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A

aamtool - package aamtool
 
aamtool.rgroup - package aamtool.rgroup
 
aamtool.rxndecoder - package aamtool.rxndecoder
 
Abstract2DSignCalculator<A> - Class in uk.ac.ebi.centres
 
Abstract2DSignCalculator() - Constructor for class uk.ac.ebi.centres.Abstract2DSignCalculator
 
AbstractAWTLayout<T> - Class in uk.ac.ebi.reactionblast.graphics.direct.awtlayout
A layout object that uses a java.awt.Graphics2D instance to work out text sizes, which makes the layout more precise than just using atom positions.
AbstractAWTLayout() - Constructor for class uk.ac.ebi.reactionblast.graphics.direct.awtlayout.AbstractAWTLayout
 
AbstractAWTReactionLayout - Class in uk.ac.ebi.reactionblast.graphics.direct.awtlayout
 
AbstractAWTReactionLayout() - Constructor for class uk.ac.ebi.reactionblast.graphics.direct.awtlayout.AbstractAWTReactionLayout
 
AbstractCanvasGenerator - Class in uk.ac.ebi.reactionblast.graphics.direct.layout
 
AbstractCanvasGenerator() - Constructor for class uk.ac.ebi.reactionblast.graphics.direct.layout.AbstractCanvasGenerator
 
AbstractChangeCalculator - Class in uk.ac.ebi.reactionblast.mechanism.interfaces
 
AbstractChangeCalculator() - Constructor for class uk.ac.ebi.reactionblast.mechanism.interfaces.AbstractChangeCalculator
 
AbstractDigraph<A> - Class in uk.ac.ebi.centres.graph
A digraph with a single immutable root.
AbstractDigraph(Ligand<A>) - Constructor for class uk.ac.ebi.centres.graph.AbstractDigraph
 
AbstractDigraph(Ligand<A>, DescriptorManager<A>) - Constructor for class uk.ac.ebi.centres.graph.AbstractDigraph
 
AbstractDirectDrawer - Class in uk.ac.ebi.reactionblast.graphics.direct
 
AbstractDirectDrawer() - Constructor for class uk.ac.ebi.reactionblast.graphics.direct.AbstractDirectDrawer
 
AbstractDirectLayout<T> - Class in uk.ac.ebi.reactionblast.graphics.direct.layout
 
AbstractDirectLayout() - Constructor for class uk.ac.ebi.reactionblast.graphics.direct.layout.AbstractDirectLayout
 
AbstractDirectLayout(boolean) - Constructor for class uk.ac.ebi.reactionblast.graphics.direct.layout.AbstractDirectLayout
 
AbstractDirectReactionLayout - Class in uk.ac.ebi.reactionblast.graphics.direct.layout
 
AbstractDirectReactionLayout() - Constructor for class uk.ac.ebi.reactionblast.graphics.direct.layout.AbstractDirectReactionLayout
 
AbstractDirectReactionLayout(boolean) - Constructor for class uk.ac.ebi.reactionblast.graphics.direct.layout.AbstractDirectReactionLayout
 
AbstractDirectReactionLayout(boolean, Vector2d) - Constructor for class uk.ac.ebi.reactionblast.graphics.direct.layout.AbstractDirectReactionLayout
 
AbstractHighlightDrawer - Class in uk.ac.ebi.reactionblast.graphics.direct
 
AbstractHighlightDrawer(Params) - Constructor for class uk.ac.ebi.reactionblast.graphics.direct.AbstractHighlightDrawer
 
AbstractLigand<A> - Class in uk.ac.ebi.centres.ligand
 
AbstractLigand(ConnectionProvider<A>, Set<A>, MutableDescriptor, int) - Constructor for class uk.ac.ebi.centres.ligand.AbstractLigand
 
AbstractLigand(Set<A>, MutableDescriptor, int) - Constructor for class uk.ac.ebi.centres.ligand.AbstractLigand
 
AbstractLigand(MutableDescriptor, int) - Constructor for class uk.ac.ebi.centres.ligand.AbstractLigand
 
AbstractPriorityRule<A> - Class in uk.ac.ebi.centres.priority
An abstract comparator that provides construction of the Comparison wrapper allowing subclasses to focus on the actual comparison of ligands.
AbstractPriorityRule(PriorityRule.Type) - Constructor for class uk.ac.ebi.centres.priority.AbstractPriorityRule
Default constructor creates an Descriptor.Type#ASYMMETRIC comparator.
AbstractPriorityRule(Descriptor.Type, PriorityRule.Type) - Constructor for class uk.ac.ebi.centres.priority.AbstractPriorityRule
Constructor creates a comparator with the specified type.
AbstractReactionLabeller - Class in uk.ac.ebi.reactionblast.tools.labelling
 
AbstractReactionLabeller() - Constructor for class uk.ac.ebi.reactionblast.tools.labelling.AbstractReactionLabeller
 
AbstractReactor - Class in uk.ac.ebi.reactionblast.mapping.helper
 
AbstractReactor() - Constructor for class uk.ac.ebi.reactionblast.mapping.helper.AbstractReactor
 
AbstractSignCalculator<A> - Class in uk.ac.ebi.centres.calculator
 
AbstractSignCalculator() - Constructor for class uk.ac.ebi.centres.calculator.AbstractSignCalculator
 
AbstractTetrahedralWedgeRule - Class in uk.ac.ebi.reactionblast.stereo.wedge
 
AbstractTetrahedralWedgeRule() - Constructor for class uk.ac.ebi.reactionblast.stereo.wedge.AbstractTetrahedralWedgeRule
 
accepts(Class) - Method in class uk.ac.ebi.reactionblast.tools.rxnfile.MDLRXNV2000Reader
 
accepts(IChemObject) - Method in class uk.ac.ebi.reactionblast.tools.rxnfile.MDLRXNV2000Reader
 
accepts(Class<? extends IChemObject>) - Method in class uk.ac.ebi.reactionblast.tools.rxnfile.MDLV2000Reader
 
accepts(Class) - Method in class uk.ac.ebi.reactionblast.tools.rxnfile.MDLV2000RXNWriter
 
accepts(Class) - Method in class uk.ac.ebi.reactionblast.tools.rxnfile.MDLV2000Writer
 
ACWTetrahedralWedgeRule - Class in uk.ac.ebi.reactionblast.stereo.wedge
 
ACWTetrahedralWedgeRule() - Constructor for class uk.ac.ebi.reactionblast.stereo.wedge.ACWTetrahedralWedgeRule
 
add(Map<Integer, Integer>) - Method in interface org.openscience.smsd.interfaces.IFinalMapping
Adds mapping to the mapping list
add(PriorityRule<A>) - Method in class uk.ac.ebi.centres.priority.CombinedRule
Add a priority rule to the compound rule.
add(Descriptor) - Method in class uk.ac.ebi.centres.priority.descriptor.DescriptorList
Adds a descriptor to the descriptor list.
add(String, IAtomContainer) - Method in class uk.ac.ebi.reactionblast.containers.MolContainer
 
add(IPatternFingerprinter) - Method in interface uk.ac.ebi.reactionblast.fingerprints.interfaces.IPatternFingerprinter
 
add(IFeature) - Method in interface uk.ac.ebi.reactionblast.fingerprints.interfaces.IPatternFingerprinter
 
add(IFeature) - Method in class uk.ac.ebi.reactionblast.fingerprints.PatternFingerprinter
 
add(IPatternFingerprinter) - Method in class uk.ac.ebi.reactionblast.fingerprints.PatternFingerprinter
 
add(String, Rectangle2D) - Method in class uk.ac.ebi.reactionblast.graphics.direct.layout.BoundsTree
Adds a rectangular bounds to the tree and updates the root bounds.
add(String, Point2D) - Method in class uk.ac.ebi.reactionblast.graphics.direct.layout.BoundsTree
 
add(String, BoundsTree) - Method in class uk.ac.ebi.reactionblast.graphics.direct.layout.BoundsTree
Add all the members of another tree, prefixing their labels with the supplied label, separated by an underscore.
add(String, IAtomContainer) - Method in interface uk.ac.ebi.reactionblast.interfaces.IMolContainer
 
add(Block) - Method in class uk.ac.ebi.reactionblast.mapping.blocks.BlockList
 
add(ITransformation<IReaction>) - Method in class uk.ac.ebi.reactionblast.tools.bulk.ReactionTransformationSequence
 
add(SuperAtoms) - Method in class uk.ac.ebi.reactionblast.tools.rxnfile.Substructure
 
add(Substructure) - Method in class uk.ac.ebi.reactionblast.tools.rxnfile.SuperAtomContainer
 
addAll(Collection<? extends Descriptor>) - Method in class uk.ac.ebi.centres.priority.descriptor.DescriptorList
Adds multiple descriptors to the descriptor list.
addBinary(BitSet) - Method in interface uk.ac.ebi.reactionblast.fingerprints.interfaces.IPatternFingerprinter
 
addBinary(BitSet) - Method in class uk.ac.ebi.reactionblast.fingerprints.PatternFingerprinter
 
addBondToAtomAnnotationPositions(IBond) - Method in class uk.ac.ebi.reactionblast.graphics.direct.LabelManager
 
addConnection(A, A, int) - Method in class uk.ac.ebi.centres.graph.BasicConnectionTable
 
addConnection(A, A, int, int) - Method in class uk.ac.ebi.centres.graph.BasicConnectionTable
 
addData(String) - Method in class uk.ac.ebi.reactionblast.mapping.container.helper.ReactionFileData
 
addData(int, String) - Method in class uk.ac.ebi.reactionblast.mapping.container.helper.ReactionFileData
 
addEdge(EdgeBuilder) - Method in class org.openscience.smsd.algorithm.vflib.builder.NodeBuilder
Adds edge to the edge list.
addEdge(EdgeBuilder) - Method in interface org.openscience.smsd.algorithm.vflib.interfaces.INode
Adds edge to the edge list.
addExplicitH(IAtomContainer) - Static method in class uk.ac.ebi.reactionblast.tools.ExtAtomContainerManipulator
 
addExplicitH(IReaction) - Static method in class uk.ac.ebi.reactionblast.tools.ExtReactionManipulatorTool
 
addHighlighter(Highlighter) - Method in class uk.ac.ebi.reactionblast.graphics.direct.DirectMoleculeDrawer
Add a highlighter to the list.
addHighlights(IAtomContainer, Color) - Method in class uk.ac.ebi.reactionblast.graphics.direct.DirectMoleculeDrawer
Set the highlights for all atoms and bonds in the highlight container to this color.
addHighlights(List<IAtom>, Color) - Method in class uk.ac.ebi.reactionblast.graphics.direct.DirectMoleculeDrawer
 
addHighlights(IAtomContainer) - Method in class uk.ac.ebi.reactionblast.graphics.direct.DirectMoleculeDrawer
Set the highlights for all atoms and bonds in the container to the color set in Params.highlightColor.
addHighlights(List<IAtom>, List<IBond>) - Method in class uk.ac.ebi.reactionblast.graphics.direct.DirectMoleculeDrawer
Set the highlights for all the atoms and bonds to the color in Params.highlightColor.
addHighlights(List<IAtom>) - Method in class uk.ac.ebi.reactionblast.graphics.direct.DirectMoleculeDrawer
Set the highlights for all the atoms in the list to the color in Params.highlightColor.
addHighlights(IAtomContainer, Color) - Method in interface uk.ac.ebi.reactionblast.graphics.direct.Highlighter
 
addHighlights(List<IAtom>, List<IBond>) - Method in interface uk.ac.ebi.reactionblast.graphics.direct.Highlighter
 
addHighlights(IAtomContainer, Color) - Method in class uk.ac.ebi.reactionblast.graphics.direct.OutlineHighlighter
 
addHighlights(List<IAtom>, List<IBond>) - Method in class uk.ac.ebi.reactionblast.graphics.direct.OutlineHighlighter
 
addHighlights(IAtomContainer, Color) - Method in class uk.ac.ebi.reactionblast.graphics.direct.SimpleHighlighter
Set the highlights for all atoms and bonds in the highlight container to this color.
addHighlights(List<IAtom>, List<IBond>) - Method in class uk.ac.ebi.reactionblast.graphics.direct.SimpleHighlighter
Set the highlights for all the atoms and bonds to the color in Params.highlightColor.
addImages(IAtomContainer, IAtomContainer, String, Map<Integer, Integer>) - Method in class uk.ac.ebi.reactionblast.tools.ImageGenerator
 
addImages(IAtomContainer, IAtomContainer, String, AtomAtomMapping) - Method in class uk.ac.ebi.reactionblast.tools.ImageGenerator
 
addImplicitHydrogens(IReaction) - Method in class uk.ac.ebi.reactionblast.tools.Reader
 
addImplicitHydrogens(IAtomContainerSet) - Method in class uk.ac.ebi.reactionblast.tools.Reader
 
addImplicitHydrogens(IAtomContainer) - Method in class uk.ac.ebi.reactionblast.tools.Reader
 
addImplicitHydrogens(IReaction) - Static method in class uk.ac.ebi.reactionblast.tools.TestUtility
 
addImplicitHydrogens(IAtomContainerSet) - Static method in class uk.ac.ebi.reactionblast.tools.TestUtility
 
addImplicitHydrogens(IAtomContainer) - Static method in class uk.ac.ebi.reactionblast.tools.TestUtility
 
addKochCliques() - Method in class org.openscience.smsd.algorithm.vflib.seeds.MCSSeedGenerator
 
addLabel(String) - Method in class org.openscience.smsd.helper.LabelContainer
Add label if its not present
addLeaf(IAtom) - Method in class uk.ac.ebi.reactionblast.graphics.direct.RootSystem
 
addMapping(IAtom, IAtom) - Method in class uk.ac.ebi.reactionblast.mapping.blocks.Block
 
addMapping(IMapping, IAtom, IAtom) - Method in class uk.ac.ebi.reactionblast.mapping.blocks.BlockPair
 
addMatrix(int, RMatrix) - Method in class uk.ac.ebi.reactionblast.mechanism.GlobalEntropyCalculator
The method adds a RMatrix to the ArrayList maintaining the set of RMatrices.
addNeighbor(NodeBuilder) - Method in class org.openscience.smsd.algorithm.vflib.builder.NodeBuilder
Adds neighbor to the Neighbors List.
addNeighbor(NodeBuilder) - Method in interface org.openscience.smsd.algorithm.vflib.interfaces.INode
Adds neighbor to the Neighbors List.
addNode(CDKRNode) - Method in class org.openscience.smsd.algorithm.rgraph.CDKRGraph
Adds a new node to the CDKRGraph.
addNode(AtomMatcher, IAtom) - Method in class org.openscience.smsd.algorithm.vflib.builder.VFQueryBuilder
Add and return a node for a query atom
addRingCenterToAtomAnnotationPosition(IAtom, List<IAtom>) - Method in class uk.ac.ebi.reactionblast.graphics.direct.LabelManager
 
addRoot(IAtom) - Method in class uk.ac.ebi.reactionblast.graphics.direct.RootSystem
 
addRootsFromBond(IBond) - Method in class uk.ac.ebi.reactionblast.graphics.direct.RootSystem
 
addScore(int, Double) - Method in class org.openscience.smsd.filters.EnergyFilter
 
addScore(int, Integer) - Method in class org.openscience.smsd.filters.FragmentFilter
 
addScore(int, T) - Method in interface org.openscience.smsd.filters.IChemicalFilter
 
addScore(int, Double) - Method in class org.openscience.smsd.filters.StereoFilter
 
addToChiralMap(Map<IAtom, IStereoAndConformation>) - Method in class uk.ac.ebi.reactionblast.graphics.direct.DirectMoleculeDrawer
 
addToHighlights(Map<IAtom, Color>) - Method in class uk.ac.ebi.reactionblast.graphics.direct.DirectMoleculeDrawer
 
addToHighlights(Map<IAtom, Color>) - Method in interface uk.ac.ebi.reactionblast.graphics.direct.Highlighter
 
addToHighlights(Map<IAtom, Color>) - Method in class uk.ac.ebi.reactionblast.graphics.direct.OutlineHighlighter
 
addToHighlights(Map<IAtom, Color>) - Method in class uk.ac.ebi.reactionblast.graphics.direct.SimpleHighlighter
Add the set of atom-to-color mappings to the highlights.
adjacencyTable - Variable in class uk.ac.ebi.reactionblast.mapping.blocks.MappingGraph
 
Algorithm - Enum in org.openscience.smsd.interfaces
This class represents various algorithm type supported by SMSD.
align(IReaction, int, int, double, double, double) - Method in class uk.ac.ebi.reactionblast.graphics.direct.DirectReactionDrawer
 
align(IAtomContainer, Vector2d) - Method in class uk.ac.ebi.reactionblast.graphics.direct.layout.AbstractDirectLayout
 
alignmentToAnnotationPosition(int) - Method in class uk.ac.ebi.reactionblast.graphics.direct.LabelManager
 
alignMolecules - Variable in class uk.ac.ebi.reactionblast.graphics.direct.Params
 
alignToAxis(IAtomContainer, Vector2d, Vector2d, Point2d) - Static method in class uk.ac.ebi.reactionblast.graphics.direct.layout.MoleculeAligner
 
alignToMaxWidth(IAtomContainer, Vector2d) - Static method in class uk.ac.ebi.reactionblast.graphics.direct.layout.MoleculeAligner
 
alignToMinAreaBox(IAtomContainer, Vector2d) - Static method in class uk.ac.ebi.reactionblast.graphics.direct.layout.MoleculeAligner
Finds the minimum-area bounding box of the atom container and uses the longest side as the central axis.
and(MolFingerprint) - Method in class uk.ac.ebi.reactionblast.fingerprints.MolFingerprint
 
annotateReactionAsText(ReactionMechanismTool, String, StringBuilder) - Method in class aamtool.Annotator
 
annotateReactionAsXML(ReactionMechanismTool, String, Document, Element) - Method in class aamtool.Annotator
 
Annotator - Class in aamtool
 
append(Collection<? extends DescriptorList>) - Method in class uk.ac.ebi.centres.priority.descriptor.DescriptorList
Appends multiple descriptor lists.
append(Byte) - Method in class uk.ac.ebi.reactionblast.fingerprints.MolFingerprint
 
append(MolFingerprint) - Method in class uk.ac.ebi.reactionblast.fingerprints.MolFingerprint
 
append(ArrayList, ArrayList) - Static method in class uk.ac.ebi.reactionblast.tools.utility.EBIArrayList
 
append(BitSet, BitSet) - Static method in class uk.ac.ebi.reactionblast.tools.utility.EBIBitSet
 
append(double[], double[]) - Static method in class uk.ac.ebi.reactionblast.tools.utility.EBIDoubleUtility
 
append(double[], double[], double[]) - Static method in class uk.ac.ebi.reactionblast.tools.utility.EBIDoubleUtility
 
Arc<A> - Class in uk.ac.ebi.centres.graph
 
Arc(Ligand<A>, Ligand<A>, MutableDescriptor) - Constructor for class uk.ac.ebi.centres.graph.Arc
 
Arc(Ligand<A>, Ligand<A>, MutableDescriptor, int) - Constructor for class uk.ac.ebi.centres.graph.Arc
 
ArcPrimaryDescriptor<A> - Class in uk.ac.ebi.centres.priority.access.descriptor
Access a descriptor on the parent arc of a ligand.
ArcPrimaryDescriptor() - Constructor for class uk.ac.ebi.centres.priority.access.descriptor.ArcPrimaryDescriptor
 
area() - Method in class uk.ac.ebi.reactionblast.graphics.direct.ConvexHull.Rectangle
 
aromatizeCDK(IAtomContainer) - Static method in class uk.ac.ebi.reactionblast.tools.ExtAtomContainerManipulator
 
aromatizeDayLight(IAtomContainer) - Static method in class uk.ac.ebi.reactionblast.tools.ExtAtomContainerManipulator
 
aromatizeMolecule(IAtomContainer) - Static method in class uk.ac.ebi.reactionblast.tools.ExtAtomContainerManipulator
This function finds rings and uses aromaticity detection code to aromatize the molecule.
arrayLeftDivide(EBIMatrix) - Method in class uk.ac.ebi.reactionblast.tools.EBIMatrix
Element-by-element left division, data = matrix.\B
arrayLeftDivideEquals(EBIMatrix) - Method in class uk.ac.ebi.reactionblast.tools.EBIMatrix
Element-by-element left division in place, matrix = matrix.\B
arrayRightDivide(EBIMatrix) - Method in class uk.ac.ebi.reactionblast.tools.EBIMatrix
Element-by-element right division, data = matrix./B
arrayRightDivideEquals(EBIMatrix) - Method in class uk.ac.ebi.reactionblast.tools.EBIMatrix
Element-by-element right division in place, matrix = matrix./B
arrayTimes(EBIMatrix) - Method in class uk.ac.ebi.reactionblast.tools.EBIMatrix
Element-by-element multiplication, data = matrix.*B
arrayTimesEquals(EBIMatrix) - Method in class uk.ac.ebi.reactionblast.tools.EBIMatrix
Element-by-element multiplication in place, matrix = matrix.*B
arrowAxis - Variable in class uk.ac.ebi.reactionblast.graphics.direct.awtlayout.AbstractAWTReactionLayout
 
arrowAxis - Variable in class uk.ac.ebi.reactionblast.graphics.direct.layout.AbstractDirectReactionLayout
 
arrowBodyWidth - Variable in class uk.ac.ebi.reactionblast.graphics.direct.Params
 
arrowGap - Variable in class uk.ac.ebi.reactionblast.graphics.direct.Params
 
arrowHeadAngle - Variable in class uk.ac.ebi.reactionblast.graphics.direct.Params
 
arrowHeadIndent - Variable in class uk.ac.ebi.reactionblast.graphics.direct.Params
 
arrowHeadLength - Variable in class uk.ac.ebi.reactionblast.graphics.direct.Params
 
arrowLength - Variable in class uk.ac.ebi.reactionblast.graphics.direct.Params
 
arrowPos - Variable in class uk.ac.ebi.reactionblast.graphics.direct.awtlayout.AbstractAWTReactionLayout
 
arrowPos - Variable in class uk.ac.ebi.reactionblast.graphics.direct.layout.AbstractDirectReactionLayout
 
arrowType - Variable in class uk.ac.ebi.reactionblast.graphics.direct.Params
 
ArrowWheel - Class in uk.ac.ebi.reactionblast.graphics.direct.layout
 
ArrowWheel(DirectArrowDrawer, IAtomContainer, List<IAtomContainer>) - Constructor for class uk.ac.ebi.reactionblast.graphics.direct.layout.ArrowWheel
 
ArrowWheel(DirectArrowDrawer, IAtomContainer, List<IAtomContainer>, List<String>) - Constructor for class uk.ac.ebi.reactionblast.graphics.direct.layout.ArrowWheel
 
atomAtomMap(IAtomContainerSet, IAtomContainerSet, Map<IAtomContainer, int[]>, Map<IAtom, IAtom>) - Method in class uk.ac.ebi.reactionblast.tools.labelling.AbstractReactionLabeller
 
atomAtomMap(IReaction, IReaction, Map<IAtomContainer, int[]>) - Method in class uk.ac.ebi.reactionblast.tools.labelling.AbstractReactionLabeller
 
AtomAtomMapping - Class in org.openscience.smsd
Holds atom-atom mappings information between source and target molecules
AtomAtomMapping(IAtomContainer, IAtomContainer) - Constructor for class org.openscience.smsd.AtomAtomMapping
 
AtomAtomMappingContainer - Class in uk.ac.ebi.reactionblast.mechanism.helper
This class maintain the atom-atom mapping of a reaction between reactants and products
AtomAtomMappingContainer(Reactor, boolean) - Constructor for class uk.ac.ebi.reactionblast.mechanism.helper.AtomAtomMappingContainer
Class constructor.
AtomAtomMappingContainer(IAtomContainerSet, IAtomContainerSet, boolean) - Constructor for class uk.ac.ebi.reactionblast.mechanism.helper.AtomAtomMappingContainer
 
AtomAtomMappingContainer(IReaction, boolean) - Constructor for class uk.ac.ebi.reactionblast.mechanism.helper.AtomAtomMappingContainer
 
atomContainer - Variable in class uk.ac.ebi.reactionblast.signature.BaseMoleculeSignature
 
atomContainer - Variable in class uk.ac.ebi.reactionblast.tools.rxnfile.RXNFileImporter
 
AtomContainerAtomPermutor - Class in uk.ac.ebi.reactionblast.tools.labelling
 
AtomContainerAtomPermutor(IAtomContainer) - Constructor for class uk.ac.ebi.reactionblast.tools.labelling.AtomContainerAtomPermutor
 
AtomContainerAtomPermutor(IAtomContainer, boolean, boolean) - Constructor for class uk.ac.ebi.reactionblast.tools.labelling.AtomContainerAtomPermutor
 
AtomContainerComparator - Class in org.openscience.smsd.tools
 
AtomContainerComparator() - Constructor for class org.openscience.smsd.tools.AtomContainerComparator
Creates a new instance of AtomContainerComparator
AtomContainerComparatorBy2DCenter - Class in uk.ac.ebi.reactionblast.graphics.direct
 
AtomContainerComparatorBy2DCenter() - Constructor for class uk.ac.ebi.reactionblast.graphics.direct.AtomContainerComparatorBy2DCenter
 
AtomContainerPrinter - Class in uk.ac.ebi.reactionblast.tools.labelling
 
AtomContainerPrinter() - Constructor for class uk.ac.ebi.reactionblast.tools.labelling.AtomContainerPrinter
 
AtomContainerSetComparator - Class in uk.ac.ebi.reactionblast.tools
GraphAtomContainer Comparator
AtomContainerSetComparator() - Constructor for class uk.ac.ebi.reactionblast.tools.AtomContainerSetComparator
Creates a new instance of AtomContainerComparator
AtomicNumberAccessor<A> - Interface in uk.ac.ebi.centres.priority.access
Wrapper provides access to a given an atom's atomic number (of type A) to priority rules that require it.
AtomicNumberRule<A> - Class in uk.ac.ebi.centres.priority
An abstract class for constitutional priority based on atomic number.
AtomicNumberRule(AtomicNumberAccessor<A>) - Constructor for class uk.ac.ebi.centres.priority.AtomicNumberRule
Constructs an atomic number comparator that uses the provided accessor to fetch the atomic number for a given atom.
atomIDFontSize - Variable in class uk.ac.ebi.reactionblast.graphics.direct.Params
 
AtomLayout - Class in uk.ac.ebi.reactionblast.graphics.direct.awtlayout
Layout an atom's symbol, and surrounding annotations, such as : charge, implicit hydrogens, etc.
AtomLayout(AbstractAWTLayout, Params, LabelManager) - Constructor for class uk.ac.ebi.reactionblast.graphics.direct.awtlayout.AtomLayout
 
AtomMatcher - Interface in org.openscience.smsd.algorithm.matchers
Interface for the AtomMatcher (atoms) in graph.
atomMatcher - Variable in class uk.ac.ebi.reactionblast.mapping.graph.MCSThread
 
atoms() - Method in class uk.ac.ebi.reactionblast.tools.rxnfile.Substructure
super atoms.
AtomStereoChangeInformation - Class in uk.ac.ebi.reactionblast.mechanism.helper
 
AtomStereoChangeInformation(IAtom, IAtom) - Constructor for class uk.ac.ebi.reactionblast.mechanism.helper.AtomStereoChangeInformation
 
AtomStereoChangeInformation(IAtom, IAtom, IStereoAndConformation, IStereoAndConformation) - Constructor for class uk.ac.ebi.reactionblast.mechanism.helper.AtomStereoChangeInformation
 
atomSymbolFontSize - Variable in class uk.ac.ebi.reactionblast.graphics.direct.Params
 
AuxiliaryDescriptor<A> - Class in uk.ac.ebi.centres.priority.access.descriptor
Access the primary descriptor on a ligand
AuxiliaryDescriptor() - Constructor for class uk.ac.ebi.centres.priority.access.descriptor.AuxiliaryDescriptor
 
axis - Variable in class uk.ac.ebi.reactionblast.graphics.direct.awtlayout.AbstractAWTReactionLayout
 
Axis - Enum in uk.ac.ebi.reactionblast.graphics.direct
 
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