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L

LabelContainer - Class in org.openscience.smsd.helper
Class that handles atoms and assigns an integer label to them.
LabelContainer() - Constructor for class org.openscience.smsd.helper.LabelContainer
 
labelGap - Variable in class uk.ac.ebi.reactionblast.graphics.direct.Params
 
LabelManager - Class in uk.ac.ebi.reactionblast.graphics.direct
 
LabelManager() - Constructor for class uk.ac.ebi.reactionblast.graphics.direct.LabelManager
 
LabelManager.AnnotationPosition - Enum in uk.ac.ebi.reactionblast.graphics.direct
 
labelPanelFont - Variable in class uk.ac.ebi.reactionblast.graphics.direct.Params
 
labelPanelFontSize - Variable in class uk.ac.ebi.reactionblast.graphics.direct.Params
 
labelPanelHeight - Variable in class uk.ac.ebi.reactionblast.graphics.direct.Params
 
labelReaction(IReaction, ICanonicalMoleculeLabeller) - Method in class uk.ac.ebi.reactionblast.tools.labelling.AbstractReactionLabeller
 
labelYGap - Variable in class uk.ac.ebi.reactionblast.graphics.direct.Params
 
layout(T, Graphics2D) - Method in class uk.ac.ebi.reactionblast.graphics.direct.awtlayout.AbstractAWTLayout
 
layout(T, String, Graphics2D) - Method in class uk.ac.ebi.reactionblast.graphics.direct.awtlayout.AbstractAWTLayout
 
layout(IAtom, Graphics2D) - Method in class uk.ac.ebi.reactionblast.graphics.direct.awtlayout.AtomLayout
 
layout(IAtom, String, Graphics2D) - Method in class uk.ac.ebi.reactionblast.graphics.direct.awtlayout.AtomLayout
 
layout(IReaction, Graphics2D) - Method in class uk.ac.ebi.reactionblast.graphics.direct.awtlayout.LeftToRightAWTReactionLayout
 
layout(IReaction, String, Graphics2D) - Method in class uk.ac.ebi.reactionblast.graphics.direct.awtlayout.LeftToRightAWTReactionLayout
 
layout(IAtomContainerSet, Graphics2D) - Method in class uk.ac.ebi.reactionblast.graphics.direct.awtlayout.LinearAtomContainerSetLayout
 
layout(IAtomContainerSet, String, Graphics2D) - Method in class uk.ac.ebi.reactionblast.graphics.direct.awtlayout.LinearAtomContainerSetLayout
 
layout(IAtomContainer, Graphics2D) - Method in class uk.ac.ebi.reactionblast.graphics.direct.awtlayout.MoleculeLayout
 
layout(IAtomContainer, String, Graphics2D) - Method in class uk.ac.ebi.reactionblast.graphics.direct.awtlayout.MoleculeLayout
 
layout(IReaction, Graphics2D) - Method in class uk.ac.ebi.reactionblast.graphics.direct.awtlayout.TopToBottomAWTReactionLayout
 
layout(IReaction, String, Graphics2D) - Method in class uk.ac.ebi.reactionblast.graphics.direct.awtlayout.TopToBottomAWTReactionLayout
 
layout(IAtomContainer, Dimension, Graphics2D) - Method in class uk.ac.ebi.reactionblast.graphics.direct.awtlayout.ZoomToFitAWTLayout
 
layout(IAtomContainer, Vector2d) - Method in class uk.ac.ebi.reactionblast.graphics.direct.awtlayout.ZoomToFitAWTLayout
 
layout(T, Vector2d) - Method in class uk.ac.ebi.reactionblast.graphics.direct.layout.AbstractDirectLayout
 
layout(List<IAtomContainer>, Dimension) - Method in interface uk.ac.ebi.reactionblast.graphics.direct.layout.CanvasGenerator
 
layout(List<IAtomContainer>, Dimension) - Method in class uk.ac.ebi.reactionblast.graphics.direct.layout.CircularCanvasGenerator
 
layout(List<IAtomContainer>, Dimension) - Method in class uk.ac.ebi.reactionblast.graphics.direct.layout.GridCanvasGenerator
 
layout(IReaction, Vector2d) - Method in class uk.ac.ebi.reactionblast.graphics.direct.layout.LeftToRightReactionLayout
 
layout(IAtomContainerSet, Vector2d) - Method in class uk.ac.ebi.reactionblast.graphics.direct.layout.LinearMoleculeSetLayout
 
layout(IAtomContainer, Vector2d) - Method in class uk.ac.ebi.reactionblast.graphics.direct.layout.SingleMoleculeLayout
 
layout(IReaction, Vector2d) - Method in class uk.ac.ebi.reactionblast.graphics.direct.layout.TopToBottomReactionLayout
 
layout(List<IAtomContainer>, Dimension, Graphics2D) - Method in class uk.ac.ebi.reactionblast.graphics.direct.layout.ZoomToFitGridLayout
 
layout(IAtomContainer, Dimension, Graphics2D) - Method in class uk.ac.ebi.reactionblast.graphics.direct.layout.ZoomToFitLayout
 
layout(IAtomContainer, Vector2d) - Method in class uk.ac.ebi.reactionblast.graphics.direct.layout.ZoomToFitLayout
 
layout(IAtomContainer) - Method in class uk.ac.ebi.reactionblast.tools.Reader
 
layout(IAtomContainer) - Static method in class uk.ac.ebi.reactionblast.tools.TestUtility
 
layoutAtomID(IAtom, IAtomContainer, Graphics2D) - Method in class uk.ac.ebi.reactionblast.graphics.direct.awtlayout.AtomLayout
 
layoutAtomSymbol(IAtom, Graphics2D) - Method in class uk.ac.ebi.reactionblast.graphics.direct.awtlayout.AtomLayout
 
LayoutCheck - Class in uk.ac.ebi.reactionblast.tools
 
layoutElectronPairs(IAtom, IAtomContainer, int, Graphics2D) - Method in class uk.ac.ebi.reactionblast.graphics.direct.awtlayout.AtomLayout
 
layoutImplicitHydrogens(IAtom, int, LabelManager.AnnotationPosition, Graphics2D) - Method in class uk.ac.ebi.reactionblast.graphics.direct.awtlayout.AtomLayout
 
layoutLeftToRight - Variable in class uk.ac.ebi.reactionblast.graphics.direct.Params
 
leftRightAlignment - Variable in class uk.ac.ebi.reactionblast.graphics.direct.Params
 
LeftToRightAWTReactionLayout - Class in uk.ac.ebi.reactionblast.graphics.direct.awtlayout
 
LeftToRightAWTReactionLayout() - Constructor for class uk.ac.ebi.reactionblast.graphics.direct.awtlayout.LeftToRightAWTReactionLayout
 
LeftToRightAWTReactionLayout(Params) - Constructor for class uk.ac.ebi.reactionblast.graphics.direct.awtlayout.LeftToRightAWTReactionLayout
 
leftToRightMoleculeLabelFontSize - Variable in class uk.ac.ebi.reactionblast.graphics.direct.Params
 
LeftToRightReactionCenterImage(IReaction, String, String) - Static method in class uk.ac.ebi.reactionblast.tools.ImageGenerator
 
LeftToRightReactionCenterImageSmall(IReaction, String, String) - Static method in class uk.ac.ebi.reactionblast.tools.ImageGenerator
 
LeftToRightReactionLayout - Class in uk.ac.ebi.reactionblast.graphics.direct.layout
Layout atoms containers by modifying the points in the molecules.
LeftToRightReactionLayout() - Constructor for class uk.ac.ebi.reactionblast.graphics.direct.layout.LeftToRightReactionLayout
 
LeftToRightReactionLayout(boolean) - Constructor for class uk.ac.ebi.reactionblast.graphics.direct.layout.LeftToRightReactionLayout
 
LeftToRightReactionLayout(boolean, Vector2d) - Constructor for class uk.ac.ebi.reactionblast.graphics.direct.layout.LeftToRightReactionLayout
 
LeftToRightReactionLayoutImage(IReaction, String, String) - Static method in class uk.ac.ebi.reactionblast.tools.ImageGenerator
 
LeftToRightReactionLayoutImageSmall(IReaction, String, String) - Static method in class uk.ac.ebi.reactionblast.tools.ImageGenerator
 
length() - Method in class uk.ac.ebi.reactionblast.fingerprints.MolFingerprint
 
lift(IAtom, IAtomContainer) - Method in class uk.ac.ebi.reactionblast.stereo.wedge.WedgeStereoLifter
 
Ligand<A> - Interface in uk.ac.ebi.centres
Defines a ligand which in the digraph is a side chain of a central atom.
LigandComparison - Class in uk.ac.ebi.centres
Simple holder for a ligand comparison.
LigandComparison(Integer, Descriptor.Type) - Constructor for class uk.ac.ebi.centres.LigandComparison
Construct a new ligand comparison with order and type.
LigandSorter<A> - Interface in uk.ac.ebi.centres
An injectable sorter for ligands.
LinearAtomContainerSetLayout - Class in uk.ac.ebi.reactionblast.graphics.direct.awtlayout
 
LinearAtomContainerSetLayout(Vector2d) - Constructor for class uk.ac.ebi.reactionblast.graphics.direct.awtlayout.LinearAtomContainerSetLayout
 
LinearAtomContainerSetLayout(Vector2d, Params) - Constructor for class uk.ac.ebi.reactionblast.graphics.direct.awtlayout.LinearAtomContainerSetLayout
 
LinearMoleculeSetLayout - Class in uk.ac.ebi.reactionblast.graphics.direct.layout
 
LinearMoleculeSetLayout(Params) - Constructor for class uk.ac.ebi.reactionblast.graphics.direct.layout.LinearMoleculeSetLayout
 
LinearMoleculeSetLayout(Params, boolean) - Constructor for class uk.ac.ebi.reactionblast.graphics.direct.layout.LinearMoleculeSetLayout
 
LinearMoleculeSetLayout(Params, boolean, Vector2d) - Constructor for class uk.ac.ebi.reactionblast.graphics.direct.layout.LinearMoleculeSetLayout
 
LipinskiRuleOfFiveDescriptor - Class in uk.ac.ebi.reactionblast.tools.descriptors
 
LipinskiRuleOfFiveDescriptor() - Constructor for class uk.ac.ebi.reactionblast.tools.descriptors.LipinskiRuleOfFiveDescriptor
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loadCML(InputStream) - Static method in class uk.ac.ebi.centres.cdk.CMLLoader
 
lonePairSeparation - Variable in class uk.ac.ebi.reactionblast.graphics.direct.Params
 
lu() - Method in class uk.ac.ebi.reactionblast.tools.EBIMatrix
LU Decomposition
LUDecomposition - Class in uk.ac.ebi.reactionblast.tools.matrix
LU Decomposition.
LUDecomposition(EBIMatrix) - Constructor for class uk.ac.ebi.reactionblast.tools.matrix.LUDecomposition
LU Decomposition
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