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 

D

dashedGapFactor - Variable in class uk.ac.ebi.reactionblast.graphics.direct.Params
 
dashedWedgeStroke - Variable in class uk.ac.ebi.reactionblast.graphics.direct.Params
 
dashedWedgeWidth - Variable in class uk.ac.ebi.reactionblast.graphics.direct.Params
 
dashedWidthFactor - Variable in class uk.ac.ebi.reactionblast.graphics.direct.Params
 
DEBUG - Static variable in class aamtool.rgroup.ECRgroupFrequency
 
Debugger - Class in uk.ac.ebi.reactionblast.mapping.helper
 
Debugger() - Constructor for class uk.ac.ebi.reactionblast.mapping.helper.Debugger
 
decrement() - Method in class org.openscience.smsd.tools.IterationManager
decrement the counter
deepClone(IReaction) - Static method in class uk.ac.ebi.reactionblast.tools.ExtReactionManipulatorTool
 
DefaultAtomMatcher - Class in org.openscience.smsd.algorithm.matchers
Checks if atom is matching between query and target molecules.
DefaultAtomMatcher(IAtom, String, boolean) - Constructor for class org.openscience.smsd.algorithm.matchers.DefaultAtomMatcher
Constructor
DefaultAtomMatcher(IAtom, boolean) - Constructor for class org.openscience.smsd.algorithm.matchers.DefaultAtomMatcher
Constructor
DefaultAtomTypeMatcher - Class in org.openscience.smsd.algorithm.matchers
Checks if atom is matching between query and target molecules.
DefaultAtomTypeMatcher(IAtom, String, boolean) - Constructor for class org.openscience.smsd.algorithm.matchers.DefaultAtomTypeMatcher
Constructor
DefaultAtomTypeMatcher(IAtom, boolean) - Constructor for class org.openscience.smsd.algorithm.matchers.DefaultAtomTypeMatcher
Constructor
DefaultBondMatcher - Class in org.openscience.smsd.algorithm.matchers
Checks if a bond is matching between query and target molecules.
DefaultBondMatcher() - Constructor for class org.openscience.smsd.algorithm.matchers.DefaultBondMatcher
Constructor
DefaultBondMatcher(IBond, boolean, boolean, boolean) - Constructor for class org.openscience.smsd.algorithm.matchers.DefaultBondMatcher
Constructor
DefaultDescriptorManager<A> - Class in uk.ac.ebi.centres.graph
 
DefaultDescriptorManager() - Constructor for class uk.ac.ebi.centres.graph.DefaultDescriptorManager
 
DefaultMatcher - Class in org.openscience.smsd.algorithm.matchers
Checks if atom is matching between query and target molecules.
DefaultPerceptor<A> - Class in uk.ac.ebi.centres
 
DefaultPerceptor(PriorityRule<A>, PriorityRule<A>, SignCalculator<A>) - Constructor for class uk.ac.ebi.centres.DefaultPerceptor
 
DefinedMapping - Class in uk.ac.ebi.reactionblast.mapping.blocks
 
DefinedMapping(int, int, int, IAtomContainer, IAtomContainer) - Constructor for class uk.ac.ebi.reactionblast.mapping.blocks.DefinedMapping
 
description() - Method in enum org.openscience.smsd.interfaces.Algorithm
Returns short description of the algorithm.
description() - Method in enum org.openscience.smsd.mcss.JobType
Returns short description of the algorithm.
description() - Method in enum uk.ac.ebi.reactionblast.mapping.interfaces.IMappingAlgorithm
Returns short description of the algorithm.
description() - Method in enum uk.ac.ebi.reactionblast.mechanism.interfaces.ECBLAST_BOND_CHANGE_FLAGS
Returns short description of the algorithm.
description() - Method in enum uk.ac.ebi.reactionblast.mechanism.interfaces.ECBLAST_FLAGS
Returns short description of the algorithm.
description() - Method in enum uk.ac.ebi.reactionblast.mechanism.interfaces.EnumBondTypeChange
 
description() - Method in enum uk.ac.ebi.reactionblast.stereo.inchi.InchiStereoAndConformation
Returns short description of the stereo.
description() - Method in enum uk.ac.ebi.reactionblast.stereo.IStereoAndConformation
Returns short description of the stereo.
Descriptor - Interface in uk.ac.ebi.centres
Defines a descriptor which can be assigned to an atom to indicate the type of chirality (if there is any).
Descriptor.Type - Enum in uk.ac.ebi.centres
Defines the type of the descriptor.
DescriptorAccessor<A> - Interface in uk.ac.ebi.centres.priority.access
Provides access to a descriptor from the provided ligand.
DescriptorList - Class in uk.ac.ebi.centres.priority.descriptor
Implementation of a descriptor list that allows descriptors to be added and ignored.
DescriptorList(Descriptor...) - Constructor for class uk.ac.ebi.centres.priority.descriptor.DescriptorList
Creates a descriptor list that ignores the provided descriptors as varargs.
DescriptorList(List<Descriptor>) - Constructor for class uk.ac.ebi.centres.priority.descriptor.DescriptorList
Creates a descriptor list that ignores the provided descriptors as a List.
DescriptorList(DescriptorList, DescriptorList) - Constructor for class uk.ac.ebi.centres.priority.descriptor.DescriptorList
Creates a new list from a provided head and tail.
DescriptorManager<A> - Interface in uk.ac.ebi.centres
 
DescriptorRule<A> - Class in uk.ac.ebi.centres.priority.descriptor
A configurable descriptor rule that allows ranking of ligands based on their descriptors.
DescriptorRule(DescriptorAccessor<A>, PriorityRule.Type, Descriptor...) - Constructor for class uk.ac.ebi.centres.priority.descriptor.DescriptorRule
Create an Descriptor.Type#ASYMMETRIC rule with a provided accessor and given ligand order.
DescriptorRule(Descriptor.Type, PriorityRule.Type, DescriptorAccessor<A>, Descriptor...) - Constructor for class uk.ac.ebi.centres.priority.descriptor.DescriptorRule
Create an rule with a provided rule type, accessor and given ligand order.
det() - Method in class uk.ac.ebi.reactionblast.tools.EBIMatrix
EBIMatrix determinant
det() - Method in class uk.ac.ebi.reactionblast.tools.matrix.LUDecomposition
Determinant
detectAromaticity(IReaction) - Static method in class uk.ac.ebi.reactionblast.tools.TestUtility
 
detectAromaticity(IAtomContainerSet) - Static method in class uk.ac.ebi.reactionblast.tools.TestUtility
 
diagonalize(int) - Method in class uk.ac.ebi.reactionblast.tools.EBIMatrix
Diagonalize this matrix with the Jacobi algorithm.
Digraph<A> - Interface in uk.ac.ebi.centres
Defines a directed graph of ligands.
DirectArrowDrawer - Class in uk.ac.ebi.reactionblast.graphics.direct
 
DirectArrowDrawer(Params) - Constructor for class uk.ac.ebi.reactionblast.graphics.direct.DirectArrowDrawer
 
DirectAtomDrawer - Class in uk.ac.ebi.reactionblast.graphics.direct
 
DirectAtomDrawer(Params, LabelManager) - Constructor for class uk.ac.ebi.reactionblast.graphics.direct.DirectAtomDrawer
 
DirectBondDrawer - Class in uk.ac.ebi.reactionblast.graphics.direct
 
DirectBondDrawer(Params, LabelManager) - Constructor for class uk.ac.ebi.reactionblast.graphics.direct.DirectBondDrawer
 
DirectHullDrawer - Class in uk.ac.ebi.reactionblast.graphics.direct
 
DirectHullDrawer() - Constructor for class uk.ac.ebi.reactionblast.graphics.direct.DirectHullDrawer
 
DirectMoleculeDrawer - Class in uk.ac.ebi.reactionblast.graphics.direct
 
DirectMoleculeDrawer(Params) - Constructor for class uk.ac.ebi.reactionblast.graphics.direct.DirectMoleculeDrawer
 
DirectMoleculeDrawer() - Constructor for class uk.ac.ebi.reactionblast.graphics.direct.DirectMoleculeDrawer
 
directMoleculeImageNaturalScale(File, IAtomContainer, String) - Method in class uk.ac.ebi.reactionblast.tools.ImageGenerator
 
directMoleculeImageZoomedToFit(File, IAtomContainer, String) - Method in class uk.ac.ebi.reactionblast.tools.ImageGenerator
 
directMoleculeImageZoomedToFit(File, IAtomContainer, String, int, int) - Method in class uk.ac.ebi.reactionblast.tools.ImageGenerator
 
DirectRBLastReactionDrawer - Class in uk.ac.ebi.reactionblast.graphics.direct
 
DirectRBLastReactionDrawer(AbstractDirectReactionLayout) - Constructor for class uk.ac.ebi.reactionblast.graphics.direct.DirectRBLastReactionDrawer
 
DirectRBLastReactionDrawer(Params, AbstractDirectReactionLayout) - Constructor for class uk.ac.ebi.reactionblast.graphics.direct.DirectRBLastReactionDrawer
 
DirectRBLastReactionDrawer(Params, AbstractDirectReactionLayout, AbstractAWTReactionLayout) - Constructor for class uk.ac.ebi.reactionblast.graphics.direct.DirectRBLastReactionDrawer
 
DirectReactionDrawer - Class in uk.ac.ebi.reactionblast.graphics.direct
Directly draw, modifying the points in the atom containers.
DirectReactionDrawer(AbstractDirectReactionLayout) - Constructor for class uk.ac.ebi.reactionblast.graphics.direct.DirectReactionDrawer
 
DirectReactionDrawer(Params) - Constructor for class uk.ac.ebi.reactionblast.graphics.direct.DirectReactionDrawer
 
DirectReactionDrawer(Params, AbstractDirectReactionLayout) - Constructor for class uk.ac.ebi.reactionblast.graphics.direct.DirectReactionDrawer
 
DirectReactionDrawer(Params, AbstractDirectReactionLayout, AbstractAWTReactionLayout) - Constructor for class uk.ac.ebi.reactionblast.graphics.direct.DirectReactionDrawer
 
dispose() - Method in interface uk.ac.ebi.centres.Centre
Clean up the digraph
dispose() - Method in interface uk.ac.ebi.centres.ConnectionProvider
Clear the digraph ready for GC
dispose() - Method in class uk.ac.ebi.centres.graph.AbstractDigraph
 
dispose() - Method in class uk.ac.ebi.centres.ligand.PlanarCentre
 
dispose() - Method in class uk.ac.ebi.centres.ligand.TetrahedralCentre
 
Distance - Class in uk.ac.ebi.reactionblast.tools
 
doubleBondGap - Variable in class uk.ac.ebi.reactionblast.graphics.direct.Params
 
doubleMarkGap - Variable in class uk.ac.ebi.reactionblast.graphics.direct.Params
 
doubleValueInAscendingOrder(Map<Double, Double>) - Static method in class uk.ac.ebi.reactionblast.tools.utility.SortMap
 
doubleValueInDescendingOrder(Map<Double, Double>) - Static method in class uk.ac.ebi.reactionblast.tools.utility.SortMap
 
draw(CanvasGenerator, Graphics2D) - Method in class uk.ac.ebi.reactionblast.graphics.direct.layout.ArrowWheel
 
draw(Map<String, String>, BoundsTree, Graphics2D) - Method in class uk.ac.ebi.reactionblast.graphics.direct.MoleculeLabelDrawer
 
draw(List<IAtomContainer>, Dimension, Graphics2D) - Method in class uk.ac.ebi.reactionblast.graphics.direct.ZoomToFitDrawer
 
draw(DirectMoleculeDrawer, IAtomContainer, String, String) - Method in class uk.ac.ebi.reactionblast.tools.Reader
 
draw(DirectMoleculeDrawer, IAtomContainer, String, String) - Static method in class uk.ac.ebi.reactionblast.tools.TestUtility
 
drawAromaticCircles - Variable in class uk.ac.ebi.reactionblast.graphics.direct.Params
 
drawArrow(Graphics2D, Point2d, Vector2d) - Method in class uk.ac.ebi.reactionblast.graphics.direct.DirectArrowDrawer
 
drawArrowFilled - Variable in class uk.ac.ebi.reactionblast.graphics.direct.Params
 
drawAtom(IAtom, IAtomContainer, int, Graphics2D) - Method in class uk.ac.ebi.reactionblast.graphics.direct.DirectAtomDrawer
 
drawAtomID(IAtom, IAtomContainer, Graphics2D) - Method in class uk.ac.ebi.reactionblast.graphics.direct.DirectAtomDrawer
 
drawAtomID - Variable in class uk.ac.ebi.reactionblast.graphics.direct.Params
 
drawAtoms(IAtomContainer, Graphics2D) - Method in class uk.ac.ebi.reactionblast.graphics.direct.DirectAtomDrawer
 
drawAtomSymbol(IAtom, Graphics2D) - Method in class uk.ac.ebi.reactionblast.graphics.direct.DirectAtomDrawer
 
drawBond(IBond, Map<IBond, IAtomContainer>, Graphics2D) - Method in class uk.ac.ebi.reactionblast.graphics.direct.DirectBondDrawer
 
drawBondChangeMarks(RBlastReaction, Graphics2D) - Method in class uk.ac.ebi.reactionblast.graphics.direct.DirectRBLastReactionDrawer
 
drawBondFormedCleavedMarks - Variable in class uk.ac.ebi.reactionblast.graphics.direct.Params
 
drawBondOrderChangedMarks - Variable in class uk.ac.ebi.reactionblast.graphics.direct.Params
 
drawBonds(IAtomContainer, Graphics2D) - Method in class uk.ac.ebi.reactionblast.graphics.direct.DirectBondDrawer
 
drawBondStereoChanges - Variable in class uk.ac.ebi.reactionblast.graphics.direct.Params
 
drawBounds - Variable in class uk.ac.ebi.reactionblast.graphics.direct.Params
 
drawCarbons - Variable in class uk.ac.ebi.reactionblast.graphics.direct.Params
 
drawDashedWedge(Point2d, Point2d, Point2d, Graphics2D) - Method in class uk.ac.ebi.reactionblast.graphics.direct.DirectBondDrawer
 
drawDashedWedge2(Point2d, Point2d, Point2d, Graphics2D) - Method in class uk.ac.ebi.reactionblast.graphics.direct.DirectBondDrawer
 
drawDoubleHeadedFatArrow(Graphics2D, Point2d, Vector2d, String) - Method in class uk.ac.ebi.reactionblast.graphics.direct.DirectArrowDrawer
 
drawElectronPairs(IAtom, IAtomContainer, int, Graphics2D) - Method in class uk.ac.ebi.reactionblast.graphics.direct.DirectAtomDrawer
 
drawExplicitHydrogens - Variable in class uk.ac.ebi.reactionblast.graphics.direct.Params
 
drawFatArrow(Graphics2D, Point2d, Vector2d, String) - Method in class uk.ac.ebi.reactionblast.graphics.direct.DirectArrowDrawer
 
drawFatArrow - Variable in class uk.ac.ebi.reactionblast.graphics.direct.Params
 
drawHighlight(IAtom, Graphics2D) - Method in class uk.ac.ebi.reactionblast.graphics.direct.SimpleHighlighter
 
drawHighlight(IAtom, Color, Graphics2D) - Method in class uk.ac.ebi.reactionblast.graphics.direct.SimpleHighlighter
 
drawHighlight(IBond, Color, Graphics2D) - Method in class uk.ac.ebi.reactionblast.graphics.direct.SimpleHighlighter
 
drawHighlightContainer(IAtomContainer, Graphics2D) - Method in class uk.ac.ebi.reactionblast.graphics.direct.SimpleHighlighter
 
drawHighlightContainer(IAtomContainer, Color, Graphics2D) - Method in class uk.ac.ebi.reactionblast.graphics.direct.SimpleHighlighter
 
drawHighlights(IAtomContainer, Graphics2D) - Method in interface uk.ac.ebi.reactionblast.graphics.direct.Highlighter
 
drawHighlights(IAtomContainer, Graphics2D) - Method in class uk.ac.ebi.reactionblast.graphics.direct.OutlineHighlighter
 
drawHighlights - Variable in class uk.ac.ebi.reactionblast.graphics.direct.Params
 
drawHighlights(IAtomContainer, Graphics2D) - Method in class uk.ac.ebi.reactionblast.graphics.direct.SimpleHighlighter
 
drawHull(IAtomContainer, int, int) - Method in class uk.ac.ebi.reactionblast.graphics.direct.DirectHullDrawer
 
drawHull(IAtomContainer, Graphics2D) - Method in class uk.ac.ebi.reactionblast.graphics.direct.DirectHullDrawer
 
drawImplicitHydrogens(IAtom, int, LabelManager.AnnotationPosition, Graphics2D) - Method in class uk.ac.ebi.reactionblast.graphics.direct.DirectAtomDrawer
 
drawImplicitHydrogens - Variable in class uk.ac.ebi.reactionblast.graphics.direct.Params
 
drawLabelPanel(Map<String, String>, BoundsTree, Graphics2D) - Method in class uk.ac.ebi.reactionblast.graphics.direct.DirectReactionDrawer
 
drawLabelPanel - Variable in class uk.ac.ebi.reactionblast.graphics.direct.Params
 
drawLeftToRightReactionCenterMoleculeImage(File, IReaction, List<String>, String) - Method in class uk.ac.ebi.reactionblast.tools.ImageGenerator
Draw a left-to-right reaction with atoms highlighted as reaction centers.
drawLeftToRightReactionLayout(String, IReaction, String) - Method in class uk.ac.ebi.reactionblast.tools.ImageGenerator
 
drawLeftToRightReactionLayout(File, IReaction, String) - Method in class uk.ac.ebi.reactionblast.tools.ImageGenerator
 
drawLine(Point2d, Point2d, Graphics2D) - Method in class uk.ac.ebi.reactionblast.graphics.direct.AbstractDirectDrawer
 
drawLonePairs - Variable in class uk.ac.ebi.reactionblast.graphics.direct.Params
 
drawMappings(IReaction, Graphics2D) - Method in class uk.ac.ebi.reactionblast.graphics.direct.DirectReactionDrawer
 
drawMappings - Variable in class uk.ac.ebi.reactionblast.graphics.direct.Params
 
drawMolecule(IAtomContainer, Graphics2D) - Method in class uk.ac.ebi.reactionblast.graphics.direct.DirectMoleculeDrawer
 
drawMoleculeID(IAtomContainer, Graphics2D) - Method in class uk.ac.ebi.reactionblast.graphics.direct.DirectMoleculeDrawer
 
drawMoleculeID - Variable in class uk.ac.ebi.reactionblast.graphics.direct.Params
 
drawMoleculeSet(IAtomContainerSet, String, double, BoundsTree, Graphics2D) - Method in class uk.ac.ebi.reactionblast.graphics.direct.DirectReactionDrawer
 
drawPlus(IAtomContainer, String, double, BoundsTree, Graphics2D) - Method in class uk.ac.ebi.reactionblast.graphics.direct.DirectReactionDrawer
 
drawRBlastReaction(RBlastReaction, int, int) - Method in class uk.ac.ebi.reactionblast.graphics.direct.DirectRBLastReactionDrawer
 
drawRBlastReaction(RBlastReaction, int, int, Graphics2D) - Method in class uk.ac.ebi.reactionblast.graphics.direct.DirectRBLastReactionDrawer
 
drawReaction(IReaction) - Method in class uk.ac.ebi.reactionblast.graphics.direct.DirectReactionDrawer
 
drawReaction(IReaction, int, int) - Method in class uk.ac.ebi.reactionblast.graphics.direct.DirectReactionDrawer
Draw a zoomed reaction.
drawReaction(IReaction, int, int, boolean) - Method in class uk.ac.ebi.reactionblast.graphics.direct.DirectReactionDrawer
Draw a zoomed reaction.
drawReaction(IReaction, boolean) - Method in class uk.ac.ebi.reactionblast.graphics.direct.DirectReactionDrawer
Draw a natural-scale reaction.
drawReaction(IReaction, BoundsTree, int, int, double, Graphics2D) - Method in class uk.ac.ebi.reactionblast.graphics.direct.DirectReactionDrawer
Draw a zoomed reaction.
drawReactionID(IReaction, int, Graphics2D) - Method in class uk.ac.ebi.reactionblast.graphics.direct.DirectReactionDrawer
 
drawReactionID - Variable in class uk.ac.ebi.reactionblast.graphics.direct.Params
 
drawRS - Variable in class uk.ac.ebi.reactionblast.graphics.direct.Params
 
drawSubgraphBoxes(RBlastReaction, Graphics2D) - Method in class uk.ac.ebi.reactionblast.graphics.direct.DirectRBLastReactionDrawer
 
drawSubgraphBoxes - Variable in class uk.ac.ebi.reactionblast.graphics.direct.Params
 
drawSubgraphMappingLines - Variable in class uk.ac.ebi.reactionblast.graphics.direct.Params
 
drawTerminalCarbons - Variable in class uk.ac.ebi.reactionblast.graphics.direct.Params
 
drawThinArrow(Graphics2D, Point2d, Vector2d, String) - Method in class uk.ac.ebi.reactionblast.graphics.direct.DirectArrowDrawer
 
drawTopToBottomReactionLayout(String, IReaction, String) - Method in class uk.ac.ebi.reactionblast.tools.ImageGenerator
 
drawTopToBottomReactionLayout(File, IReaction, String) - Method in class uk.ac.ebi.reactionblast.tools.ImageGenerator
 
drawWigglyLine(Point2d, Point2d, Graphics2D) - Method in class uk.ac.ebi.reactionblast.graphics.direct.DirectBondDrawer
 
duplicate() - Method in class uk.ac.ebi.reactionblast.tools.EBIMatrix
Make a deep duplicate of a matrix
DuplicateAtomRule<A> - Class in uk.ac.ebi.centres.priority
 
DuplicateAtomRule() - Constructor for class uk.ac.ebi.centres.priority.DuplicateAtomRule
 
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