- 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 uk.ac.ebi.aamtool.Annotator
-
- annotateReactionAsXML(ReactionMechanismTool, String, Document, Element) - Method in class uk.ac.ebi.aamtool.Annotator
-
- Annotator - Class in uk.ac.ebi.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
-