- 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
-