- 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
-