java.util.Comparator<T>, uk.ac.ebi.reactionblast.fingerprints.interfaces.
IPatternFingerprinter
, java.io.Serializable)
uk.ac.ebi.reactionblast.tools.labelling.
Permutor
uk.ac.ebi.reactionblast.tools.labelling.
AtomContainerAtomPermutor
(implements java.util.Iterator<E>)
org.openscience.smsd.filters.
PostFilter
uk.ac.ebi.centres.priority.access.descriptor.
PrimaryDescriptor
<A> (implements uk.ac.ebi.centres.priority.access.
DescriptorAccessor
<A>)
uk.ac.ebi.centres.
Priority
uk.ac.ebi.centres.priority.access.
PsuedoAtomicNumberModifier
<A> (implements uk.ac.ebi.centres.priority.access.
AtomicNumberAccessor
<A>)
uk.ac.ebi.reactionblast.tools.matrix.
QRDecomposition
(implements java.io.Serializable)
org.openscience.smsd.algorithm.vflib.query.
QueryCompiler
(implements org.openscience.smsd.algorithm.vflib.interfaces.
IQueryCompiler
)
org.openscience.smsd.algorithm.mcgregor.
QueryProcessor
uk.ac.ebi.reactionblast.fingerprints.
RandomNumber
(implements java.io.Serializable)
uk.ac.ebi.reactionblast.signature.
RBlastAtomSignatureLabellingAdaptor
(implements uk.ac.ebi.reactionblast.tools.labelling.
ICanonicalMoleculeLabeller
)
uk.ac.ebi.reactionblast.tools.labelling.
RBlastMoleculeLabeller
(implements uk.ac.ebi.reactionblast.tools.labelling.
ICanonicalMoleculeLabeller
)
uk.ac.ebi.reactionblast.signature.
RBlastMoleculeSignatureLabellingAdaptor
(implements uk.ac.ebi.reactionblast.tools.labelling.
ICanonicalMoleculeLabeller
)
uk.ac.ebi.reactionblast.mapping.helper.
RBlastReaction
uk.ac.ebi.reactionblast.signature.
RBlastSmilesGenerator
uk.ac.ebi.reactionblast.mechanism.helper.
ReactantProductPair
(implements java.lang.Comparable<T>, java.util.Comparator<T>, java.io.Serializable)
uk.ac.ebi.reactionblast.tools.bulk.
ReactionAromatizationTransformation
(implements uk.ac.ebi.reactionblast.interfaces.
ITransformation
<T>)
uk.ac.ebi.reactionblast.tools.bulk.
ReactionAtomIDTransformation
(implements uk.ac.ebi.reactionblast.interfaces.
ITransformation
<T>)
uk.ac.ebi.reactionblast.tools.bulk.
ReactionCanonicalizationTransformation
(implements uk.ac.ebi.reactionblast.interfaces.
ITransformation
<T>)
uk.ac.ebi.reactionblast.mechanism.helper.
ReactionCenterFragment
(implements java.io.Serializable)
uk.ac.ebi.reactionblast.mapping.container.
ReactionContainer
(implements java.lang.Cloneable, java.io.Serializable)
uk.ac.ebi.reactionblast.containers.
ReactionDBContainer
(implements java.io.Serializable)
uk.ac.ebi.reactionblast.mapping.container.helper.
ReactionFileData
(implements java.io.Serializable)
uk.ac.ebi.reactionblast.fingerprints.
ReactionFingerprinter
(implements java.io.Serializable)
uk.ac.ebi.reactionblast.tools.bulk.
ReactionIdentityTransformation
(implements uk.ac.ebi.reactionblast.interfaces.
ITransformation
<T>)
uk.ac.ebi.reactionblast.tools.bulk.
ReactionImplicitHydrogenTransformation
(implements uk.ac.ebi.reactionblast.interfaces.
ITransformation
<T>)
uk.ac.ebi.reactionblast.containers.
ReactionInfoCollector
(implements java.io.Serializable)
uk.ac.ebi.reactionblast.mapping.algorithm.checks.
ReactionIsomorphismHandler
(implements java.io.Serializable)
org.openscience.cdk.tools.manipulator.ReactionManipulator
uk.ac.ebi.reactionblast.tools.
ExtReactionManipulatorTool
uk.ac.ebi.reactionblast.mechanism.
ReactionMechanismTool
(implements java.io.Serializable)
uk.ac.ebi.reactionblast.tools.
ReactionSimilarityTool
uk.ac.ebi.reactionblast.tools.bulk.
ReactionTransformationSequence
(implements uk.ac.ebi.reactionblast.interfaces.
ITransformation
<T>)
uk.ac.ebi.reactionblast.tools.
Reader
org.openscience.smsd.ring.
RingFilter
uk.ac.ebi.reactionblast.graphics.direct.
RootSystem
uk.ac.ebi.reactionblast.mapping.algorithm.checks.
RuleBasedMappingHandler
(implements java.io.Serializable)
uk.ac.ebi.reactionblast.tools.rxnfile.
RXNFileImporter
uk.ac.ebi.reactionblast.mapping.algorithm.checks.
Selector
(implements java.io.Serializable)
uk.ac.ebi.reactionblast.mapping.algorithm.checks.
ChooseWinner
(implements java.io.Serializable)
uk.ac.ebi.reactionblast.mapping.algorithm.checks.
IsomorphismMax
(implements uk.ac.ebi.reactionblast.mapping.interfaces.
IResult
)
uk.ac.ebi.reactionblast.mapping.algorithm.checks.
IsomorphismMin
(implements uk.ac.ebi.reactionblast.mapping.interfaces.
IResult
)
uk.ac.ebi.reactionblast.signature.
SignatureMatcher
uk.ac.ebi.reactionblast.tools.labelling.
SignatureMoleculeLabeller
(implements uk.ac.ebi.reactionblast.tools.labelling.
ICanonicalMoleculeLabeller
)
uk.ac.ebi.reactionblast.graphics.direct.
SignatureRootFinder
uk.ac.ebi.reactionblast.fingerprints.tools.
Similarity
uk.ac.ebi.aamtool.
SimilarityResult
org.openscience.smsd.algorithm.single.
SingleMapping
org.openscience.smsd.algorithm.single.
SingleMappingHandler
(implements org.openscience.smsd.interfaces.
IResults
)
uk.ac.ebi.reactionblast.tools.matrix.
SingularValueDecomposition
(implements java.io.Serializable)
uk.ac.ebi.reactionblast.tools.labelling.
SmilesMoleculeLabeller
(implements uk.ac.ebi.reactionblast.tools.labelling.
ICanonicalMoleculeLabeller
)
uk.ac.ebi.reactionblast.tools.utility.
SortMap
org.openscience.smsd.filters.
Sotter
org.openscience.smsd.filters.
EnergyFilter
(implements org.openscience.smsd.filters.
IChemicalFilter
<T>)
org.openscience.smsd.filters.
FragmentFilter
(implements org.openscience.smsd.filters.
IChemicalFilter
<T>)
org.openscience.smsd.filters.
StereoFilter
(implements org.openscience.smsd.filters.
IChemicalFilter
<T>)
uk.ac.ebi.reactionblast.tools.
StandardizeReaction
(implements uk.ac.ebi.reactionblast.interfaces.
IStandardizer
)
uk.ac.ebi.reactionblast.stereo.compare.
StereoCenterAnalyser
uk.ac.ebi.reactionblast.mechanism.
StereoChange
(implements java.io.Serializable)
uk.ac.ebi.reactionblast.mechanism.
StereogenicCenterCalculator
(implements java.io.Serializable)
uk.ac.ebi.reactionblast.tools.rxnfile.
Substructure
uk.ac.ebi.reactionblast.tools.utility.
Suffix
uk.ac.ebi.reactionblast.tools.rxnfile.
SuperAtomContainer
uk.ac.ebi.reactionblast.tools.rxnfile.
SuperAtoms
uk.ac.ebi.reactionblast.tools.rxnfile.
SuperBonds
org.openscience.smsd.algorithm.mcgregor.
TargetProcessor
uk.ac.ebi.reactionblast.tools.
TestUtility
uk.ac.ebi.reactionblast.tools.
MappingUtility
java.lang.Throwable (implements java.io.Serializable)
java.lang.Exception
java.lang.RuntimeException
uk.ac.ebi.centres.exception.
WarpCoreEjection
uk.ac.ebi.reactionblast.stereo.wedge.
StereoMatchException
org.openscience.smsd.tools.
TimeManager
uk.ac.ebi.reactionblast.tools.
ValencyCalculator
org.openscience.smsd.algorithm.vflib.substructure.
VF2
(implements org.openscience.smsd.interfaces.
IResults
)
org.openscience.smsd.algorithm.vflib.
VF2Sub
(implements org.openscience.smsd.interfaces.
IResults
)
org.openscience.smsd.algorithm.vflib.map.
VFMapper
(implements org.openscience.smsd.algorithm.vflib.interfaces.
IMapper
)
org.openscience.smsd.algorithm.vflib.map.
VFMCSMapper
(implements org.openscience.smsd.algorithm.vflib.interfaces.
IMapper
)
org.openscience.smsd.algorithm.vflib.map.
VFMCSState
(implements org.openscience.smsd.algorithm.vflib.interfaces.
IState
)
org.openscience.smsd.algorithm.vflib.builder.
VFQueryBuilder
(implements org.openscience.smsd.algorithm.vflib.interfaces.
IQuery
)
org.openscience.smsd.algorithm.vflib.map.
VFState
(implements org.openscience.smsd.algorithm.vflib.interfaces.
IState
)
uk.ac.ebi.reactionblast.stereo.wedge.
WedgeRule
uk.ac.ebi.reactionblast.stereo.wedge.
AbstractTetrahedralWedgeRule
uk.ac.ebi.reactionblast.stereo.wedge.
ACWTetrahedralWedgeRule
uk.ac.ebi.reactionblast.stereo.wedge.
CWTetrahedralWedgeRule
uk.ac.ebi.reactionblast.stereo.wedge.
FullTetrahedralWedgeRule
uk.ac.ebi.reactionblast.stereo.wedge.
ExplicitHydrogenSingleDownWedgeRule
uk.ac.ebi.reactionblast.stereo.wedge.
ExplicitHydrogenSingleUpWedgeRule
uk.ac.ebi.reactionblast.stereo.wedge.
SingleDownWedgeRule
uk.ac.ebi.reactionblast.stereo.wedge.
SingleUpWedgeRule
uk.ac.ebi.reactionblast.stereo.wedge.
WedgeStereoAnalyser
uk.ac.ebi.reactionblast.stereo.compare.
WedgeStereoComparisonResult
uk.ac.ebi.reactionblast.stereo.compare.
WedgeStereoComparisonTool
uk.ac.ebi.reactionblast.stereo.wedge.
WedgeStereoLifter
uk.ac.ebi.reactionblast.graphics.direct.
ZoomToFitDrawer
uk.ac.ebi.reactionblast.graphics.direct.layout.
ZoomToFitGridLayout
Interface Hierarchy
uk.ac.ebi.centres.priority.access.
AtomicNumberAccessor
<A>
org.openscience.smsd.algorithm.matchers.
AtomMatcher
org.openscience.smsd.algorithm.matchers.
BondMatcher
uk.ac.ebi.reactionblast.graphics.direct.layout.
CanvasGenerator
uk.ac.ebi.centres.
CentreProvider
<A>
uk.ac.ebi.reactionblast.stereo.compare.
ChiralityTool
java.lang.Comparable<T>
uk.ac.ebi.reactionblast.fingerprints.interfaces.
IFeature
uk.ac.ebi.reactionblast.mapping.interfaces.
IKey
(also extends java.util.Comparator<T>)
uk.ac.ebi.reactionblast.fingerprints.interfaces.
IPatternFingerprinter
java.util.Comparator<T>
uk.ac.ebi.reactionblast.mapping.interfaces.
IKey
(also extends java.lang.Comparable<T>)
uk.ac.ebi.centres.
PriorityRule
<A>
uk.ac.ebi.centres.
Comparison
uk.ac.ebi.centres.
ConnectionProvider
<A>
uk.ac.ebi.centres.
ConnectionTable
<A>
uk.ac.ebi.centres.
Descriptor
uk.ac.ebi.centres.priority.access.
DescriptorAccessor
<A>
uk.ac.ebi.centres.
DescriptorManager
<A>
uk.ac.ebi.centres.
Digraph
<A>
uk.ac.ebi.reactionblast.graphics.direct.
Highlighter
org.openscience.smsd.interfaces.
IAtomMapping
uk.ac.ebi.reactionblast.tools.labelling.
ICanonicalMoleculeLabeller
uk.ac.ebi.reactionblast.tools.labelling.
ICanonicalReactionLabeller
uk.ac.ebi.reactionblast.mechanism.interfaces.
IChangeCalculator
org.openscience.smsd.filters.
IChemicalFilter
<T>
uk.ac.ebi.reactionblast.interfaces.
IDataSource
<T>
uk.ac.ebi.reactionblast.interfaces.
IDataStore
<T>
org.openscience.smsd.algorithm.vflib.interfaces.
IEdge
org.openscience.smsd.interfaces.
IFinalMapping
uk.ac.ebi.reactionblast.interfaces.
IFingerPrintContainer
org.openscience.cdk.fingerprint.IFingerprinter
uk.ac.ebi.reactionblast.fingerprints.interfaces.
IFingerprinter
uk.ac.ebi.reactionblast.fingerprints.interfaces.
ISPFingerprinter
uk.ac.ebi.reactionblast.fingerprints.interfaces.
IFingerprintGenerator
uk.ac.ebi.reactionblast.mapping.interfaces.
IGameTheory
uk.ac.ebi.reactionblast.mapping.interfaces.
IGraphTheoryMatrix
uk.ac.ebi.reactionblast.interfaces.
IInChIContainer
org.openscience.smsd.algorithm.vflib.interfaces.
IMapper
uk.ac.ebi.reactionblast.interfaces.
IMolContainer
uk.ac.ebi.reactionblast.interfaces.
IMolDescriptors
org.openscience.smsd.algorithm.vflib.interfaces.
INode
org.openscience.smsd.algorithm.vflib.interfaces.
IQuery
org.openscience.smsd.algorithm.vflib.interfaces.
IQueryCompiler
uk.ac.ebi.reactionblast.fingerprints.
IQueryTool
uk.ac.ebi.reactionblast.interfaces.
IReactionBuilder
uk.ac.ebi.reactionblast.mapping.interfaces.
IResult
org.openscience.smsd.interfaces.
IResults
uk.ac.ebi.reactionblast.interfaces.
IStandardizer
org.openscience.smsd.algorithm.vflib.interfaces.
IState
org.openscience.smsd.interfaces.
ITimeOut
uk.ac.ebi.reactionblast.interfaces.
ITransformation
<T>
uk.ac.ebi.reactionblast.fingerprints.interfaces.
IWalker
uk.ac.ebi.centres.
Ligand
<A>
uk.ac.ebi.centres.
Centre
<A>
uk.ac.ebi.centres.
LigandSorter
<A>
uk.ac.ebi.centres.priority.access.
MassNumberAccessor
<A>
uk.ac.ebi.centres.
Perceptor
<A>
java.io.Serializable
uk.ac.ebi.reactionblast.fingerprints.interfaces.
ISPWalker
uk.ac.ebi.centres.
SignCalculator
<A>
Enum Hierarchy
java.lang.Object
java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
org.openscience.smsd.algorithm.vflib.
SortOrder
org.openscience.smsd.interfaces.
Algorithm
(implements java.lang.Comparable<T>)
org.openscience.smsd.mcss.
JobType
(implements java.lang.Comparable<T>)
uk.ac.ebi.centres.
Descriptor.Type
uk.ac.ebi.centres.
PriorityRule.Type
uk.ac.ebi.centres.descriptor.
General
(implements uk.ac.ebi.centres.
Descriptor
)
uk.ac.ebi.centres.descriptor.
Planar
(implements uk.ac.ebi.centres.
Descriptor
)
uk.ac.ebi.centres.descriptor.
Tetrahedral
(implements uk.ac.ebi.centres.
Descriptor
)
uk.ac.ebi.centres.descriptor.
Trigonal
(implements uk.ac.ebi.centres.
Descriptor
)
uk.ac.ebi.reactionblast.graphics.direct.
Axis
uk.ac.ebi.reactionblast.graphics.direct.
LabelManager.AnnotationPosition
uk.ac.ebi.reactionblast.graphics.direct.
Params.BondStrokeCap
uk.ac.ebi.reactionblast.graphics.direct.
Params.BondStrokeJoin
uk.ac.ebi.reactionblast.graphics.direct.
Params.XAlign
uk.ac.ebi.reactionblast.graphics.direct.
Params.YAlign
uk.ac.ebi.reactionblast.graphics.direct.
Params.ArrowType
uk.ac.ebi.reactionblast.graphics.direct.
Params.MoleculeAlignMethod
uk.ac.ebi.reactionblast.interfaces.
ITransformation.TargetType
uk.ac.ebi.reactionblast.mapping.interfaces.
IMappingAlgorithm
uk.ac.ebi.reactionblast.mechanism.interfaces.
ECBLAST_BOND_CHANGE_FLAGS
uk.ac.ebi.reactionblast.mechanism.interfaces.
ECBLAST_FLAGS
uk.ac.ebi.reactionblast.mechanism.interfaces.
EnumBondTypeChange
uk.ac.ebi.reactionblast.mechanism.interfaces.
EnumSubstrateProduct
uk.ac.ebi.reactionblast.stereo.
IStereoAndConformation
(implements java.lang.Comparable<T>)
uk.ac.ebi.reactionblast.stereo.inchi.
InchiStereoAndConformation
uk.ac.ebi.reactionblast.stereo.wedge.
WedgeStereoAnalysisResult
uk.ac.ebi.reactionblast.tools.rxnfile.
MDLV2000Writer.SPIN_MULTIPLICITY
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