- s -

• SASEdge() : BALL::SASEdge
• SASFace() : BALL::SASFace
• SASTriangulator() : BALL::SASTriangulator
• SASVertex() : BALL::SASVertex
• saveBALLViewProjectFile() : BALL::VIEW::MainControl
• savePositions() : BALL::AtomVector
• scale() : BALL::PeakList< PT > , BALL::TMatrix4x4< T >
• Scene() : BALL::VIEW::Scene
• SceneMessage() : BALL::VIEW::SceneMessage
• Scoring_() : BALL::DockResult::DockResult::Scoring_
• scoringAdvancedPressed() : BALL::VIEW::DockDialog
• scoringClicked() : BALL::VIEW::DockResultDialog
• scoringFuncChosen() : BALL::VIEW::DockDialog , BALL::VIEW::DockResultDialog
• scriptDialog() : BALL::VIEW::PyWidget
• SCWRLRotamerFile() : BALL::SCWRLRotamerFile
• SDFile() : BALL::SDFile
• SDGenerator() : BALL::SDGenerator
• search() : BALL::LineBasedFile
• SecondaryStructure() : BALL::SecondaryStructure
• select() : BALL::Composite , BALL::Selectable , BALL::VIEW::MolecularControl
• Selectable() : BALL::Selectable
• selectAllModels() : BALL::PDBFile
• selectColoringMethod() : BALL::VIEW::DisplayProperties
• selectCompositeRecursive() : BALL::VIEW::MainControl
• selectedForceField() : BALL::VIEW::MinimizationDialog , BALL::VIEW::MolecularDynamicsDialog
• selectFile_() : BALL::VIEW::DockDialog
• selectFont() : BALL::VIEW::MainControlPreferences
• selectForceField() : BALL::VIEW::MinimizationDialog , BALL::VIEW::MolecularDynamicsDialog
• selectMode() : BALL::VIEW::DisplayProperties
• selectModel() : BALL::PDBFile , BALL::VIEW::DisplayProperties
• Selector() : BALL::Selector
• sendMessage() : BALL::VIEW::MainControl
• sendMessage_() : BALL::VIEW::BALLThread
• sendObject() : BALL::VIEW::ServerWidget::ServerWidget::BALLViewServer
• sequenceRings() : BALL::SDGenerator
• ServerPreferences() : BALL::VIEW::ServerPreferences
• ServerWidget() : BALL::VIEW::ServerWidget
• SESComputer() : BALL::SESComputer
• SESEdge() : BALL::SESEdge
• SESFace() : BALL::SESFace
• SESSingularityCleaner() : BALL::SESSingularityCleaner
• SESTriangulator() : BALL::SESTriangulator
• SESVertex() : BALL::SESVertex
• set() : BALL::TAngle< T > , BALL::VIEW::TwoColoredTube , BALL::VIEW::Scene , BALL::TBox3< T > , BALL::TCircle3< T > , BALL::TLine3< T > , BALL::TMatrix4x4< T > , BALL::PiecewisePolynomial , BALL::TPlane3< T > , BALL::TQuaternion< T > , BALL::TSimpleBox3< T > , BALL::TSphere3< T > , BALL::TVector2< T > , BALL::TVector3< T > , BALL::TVector4< T > , BALL::Exception::GlobalExceptionHandler , BALL::TVector4< T > , BALL::Composite , BALL::TVector4< T > , BALL::AtomVector , BALL::PropertyManager , BALL::AtomVector , BALL::Gradient , BALL::Selectable , BALL::Gradient , BALL::MolecularDynamics , BALL::PreciseTime , BALL::GraphEdge< Vertex, Edge, Face > , BALL::PreciseTime , BALL::GraphFace< Vertex, Edge, Face > , BALL::GraphTriangle< Vertex, Edge, Face > , BALL::BitVector , BALL::GraphTriangle< Vertex, Edge, Face > , BALL::GraphVertex< Vertex, Edge, Face > , BALL::BitVector , BALL::ReducedSurface , BALL::RSEdge , BALL::HashGrid3< Item > , BALL::RSEdge , BALL::RSFace , BALL::HashGrid3< Item > , BALL::RSFace , BALL::RSVertex , BALL::HashGrid3< Item > , BALL::SASEdge , BALL::HashSet< Key > , BALL::SASFace , BALL::SASVertex , BALL::List< Value > , BALL::SASVertex , BALL::SESEdge , BALL::Options , BALL::SESEdge , BALL::SESFace , BALL::RegularExpression , BALL::SESVertex , BALL::RegularExpression , BALL::StructureMapper , BALL::Triangle , BALL::String , BALL::TrianglePoint , BALL::TriangulatedSAS , BALL::String , BALL::TriangulatedSES , BALL::TriangulatedSurface , BALL::String , BALL::TriangulatedSphere , BALL::Directory , BALL::String , BALL::Directory , BALL::TCPTransfer , BALL::String , BALL::TCPTransfer , BALL::VIEW::ColorExtension2 , BALL::String , BALL::VIEW::MultiColorExtension , BALL::VIEW::ColorHSV , BALL::String , BALL::VIEW::ColorHSV , BALL::String , BALL::VIEW::ColorHSV , BALL::String , BALL::VIEW::ColorRGBA , BALL::String , BALL::VIEW::ColorRGBA , BALL::String , BALL::VIEW::ColorRGBA , BALL::String , BALL::VIEW::ColorUnit , BALL::String , BALL::VIEW::ColorUnit , BALL::String , BALL::VIEW::ColorUnit , BALL::String , BALL::VIEW::ColorUnit , BALL::Substring , BALL::VIEW::ColorUnit , BALL::Substring , BALL::VIEW::ColorUnit , BALL::Substring , BALL::VIEW::ColorUnitHue , BALL::StringHashMap< Value > , BALL::VIEW::ColorUnitHue , BALL::ResourceEntry , BALL::VIEW::ColorUnitHue , BALL::Atom , BALL::VIEW::ColorUnitHue , BALL::AtomContainer , BALL::VIEW::ColorUnitHue , BALL::Chain , BALL::VIEW::ColorUnitHue , BALL::Molecule , BALL::VIEW::Dataset , BALL::VIEW::Vertex , BALL::NucleicAcid , BALL::VIEW::Vertex2 , BALL::VIEW::GeometricObject , BALL::Nucleotide , BALL::VIEW::AtomBondModelBaseProcessor , BALL::VIEW::AddBallAndStickModel , BALL::PDBAtom , BALL::VIEW::ColorProcessor , BALL::VIEW::HBondModelProcessor , BALL::Protein , BALL::VIEW::Box , BALL::VIEW::Disc , BALL::Residue , BALL::VIEW::Label , BALL::VIEW::Line , BALL::SecondaryStructure , BALL::VIEW::Mesh , BALL::VIEW::Point , BALL::System , BALL::VIEW::SimpleBox , BALL::VIEW::Sphere , BALL::TAngle< T > , BALL::VIEW::Tube , BALL::VIEW::TwoColoredLine
• setAlpha() : BALL::LineSearch , BALL::VIEW::ColorRGBA
• setAlphaBlending() : BALL::VIEW::ColorMap
• setAlphas() : BALL::VIEW::MultiColorExtension
• setAlternateLocationIndicator() : BALL::PDBAtom
• setAmberDialog() : BALL::VIEW::MinimizationDialog
• setAminoAcidType() : BALL::Peptides::AminoAcidDescriptor
• setAngle() : BALL::RSEdge , BALL::SASEdge , BALL::VIEW::LightSource
• setAntialiasing() : BALL::VIEW::GLRenderer
• setArgument() : BALL::ExpressionPredicate , BALL::ConnectedToPredicate
• setAtom() : BALL::Peak< PositionType > , BALL::RSVertex , BALL::SESVertex
• setAtomForces() : BALL::SnapShot
• setAtomicNumber() : BALL::Element
• setAtomicRadius() : BALL::Element
• setAtomicWeight() : BALL::Element
• setAtomPositions() : BALL::SnapShot
• setAtomTypeSmarts() : BALL::HybridisationProcessor
• setAtomVelocities() : BALL::SnapShot
• setAtomVelocitites() : BALL::SnapShot
• setAttenuation() : BALL::VIEW::LightSource
• setAutoDeletable() : BALL::AutoDeletable
• setBackboneDependent() : BALL::RotamerLibrary
• setBackgroundColor() : BALL::VIEW::Stage
• setBallRadius() : BALL::VIEW::AddBallAndStickModel
• setBaseColors() : BALL::VIEW::ColorMap
• setBathRelaxationTime() : BALL::CanonicalMD
• setBeta() : BALL::LineSearch
• setBit() : BALL::BitVector
• setBlue() : BALL::VIEW::ColorRGBA
• setBondLengths() : BALL::BuildBondsProcessor
• setBondOrder() : BALL::SmartsParser::SmartsParser::SPBond
• setBool() : BALL::Options
• setBox() : BALL::PeriodicBoundary
• setBracketedFlag() : BALL::LineSearch
• setBranchDesignator() : BALL::PDBAtom
• setBusyMode_() : BALL::VIEW::MainControl
• setCamera() : BALL::VIEW::Stage
• setCenter() : BALL::RSFace
• setCenterOfTorus() : BALL::RSEdge
• setChainName() : BALL::Peptides::PeptideBuilder
• setCharge() : BALL::Atom
• setCharmmDialog() : BALL::VIEW::MinimizationDialog
• setCircle() : BALL::SASEdge , BALL::SESEdge
• setCoefficients() : BALL::PiecewiseFunction
• setColor() : BALL::VIEW::LightSource
• setColor2() : BALL::VIEW::ColorExtension2
• setColors() : BALL::VIEW::MultiColorExtension
• setColumn() : BALL::TMatrix4x4< T >
• setCompareMode() : BALL::String
• setComponentGrouping() : BALL::SmartsParser
• setComponentNumber() : BALL::SmartsParser::SmartsParser::SPNode
• setComposite() : BALL::FragmentDistanceCollector , BALL::VIEW::CompositeMessage
• setCompositeName() : BALL::VIEW::CompositeMessage
• setComposites() : BALL::VIEW::ColorProcessor
• setConformationSet() : BALL::DockResult
• setConstant() : BALL::MutableConstant< DataType >
• setConstants() : BALL::Pair6_12RDFIntegrator , BALL::PairExpRDFIntegrator
• setContactCircle() : BALL::RSEdge
• setCorrectionParameter() : BALL::ShiftedLVMMMinimizer
• setCovalentRadius() : BALL::Element
• setCurrent() : BALL::Directory
• setCurrentModel() : BALL::PDBInfo
• setCurrentRepresentation() : BALL::VIEW::MaterialSettings
• setCurrentTime() : BALL::MolecularDynamics
• setData() : BALL::TFFT1D< ComplexTraits > , BALL::TFFT2D< ComplexTraits > , BALL::TFFT3D< ComplexTraits > , BALL::BinaryFileAdaptor< T >
• setDataPath() : BALL::Path
• setDefault() : BALL::Options
• setDefaultBool() : BALL::Options
• setDefaultColor() : BALL::VIEW::ColorProcessor
• setDefaultInteger() : BALL::Options
• setDefaultOptions() : BALL::AromaticityProcessor , BALL::RingPerceptionProcessor , BALL::AssignBondOrderProcessor , BALL::BuildBondsProcessor , BALL::HybridisationProcessor , BALL::SDGenerator
• setDefaultPeak() : BALL::Experiment< PeakListType >
• setDefaultReal() : BALL::Options
• setDefaultVertex1Address() : BALL::VIEW::Vertex2
• setDefaultVertex2Address() : BALL::VIEW::Vertex2
• setDefaultVertexAddress() : BALL::VIEW::Vertex
• setDefaultVertexAddresses() : BALL::VIEW::Vertex2
• setDegree() : BALL::PiecewisePolynomial
• setDeletable() : BALL::VIEW::Message
• setDeleteEntryEnabled() : BALL::VIEW::MainControl
• setDensity() : BALL::TriangulatedSAS , BALL::TriangulatedSES
• setDepth() : BALL::TBox3< T >
• setDimension() : BALL::TRegularData1D< ValueType > , BALL::TRegularData2D< ValueType > , BALL::TRegularData3D< ValueType >
• setDirection() : BALL::VIEW::LightSource
• setDistance() : BALL::FragmentDistanceCollector , BALL::VIEW::AtomDistanceColorProcessor
• setDockedSystem() : BALL::VIEW::DockResultDialog
• setDockingAlgorithm() : BALL::VIEW::DockProgressDialog
• setDockResult() : BALL::VIEW::DockResultDialog
• setDuplicateKeyCheck() : BALL::INIFile
• setEdge() : BALL::GraphTriangle< Vertex, Edge, Face >
• setElectronegativity() : BALL::Element
• setElement() : BALL::Atom
• setEnergyDifferenceBound() : BALL::EnergyMinimizer
• setEnergyOutputFrequency() : BALL::MolecularDynamics , BALL::EnergyMinimizer
• setEnergyToAbort() : BALL::MolecularDynamics , BALL::EnergyMinimizer
• setEpsilon() : BALL::RombergIntegrator< Function, DataType >
• setExponent() : BALL::MutablePower< Function, DataType >
• setExpression() : BALL::Expression , BALL::Selector
• setEyeDistance() : BALL::VIEW::Stage
• setFace() : BALL::GraphEdge< Vertex, Edge, Face >
• setFile() : BALL::Exception::GlobalExceptionHandler
• setFilename() : BALL::INIFile , BALL::Parameters , BALL::PDBInfo , BALL::ShiftModel , BALL::AssignRadiusProcessor , BALL::FragmentDB , BALL::VIEW::PythonSettings
• setFileName() : BALL::VIEW::POVRenderer , BALL::VIEW::STLRenderer , BALL::VIEW::VRMLRenderer , BALL::VIEW::FileObserver
• setFirst() : BALL::Addition< First, Second, DataType > , BALL::Subtraction< First, Second, DataType > , BALL::Product< First, Second, DataType > , BALL::Division< First, Second, DataType >
• setFirstAtom() : BALL::Bond
• setFirstEdge() : BALL::SmartsParser::SmartsParser::SPNode
• setFirstSPEdge() : BALL::SmartsParser::SmartsParser::SPEdge
• setFirstSPNode() : BALL::SmartsParser::SmartsParser::SPEdge
• setFlushToDiskFrequency() : BALL::SnapShotManager
• setFocalDistance() : BALL::VIEW::Stage
• setFont() : BALL::VIEW::MainControlPreferences
• setForce() : BALL::Atom
• setForceField() : BALL::ForceFieldComponent , BALL::SnapShotManager , BALL::AmberEvaluation , BALL::ForceFieldEvaluation
• setFormalCharge() : BALL::Atom
• setFragmentDB() : BALL::FragmentDB::FragmentDB::NormalizeNamesProcessor , BALL::FragmentDB::FragmentDB::BuildBondsProcessor , BALL::ReconstructFragmentProcessor
• setFrameBufferFormat() : BALL::VIEW::BufferedRenderer
• setFunction() : BALL::Reciprocal< Function, DataType > , BALL::SquareFunction< Function, DataType > , BALL::CubicFunction< Function, DataType > , BALL::MutablePower< Function, DataType > , BALL::NumericalIntegrator< Function, DataType >
• setGLRenderer() : BALL::VIEW::MeshBuffer , BALL::VIEW::Scene
• setGreen() : BALL::VIEW::ColorRGBA
• setGroup() : BALL::Element
• setGuest() : BALL::VIEW::DockWidget
• setHandleStreamsExternally() : BALL::XDRPersistenceManager
• setHeight() : BALL::TBox3< T > , BALL::VIEW::FrameBufferFormat
• setHeightVector() : BALL::TBox3< T >
• setHue() : BALL::VIEW::ColorHSV
• setIcon() : BALL::VIEW::ModularWidget
• setID() : BALL::PDBInfo , BALL::NucleicAcid , BALL::Nucleotide , BALL::Protein , BALL::Residue
• setIdentifier() : BALL::Embeddable
• setIdentity() : BALL::TMatrix4x4< T > , BALL::TQuaternion< T >
• setImprovedFlag() : BALL::StrangLBFGSMinimizer
• setIndex() : BALL::SnapShot , BALL::GraphEdge< Vertex, Edge, Face > , BALL::GraphFace< Vertex, Edge, Face > , BALL::GraphTriangle< Vertex, Edge, Face > , BALL::GraphVertex< Vertex, Edge, Face >
• setIndices() : BALL::TriangulatedSurface
• setInfoColor() : BALL::VIEW::Stage
• setINIFileSectionName() : BALL::VIEW::PreferencesEntry
• setInsertionCode() : BALL::Nucleotide , BALL::Residue
• setInteger() : BALL::Options
• setIntensity() : BALL::Peak< PositionType > , BALL::VIEW::LightSource
• setInternal() : BALL::SmartsParser::SmartsParser::SPEdge , BALL::SmartsParser::SmartsParser::SPNode
• setInterpolationBoundaries() : BALL::VIEW::ColorMap
• setIntersectionPoint() : BALL::RSEdge
• setIntervals() : BALL::PiecewiseFunction
• setIstream() : BALL::PersistenceManager
• setKineticEnergy() : BALL::SnapShot
• setLevel() : BALL::LogStream
• setLights() : BALL::VIEW::GLRenderer , BALL::VIEW::Renderer , BALL::VIEW::RenderSetup , BALL::VIEW::TilingRenderer
• setLine() : BALL::Exception::GlobalExceptionHandler , BALL::INIFile
• setLocked() : BALL::VIEW::ServerWidget::ServerWidget::BALLViewServer
• setLoggingFilename() : BALL::VIEW::MainControl
• setLogicalOperator() : BALL::SmartsParser::SmartsParser::SPEdge , BALL::SmartsParser::SmartsParser::SPNode
• setLookAtPosition() : BALL::VIEW::Camera
• setLookUpVector() : BALL::VIEW::Camera
• setLowerBound() : BALL::LineSearch
• setMajorRadiusOfTorus() : BALL::RSEdge
• setMaxDistanceColor() : BALL::VIEW::AtomDistanceColorProcessor
• setMaxGradient() : BALL::EnergyMinimizer
• setMaximalNumberOfIterations() : BALL::MolecularDynamics
• setMaximalSimulationTime() : BALL::MolecularDynamics
• setMaximumDisplacement() : BALL::EnergyMinimizer
• setMaximumNumberOfErrors() : BALL::ForceField
• setMaximumUnassignedAtoms() : BALL::AssignBaseProcessor , BALL::Templates
• setMaxIterations() : BALL::VIEW::MinimizationDialog
• setMaxLevel() : BALL::LogStream
• setMaxNumberOfIterations() : BALL::EnergyMinimizer
• setMaxNumOfColumns() : BALL::ShiftedLVMMMinimizer
• setMaxNumOfStoredVectPairs() : BALL::StrangLBFGSMinimizer
• setMaxNumSteps() : BALL::RombergIntegrator< Function, DataType >
• setMaxSameEnergy() : BALL::EnergyMinimizer
• setMaxSteps() : BALL::LineSearch
• setMenuHelp() : BALL::VIEW::ModularWidget
• setMenuHint() : BALL::VIEW::MainControl , BALL::VIEW::ModularWidget
• setMesh() : BALL::VIEW::MeshBuffer
• setMessage() : BALL::Exception::GeneralException , BALL::Exception::GlobalExceptionHandler
• setMinimizer() : BALL::LineSearch
• setMinLevel() : BALL::LogStream
• setMinMaxColors() : BALL::VIEW::ColorMap
• setModelInformation() : BALL::VIEW::Representation
• setMultithreading() : BALL::VIEW::MainControl
• setName() : BALL::ForceFieldComponent , BALL::ShiftModule , BALL::SolventDescriptor , BALL::ResidueRotamerSet , BALL::File , BALL::Exception::GlobalExceptionHandler , BALL::Options , BALL::PDBInfo , BALL::Atom , BALL::AtomContainer , BALL::Bond , BALL::Element , BALL::ForceField
• setNeedsSSSR() : BALL::SmartsParser
• setNegate() : BALL::ExpressionTree
• setNextComponentNumberToSubTree() : BALL::SmartsParser
• setNormal() : BALL::RSFace , BALL::SESVertex , BALL::TrianglePoint
• setNot() : BALL::SmartsParser::SmartsParser::SPBond , BALL::SmartsParser::SmartsParser::SPEdge , BALL::SmartsParser::SmartsParser::SPNode
• setNotProperty() : BALL::SmartsParser::SmartsParser::SPAtom
• setNullDistanceColor() : BALL::VIEW::AtomDistanceColorProcessor
• setNumberDensity() : BALL::SolventDescriptor
• setNumberOfATOMRecords() : BALL::PDBInfo
• setNumberOfAtoms() : BALL::SnapShot
• setNumberOfColors() : BALL::VIEW::ColorMap
• setNumberOfHETATMRecords() : BALL::PDBInfo
• setNumberOfIteration() : BALL::MolecularDynamics
• setNumberOfIterations() : BALL::EnergyMinimizer
• setNumberOfModels() : BALL::PDBInfo
• setNumberOfRecords() : BALL::PDBInfo
• setNumberOfTorsions() : BALL::ResidueRotamerSet
• setOccupancy() : BALL::PDBAtom
• setOffset() : BALL::VIEW::RenderSetup
• setOmega() : BALL::Peptides::AminoAcidDescriptor
• setOrder() : BALL::Bond
• setOrigin() : BALL::TRegularData1D< ValueType > , BALL::TRegularData2D< ValueType > , BALL::TRegularData3D< ValueType >
• setOstream() : BALL::PersistenceManager , BALL::VIEW::POVRenderer
• setParameters() : BALL::ShiftModule
• setPeriod() : BALL::Element
• setPhi() : BALL::Peptides::AminoAcidDescriptor
• setPhysStepWidth() : BALL::TFFT1D< ComplexTraits > , BALL::TFFT2D< ComplexTraits > , BALL::TFFT3D< ComplexTraits >
• setPitch() : BALL::VIEW::FrameBufferFormat
• setPixelFormat() : BALL::VIEW::FrameBufferFormat
• setPoint() : BALL::TBox3< T > , BALL::SASVertex , BALL::SESVertex , BALL::Triangle , BALL::TriangleEdge , BALL::TrianglePoint
• setPort() : BALL::VIEW::ServerWidget
• setPosition() : BALL::Atom , BALL::Peak< PositionType > , BALL::VIEW::LightSource
• setPotentialEnergy() : BALL::SnapShot
• setPredicate() : BALL::ExpressionTree , BALL::CompositeIteratorTraits
• setPrefix() : BALL::LogStream , BALL::RuleEvaluator , BALL::VIEW::DownloadPDBFile
• setPreview() : BALL::VIEW::Scene
• setPreviewMode() : BALL::VIEW::Renderer
• setProbeRadius() : BALL::SurfaceProcessor
• setProperty() : BALL::PropertyManager , BALL::SmartsParser::SmartsParser::SPAtom , BALL::PropertyManager , BALL::SmartsParser::SmartsParser::SPAtom
• setProteinName() : BALL::Peptides::PeptideBuilder
• setProxy() : BALL::VIEW::MainControl
• setPsi() : BALL::Peptides::AminoAcidDescriptor
• setRadius() : BALL::Atom , BALL::VIEW::Tube , BALL::VIEW::TwoColoredTube
• setRange() : BALL::VIEW::ColorMap
• setRDF() : BALL::RDFIntegrator
• setRDFIntegrator() : BALL::Pair6_12InteractionEnergyProcessor
• setRDFParameters() : BALL::Pair6_12InteractionEnergyProcessor
• setReal() : BALL::Options
• setReceiveBufferUpdates() : BALL::VIEW::RenderSetup
• setRecursive() : BALL::SmartsParser::SmartsParser::SPNode , BALL::SmartsParser
• setRed() : BALL::VIEW::ColorRGBA
• setReferenceTemperature() : BALL::MolecularDynamics
• setRefresh() : BALL::VIEW::MinimizationDialog
• setRelativeToCamera() : BALL::VIEW::LightSource
• setRemotenessIndicator() : BALL::PDBAtom
• setRepresentation() : BALL::RadialDistributionFunction
• setRightVector() : BALL::TBox3< T >
• setRingSize() : BALL::RingFinder
• setRoot() : BALL::SmartsParser
• setRotamer() : BALL::ResidueRotamerSet
• setRotation() : BALL::TMatrix4x4< T >
• setRotationX() : BALL::TMatrix4x4< T >
• setRotationY() : BALL::TMatrix4x4< T >
• setRotationZ() : BALL::TMatrix4x4< T >
• setRow() : BALL::TMatrix4x4< T >
• setRSEdge() : BALL::SESEdge , BALL::SESFace
• setRSFace() : BALL::SESFace
• setRSVertex() : BALL::SESFace
• setSaturation() : BALL::VIEW::ColorHSV
• setScale() : BALL::TMatrix4x4< T >
• setScalingFactorFile() : BALL::GeneralizedBornModel
• setScoring() : BALL::ConformationSet
• setSecond() : BALL::Subtraction< First, Second, DataType > , BALL::Addition< First, Second, DataType > , BALL::Product< First, Second, DataType > , BALL::Division< First, Second, DataType >
• setSecondAtom() : BALL::Bond
• setSecondEdge() : BALL::SmartsParser::SmartsParser::SPNode
• setSecondSPEdge() : BALL::SmartsParser::SmartsParser::SPEdge
• setSecondSPNode() : BALL::SmartsParser::SmartsParser::SPEdge
• setSelected() : BALL::Selectable , BALL::VIEW::GeometricObjectSelectionMessage
• setSelection() : BALL::VIEW::GenericSelectionMessage , BALL::VIEW::GeometricObjectSelectionMessage
• setSelection_() : BALL::VIEW::MolecularControl
• setSender() : BALL::VIEW::Message
• setShiftRange() : BALL::Bruker2DFile
• setSimulationThread() : BALL::VIEW::MainControl
• setSingular() : BALL::RSFace , BALL::RSEdge
• setSize() : BALL::BitVector , BALL::VIEW::GLRenderer , BALL::VIEW::Renderer , BALL::VIEW::TilingRenderer
• setSmoothLines() : BALL::VIEW::GLRenderer
• setSnapShotFrequency() : BALL::MolecularDynamics , BALL::EnergyMinimizer
• setSnapShotManager() : BALL::VIEW::SnapshotVisualisationDialog
• setSoluteDC() : BALL::GeneralizedBornModel
• setSolventAtomDescriptorList() : BALL::SolventDescriptor
• setSolventDC() : BALL::GeneralizedBornModel
• setSolventDescriptor() : BALL::Pair6_12InteractionEnergyProcessor
• setSPAtom() : BALL::SmartsParser::SmartsParser::SPNode
• setSPBond() : BALL::SmartsParser::SmartsParser::SPEdge
• setSphere() : BALL::SASFace
• setSSSR() : BALL::SmartsParser
• setStage() : BALL::VIEW::SceneMessage , BALL::VIEW::Renderer
• setStatusbarText() : BALL::VIEW::MainControl , BALL::VIEW::ModularWidget
• setStereoMode() : BALL::VIEW::RenderSetup
• setStickRadius() : BALL::VIEW::AddBallAndStickModel
• setSuffix() : BALL::VIEW::DownloadPDBFile
• setSwapEndian() : BALL::BinaryFileAdaptor< T >
• setSwapSideBySideStereo() : BALL::VIEW::Stage
• setSymbol() : BALL::Element
• setSysPath() : BALL::PyInterpreter
• setSystem() : BALL::SnapShotManager , BALL::VIEW::FDPBDialog
• setSystems() : BALL::VIEW::DockDialog
• setTemperatureFactor() : BALL::PDBAtom
• setTemplateResidue() : BALL::ResidueRotamerSet
• setText() : BALL::VIEW::Label
• setTimeStep() : BALL::CanonicalMD , BALL::MicroCanonicalMD , BALL::MolecularDynamics
• setTorsionAngle_() : BALL::ResidueRotamerSet
• setTraits() : BALL::BaseIterator< Container, DataType, Position, Traits >
• setTrajectoryFile() : BALL::SnapShotManager
• setTransformation() : BALL::TransformationProcessor
• setTranslation() : BALL::TMatrix4x4< T > , BALL::TranslationProcessor
• setTransparency() : BALL::VIEW::Representation , BALL::VIEW::ColorProcessor , BALL::VIEW::ElementColorProcessor , BALL::VIEW::ResidueNameColorProcessor , BALL::VIEW::ResidueTypeColorProcessor , BALL::VIEW::SecondaryStructureColorProcessor
• setTriangle() : BALL::TriangleEdge
• setType() : BALL::Atom , BALL::ExpressionTree , BALL::SecondaryStructure , BALL::SESEdge , BALL::SurfaceProcessor , BALL::VIEW::SceneMessage , BALL::VIEW::LightSource , BALL::VIEW::AddSurfaceModel , BALL::SESFace , BALL::Bond
• setTypeName() : BALL::Atom
• setUnsignedChar() : BALL::BitVector
• setUnsignedInt() : BALL::BitVector
• setUnsignedLong() : BALL::BitVector
• setUnsignedShort() : BALL::BitVector
• setup() : BALL::AmberBend , BALL::AmberNonBonded , BALL::AmberTorsion , BALL::CharmmBend , BALL::CharmmImproperTorsion , BALL::CharmmStretch , BALL::CharmmTorsion , BALL::ForceField , BALL::ForceFieldComponent , BALL::PeriodicBoundary , BALL::SnapShotManager , BALL::CanonicalMD , BALL::MicroCanonicalMD , BALL::MolecularDynamics , BALL::EnergyMinimizer , BALL::MMFF94NonBonded , BALL::MMFF94OutOfPlaneBend , BALL::MMFF94StretchBend , BALL::MMFF94Torsion , BALL::BuriedPolar , BALL::HydrogenBond , BALL::Lipophilic , BALL::ChemScoreMetal , BALL::PolarSolvation , BALL::RotationalEntropyLoss , BALL::GeneralizedBornModel , BALL::FDPB , BALL::AtomTyper , BALL::ConformationSet , BALL::DockingAlgorithm , BALL::GeometricFit , BALL::FDPB , BALL::NonpolarSolvation , BALL::CHPI , BALL::EnergyMinimizer , BALL::MicroCanonicalMD , BALL::SnapShotManager , BALL::CharmmNonBonded , BALL::AmberStretch
• setupAtomArray() : BALL::FDPB
• setupBoundary() : BALL::FDPB
• setUpdateInterval() : BALL::VIEW::FileObserver
• setUpdateMethod() : BALL::ConjugateGradientMinimizer , BALL::ShiftedLVMMMinimizer
• setupEpsGrid() : BALL::FDPB
• setupForceField() : BALL::VIEW::MolecularStructure
• setupKappaGrid() : BALL::FDPB
• setupPhiGrid() : BALL::FDPB
• setupQGrid() : BALL::FDPB
• setupSASGrid() : BALL::FDPB
• setupStereo() : BALL::VIEW::Renderer , BALL::VIEW::GLRenderer
• setUsePotentialGrid() : BALL::VIEW::FieldLineCreator
• setValue() : BALL::VIEW::QColorTable , BALL::VIEW::HotkeyTable , BALL::ResourceEntry , BALL::PreferencesObject , BALL::INIFile , BALL::PluginManager , BALL::VIEW::ColorHSV , BALL::VIEW::PreferencesEntry::PreferencesEntry::ExtendedPreferencesObject , BALL::VIEW::ShortcutRegistry
• setVanDerWaalsRadius() : BALL::Element
• setVDWRadiusFactor() : BALL::VIEW::AddVanDerWaalsModel
• setVector() : BALL::Options
• setVelocity() : BALL::Atom
• setVertex() : BALL::VIEW::Vertex , BALL::GraphTriangle< Vertex, Edge, Face > , BALL::GraphEdge< Vertex, Edge, Face > , BALL::VIEW::Vertex
• setVertex1() : BALL::VIEW::Vertex2
• setVertex1Address() : BALL::VIEW::Vertex2
• setVertex2() : BALL::VIEW::Vertex2
• setVertex2Address() : BALL::VIEW::Vertex2
• setVertexAddress() : BALL::VIEW::Vertex
• setVertexAddresses() : BALL::VIEW::Vertex2
• setVertices() : BALL::VIEW::Vertex2
• setViewPoint() : BALL::VIEW::Camera
• setViewPoint_() : BALL::VIEW::Scene
• setWidgetStack() : BALL::VIEW::PreferencesEntry
• setWidgetStackName() : BALL::VIEW::PreferencesEntry
• setWidgetVisible() : BALL::VIEW::DockWidget
• setWidth() : BALL::TBox3< T > , BALL::VIEW::FrameBufferFormat , BALL::Peak< PositionType >
• setWorkingDir() : BALL::VIEW::MainControl , BALL::VIEW::ModularWidget
• setXTol() : BALL::LineSearch
• setZEType() : BALL::SmartsParser::SmartsParser::SPBond
• shift() : BALL::TriangulatedSurface
• ShiftedLVMMMinimizer() : BALL::ShiftedLVMMMinimizer
• ShiftModel() : BALL::ShiftModel
• ShiftModule() : BALL::ShiftModule
• ShortcutDialog() : BALL::VIEW::ShortcutDialog
• show() : BALL::VIEW::GeometricFitDialog , BALL::VIEW::LabelDialog , BALL::VIEW::DisplayProperties , BALL::VIEW::MainControl , BALL::VIEW::AssignBondOrderResultsDialog , BALL::VIEW::DockProgressDialog , BALL::VIEW::Preferences , BALL::VIEW::PubChemDialog , BALL::VIEW::DockResultDialog
• showAmberForceFieldOptions() : BALL::VIEW::MolecularStructure
• showBondOrderAssignmentResults() : BALL::VIEW::MolecularStructure
• showCharmmForceFieldOptions() : BALL::VIEW::MolecularStructure
• showCoordinateSystem() : BALL::VIEW::Stage
• showDockingOptions() : BALL::VIEW::DockResultDialog
• showDocumentationForObject() : BALL::VIEW::HelpViewer
• showEntry() : BALL::VIEW::Preferences
• showExportPNGDialog() : BALL::VIEW::Scene
• showExportVRMLDialog() : BALL::VIEW::Scene
• showFilename() : BALL::VIEW::MolecularControl
• showHelp() : BALL::VIEW::HelpViewer
• showHelpFor() : BALL::VIEW::HelpViewer
• showInfos() : BALL::VIEW::Scene
• showLightSources() : BALL::VIEW::Renderer
• showOnlyInLogView() : BALL::VIEW::LogEvent
• showRuler() : BALL::VIEW::RenderSetup
• showScoringOptions_() : BALL::VIEW::DockResultDialog
• showSelectorHelp() : BALL::VIEW::MolecularControl
• showSnapshot() : BALL::VIEW::DockResultDialog
• showStackPage() : BALL::VIEW::PreferencesEntry
• showText() : BALL::VIEW::Scene
• showViewPoint_() : BALL::VIEW::Scene
• shrink() : BALL::TriangulatedSurface
• SimpleBase() : BALL::SimpleBase
• SimpleBox() : BALL::VIEW::SimpleBox
• SimpleExperiment1D() : BALL::SimpleExperiment1D
• simulate() : BALL::MolecularDynamics
• simulateIterations() : BALL::MicroCanonicalMD , BALL::MolecularDynamics , BALL::CanonicalMD
• simulateTime() : BALL::MolecularDynamics
• size() : BALL::Substring , BALL::HashSet< Key > , BALL::ConformationSet
• SizeOfSSSR() : BALL::SizeOfSSSR
• skipCurrentRecord() : BALL::PDBFile
• skipLines() : BALL::LineBasedFile
• SLICKEnergy() : BALL::SLICKEnergy
• SLICKScore() : BALL::SLICKScore
• SmartsParser() : BALL::SmartsParser
• SnapShot() : BALL::SnapShot
• snapShotInputTest() : BALL::VIEW::SnapshotVisualisationDialog
• SnapShotManager() : BALL::SnapShotManager
• SnapshotVisualisationDialog() : BALL::VIEW::SnapshotVisualisationDialog
• solve() : BALL::FDPB
• SolventAccessibleSurface() : BALL::SolventAccessibleSurface
• SolventDescriptor() : BALL::SolventDescriptor
• SolventExcludedSurface() : BALL::SolventExcludedSurface
• SolventParameter() : BALL::SolventParameter
• sort() : BALL::RotamerLibrary , BALL::ResidueRotamerSet
• sortTable() : BALL::VIEW::DockResultDialog
• SPAtom() : BALL::SmartsParser::SmartsParser::SPAtom
• SPBond() : BALL::SmartsParser::SmartsParser::SPBond
• specificSetup() : BALL::CanonicalMD , BALL::MolecularDynamics , BALL::EnergyMinimizer , BALL::MMFF94 , BALL::SLICKEnergy , BALL::SLICKScore , BALL::ConjugateGradientMinimizer , BALL::StrangLBFGSMinimizer , BALL::ShiftedLVMMMinimizer , BALL::SteepestDescentMinimizer , BALL::CharmmFF , BALL::MicroCanonicalMD , BALL::ForceField , BALL::AmberFF
• specificSetup_() : BALL::AtomTyper , BALL::PluginHandler , BALL::VIEW::InputDevPluginHandler
• specificShutdown_() : BALL::PluginHandler , BALL::VIEW::InputDevPluginHandler
• Spectrum() : BALL::Spectrum< DataT, PeakT, PositionT >
• SPEdge() : BALL::SmartsParser::SmartsParser::SPEdge
• Sphere() : BALL::VIEW::Sphere
• splice() : BALL::Residue , BALL::System , BALL::SecondaryStructure , BALL::Chain , BALL::Molecule , BALL::AtomContainer , BALL::Nucleotide , BALL::Composite
• spliceAfter() : BALL::AtomContainer , BALL::Composite , BALL::Chain , BALL::Nucleotide , BALL::Molecule , BALL::System , BALL::SecondaryStructure , BALL::Residue
• spliceBefore() : BALL::Composite , BALL::Nucleotide , BALL::Chain , BALL::Residue , BALL::AtomContainer , BALL::SecondaryStructure , BALL::System , BALL::Molecule
• split() : BALL::String
• splitQuoted() : BALL::String
• SPNode() : BALL::SmartsParser::SmartsParser::SPNode
• SquareFunction() : BALL::SquareFunction< Function, DataType >
• Stage() : BALL::VIEW::Stage
• StageSettings() : BALL::VIEW::StageSettings
• stamp() : BALL::TimeStamp , BALL::Composite
• start() : BALL::ReconstructFragmentProcessor , BALL::SimpleExperiment1D , BALL::VIEW::AddBackboneModel , BALL::AromaticityProcessor , BALL::ShiftModule , BALL::BuildBondsProcessor , BALL::VIEW::FileObserver , BALL::BinaryProcessor< T1, T2 > , BALL::UnaryProcessor< T > , BALL::Timer , BALL::ResidueChecker , BALL::VIEW::ResidueNumberColorProcessor , BALL::VIEW::ColorProcessor , BALL::BoundingBoxProcessor , BALL::AssignBondOrderProcessor , BALL::GeometricCenterProcessor , BALL::JohnsonBoveyShiftProcessor , BALL::EnergyProcessor , BALL::AssignRadiusProcessor , BALL::AssignChargeProcessor , BALL::FragmentDB::FragmentDB::NormalizeNamesProcessor , BALL::HybridisationProcessor , BALL::RuleProcessor , BALL::AddHydrogenProcessor , BALL::VIEW::InterpolateColorProcessor , BALL::HBondShiftProcessor , BALL::CreateSpectrumProcessor , BALL::GeometricFit , BALL::FragmentDB::FragmentDB::BuildBondsProcessor , BALL::ShiftModel , BALL::EFShiftProcessor , BALL::Selector , BALL::AssignShiftProcessor , BALL::FragmentDistanceCollector , BALL::MMFF94ChargeProcessor , BALL::SurfaceProcessor
• startDefinition() : BALL::VIEW::GLDisplayList
• startDocking() : BALL::VIEW::DockingController
• startInterpreter() : BALL::VIEW::PyWidget
• startOutput() : BALL::PersistenceManager
• startPlugin() : BALL::PluginManager , BALL::PluginHandler , BALL::PluginManager
• startRendering() : BALL::VIEW::RenderSetup
• startsWith() : BALL::LineBasedFile
• SteepestDescentMinimizer() : BALL::SteepestDescentMinimizer
• STLRenderer() : BALL::VIEW::STLRenderer
• stop() : BALL::Timer , BALL::VIEW::FileObserver
• stopedSimulation() : BALL::VIEW::MainControl
• stopPlugin() : BALL::PluginManager , BALL::PluginHandler , BALL::PluginManager
• stopSimulation() : BALL::VIEW::MainControl
• storeConnections_() : BALL::FragmentDB::FragmentDB::BuildBondsProcessor
• storeGradientEnergy() : BALL::EnergyMinimizer
• storeOriginalConfiguration_() : BALL::AssignBondOrderProcessor
• storeValues() : BALL::VIEW::PreferencesEntry
• StrangLBFGSMinimizer() : BALL::StrangLBFGSMinimizer
• String() : BALL::String
• StringHashMap() : BALL::StringHashMap< Value >
• StructureMapper() : BALL::StructureMapper
• substitute() : BALL::GraphEdge< Vertex, Edge, Face > , BALL::GraphFace< Vertex, Edge, Face > , BALL::String , BALL::GraphVertex< Vertex, Edge, Face > , BALL::GraphTriangle< Vertex, Edge, Face > , BALL::GraphEdge< Vertex, Edge, Face > , BALL::GraphFace< Vertex, Edge, Face > , BALL::GraphTriangle< Vertex, Edge, Face >
• Substring() : BALL::Substring
• Subtraction() : BALL::Subtraction< First, Second, DataType >
• supports() : BALL::VIEW::BufferedRenderer
• SurfaceBase() : BALL::SurfaceBase
• SurfaceProcessor() : BALL::SurfaceProcessor
• swap() : BALL::TSimpleBox3< T > , BALL::VIEW::Point , BALL::Atom , BALL::Bond , BALL::BaseIterator< Container, DataType, Position, Traits > , BALL::VIEW::Line , BALL::VIEW::ColorExtension2 , BALL::VIEW::Mesh , BALL::VIEW::ColorRGBA , BALL::TVector4< T > , BALL::VIEW::MultiColorExtension , BALL::VIEW::TwoColoredLine , BALL::VIEW::Label , BALL::Selectable , BALL::VIEW::TwoColoredTube , BALL::VIEW::Vertex2 , BALL::Molecule , BALL::TBox3< T > , BALL::TMatrix4x4< T > , BALL::VIEW::Disc , BALL::Chain , BALL::AtomContainer , BALL::VIEW::ColorUnitHue , BALL::Residue , BALL::Composite , BALL::VIEW::Sphere , BALL::TLine3< T > , BALL::NucleicAcid , BALL::PDBAtom , BALL::TSphere3< T > , BALL::VIEW::GeometricObject , BALL::PropertyManager , BALL::TVector3< T > , BALL::HashSet< Key > , BALL::SecondaryStructure , BALL::TQuaternion< T > , BALL::TCircle3< T > , BALL::VIEW::Tube , BALL::TAngle< T > , BALL::VIEW::ColorUnit , BALL::VIEW::Vertex , BALL::VIEW::ColorHSV , BALL::Protein , BALL::Nucleotide , BALL::List< Value > , BALL::StringHashMap< Value > , BALL::String
• swapSideBySideStereo() : BALL::VIEW::Stage
• swapValues_() : BALL::VIEW::DockDialog , BALL::VIEW::GeometricFitDialog
• switchShowWidget() : BALL::VIEW::Scene
• switchString() : BALL::LineBasedFile
• switchView() : BALL::VIEW::AssignBondOrderResultsDialog
• sync() : BALL::LogStreamBuf
• SyntaxTree() : BALL::ExpressionParser::ExpressionParser::SyntaxTree
• System() : BALL::System