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allclasses-noframe.html
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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
<!-- NewPage -->
<html lang="en">
<head>
<!-- Generated by javadoc (1.8.0_202) on Mon Jul 15 17:15:34 CEST 2019 -->
<title>All Classes</title>
<meta name="date" content="2019-07-15">
<link rel="stylesheet" type="text/css" href="stylesheet.css" title="Style">
<script type="text/javascript" src="script.js"></script>
</head>
<body>
<h1 class="bar">All Classes</h1>
<div class="indexContainer">
<ul>
<li><a href="bio/singa/javafx/geometry/AbacusVisualization.html" title="class in bio.singa.javafx.geometry">AbacusVisualization</a></li>
<li><a href="bio/singa/chemistry/entities/AbstractChemicalEntity.html" title="class in bio.singa.chemistry.entities">AbstractChemicalEntity</a></li>
<li><a href="bio/singa/chemistry/entities/AbstractChemicalEntity.Builder.html" title="class in bio.singa.chemistry.entities">AbstractChemicalEntity.Builder</a></li>
<li><a href="bio/singa/simulation/model/modules/concentration/functions/AbstractDeltaFunction.html" title="class in bio.singa.simulation.model.modules.concentration.functions">AbstractDeltaFunction</a></li>
<li><a href="bio/singa/mathematics/graphs/model/AbstractEdge.html" title="class in bio.singa.mathematics.graphs.model">AbstractEdge</a></li>
<li><a href="bio/singa/features/model/AbstractFeature.html" title="class in bio.singa.features.model">AbstractFeature</a></li>
<li><a href="bio/singa/mathematics/forces/AbstractForce.html" title="class in bio.singa.mathematics.forces">AbstractForce</a></li>
<li><a href="bio/singa/mathematics/graphs/grid/AbstractGridGraph.html" title="class in bio.singa.mathematics.graphs.grid">AbstractGridGraph</a></li>
<li><a href="bio/singa/core/parser/AbstractHTMLParser.html" title="class in bio.singa.core.parser">AbstractHTMLParser</a></li>
<li><a href="bio/singa/features/identifiers/model/AbstractIdentifier.html" title="class in bio.singa.features.identifiers.model">AbstractIdentifier</a></li>
<li><a href="bio/singa/simulation/model/modules/concentration/imlementations/reactions/behaviors/kineticlaws/AbstractKineticLaw.html" title="class in bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.kineticlaws">AbstractKineticLaw</a></li>
<li><a href="bio/singa/mathematics/graphs/model/AbstractMapGraph.html" title="class in bio.singa.mathematics.graphs.model">AbstractMapGraph</a></li>
<li><a href="bio/singa/chemistry/entities/modification/AbstractModification.html" title="class in bio.singa.chemistry.entities.modification">AbstractModification</a></li>
<li><a href="bio/singa/mathematics/graphs/model/AbstractNode.html" title="class in bio.singa.mathematics.graphs.model">AbstractNode</a></li>
<li><a href="bio/singa/core/parser/AbstractParser.html" title="class in bio.singa.core.parser">AbstractParser</a></li>
<li><a href="bio/singa/structure/algorithms/superimposition/fit3d/representations/AbstractRepresentationScheme.html" title="class in bio.singa.structure.algorithms.superimposition.fit3d.representations">AbstractRepresentationScheme</a></li>
<li><a href="bio/singa/sequence/model/AbstractSequence.html" title="class in bio.singa.sequence.model">AbstractSequence</a></li>
<li><a href="bio/singa/core/parser/AbstractUniProtIdentifierMappingParser.html" title="class in bio.singa.core.parser">AbstractUniProtIdentifierMappingParser</a></li>
<li><a href="bio/singa/core/parser/AbstractXMLParser.html" title="class in bio.singa.core.parser">AbstractXMLParser</a></li>
<li><a href="bio/singa/simulation/features/ActinBoostVelocity.html" title="class in bio.singa.simulation.features">ActinBoostVelocity</a></li>
<li><a href="bio/singa/simulation/model/modules/qualitative/implementations/ActinCortexDiffusivityScaling.html" title="class in bio.singa.simulation.model.modules.qualitative.implementations">ActinCortexDiffusivityScaling</a></li>
<li><a href="bio/singa/mathematics/concepts/Addable.html" title="interface in bio.singa.mathematics.concepts"><span class="interfaceName">Addable</span></a></li>
<li><a href="uk/co/cogitolearning/cogpar/AdditionExpressionNode.html" title="class in uk.co.cogitolearning.cogpar">AdditionExpressionNode</a></li>
<li><a href="bio/singa/mathematics/concepts/AdditivelyInvertible.html" title="interface in bio.singa.mathematics.concepts"><span class="interfaceName">AdditivelyInvertible</span></a></li>
<li><a href="bio/singa/chemistry/entities/modification/AddModification.html" title="class in bio.singa.chemistry.entities.modification">AddModification</a></li>
<li><a href="bio/singa/simulation/features/AffectedRegion.html" title="class in bio.singa.simulation.features">AffectedRegion</a></li>
<li><a href="bio/singa/structure/algorithms/superimposition/affinity/AffinityAlignment.html" title="class in bio.singa.structure.algorithms.superimposition.affinity">AffinityAlignment</a></li>
<li><a href="bio/singa/structure/algorithms/superimposition/affinity/AffinityAlignment.AtomStep.html" title="interface in bio.singa.structure.algorithms.superimposition.affinity"><span class="interfaceName">AffinityAlignment.AtomStep</span></a></li>
<li><a href="bio/singa/structure/algorithms/superimposition/affinity/AffinityAlignment.Builder.html" title="class in bio.singa.structure.algorithms.superimposition.affinity">AffinityAlignment.Builder</a></li>
<li><a href="bio/singa/structure/algorithms/superimposition/affinity/AffinityAlignment.InputStep.html" title="interface in bio.singa.structure.algorithms.superimposition.affinity"><span class="interfaceName">AffinityAlignment.InputStep</span></a></li>
<li><a href="bio/singa/structure/algorithms/superimposition/affinity/AffinityAlignment.ParameterStep.html" title="interface in bio.singa.structure.algorithms.superimposition.affinity"><span class="interfaceName">AffinityAlignment.ParameterStep</span></a></li>
<li><a href="bio/singa/mathematics/algorithms/clustering/AffinityPropagation.html" title="class in bio.singa.mathematics.algorithms.clustering">AffinityPropagation</a></li>
<li><a href="bio/singa/mathematics/algorithms/clustering/AffinityPropagation.Builder.html" title="class in bio.singa.mathematics.algorithms.clustering">AffinityPropagation.Builder</a></li>
<li><a href="bio/singa/mathematics/algorithms/clustering/AffinityPropagation.DataStep.html" title="interface in bio.singa.mathematics.algorithms.clustering"><span class="interfaceName">AffinityPropagation.DataStep</span></a></li>
<li><a href="bio/singa/mathematics/algorithms/clustering/AffinityPropagation.DistanceStep.html" title="interface in bio.singa.mathematics.algorithms.clustering"><span class="interfaceName">AffinityPropagation.DistanceStep</span></a></li>
<li><a href="bio/singa/mathematics/algorithms/clustering/AffinityPropagation.MatrixStep.html" title="interface in bio.singa.mathematics.algorithms.clustering"><span class="interfaceName">AffinityPropagation.MatrixStep</span></a></li>
<li><a href="bio/singa/mathematics/algorithms/clustering/AffinityPropagation.ParameterStep.html" title="interface in bio.singa.mathematics.algorithms.clustering"><span class="interfaceName">AffinityPropagation.ParameterStep</span></a></li>
<li><a href="bio/singa/mathematics/algorithms/clustering/AffinityPropagationSampler.html" title="class in bio.singa.mathematics.algorithms.clustering">AffinityPropagationSampler</a></li>
<li><a href="bio/singa/structure/algorithms/superimposition/fit3d/representations/AlphaCarbonRepresentationScheme.html" title="class in bio.singa.structure.algorithms.superimposition.fit3d.representations">AlphaCarbonRepresentationScheme</a></li>
<li><a href="bio/singa/structure/model/interfaces/AminoAcid.html" title="interface in bio.singa.structure.model.interfaces"><span class="interfaceName">AminoAcid</span></a></li>
<li><a href="bio/singa/structure/model/families/AminoAcidFamily.html" title="enum in bio.singa.structure.model.families">AminoAcidFamily</a></li>
<li><a href="bio/singa/structure/model/oak/AminoAcids.html" title="class in bio.singa.structure.model.oak">AminoAcids</a></li>
<li><a href="bio/singa/mathematics/metrics/implementations/AngularDistance.html" title="class in bio.singa.mathematics.metrics.implementations">AngularDistance</a></li>
<li><a href="bio/singa/chemistry/annotations/Annotatable.html" title="interface in bio.singa.chemistry.annotations"><span class="interfaceName">Annotatable</span></a></li>
<li><a href="bio/singa/chemistry/annotations/Annotation.html" title="class in bio.singa.chemistry.annotations">Annotation</a></li>
<li><a href="bio/singa/chemistry/annotations/AnnotationType.html" title="enum in bio.singa.chemistry.annotations">AnnotationType</a></li>
<li><a href="bio/singa/simulation/features/AppliedVesicleState.html" title="class in bio.singa.simulation.features">AppliedVesicleState</a></li>
<li><a href="bio/singa/simulation/model/rules/AssignmentRule.html" title="class in bio.singa.simulation.model.rules">AssignmentRule</a></li>
<li><a href="bio/singa/simulation/model/rules/AssignmentRules.html" title="class in bio.singa.simulation.model.rules">AssignmentRules</a></li>
<li><a href="bio/singa/structure/model/interfaces/Atom.html" title="interface in bio.singa.structure.model.interfaces"><span class="interfaceName">Atom</span></a></li>
<li><a href="bio/singa/structure/model/interfaces/AtomContainer.html" title="interface in bio.singa.structure.model.interfaces"><span class="interfaceName">AtomContainer</span></a></li>
<li><a href="bio/singa/structure/model/oak/AtomName.html" title="enum in bio.singa.structure.model.oak">AtomName</a></li>
<li><a href="bio/singa/structure/parser/pdb/structures/tokens/AtomToken.html" title="enum in bio.singa.structure.parser.pdb.structures.tokens">AtomToken</a></li>
<li><a href="bio/singa/simulation/features/AttachedFilament.html" title="class in bio.singa.simulation.features">AttachedFilament</a></li>
<li><a href="bio/singa/simulation/features/AttachedMotor.html" title="class in bio.singa.simulation.features">AttachedMotor</a></li>
<li><a href="bio/singa/simulation/features/AttachmentDistance.html" title="class in bio.singa.simulation.features">AttachmentDistance</a></li>
<li><a href="bio/singa/mathematics/forces/AttractiveForce.html" title="class in bio.singa.mathematics.forces">AttractiveForce</a></li>
<li><a href="bio/singa/simulation/model/graphs/AutomatonEdge.html" title="class in bio.singa.simulation.model.graphs">AutomatonEdge</a></li>
<li><a href="bio/singa/simulation/model/graphs/AutomatonGraph.html" title="class in bio.singa.simulation.model.graphs">AutomatonGraph</a></li>
<li><a href="bio/singa/simulation/model/graphs/AutomatonGraphs.html" title="class in bio.singa.simulation.model.graphs">AutomatonGraphs</a></li>
<li><a href="bio/singa/simulation/model/graphs/AutomatonNode.html" title="class in bio.singa.simulation.model.graphs">AutomatonNode</a></li>
<li><a href="bio/singa/chemistry/features/reactions/BackwardsRateConstant.html" title="interface in bio.singa.chemistry.features.reactions"><span class="interfaceName">BackwardsRateConstant</span></a></li>
<li><a href="bio/singa/mathematics/algorithms/voronoi/model/BeachLine.html" title="class in bio.singa.mathematics.algorithms.voronoi.model">BeachLine</a></li>
<li><a href="bio/singa/mathematics/algorithms/voronoi/model/BeachSection.html" title="class in bio.singa.mathematics.algorithms.voronoi.model">BeachSection</a></li>
<li><a href="bio/singa/structure/algorithms/superimposition/fit3d/representations/BetaCarbonRepresentationScheme.html" title="class in bio.singa.structure.algorithms.superimposition.fit3d.representations">BetaCarbonRepresentationScheme</a></li>
<li><a href="bio/singa/mathematics/graphs/trees/BinaryTree.html" title="class in bio.singa.mathematics.graphs.trees">BinaryTree</a></li>
<li><a href="bio/singa/mathematics/graphs/trees/BinaryTreeNode.html" title="class in bio.singa.mathematics.graphs.trees">BinaryTreeNode</a></li>
<li><a href="bio/singa/mathematics/algorithms/geometry/BitPlane.html" title="class in bio.singa.mathematics.algorithms.geometry">BitPlane</a></li>
<li><a href="bio/singa/mathematics/vectors/BitVector.html" title="interface in bio.singa.mathematics.vectors"><span class="interfaceName">BitVector</span></a></li>
<li><a href="bio/singa/mathematics/vectors/BitVectors.html" title="class in bio.singa.mathematics.vectors">BitVectors</a></li>
<li><a href="bio/singa/mathematics/transformations/model/BitvectorTransformation.html" title="interface in bio.singa.mathematics.transformations.model"><span class="interfaceName">BitvectorTransformation</span></a></li>
<li><a href="bio/singa/simulation/features/BlackListVesicleStates.html" title="class in bio.singa.simulation.features">BlackListVesicleStates</a></li>
<li><a href="bio/singa/structure/model/oak/BondType.html" title="enum in bio.singa.structure.model.oak">BondType</a></li>
<li><a href="bio/singa/simulation/features/BoostMediatingEntity.html" title="class in bio.singa.simulation.features">BoostMediatingEntity</a></li>
<li><a href="bio/singa/core/utility/Bounded.html" title="interface in bio.singa.core.utility"><span class="interfaceName">Bounded</span></a></li>
<li><a href="bio/singa/simulation/features/Cargo.html" title="class in bio.singa.simulation.features">Cargo</a></li>
<li><a href="bio/singa/simulation/features/CargoAdditionRate.html" title="class in bio.singa.simulation.features">CargoAdditionRate</a></li>
<li><a href="bio/singa/simulation/features/Cargoes.html" title="class in bio.singa.simulation.features">Cargoes</a></li>
<li><a href="bio/singa/simulation/model/sections/CellRegion.html" title="class in bio.singa.simulation.model.sections">CellRegion</a></li>
<li><a href="bio/singa/simulation/model/sections/CellRegions.html" title="class in bio.singa.simulation.model.sections">CellRegions</a></li>
<li><a href="bio/singa/simulation/model/sections/CellSubsection.html" title="class in bio.singa.simulation.model.sections">CellSubsection</a></li>
<li><a href="bio/singa/simulation/model/sections/CellSubsections.html" title="class in bio.singa.simulation.model.sections">CellSubsections</a></li>
<li><a href="bio/singa/simulation/model/sections/CellTopology.html" title="enum in bio.singa.simulation.model.sections">CellTopology</a></li>
<li><a href="bio/singa/structure/algorithms/superimposition/fit3d/representations/CentroidRepresentationScheme.html" title="class in bio.singa.structure.algorithms.superimposition.fit3d.representations">CentroidRepresentationScheme</a></li>
<li><a href="bio/singa/structure/model/interfaces/Chain.html" title="interface in bio.singa.structure.model.interfaces"><span class="interfaceName">Chain</span></a></li>
<li><a href="bio/singa/structure/model/interfaces/ChainContainer.html" title="interface in bio.singa.structure.model.interfaces"><span class="interfaceName">ChainContainer</span></a></li>
<li><a href="bio/singa/structure/parser/pdb/structures/tokens/ChainTerminatorToken.html" title="enum in bio.singa.structure.parser.pdb.structures.tokens">ChainTerminatorToken</a></li>
<li><a href="bio/singa/chemistry/features/databases/chebi/ChEBIContentHandler.html" title="class in bio.singa.chemistry.features.databases.chebi">ChEBIContentHandler</a></li>
<li><a href="bio/singa/chemistry/features/databases/chebi/ChEBIDatabase.html" title="class in bio.singa.chemistry.features.databases.chebi">ChEBIDatabase</a></li>
<li><a href="bio/singa/features/identifiers/ChEBIIdentifier.html" title="class in bio.singa.features.identifiers">ChEBIIdentifier</a></li>
<li><a href="bio/singa/chemistry/features/databases/chebi/ChEBIImageService.html" title="class in bio.singa.chemistry.features.databases.chebi">ChEBIImageService</a></li>
<li><a href="bio/singa/chemistry/features/databases/chebi/ChEBIParserService.html" title="class in bio.singa.chemistry.features.databases.chebi">ChEBIParserService</a></li>
<li><a href="bio/singa/chemistry/features/identifiers/ChEBIToInChIKey.html" title="class in bio.singa.chemistry.features.identifiers">ChEBIToInChIKey</a></li>
<li><a href="bio/singa/chemistry/entities/ChemicalEntities.html" title="class in bio.singa.chemistry.entities">ChemicalEntities</a></li>
<li><a href="bio/singa/chemistry/entities/ChemicalEntity.html" title="interface in bio.singa.chemistry.entities"><span class="interfaceName">ChemicalEntity</span></a></li>
<li><a href="bio/singa/chemistry/features/ChemistryFeatureContainer.html" title="class in bio.singa.chemistry.features">ChemistryFeatureContainer</a></li>
<li><a href="bio/singa/structure/parser/pdb/ligands/CifFileParser.html" title="class in bio.singa.structure.parser.pdb.ligands">CifFileParser</a></li>
<li><a href="bio/singa/mathematics/geometry/faces/Circle.html" title="class in bio.singa.mathematics.geometry.faces">Circle</a></li>
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<li><a href="bio/singa/structure/parser/pdb/structures/tokens/ModelToken.html" title="enum in bio.singa.structure.parser.pdb.structures.tokens">ModelToken</a></li>
<li><a href="bio/singa/chemistry/entities/modification/ModificationBuilder.html" title="class in bio.singa.chemistry.entities.modification">ModificationBuilder</a></li>
<li><a href="bio/singa/chemistry/entities/ModificationSite.html" title="class in bio.singa.chemistry.entities">ModificationSite</a></li>
<li><a href="bio/singa/chemistry/entities/ModificationSite.Builder.html" title="class in bio.singa.chemistry.entities">ModificationSite.Builder</a></li>
<li><a href="bio/singa/simulation/features/ModifiedDiffusivity.html" title="class in bio.singa.simulation.features">ModifiedDiffusivity</a></li>
<li><a href="bio/singa/simulation/model/modules/concentration/ModuleBuilder.html" title="interface in bio.singa.simulation.model.modules.concentration"><span class="interfaceName">ModuleBuilder</span></a></li>
<li><a href="bio/singa/simulation/exceptions/ModuleCalculationException.html" title="class in bio.singa.simulation.exceptions">ModuleCalculationException</a></li>
<li><a href="bio/singa/simulation/model/modules/concentration/ModuleFactory.html" title="class in bio.singa.simulation.model.modules.concentration">ModuleFactory</a></li>
<li><a href="bio/singa/simulation/model/modules/concentration/ModuleFactory.Scope.html" title="enum in bio.singa.simulation.model.modules.concentration">ModuleFactory.Scope</a></li>
<li><a href="bio/singa/simulation/model/modules/concentration/ModuleFactory.Specificity.html" title="enum in bio.singa.simulation.model.modules.concentration">ModuleFactory.Specificity</a></li>
<li><a href="bio/singa/simulation/features/variation/ModuleFeatureVariation.html" title="class in bio.singa.simulation.features.variation">ModuleFeatureVariation</a></li>
<li><a href="bio/singa/simulation/features/variation/ModuleFeatureVariationEntry.html" title="class in bio.singa.simulation.features.variation">ModuleFeatureVariationEntry</a></li>
<li><a href="bio/singa/simulation/model/modules/concentration/ModuleState.html" title="enum in bio.singa.simulation.model.modules.concentration">ModuleState</a></li>
<li><a href="bio/singa/features/quantities/MolarConcentration.html" title="class in bio.singa.features.quantities">MolarConcentration</a></li>
<li><a href="bio/singa/structure/features/molarmass/MolarMass.html" title="class in bio.singa.structure.features.molarmass">MolarMass</a></li>
<li><a href="bio/singa/chemistry/features/molarmass/MolarMassProvider.html" title="class in bio.singa.chemistry.features.molarmass">MolarMassProvider</a></li>
<li><a href="bio/singa/features/quantities/MolarVolume.html" title="class in bio.singa.features.quantities">MolarVolume</a></li>
<li><a href="bio/singa/chemistry/features/molarvolume/MolarVolumePredictor.html" title="class in bio.singa.chemistry.features.molarvolume">MolarVolumePredictor</a></li>
<li><a href="bio/singa/structure/model/molecules/MoleculeAtom.html" title="class in bio.singa.structure.model.molecules">MoleculeAtom</a></li>
<li><a href="bio/singa/structure/model/molecules/MoleculeBond.html" title="class in bio.singa.structure.model.molecules">MoleculeBond</a></li>
<li><a href="bio/singa/structure/model/molecules/MoleculeBondType.html" title="enum in bio.singa.structure.model.molecules">MoleculeBondType</a></li>
<li><a href="bio/singa/features/formatter/MoleculeFormatter.html" title="class in bio.singa.features.formatter">MoleculeFormatter</a></li>
<li><a href="bio/singa/structure/model/molecules/MoleculeGraph.html" title="class in bio.singa.structure.model.molecules">MoleculeGraph</a></li>
<li><a href="bio/singa/javafx/renderer/molecules/MoleculeGraphRenderer.html" title="class in bio.singa.javafx.renderer.molecules">MoleculeGraphRenderer</a></li>
<li><a href="bio/singa/structure/model/molecules/MoleculeGraphs.html" title="class in bio.singa.structure.model.molecules">MoleculeGraphs</a></li>
<li><a href="bio/singa/structure/algorithms/molecules/MoleculeIsomorphism.html" title="class in bio.singa.structure.algorithms.molecules">MoleculeIsomorphism</a></li>
<li><a href="bio/singa/structure/algorithms/molecules/MoleculeIsomorphismFinder.html" title="class in bio.singa.structure.algorithms.molecules">MoleculeIsomorphismFinder</a></li>
<li><a href="bio/singa/structure/algorithms/molecules/MoleculeIsomorphismFinder.AtomConditions.html" title="class in bio.singa.structure.algorithms.molecules">MoleculeIsomorphismFinder.AtomConditions</a></li>
<li><a href="bio/singa/structure/algorithms/molecules/MoleculeIsomorphismFinder.BondConditions.html" title="class in bio.singa.structure.algorithms.molecules">MoleculeIsomorphismFinder.BondConditions</a></li>
<li><a href="bio/singa/javafx/viewer/MoleculeIsomorphismTest.html" title="class in bio.singa.javafx.viewer">MoleculeIsomorphismTest</a></li>
<li><a href="bio/singa/structure/algorithms/molecules/MoleculePathFinder.html" title="class in bio.singa.structure.algorithms.molecules">MoleculePathFinder</a></li>
<li><a href="bio/singa/javafx/renderer/molecules/MoleculeRendererOptions.html" title="class in bio.singa.javafx.renderer.molecules">MoleculeRendererOptions</a></li>
<li><a href="bio/singa/chemistry/features/structure3d/MolStructureParser.html" title="class in bio.singa.chemistry.features.structure3d">MolStructureParser</a></li>
<li><a href="bio/singa/mathematics/topology/grids/rectangular/MooreRectangularDirection.html" title="enum in bio.singa.mathematics.topology.grids.rectangular">MooreRectangularDirection</a></li>
<li><a href="bio/singa/simulation/features/MotorMovementVelocity.html" title="class in bio.singa.simulation.features">MotorMovementVelocity</a></li>
<li><a href="bio/singa/simulation/features/MotorPullDirection.html" title="class in bio.singa.simulation.features">MotorPullDirection</a></li>
<li><a href="bio/singa/mathematics/concepts/MultiDimensional.html" title="interface in bio.singa.mathematics.concepts"><span class="interfaceName">MultiDimensional</span></a></li>
<li><a href="bio/singa/simulation/features/MultiEntityFeature.html" title="class in bio.singa.simulation.features">MultiEntityFeature</a></li>
<li><a href="bio/singa/mathematics/concepts/Multipliable.html" title="interface in bio.singa.mathematics.concepts"><span class="interfaceName">Multipliable</span></a></li>
<li><a href="uk/co/cogitolearning/cogpar/MultiplicationExpressionNode.html" title="class in uk.co.cogitolearning.cogpar">MultiplicationExpressionNode</a></li>
<li><a href="bio/singa/mathematics/concepts/MultiplicativelyInvertible.html" title="interface in bio.singa.mathematics.concepts"><span class="interfaceName">MultiplicativelyInvertible</span></a></li>
<li><a href="bio/singa/simulation/features/MultiStringFeature.html" title="class in bio.singa.simulation.features">MultiStringFeature</a></li>
<li><a href="bio/singa/mathematics/graphs/trees/MultiTree.html" title="class in bio.singa.mathematics.graphs.trees">MultiTree</a></li>
<li><a href="bio/singa/mathematics/graphs/trees/MultiTreeNode.html" title="class in bio.singa.mathematics.graphs.trees">MultiTreeNode</a></li>
<li><a href="bio/singa/features/quantities/NaturalConstants.html" title="class in bio.singa.features.quantities">NaturalConstants</a></li>
<li><a href="bio/singa/features/identifiers/NCBITaxonomyIdentifier.html" title="class in bio.singa.features.identifiers">NCBITaxonomyIdentifier</a></li>
<li><a href="bio/singa/sequence/algorithms/alignment/NeedlemanWunschAlignment.html" title="class in bio.singa.sequence.algorithms.alignment">NeedlemanWunschAlignment</a></li>
<li><a href="bio/singa/mathematics/algorithms/graphs/NeighbourhoodExtractor.html" title="class in bio.singa.mathematics.algorithms.graphs">NeighbourhoodExtractor</a></li>
<li><a href="bio/singa/simulation/trajectories/nested/NestedUpdateRecorder.html" title="class in bio.singa.simulation.trajectories.nested">NestedUpdateRecorder</a></li>
<li><a href="bio/singa/mathematics/topology/grids/rectangular/NeumannRectangularDirection.html" title="enum in bio.singa.mathematics.topology.grids.rectangular">NeumannRectangularDirection</a></li>
<li><a href="bio/singa/mathematics/graphs/trees/NewickParser.html" title="class in bio.singa.mathematics.graphs.trees">NewickParser</a></li>
<li><a href="bio/singa/mathematics/graphs/model/Node.html" title="interface in bio.singa.mathematics.graphs.model"><span class="interfaceName">Node</span></a></li>
<li><a href="bio/singa/simulation/model/modules/concentration/imlementations/reactions/behaviors/deltas/NodeBehavior.html" title="class in bio.singa.simulation.model.modules.concentration.imlementations.reactions.behaviors.deltas">NodeBehavior</a></li>
<li><a href="bio/singa/simulation/events/NodeEventEmitter.html" title="class in bio.singa.simulation.events">NodeEventEmitter</a></li>
<li><a href="bio/singa/mathematics/graphs/model/Nodes.html" title="class in bio.singa.mathematics.graphs.model">Nodes</a></li>
<li><a href="bio/singa/structure/model/interfaces/Nucleotide.html" title="interface in bio.singa.structure.model.interfaces"><span class="interfaceName">Nucleotide</span></a></li>
<li><a href="bio/singa/structure/model/families/NucleotideFamily.html" title="enum in bio.singa.structure.model.families">NucleotideFamily</a></li>
<li><a href="bio/singa/sequence/model/NucleotideSequence.html" title="class in bio.singa.sequence.model">NucleotideSequence</a></li>
<li><a href="bio/singa/mathematics/exceptions/NumberOfInterceptsException.html" title="class in bio.singa.mathematics.exceptions">NumberOfInterceptsException</a></li>
<li><a href="bio/singa/simulation/exceptions/NumericalInstabilityException.html" title="class in bio.singa.simulation.exceptions">NumericalInstabilityException</a></li>
<li><a href="bio/singa/structure/model/oak/OakAminoAcid.html" title="class in bio.singa.structure.model.oak">OakAminoAcid</a></li>
<li><a href="bio/singa/structure/model/oak/OakAtom.html" title="class in bio.singa.structure.model.oak">OakAtom</a></li>
<li><a href="bio/singa/structure/model/oak/OakBond.html" title="class in bio.singa.structure.model.oak">OakBond</a></li>
<li><a href="bio/singa/structure/model/oak/OakChain.html" title="class in bio.singa.structure.model.oak">OakChain</a></li>
<li><a href="bio/singa/structure/model/oak/OakLeafSubstructure.html" title="class in bio.singa.structure.model.oak">OakLeafSubstructure</a></li>
<li><a href="bio/singa/structure/model/oak/OakLigand.html" title="class in bio.singa.structure.model.oak">OakLigand</a></li>
<li><a href="bio/singa/structure/model/oak/OakModel.html" title="class in bio.singa.structure.model.oak">OakModel</a></li>
<li><a href="bio/singa/structure/model/oak/OakNucleotide.html" title="class in bio.singa.structure.model.oak">OakNucleotide</a></li>
<li><a href="bio/singa/structure/model/oak/OakStructure.html" title="class in bio.singa.structure.model.oak">OakStructure</a></li>
<li><a href="bio/singa/simulation/model/agents/organelles/OrganelleImageParser.html" title="class in bio.singa.simulation.model.agents.organelles">OrganelleImageParser</a></li>
<li><a href="bio/singa/simulation/model/agents/organelles/OrganelleTemplate.html" title="class in bio.singa.simulation.model.agents.organelles">OrganelleTemplate</a></li>
<li><a href="bio/singa/simulation/model/agents/organelles/OrganelleTypes.html" title="enum in bio.singa.simulation.model.agents.organelles">OrganelleTypes</a></li>
<li><a href="bio/singa/chemistry/annotations/taxonomy/Organism.html" title="class in bio.singa.chemistry.annotations.taxonomy">Organism</a></li>
<li><a href="bio/singa/simulation/features/OriginalDiffusivity.html" title="class in bio.singa.simulation.features">OriginalDiffusivity</a></li>
<li><a href="bio/singa/chemistry/features/permeability/OsmoticPermeability.html" title="class in bio.singa.chemistry.features.permeability">OsmoticPermeability</a></li>
<li><a href="bio/singa/core/utility/Pair.html" title="class in bio.singa.core.utility">Pair</a></li>
<li><a href="bio/singa/mathematics/geometry/edges/Parabola.html" title="class in bio.singa.mathematics.geometry.edges">Parabola</a></li>
<li><a href="bio/singa/simulation/model/parameters/Parameter.html" title="class in bio.singa.simulation.model.parameters">Parameter</a></li>
<li><a href="bio/singa/simulation/model/parameters/ParameterStorage.html" title="class in bio.singa.simulation.model.parameters">ParameterStorage</a></li>
<li><a href="bio/singa/core/parser/Parser.html" title="interface in bio.singa.core.parser"><span class="interfaceName">Parser</span></a></li>
<li><a href="uk/co/cogitolearning/cogpar/ParserException.html" title="class in uk.co.cogitolearning.cogpar">ParserException</a></li>
<li><a href="bio/singa/structure/parser/sifts/PDBEnzymeMapper.html" title="class in bio.singa.structure.parser.sifts">PDBEnzymeMapper</a></li>
<li><a href="bio/singa/structure/model/identifiers/PDBIdentifier.html" title="class in bio.singa.structure.model.identifiers">PDBIdentifier</a></li>
<li><a href="bio/singa/chemistry/features/identifiers/PDBLigandIdentiferProvider.html" title="class in bio.singa.chemistry.features.identifiers">PDBLigandIdentiferProvider</a></li>
<li><a href="bio/singa/features/identifiers/PDBLigandIdentifier.html" title="class in bio.singa.features.identifiers">PDBLigandIdentifier</a></li>
<li><a href="bio/singa/structure/parser/sifts/PDBPfamMapper.html" title="class in bio.singa.structure.parser.sifts">PDBPfamMapper</a></li>
<li><a href="bio/singa/structure/parser/pdb/rest/PDBRestEndpoint.html" title="class in bio.singa.structure.parser.pdb.rest">PDBRestEndpoint</a></li>
<li><a href="bio/singa/structure/parser/pdb/rest/cluster/PDBSequenceCluster.html" title="class in bio.singa.structure.parser.pdb.rest.cluster">PDBSequenceCluster</a></li>
<li><a href="bio/singa/structure/parser/pdb/rest/cluster/PDBSequenceCluster.PDBSequenceClusterIdentity.html" title="enum in bio.singa.structure.parser.pdb.rest.cluster">PDBSequenceCluster.PDBSequenceClusterIdentity</a></li>
<li><a href="bio/singa/structure/parser/pdb/rest/cluster/PDBSequenceClusterMember.html" title="class in bio.singa.structure.parser.pdb.rest.cluster">PDBSequenceClusterMember</a></li>
<li><a href="bio/singa/structure/parser/pdb/structures/tokens/PDBToken.html" title="interface in bio.singa.structure.parser.pdb.structures.tokens"><span class="interfaceName">PDBToken</span></a></li>
<li><a href="bio/singa/structure/parser/sifts/PDBUniProtMapper.html" title="class in bio.singa.structure.parser.sifts">PDBUniProtMapper</a></li>
<li><a href="bio/singa/features/identifiers/PfamIdentifier.html" title="class in bio.singa.features.identifiers">PfamIdentifier</a></li>
<li><a href="bio/singa/structure/parser/pfam/PfamParser.html" title="class in bio.singa.structure.parser.pfam">PfamParser</a></li>
<li><a href="bio/singa/structure/parser/pfam/PfamParser.Builder.html" title="class in bio.singa.structure.parser.pfam">PfamParser.Builder</a></li>
<li><a href="bio/singa/structure/parser/pfam/PfamParser.ChainStep.html" title="interface in bio.singa.structure.parser.pfam"><span class="interfaceName">PfamParser.ChainStep</span></a></li>
<li><a href="bio/singa/structure/parser/pfam/PfamParser.DomainStep.html" title="interface in bio.singa.structure.parser.pfam"><span class="interfaceName">PfamParser.DomainStep</span></a></li>
<li><a href="bio/singa/structure/parser/pfam/PfamParser.FamilyStep.html" title="interface in bio.singa.structure.parser.pfam"><span class="interfaceName">PfamParser.FamilyStep</span></a></li>
<li><a href="bio/singa/structure/parser/pfam/PfamParser.PfamVersion.html" title="enum in bio.singa.structure.parser.pfam">PfamParser.PfamVersion</a></li>
<li><a href="bio/singa/structure/parser/pfam/PfamParser.VersionStep.html" title="interface in bio.singa.structure.parser.pfam"><span class="interfaceName">PfamParser.VersionStep</span></a></li>
<li><a href="bio/singa/structure/parser/pfam/tokens/PfamToken.html" title="interface in bio.singa.structure.parser.pfam.tokens"><span class="interfaceName">PfamToken</span></a></li>
<li><a href="bio/singa/structure/parser/pfam/tokens/PfamToken.IdentifierToken.html" title="enum in bio.singa.structure.parser.pfam.tokens">PfamToken.IdentifierToken</a></li>
<li><a href="bio/singa/structure/parser/pfam/tokens/PfamToken.PDBToken.html" title="enum in bio.singa.structure.parser.pfam.tokens">PfamToken.PDBToken</a></li>
<li><a href="bio/singa/structure/parser/plip/PiCation.html" title="class in bio.singa.structure.parser.plip">PiCation</a></li>
<li><a href="bio/singa/structure/parser/plip/PiStacking.html" title="class in bio.singa.structure.parser.plip">PiStacking</a></li>
<li><a href="bio/singa/simulation/features/PitFormationRate.html" title="class in bio.singa.simulation.features">PitFormationRate</a></li>
<li><a href="bio/singa/structure/parser/plip/PlipContentHandler.html" title="class in bio.singa.structure.parser.plip">PlipContentHandler</a></li>
<li><a href="bio/singa/structure/parser/plip/PlipCountFingerprint.html" title="class in bio.singa.structure.parser.plip">PlipCountFingerprint</a></li>
<li><a href="bio/singa/structure/parser/plip/PlipParser.html" title="class in bio.singa.structure.parser.plip">PlipParser</a></li>
<li><a href="bio/singa/structure/parser/plip/PlipShellGenerator.html" title="class in bio.singa.structure.parser.plip">PlipShellGenerator</a></li>
<li><a href="bio/singa/structure/parser/plip/PlipShellGenerator.InteractionShell.html" title="enum in bio.singa.structure.parser.plip">PlipShellGenerator.InteractionShell</a></li>
<li><a href="bio/singa/mathematics/geometry/model/Polygon.html" title="interface in bio.singa.mathematics.geometry.model"><span class="interfaceName">Polygon</span></a></li>
<li><a href="bio/singa/mathematics/geometry/faces/Polygons.html" title="class in bio.singa.mathematics.geometry.faces">Polygons</a></li>
<li><a href="bio/singa/mathematics/geometry/model/Polytope.html" title="interface in bio.singa.mathematics.geometry.model"><span class="interfaceName">Polytope</span></a></li>
<li><a href="bio/singa/mathematics/algorithms/primes/Primes.html" title="class in bio.singa.mathematics.algorithms.primes">Primes</a></li>
<li><a href="bio/singa/chemistry/entities/Protein.html" title="class in bio.singa.chemistry.entities">Protein</a></li>
<li><a href="bio/singa/chemistry/entities/Protein.Builder.html" title="class in bio.singa.chemistry.entities">Protein.Builder</a></li>
<li><a href="bio/singa/sequence/model/ProteinSequence.html" title="class in bio.singa.sequence.model">ProteinSequence</a></li>
<li><a href="bio/singa/structure/algorithms/superimposition/scores/PsScore.html" title="class in bio.singa.structure.algorithms.superimposition.scores">PsScore</a></li>
<li><a href="bio/singa/chemistry/features/databases/pubchem/PubChemDatabase.html" title="class in bio.singa.chemistry.features.databases.pubchem">PubChemDatabase</a></li>
<li><a href="bio/singa/features/identifiers/PubChemIdentifier.html" title="class in bio.singa.features.identifiers">PubChemIdentifier</a></li>
<li><a href="bio/singa/chemistry/features/identifiers/PubChemIdentifierProvider.html" title="class in bio.singa.chemistry.features.identifiers">PubChemIdentifierProvider</a></li>
<li><a href="bio/singa/chemistry/features/databases/pubchem/PubChemParserService.html" title="class in bio.singa.chemistry.features.databases.pubchem">PubChemParserService</a></li>
<li><a href="bio/singa/chemistry/features/identifiers/PubChemToChEBI.html" title="class in bio.singa.chemistry.features.identifiers">PubChemToChEBI</a></li>
<li><a href="bio/singa/chemistry/features/identifiers/PubChemToInChIKey.html" title="class in bio.singa.chemistry.features.identifiers">PubChemToInChIKey</a></li>
<li><a href="bio/singa/mathematics/algorithms/matrix/QRDecomposition.html" title="class in bio.singa.mathematics.algorithms.matrix">QRDecomposition</a></li>
<li><a href="bio/singa/features/model/QualitativeFeature.html" title="class in bio.singa.features.model">QualitativeFeature</a></li>
<li><a href="bio/singa/simulation/model/modules/qualitative/QualitativeModule.html" title="class in bio.singa.simulation.model.modules.qualitative">QualitativeModule</a></li>
<li><a href="bio/singa/features/model/QuantitativeFeature.html" title="class in bio.singa.features.model">QuantitativeFeature</a></li>
<li><a href="bio/singa/features/formatter/QuantityFormatter.html" title="interface in bio.singa.features.formatter"><span class="interfaceName">QuantityFormatter</span></a></li>
<li><a href="bio/singa/mathematics/quaternions/Quaternion.html" title="interface in bio.singa.mathematics.quaternions"><span class="interfaceName">Quaternion</span></a></li>
<li><a href="bio/singa/mathematics/quaternions/Quaternions.html" title="class in bio.singa.mathematics.quaternions">Quaternions</a></li>
<li><a href="bio/singa/core/utility/Range.html" title="class in bio.singa.core.utility">Range</a></li>
<li><a href="bio/singa/mathematics/similarities/RankBiasedOverlap.html" title="class in bio.singa.mathematics.similarities">RankBiasedOverlap</a></li>
<li><a href="bio/singa/chemistry/features/reactions/RateConstant.html" title="class in bio.singa.chemistry.features.reactions">RateConstant</a></li>
<li><a href="bio/singa/chemistry/features/reactions/RateConstant.BuilderStep.html" title="interface in bio.singa.chemistry.features.reactions"><span class="interfaceName">RateConstant.BuilderStep</span></a></li>
<li><a href="bio/singa/chemistry/features/reactions/RateConstant.ConcentrationStep.html" title="interface in bio.singa.chemistry.features.reactions"><span class="interfaceName">RateConstant.ConcentrationStep</span></a></li>
<li><a href="bio/singa/chemistry/features/reactions/RateConstant.Direction.html" title="enum in bio.singa.chemistry.features.reactions">RateConstant.Direction</a></li>
<li><a href="bio/singa/chemistry/features/reactions/RateConstant.DirectionStep.html" title="interface in bio.singa.chemistry.features.reactions"><span class="interfaceName">RateConstant.DirectionStep</span></a></li>
<li><a href="bio/singa/chemistry/features/reactions/RateConstant.Order.html" title="enum in bio.singa.chemistry.features.reactions">RateConstant.Order</a></li>
<li><a href="bio/singa/chemistry/features/reactions/RateConstant.OrderStep.html" title="interface in bio.singa.chemistry.features.reactions"><span class="interfaceName">RateConstant.OrderStep</span></a></li>
<li><a href="bio/singa/chemistry/features/reactions/RateConstant.OriginStep.html" title="interface in bio.singa.chemistry.features.reactions"><span class="interfaceName">RateConstant.OriginStep</span></a></li>
<li><a href="bio/singa/chemistry/features/reactions/RateConstant.RateBuilder.html" title="class in bio.singa.chemistry.features.reactions">RateConstant.RateBuilder</a></li>
<li><a href="bio/singa/chemistry/features/reactions/RateConstant.TimeStep.html" title="interface in bio.singa.chemistry.features.reactions"><span class="interfaceName">RateConstant.TimeStep</span></a></li>
<li><a href="bio/singa/simulation/features/Ratio.html" title="class in bio.singa.simulation.features">Ratio</a></li>
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<li><a href="bio/singa/chemistry/features/variants/SequenceVariants.html" title="class in bio.singa.chemistry.features.variants">SequenceVariants</a></li>
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<li><a href="bio/singa/mathematics/algorithms/graphs/ShortestPathFinder.html" title="class in bio.singa.mathematics.algorithms.graphs">ShortestPathFinder</a></li>
<li><a href="bio/singa/mathematics/metrics/implementations/ShortestPathMetric.html" title="class in bio.singa.mathematics.metrics.implementations">ShortestPathMetric</a></li>
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<li><a href="bio/singa/structure/model/families/StructuralFamily.html" title="interface in bio.singa.structure.model.families"><span class="interfaceName">StructuralFamily</span></a></li>
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