Skip navigation links
A B C D E F G H I J K L M N O P Q R S T U V W X Y Z 

T

target - Variable in class org.openscience.smsd.algorithm.vflib.BaseMCS
 
targetPosition - Variable in class uk.ac.ebi.reactionblast.mapping.graph.MCSThread
 
TargetProcessor - Class in org.openscience.smsd.algorithm.mcgregor
Class to handle mappings of target molecule based on the query.
TargetProcessor(List<String>, String[], int, int, List<Integer>, List<String>, int, List<Integer>, List<String>) - Constructor for class org.openscience.smsd.algorithm.mcgregor.TargetProcessor
 
TerminalLigand<A> - Class in uk.ac.ebi.centres.ligand
 
TerminalLigand(ConnectionProvider<A>, MutableDescriptor, A, A, int) - Constructor for class uk.ac.ebi.centres.ligand.TerminalLigand
 
TerminalLigand(ConnectionProvider<A>, MutableDescriptor, Set<A>, A, A, int) - Constructor for class uk.ac.ebi.centres.ligand.TerminalLigand
 
testIsSubgraphHeuristics(IAtomContainer, IAtomContainer, boolean) - Static method in class org.openscience.smsd.helper.MoleculeInitializer
Checks some simple heuristics for whether the subgraph query can realistically be atom subgraph of the supergraph.
testRCReactions(String, String) - Method in class uk.ac.ebi.reactionblast.tools.MappingUtility
 
testReactions(String, String) - Method in class uk.ac.ebi.reactionblast.tools.MappingUtility
 
TestUtility - Class in uk.ac.ebi.reactionblast.tools
 
TestUtility() - Constructor for class uk.ac.ebi.reactionblast.tools.TestUtility
 
Tetrahedral - Enum in uk.ac.ebi.centres.descriptor
Enumeration of asymmetric and pseudo-asymmetric tetrahedral descriptors.
TetrahedralCentre<A> - Class in uk.ac.ebi.centres.ligand
 
TetrahedralCentre(MutableDescriptor, A) - Constructor for class uk.ac.ebi.centres.ligand.TetrahedralCentre
 
theory - Variable in class uk.ac.ebi.reactionblast.mapping.graph.MCSThread
 
ThreeDimensionalSignCalculator<A> - Class in uk.ac.ebi.centres.calculator
 
ThreeDimensionalSignCalculator() - Constructor for class uk.ac.ebi.centres.calculator.ThreeDimensionalSignCalculator
 
TimeManager - Class in org.openscience.smsd.tools
Class that handles execution time of the MCS search.
TimeManager() - Constructor for class org.openscience.smsd.tools.TimeManager
Constructor for storing execution time
timeout - Static variable in class org.openscience.smsd.algorithm.rgraph.CDKMCS
 
times(double) - Method in class uk.ac.ebi.reactionblast.tools.EBIMatrix
Multiply a matrix by a scalar, data = s*matrix
times(EBIMatrix) - Method in class uk.ac.ebi.reactionblast.tools.EBIMatrix
Linear algebraic matrix multiplication, matrix * B
timesEquals(double) - Method in class uk.ac.ebi.reactionblast.tools.EBIMatrix
Multiply a matrix by a scalar in place, matrix = s*matrix
topBottomAlignment - Variable in class uk.ac.ebi.reactionblast.graphics.direct.Params
 
TopToBottomAWTReactionLayout - Class in uk.ac.ebi.reactionblast.graphics.direct.awtlayout
 
TopToBottomAWTReactionLayout() - Constructor for class uk.ac.ebi.reactionblast.graphics.direct.awtlayout.TopToBottomAWTReactionLayout
 
TopToBottomAWTReactionLayout(Params) - Constructor for class uk.ac.ebi.reactionblast.graphics.direct.awtlayout.TopToBottomAWTReactionLayout
 
topToBottomMoleculeLabelFontSize - Variable in class uk.ac.ebi.reactionblast.graphics.direct.Params
 
TopToBottomReactionLayout - Class in uk.ac.ebi.reactionblast.graphics.direct.layout
 
TopToBottomReactionLayout() - Constructor for class uk.ac.ebi.reactionblast.graphics.direct.layout.TopToBottomReactionLayout
 
TopToBottomReactionLayout(boolean) - Constructor for class uk.ac.ebi.reactionblast.graphics.direct.layout.TopToBottomReactionLayout
 
TopToBottomReactionLayout(boolean, Vector2d) - Constructor for class uk.ac.ebi.reactionblast.graphics.direct.layout.TopToBottomReactionLayout
 
TopToBottomReactionLayoutImage(IReaction, String, String) - Static method in class uk.ac.ebi.reactionblast.tools.ImageGenerator
 
TopToBottomReactionLayoutImageSmall(IReaction, String, String) - Static method in class uk.ac.ebi.reactionblast.tools.ImageGenerator
 
toSmiles(IAtomContainer) - Static method in class org.openscience.smsd.mcss.Fragment
Return SMILES
toString() - Method in class org.openscience.smsd.algorithm.rgraph.CDKRGraph
Returns a string representation of the CDKRGraph.
toString() - Method in class org.openscience.smsd.algorithm.rgraph.CDKRNode
Returns a string representation of the RNode
toString() - Method in class org.openscience.smsd.algorithm.vflib.builder.NodeBuilder
 
toString() - Method in class org.openscience.smsd.algorithm.vflib.map.Match
 
toString() - Method in class org.openscience.smsd.algorithm.vflib.substructure.Pair
 
toString() - Method in class org.openscience.smsd.AtomAtomMapping
Returns String.
toString() - Method in interface org.openscience.smsd.interfaces.IAtomMapping
Convert to String
toString() - Method in class uk.ac.ebi.centres.graph.Arc
 
toString() - Method in class uk.ac.ebi.centres.graph.DefaultDescriptorManager
 
toString() - Method in class uk.ac.ebi.centres.ligand.AbstractLigand
 
toString() - Method in class uk.ac.ebi.centres.ligand.PlanarCentre
 
toString() - Method in class uk.ac.ebi.centres.ligand.TerminalLigand
 
toString() - Method in class uk.ac.ebi.centres.priority.CombinedRule
 
toString() - Method in class uk.ac.ebi.centres.priority.descriptor.DescriptorList
 
toString() - Method in class uk.ac.ebi.reactionblast.fingerprints.Feature
Return weighted fingerprint
toString() - Method in interface uk.ac.ebi.reactionblast.fingerprints.interfaces.IFeature
Return weighted fingerprint
toString() - Method in interface uk.ac.ebi.reactionblast.fingerprints.interfaces.IPatternFingerprinter
 
toString() - Method in interface uk.ac.ebi.reactionblast.fingerprints.interfaces.ISPWalker
 
toString() - Method in class uk.ac.ebi.reactionblast.fingerprints.MolFingerprint
 
toString() - Method in class uk.ac.ebi.reactionblast.fingerprints.PatternFingerprinter
 
toString() - Method in class uk.ac.ebi.reactionblast.graphics.direct.ConvexHull.Rectangle
 
toString(Point2d...) - Method in class uk.ac.ebi.reactionblast.graphics.direct.ConvexHull
 
toString(Rectangle2D) - Static method in class uk.ac.ebi.reactionblast.graphics.direct.layout.BoundsPrinter
DEBUG method for printing readable rectangle 2Ds
toString() - Method in class uk.ac.ebi.reactionblast.graphics.direct.layout.BoundsTree
 
toString() - Method in class uk.ac.ebi.reactionblast.graphics.direct.RootSystem
 
toString() - Method in class uk.ac.ebi.reactionblast.mapping.blocks.Block
 
toString() - Method in class uk.ac.ebi.reactionblast.mapping.blocks.BlockList
 
toString() - Method in class uk.ac.ebi.reactionblast.mapping.blocks.BlockMapping
 
toString() - Method in class uk.ac.ebi.reactionblast.mapping.blocks.BlockPair
 
toString() - Method in class uk.ac.ebi.reactionblast.mapping.blocks.DefinedMapping
 
toString() - Method in class uk.ac.ebi.reactionblast.mapping.container.BestMatchContainer
 
toString() - Method in class uk.ac.ebi.reactionblast.mapping.container.CDKReactionBuilder
 
toString() - Method in class uk.ac.ebi.reactionblast.mapping.container.helper.Key
 
toString() - Method in class uk.ac.ebi.reactionblast.mapping.container.helper.MolMapping
 
toString() - Method in class uk.ac.ebi.reactionblast.mapping.container.helper.ReactionFileData
Print the data
toString() - Method in class uk.ac.ebi.reactionblast.mapping.container.HydrogenFreeFingerPrintContainer
 
toString() - Method in class uk.ac.ebi.reactionblast.mapping.container.MoleculeMoleculeMapping
 
toString() - Method in class uk.ac.ebi.reactionblast.mapping.container.ReactionContainer
 
toString() - Method in class uk.ac.ebi.reactionblast.mapping.graph.Combination
 
toString() - Method in interface uk.ac.ebi.reactionblast.mapping.interfaces.IKey
 
toString() - Method in class uk.ac.ebi.reactionblast.mapping.Reactor
 
toString() - Method in class uk.ac.ebi.reactionblast.mechanism.BEMatrix
 
toString() - Method in class uk.ac.ebi.reactionblast.mechanism.BondChangeCalculator
Print the atom changes
toString() - Method in class uk.ac.ebi.reactionblast.mechanism.helper.AtomAtomMappingContainer
This method prints the matrix to the standard output
toString() - Method in class uk.ac.ebi.reactionblast.mechanism.helper.BondChange
 
toString() - Method in class uk.ac.ebi.reactionblast.mechanism.helper.MoleculeMoleculePair
 
toString() - Method in class uk.ac.ebi.reactionblast.mechanism.helper.ReactantProductPair
 
toString() - Method in class uk.ac.ebi.reactionblast.mechanism.helper.ReactionCenterFragment
 
toString() - Method in class uk.ac.ebi.reactionblast.mechanism.MappingSolution
 
toString() - Method in class uk.ac.ebi.reactionblast.mechanism.RMatrix
 
toString() - Method in class uk.ac.ebi.reactionblast.mechanism.StereoChange
 
toString() - Method in class uk.ac.ebi.reactionblast.stereo.compare.WedgeStereoComparisonResult
 
toString() - Method in class uk.ac.ebi.reactionblast.tools.EBIMatrix
Return a matrix as a String.
toString(IAtomContainer) - Method in class uk.ac.ebi.reactionblast.tools.labelling.AtomContainerPrinter
 
toVector(A, A) - Method in class uk.ac.ebi.centres.calculator.TwoDimensionalSignCalculator
Constructs a two dimensional vector from the base atom to the 'atom'
trace() - Method in class uk.ac.ebi.reactionblast.tools.EBIMatrix
EBIMatrix trace.
transform(AffineTransform) - Method in class uk.ac.ebi.reactionblast.graphics.direct.layout.BoundsTree
 
transform(T) - Method in interface uk.ac.ebi.reactionblast.interfaces.ITransformation
 
transform(IReaction) - Method in class uk.ac.ebi.reactionblast.tools.bulk.BondChangeCalculationTransformation
 
transform(IDataSource, IDataStore) - Method in class uk.ac.ebi.reactionblast.tools.bulk.BulkTransformer
Transform all the entries in the datasource.
transform(IReaction) - Method in class uk.ac.ebi.reactionblast.tools.bulk.MappingTransformation
 
transform(IAtomContainer) - Method in class uk.ac.ebi.reactionblast.tools.bulk.MoleculeCanonicalizationTransformation
 
transform(IReaction) - Method in class uk.ac.ebi.reactionblast.tools.bulk.ReactionAromatizationTransformation
 
transform(IReaction) - Method in class uk.ac.ebi.reactionblast.tools.bulk.ReactionAtomIDTransformation
 
transform(IReaction) - Method in class uk.ac.ebi.reactionblast.tools.bulk.ReactionCanonicalizationTransformation
 
transform(IReaction) - Method in class uk.ac.ebi.reactionblast.tools.bulk.ReactionIdentityTransformation
 
transform(IReaction) - Method in class uk.ac.ebi.reactionblast.tools.bulk.ReactionImplicitHydrogenTransformation
 
transform(IReaction) - Method in class uk.ac.ebi.reactionblast.tools.bulk.ReactionTransformationSequence
 
translateTo(IAtomContainer, double, double, BoundsTree) - Method in class uk.ac.ebi.reactionblast.graphics.direct.awtlayout.AbstractAWTLayout
 
translateTo(IAtomContainer, double, double, Rectangle2D) - Method in class uk.ac.ebi.reactionblast.graphics.direct.layout.AbstractDirectLayout
 
translucentHighlightColor - Variable in class uk.ac.ebi.reactionblast.graphics.direct.AbstractHighlightDrawer
 
transpose() - Method in class uk.ac.ebi.centres.graph.Arc
 
transpose() - Method in class uk.ac.ebi.reactionblast.tools.EBIMatrix
EBIMatrix transpose.
Trigonal - Enum in uk.ac.ebi.centres.descriptor
Enumeration of asymmetric and pseudo-asymmetric trigonal planar descriptors.
tripleBondGap - Variable in class uk.ac.ebi.reactionblast.graphics.direct.Params
 
TwoDimensionalSignCalculator<A> - Class in uk.ac.ebi.centres.calculator
 
TwoDimensionalSignCalculator() - Constructor for class uk.ac.ebi.centres.calculator.TwoDimensionalSignCalculator
 
type() - Method in enum org.openscience.smsd.interfaces.Algorithm
Returns type of algorithm.
type() - Method in enum org.openscience.smsd.mcss.JobType
Returns type of algorithm.
type() - Method in enum uk.ac.ebi.reactionblast.mapping.interfaces.IMappingAlgorithm
Returns type of algorithm.
type() - Method in enum uk.ac.ebi.reactionblast.mechanism.interfaces.ECBLAST_BOND_CHANGE_FLAGS
Returns type of algorithm.
type() - Method in enum uk.ac.ebi.reactionblast.mechanism.interfaces.ECBLAST_FLAGS
Returns type of algorithm.
type() - Method in enum uk.ac.ebi.reactionblast.mechanism.interfaces.EnumBondTypeChange
 
type() - Method in enum uk.ac.ebi.reactionblast.stereo.inchi.InchiStereoAndConformation
Returns type of stereo.
type() - Method in enum uk.ac.ebi.reactionblast.stereo.IStereoAndConformation
Returns type of stereo.
typeAtoms(IAtomContainer) - Method in class uk.ac.ebi.reactionblast.tools.Reader
 
typeAtoms(IAtomContainer) - Static method in class uk.ac.ebi.reactionblast.tools.TestUtility
 
A B C D E F G H I J K L M N O P Q R S T U V W X Y Z 
Skip navigation links