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allclasses-frame.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" target="classFrame">AbacusVisualization</a></li>
<li><a href="bio/singa/chemistry/entities/AbstractChemicalEntity.html" title="class in bio.singa.chemistry.entities" target="classFrame">AbstractChemicalEntity</a></li>
<li><a href="bio/singa/chemistry/entities/AbstractChemicalEntity.Builder.html" title="class in bio.singa.chemistry.entities" target="classFrame">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" target="classFrame">AbstractDeltaFunction</a></li>
<li><a href="bio/singa/mathematics/graphs/model/AbstractEdge.html" title="class in bio.singa.mathematics.graphs.model" target="classFrame">AbstractEdge</a></li>
<li><a href="bio/singa/features/model/AbstractFeature.html" title="class in bio.singa.features.model" target="classFrame">AbstractFeature</a></li>
<li><a href="bio/singa/mathematics/forces/AbstractForce.html" title="class in bio.singa.mathematics.forces" target="classFrame">AbstractForce</a></li>
<li><a href="bio/singa/mathematics/graphs/grid/AbstractGridGraph.html" title="class in bio.singa.mathematics.graphs.grid" target="classFrame">AbstractGridGraph</a></li>
<li><a href="bio/singa/core/parser/AbstractHTMLParser.html" title="class in bio.singa.core.parser" target="classFrame">AbstractHTMLParser</a></li>
<li><a href="bio/singa/features/identifiers/model/AbstractIdentifier.html" title="class in bio.singa.features.identifiers.model" target="classFrame">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" target="classFrame">AbstractKineticLaw</a></li>
<li><a href="bio/singa/mathematics/graphs/model/AbstractMapGraph.html" title="class in bio.singa.mathematics.graphs.model" target="classFrame">AbstractMapGraph</a></li>
<li><a href="bio/singa/chemistry/entities/modification/AbstractModification.html" title="class in bio.singa.chemistry.entities.modification" target="classFrame">AbstractModification</a></li>
<li><a href="bio/singa/mathematics/graphs/model/AbstractNode.html" title="class in bio.singa.mathematics.graphs.model" target="classFrame">AbstractNode</a></li>
<li><a href="bio/singa/core/parser/AbstractParser.html" title="class in bio.singa.core.parser" target="classFrame">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" target="classFrame">AbstractRepresentationScheme</a></li>
<li><a href="bio/singa/sequence/model/AbstractSequence.html" title="class in bio.singa.sequence.model" target="classFrame">AbstractSequence</a></li>
<li><a href="bio/singa/core/parser/AbstractUniProtIdentifierMappingParser.html" title="class in bio.singa.core.parser" target="classFrame">AbstractUniProtIdentifierMappingParser</a></li>
<li><a href="bio/singa/core/parser/AbstractXMLParser.html" title="class in bio.singa.core.parser" target="classFrame">AbstractXMLParser</a></li>
<li><a href="bio/singa/simulation/features/ActinBoostVelocity.html" title="class in bio.singa.simulation.features" target="classFrame">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" target="classFrame">ActinCortexDiffusivityScaling</a></li>
<li><a href="bio/singa/mathematics/concepts/Addable.html" title="interface in bio.singa.mathematics.concepts" target="classFrame"><span class="interfaceName">Addable</span></a></li>
<li><a href="uk/co/cogitolearning/cogpar/AdditionExpressionNode.html" title="class in uk.co.cogitolearning.cogpar" target="classFrame">AdditionExpressionNode</a></li>
<li><a href="bio/singa/mathematics/concepts/AdditivelyInvertible.html" title="interface in bio.singa.mathematics.concepts" target="classFrame"><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" target="classFrame">AddModification</a></li>
<li><a href="bio/singa/simulation/features/AffectedRegion.html" title="class in bio.singa.simulation.features" target="classFrame">AffectedRegion</a></li>
<li><a href="bio/singa/structure/algorithms/superimposition/affinity/AffinityAlignment.html" title="class in bio.singa.structure.algorithms.superimposition.affinity" target="classFrame">AffinityAlignment</a></li>
<li><a href="bio/singa/structure/algorithms/superimposition/affinity/AffinityAlignment.AtomStep.html" title="interface in bio.singa.structure.algorithms.superimposition.affinity" target="classFrame"><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" target="classFrame">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" target="classFrame"><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" target="classFrame"><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" target="classFrame">AffinityPropagation</a></li>
<li><a href="bio/singa/mathematics/algorithms/clustering/AffinityPropagation.Builder.html" title="class in bio.singa.mathematics.algorithms.clustering" target="classFrame">AffinityPropagation.Builder</a></li>
<li><a href="bio/singa/mathematics/algorithms/clustering/AffinityPropagation.DataStep.html" title="interface in bio.singa.mathematics.algorithms.clustering" target="classFrame"><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" target="classFrame"><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" target="classFrame"><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" target="classFrame"><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" target="classFrame">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" target="classFrame">AlphaCarbonRepresentationScheme</a></li>
<li><a href="bio/singa/structure/model/interfaces/AminoAcid.html" title="interface in bio.singa.structure.model.interfaces" target="classFrame"><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" target="classFrame">AminoAcidFamily</a></li>
<li><a href="bio/singa/structure/model/oak/AminoAcids.html" title="class in bio.singa.structure.model.oak" target="classFrame">AminoAcids</a></li>
<li><a href="bio/singa/mathematics/metrics/implementations/AngularDistance.html" title="class in bio.singa.mathematics.metrics.implementations" target="classFrame">AngularDistance</a></li>
<li><a href="bio/singa/chemistry/annotations/Annotatable.html" title="interface in bio.singa.chemistry.annotations" target="classFrame"><span class="interfaceName">Annotatable</span></a></li>
<li><a href="bio/singa/chemistry/annotations/Annotation.html" title="class in bio.singa.chemistry.annotations" target="classFrame">Annotation</a></li>
<li><a href="bio/singa/chemistry/annotations/AnnotationType.html" title="enum in bio.singa.chemistry.annotations" target="classFrame">AnnotationType</a></li>
<li><a href="bio/singa/simulation/features/AppliedVesicleState.html" title="class in bio.singa.simulation.features" target="classFrame">AppliedVesicleState</a></li>
<li><a href="bio/singa/simulation/model/rules/AssignmentRule.html" title="class in bio.singa.simulation.model.rules" target="classFrame">AssignmentRule</a></li>
<li><a href="bio/singa/simulation/model/rules/AssignmentRules.html" title="class in bio.singa.simulation.model.rules" target="classFrame">AssignmentRules</a></li>
<li><a href="bio/singa/structure/model/interfaces/Atom.html" title="interface in bio.singa.structure.model.interfaces" target="classFrame"><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" target="classFrame"><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" target="classFrame">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" target="classFrame">AtomToken</a></li>
<li><a href="bio/singa/simulation/features/AttachedFilament.html" title="class in bio.singa.simulation.features" target="classFrame">AttachedFilament</a></li>
<li><a href="bio/singa/simulation/features/AttachedMotor.html" title="class in bio.singa.simulation.features" target="classFrame">AttachedMotor</a></li>
<li><a href="bio/singa/simulation/features/AttachmentDistance.html" title="class in bio.singa.simulation.features" target="classFrame">AttachmentDistance</a></li>
<li><a href="bio/singa/mathematics/forces/AttractiveForce.html" title="class in bio.singa.mathematics.forces" target="classFrame">AttractiveForce</a></li>
<li><a href="bio/singa/simulation/model/graphs/AutomatonEdge.html" title="class in bio.singa.simulation.model.graphs" target="classFrame">AutomatonEdge</a></li>
<li><a href="bio/singa/simulation/model/graphs/AutomatonGraph.html" title="class in bio.singa.simulation.model.graphs" target="classFrame">AutomatonGraph</a></li>
<li><a href="bio/singa/simulation/model/graphs/AutomatonGraphs.html" title="class in bio.singa.simulation.model.graphs" target="classFrame">AutomatonGraphs</a></li>
<li><a href="bio/singa/simulation/model/graphs/AutomatonNode.html" title="class in bio.singa.simulation.model.graphs" target="classFrame">AutomatonNode</a></li>
<li><a href="bio/singa/chemistry/features/reactions/BackwardsRateConstant.html" title="interface in bio.singa.chemistry.features.reactions" target="classFrame"><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" target="classFrame">BeachLine</a></li>
<li><a href="bio/singa/mathematics/algorithms/voronoi/model/BeachSection.html" title="class in bio.singa.mathematics.algorithms.voronoi.model" target="classFrame">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" target="classFrame">BetaCarbonRepresentationScheme</a></li>
<li><a href="bio/singa/mathematics/graphs/trees/BinaryTree.html" title="class in bio.singa.mathematics.graphs.trees" target="classFrame">BinaryTree</a></li>
<li><a href="bio/singa/mathematics/graphs/trees/BinaryTreeNode.html" title="class in bio.singa.mathematics.graphs.trees" target="classFrame">BinaryTreeNode</a></li>
<li><a href="bio/singa/mathematics/algorithms/geometry/BitPlane.html" title="class in bio.singa.mathematics.algorithms.geometry" target="classFrame">BitPlane</a></li>
<li><a href="bio/singa/mathematics/vectors/BitVector.html" title="interface in bio.singa.mathematics.vectors" target="classFrame"><span class="interfaceName">BitVector</span></a></li>
<li><a href="bio/singa/mathematics/vectors/BitVectors.html" title="class in bio.singa.mathematics.vectors" target="classFrame">BitVectors</a></li>
<li><a href="bio/singa/mathematics/transformations/model/BitvectorTransformation.html" title="interface in bio.singa.mathematics.transformations.model" target="classFrame"><span class="interfaceName">BitvectorTransformation</span></a></li>
<li><a href="bio/singa/simulation/features/BlackListVesicleStates.html" title="class in bio.singa.simulation.features" target="classFrame">BlackListVesicleStates</a></li>
<li><a href="bio/singa/structure/model/oak/BondType.html" title="enum in bio.singa.structure.model.oak" target="classFrame">BondType</a></li>
<li><a href="bio/singa/simulation/features/BoostMediatingEntity.html" title="class in bio.singa.simulation.features" target="classFrame">BoostMediatingEntity</a></li>
<li><a href="bio/singa/core/utility/Bounded.html" title="interface in bio.singa.core.utility" target="classFrame"><span class="interfaceName">Bounded</span></a></li>
<li><a href="bio/singa/simulation/features/Cargo.html" title="class in bio.singa.simulation.features" target="classFrame">Cargo</a></li>
<li><a href="bio/singa/simulation/features/CargoAdditionRate.html" title="class in bio.singa.simulation.features" target="classFrame">CargoAdditionRate</a></li>
<li><a href="bio/singa/simulation/features/Cargoes.html" title="class in bio.singa.simulation.features" target="classFrame">Cargoes</a></li>
<li><a href="bio/singa/simulation/model/sections/CellRegion.html" title="class in bio.singa.simulation.model.sections" target="classFrame">CellRegion</a></li>
<li><a href="bio/singa/simulation/model/sections/CellRegions.html" title="class in bio.singa.simulation.model.sections" target="classFrame">CellRegions</a></li>
<li><a href="bio/singa/simulation/model/sections/CellSubsection.html" title="class in bio.singa.simulation.model.sections" target="classFrame">CellSubsection</a></li>
<li><a href="bio/singa/simulation/model/sections/CellSubsections.html" title="class in bio.singa.simulation.model.sections" target="classFrame">CellSubsections</a></li>
<li><a href="bio/singa/simulation/model/sections/CellTopology.html" title="enum in bio.singa.simulation.model.sections" target="classFrame">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" target="classFrame">CentroidRepresentationScheme</a></li>
<li><a href="bio/singa/structure/model/interfaces/Chain.html" title="interface in bio.singa.structure.model.interfaces" target="classFrame"><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" target="classFrame"><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" target="classFrame">ChainTerminatorToken</a></li>
<li><a href="bio/singa/chemistry/features/databases/chebi/ChEBIContentHandler.html" title="class in bio.singa.chemistry.features.databases.chebi" target="classFrame">ChEBIContentHandler</a></li>
<li><a href="bio/singa/chemistry/features/databases/chebi/ChEBIDatabase.html" title="class in bio.singa.chemistry.features.databases.chebi" target="classFrame">ChEBIDatabase</a></li>
<li><a href="bio/singa/features/identifiers/ChEBIIdentifier.html" title="class in bio.singa.features.identifiers" target="classFrame">ChEBIIdentifier</a></li>
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<li><a href="bio/singa/simulation/model/agents/surfacelike/MembraneLayer.html" title="class in bio.singa.simulation.model.agents.surfacelike" target="classFrame">MembraneLayer</a></li>
<li><a href="bio/singa/chemistry/features/permeability/MembranePermeability.html" title="class in bio.singa.chemistry.features.permeability" target="classFrame">MembranePermeability</a></li>
<li><a href="bio/singa/simulation/model/agents/surfacelike/MembraneSegment.html" title="class in bio.singa.simulation.model.agents.surfacelike" target="classFrame">MembraneSegment</a></li>
<li><a href="bio/singa/simulation/model/agents/surfacelike/MembraneTracer.html" title="class in bio.singa.simulation.model.agents.surfacelike" target="classFrame">MembraneTracer</a></li>
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<li><a href="bio/singa/mathematics/metrics/implementations/MinkowskiMetric.html" title="class in bio.singa.mathematics.metrics.implementations" target="classFrame">MinkowskiMetric</a></li>
<li><a href="bio/singa/structure/model/mmtf/MmtfAminoAcid.html" title="class in bio.singa.structure.model.mmtf" target="classFrame">MmtfAminoAcid</a></li>
<li><a href="bio/singa/structure/model/mmtf/MmtfAtom.html" title="class in bio.singa.structure.model.mmtf" target="classFrame">MmtfAtom</a></li>
<li><a href="bio/singa/structure/model/mmtf/MmtfChain.html" title="class in bio.singa.structure.model.mmtf" target="classFrame">MmtfChain</a></li>
<li><a href="bio/singa/structure/model/mmtf/MmtfLeafSubstructure.html" title="class in bio.singa.structure.model.mmtf" target="classFrame">MmtfLeafSubstructure</a></li>
<li><a href="bio/singa/structure/model/mmtf/MmtfLigand.html" title="class in bio.singa.structure.model.mmtf" target="classFrame">MmtfLigand</a></li>
<li><a href="bio/singa/structure/model/mmtf/MmtfModel.html" title="class in bio.singa.structure.model.mmtf" target="classFrame">MmtfModel</a></li>
<li><a href="bio/singa/structure/model/mmtf/MmtfNucleotide.html" title="class in bio.singa.structure.model.mmtf" target="classFrame">MmtfNucleotide</a></li>
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<li><a href="bio/singa/structure/model/mmtf/MmtfSecondaryStructure.html" title="enum in bio.singa.structure.model.mmtf" target="classFrame">MmtfSecondaryStructure</a></li>
<li><a href="bio/singa/structure/model/mmtf/MmtfStructure.html" title="class in bio.singa.structure.model.mmtf" target="classFrame">MmtfStructure</a></li>
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<li><a href="bio/singa/chemistry/entities/modification/ModificationBuilder.html" title="class in bio.singa.chemistry.entities.modification" target="classFrame">ModificationBuilder</a></li>
<li><a href="bio/singa/chemistry/entities/ModificationSite.html" title="class in bio.singa.chemistry.entities" target="classFrame">ModificationSite</a></li>
<li><a href="bio/singa/chemistry/entities/ModificationSite.Builder.html" title="class in bio.singa.chemistry.entities" target="classFrame">ModificationSite.Builder</a></li>
<li><a href="bio/singa/simulation/features/ModifiedDiffusivity.html" title="class in bio.singa.simulation.features" target="classFrame">ModifiedDiffusivity</a></li>
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<li><a href="bio/singa/simulation/model/modules/concentration/ModuleFactory.Scope.html" title="enum in bio.singa.simulation.model.modules.concentration" target="classFrame">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" target="classFrame">ModuleFactory.Specificity</a></li>
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<li><a href="bio/singa/simulation/features/variation/ModuleFeatureVariationEntry.html" title="class in bio.singa.simulation.features.variation" target="classFrame">ModuleFeatureVariationEntry</a></li>
<li><a href="bio/singa/simulation/model/modules/concentration/ModuleState.html" title="enum in bio.singa.simulation.model.modules.concentration" target="classFrame">ModuleState</a></li>
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<li><a href="bio/singa/structure/features/molarmass/MolarMass.html" title="class in bio.singa.structure.features.molarmass" target="classFrame">MolarMass</a></li>
<li><a href="bio/singa/chemistry/features/molarmass/MolarMassProvider.html" title="class in bio.singa.chemistry.features.molarmass" target="classFrame">MolarMassProvider</a></li>
<li><a href="bio/singa/features/quantities/MolarVolume.html" title="class in bio.singa.features.quantities" target="classFrame">MolarVolume</a></li>
<li><a href="bio/singa/chemistry/features/molarvolume/MolarVolumePredictor.html" title="class in bio.singa.chemistry.features.molarvolume" target="classFrame">MolarVolumePredictor</a></li>
<li><a href="bio/singa/structure/model/molecules/MoleculeAtom.html" title="class in bio.singa.structure.model.molecules" target="classFrame">MoleculeAtom</a></li>
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<li><a href="bio/singa/structure/model/molecules/MoleculeBondType.html" title="enum in bio.singa.structure.model.molecules" target="classFrame">MoleculeBondType</a></li>
<li><a href="bio/singa/features/formatter/MoleculeFormatter.html" title="class in bio.singa.features.formatter" target="classFrame">MoleculeFormatter</a></li>
<li><a href="bio/singa/structure/model/molecules/MoleculeGraph.html" title="class in bio.singa.structure.model.molecules" target="classFrame">MoleculeGraph</a></li>
<li><a href="bio/singa/javafx/renderer/molecules/MoleculeGraphRenderer.html" title="class in bio.singa.javafx.renderer.molecules" target="classFrame">MoleculeGraphRenderer</a></li>
<li><a href="bio/singa/structure/model/molecules/MoleculeGraphs.html" title="class in bio.singa.structure.model.molecules" target="classFrame">MoleculeGraphs</a></li>
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<li><a href="bio/singa/structure/algorithms/molecules/MoleculeIsomorphismFinder.html" title="class in bio.singa.structure.algorithms.molecules" target="classFrame">MoleculeIsomorphismFinder</a></li>
<li><a href="bio/singa/structure/algorithms/molecules/MoleculeIsomorphismFinder.AtomConditions.html" title="class in bio.singa.structure.algorithms.molecules" target="classFrame">MoleculeIsomorphismFinder.AtomConditions</a></li>
<li><a href="bio/singa/structure/algorithms/molecules/MoleculeIsomorphismFinder.BondConditions.html" title="class in bio.singa.structure.algorithms.molecules" target="classFrame">MoleculeIsomorphismFinder.BondConditions</a></li>
<li><a href="bio/singa/javafx/viewer/MoleculeIsomorphismTest.html" title="class in bio.singa.javafx.viewer" target="classFrame">MoleculeIsomorphismTest</a></li>
<li><a href="bio/singa/structure/algorithms/molecules/MoleculePathFinder.html" title="class in bio.singa.structure.algorithms.molecules" target="classFrame">MoleculePathFinder</a></li>
<li><a href="bio/singa/javafx/renderer/molecules/MoleculeRendererOptions.html" title="class in bio.singa.javafx.renderer.molecules" target="classFrame">MoleculeRendererOptions</a></li>
<li><a href="bio/singa/chemistry/features/structure3d/MolStructureParser.html" title="class in bio.singa.chemistry.features.structure3d" target="classFrame">MolStructureParser</a></li>
<li><a href="bio/singa/mathematics/topology/grids/rectangular/MooreRectangularDirection.html" title="enum in bio.singa.mathematics.topology.grids.rectangular" target="classFrame">MooreRectangularDirection</a></li>
<li><a href="bio/singa/simulation/features/MotorMovementVelocity.html" title="class in bio.singa.simulation.features" target="classFrame">MotorMovementVelocity</a></li>
<li><a href="bio/singa/simulation/features/MotorPullDirection.html" title="class in bio.singa.simulation.features" target="classFrame">MotorPullDirection</a></li>
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<li><a href="bio/singa/mathematics/concepts/MultiplicativelyInvertible.html" title="interface in bio.singa.mathematics.concepts" target="classFrame"><span class="interfaceName">MultiplicativelyInvertible</span></a></li>
<li><a href="bio/singa/simulation/features/MultiStringFeature.html" title="class in bio.singa.simulation.features" target="classFrame">MultiStringFeature</a></li>
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<li><a href="bio/singa/mathematics/graphs/trees/MultiTreeNode.html" title="class in bio.singa.mathematics.graphs.trees" target="classFrame">MultiTreeNode</a></li>
<li><a href="bio/singa/features/quantities/NaturalConstants.html" title="class in bio.singa.features.quantities" target="classFrame">NaturalConstants</a></li>
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<li><a href="bio/singa/sequence/algorithms/alignment/NeedlemanWunschAlignment.html" title="class in bio.singa.sequence.algorithms.alignment" target="classFrame">NeedlemanWunschAlignment</a></li>
<li><a href="bio/singa/mathematics/algorithms/graphs/NeighbourhoodExtractor.html" title="class in bio.singa.mathematics.algorithms.graphs" target="classFrame">NeighbourhoodExtractor</a></li>
<li><a href="bio/singa/simulation/trajectories/nested/NestedUpdateRecorder.html" title="class in bio.singa.simulation.trajectories.nested" target="classFrame">NestedUpdateRecorder</a></li>
<li><a href="bio/singa/mathematics/topology/grids/rectangular/NeumannRectangularDirection.html" title="enum in bio.singa.mathematics.topology.grids.rectangular" target="classFrame">NeumannRectangularDirection</a></li>
<li><a href="bio/singa/mathematics/graphs/trees/NewickParser.html" title="class in bio.singa.mathematics.graphs.trees" target="classFrame">NewickParser</a></li>
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<li><a href="bio/singa/mathematics/graphs/model/Nodes.html" title="class in bio.singa.mathematics.graphs.model" target="classFrame">Nodes</a></li>
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<li><a href="bio/singa/sequence/model/NucleotideSequence.html" title="class in bio.singa.sequence.model" target="classFrame">NucleotideSequence</a></li>
<li><a href="bio/singa/mathematics/exceptions/NumberOfInterceptsException.html" title="class in bio.singa.mathematics.exceptions" target="classFrame">NumberOfInterceptsException</a></li>
<li><a href="bio/singa/simulation/exceptions/NumericalInstabilityException.html" title="class in bio.singa.simulation.exceptions" target="classFrame">NumericalInstabilityException</a></li>
<li><a href="bio/singa/structure/model/oak/OakAminoAcid.html" title="class in bio.singa.structure.model.oak" target="classFrame">OakAminoAcid</a></li>
<li><a href="bio/singa/structure/model/oak/OakAtom.html" title="class in bio.singa.structure.model.oak" target="classFrame">OakAtom</a></li>
<li><a href="bio/singa/structure/model/oak/OakBond.html" title="class in bio.singa.structure.model.oak" target="classFrame">OakBond</a></li>
<li><a href="bio/singa/structure/model/oak/OakChain.html" title="class in bio.singa.structure.model.oak" target="classFrame">OakChain</a></li>
<li><a href="bio/singa/structure/model/oak/OakLeafSubstructure.html" title="class in bio.singa.structure.model.oak" target="classFrame">OakLeafSubstructure</a></li>
<li><a href="bio/singa/structure/model/oak/OakLigand.html" title="class in bio.singa.structure.model.oak" target="classFrame">OakLigand</a></li>
<li><a href="bio/singa/structure/model/oak/OakModel.html" title="class in bio.singa.structure.model.oak" target="classFrame">OakModel</a></li>
<li><a href="bio/singa/structure/model/oak/OakNucleotide.html" title="class in bio.singa.structure.model.oak" target="classFrame">OakNucleotide</a></li>
<li><a href="bio/singa/structure/model/oak/OakStructure.html" title="class in bio.singa.structure.model.oak" target="classFrame">OakStructure</a></li>
<li><a href="bio/singa/simulation/model/agents/organelles/OrganelleImageParser.html" title="class in bio.singa.simulation.model.agents.organelles" target="classFrame">OrganelleImageParser</a></li>
<li><a href="bio/singa/simulation/model/agents/organelles/OrganelleTemplate.html" title="class in bio.singa.simulation.model.agents.organelles" target="classFrame">OrganelleTemplate</a></li>
<li><a href="bio/singa/simulation/model/agents/organelles/OrganelleTypes.html" title="enum in bio.singa.simulation.model.agents.organelles" target="classFrame">OrganelleTypes</a></li>
<li><a href="bio/singa/chemistry/annotations/taxonomy/Organism.html" title="class in bio.singa.chemistry.annotations.taxonomy" target="classFrame">Organism</a></li>
<li><a href="bio/singa/simulation/features/OriginalDiffusivity.html" title="class in bio.singa.simulation.features" target="classFrame">OriginalDiffusivity</a></li>
<li><a href="bio/singa/chemistry/features/permeability/OsmoticPermeability.html" title="class in bio.singa.chemistry.features.permeability" target="classFrame">OsmoticPermeability</a></li>
<li><a href="bio/singa/core/utility/Pair.html" title="class in bio.singa.core.utility" target="classFrame">Pair</a></li>
<li><a href="bio/singa/mathematics/geometry/edges/Parabola.html" title="class in bio.singa.mathematics.geometry.edges" target="classFrame">Parabola</a></li>
<li><a href="bio/singa/simulation/model/parameters/Parameter.html" title="class in bio.singa.simulation.model.parameters" target="classFrame">Parameter</a></li>
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<li><a href="bio/singa/core/parser/Parser.html" title="interface in bio.singa.core.parser" target="classFrame"><span class="interfaceName">Parser</span></a></li>
<li><a href="uk/co/cogitolearning/cogpar/ParserException.html" title="class in uk.co.cogitolearning.cogpar" target="classFrame">ParserException</a></li>
<li><a href="bio/singa/structure/parser/sifts/PDBEnzymeMapper.html" title="class in bio.singa.structure.parser.sifts" target="classFrame">PDBEnzymeMapper</a></li>
<li><a href="bio/singa/structure/model/identifiers/PDBIdentifier.html" title="class in bio.singa.structure.model.identifiers" target="classFrame">PDBIdentifier</a></li>
<li><a href="bio/singa/chemistry/features/identifiers/PDBLigandIdentiferProvider.html" title="class in bio.singa.chemistry.features.identifiers" target="classFrame">PDBLigandIdentiferProvider</a></li>
<li><a href="bio/singa/features/identifiers/PDBLigandIdentifier.html" title="class in bio.singa.features.identifiers" target="classFrame">PDBLigandIdentifier</a></li>
<li><a href="bio/singa/structure/parser/sifts/PDBPfamMapper.html" title="class in bio.singa.structure.parser.sifts" target="classFrame">PDBPfamMapper</a></li>
<li><a href="bio/singa/structure/parser/pdb/rest/PDBRestEndpoint.html" title="class in bio.singa.structure.parser.pdb.rest" target="classFrame">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" target="classFrame">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" target="classFrame">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" target="classFrame">PDBSequenceClusterMember</a></li>
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<li><a href="bio/singa/structure/parser/sifts/PDBUniProtMapper.html" title="class in bio.singa.structure.parser.sifts" target="classFrame">PDBUniProtMapper</a></li>
<li><a href="bio/singa/features/identifiers/PfamIdentifier.html" title="class in bio.singa.features.identifiers" target="classFrame">PfamIdentifier</a></li>
<li><a href="bio/singa/structure/parser/pfam/PfamParser.html" title="class in bio.singa.structure.parser.pfam" target="classFrame">PfamParser</a></li>
<li><a href="bio/singa/structure/parser/pfam/PfamParser.Builder.html" title="class in bio.singa.structure.parser.pfam" target="classFrame">PfamParser.Builder</a></li>
<li><a href="bio/singa/structure/parser/pfam/PfamParser.ChainStep.html" title="interface in bio.singa.structure.parser.pfam" target="classFrame"><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" target="classFrame"><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" target="classFrame"><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" target="classFrame">PfamParser.PfamVersion</a></li>
<li><a href="bio/singa/structure/parser/pfam/PfamParser.VersionStep.html" title="interface in bio.singa.structure.parser.pfam" target="classFrame"><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" target="classFrame"><span class="interfaceName">PfamToken</span></a></li>
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