Here is a list of all documented class members with links to the class documentation for each member:

- a -

• a : TSimpleBox3< T >
• a0 : Constant
• a_ : HBondShiftProcessor
• a_i_ : ConjugateGradientMinimizer
• ABORT : Processor
• abort() : TCPTransfer
• abortClicked() : VIEW::DockProgressDialog
• aboutToExit() : VIEW::MainControl
• ABSOLUTE_TEMPERATURE : ReissCavFreeEnergyProcessor::Default, ReissCavFreeEnergyProcessor::Option, PierottiCavFreeEnergyProcessor::Default, PierottiCavFreeEnergyProcessor::Option, PCMCavFreeEnergyProcessor::Default, PCMCavFreeEnergyProcessor::Option
• accept() : VIEW::LabelDialog, VIEW::AtomOverview
• acceptor_list_ : HBondShiftProcessor
• activate() : VIEW::Server
• ACTIVE_STEREO : VIEW::GLRenderer
• ADD : VIEW::RepresentationMessage, VIEW::DatasetMessage
• add() : SmartsMatcher::RecStruct_
• add_hydrogens : FragmentDB
• ADD_TO_GEOMETRIC_CONTROL : VIEW::RepresentationMessage
• ADD_VARIANT_EXTENSIONS : Residue
• addAlgorithm() : VIEW::DockDialog
• addAllRecords_() : PDBFile
• addAminoAcid() : Peptides::PeptideBuilder
• addAtom() : VIEW::AtomDistanceColorProcessor
• AddBackboneModel() : VIEW::AddBackboneModel
• AddBallAndStickModel() : VIEW::AddBallAndStickModel
• AddCartoonModel() : VIEW::AddCartoonModel
• addComponent() : ComposedEnergyProcessor
• addComposite() : VIEW::MolecularControl
• addDataPath() : Path
• addEdge() : SmartsParser
• addHydrogens() : VIEW::MolecularStructure
• Addition() : Addition< First, Second, DataType >
• addLightPressed() : VIEW::LightSettings
• addLightSource() : VIEW::Stage
• AddLineModel() : VIEW::AddLineModel
• addModularWidget() : VIEW::MainControl
• addMovable_() : ResidueRotamerSet
• addNode() : SmartsParser
• addPropertiesFromSPAtom() : SmartsParser::SPAtom
• addRecursiveEdge() : SmartsParser
• addRepresentation() : VIEW::GeometricControl
• addRingConnection() : SmartsParser
• addRotamer() : RotamerLibrary, ResidueRotamerSet
• addScoring() : DockResult
• addScoringFunction() : VIEW::DockResultDialog, VIEW::DockDialog
• addSolvent() : PeriodicBoundary
• addSPEdge() : SmartsParser::SPNode
• AddSurfaceModel() : VIEW::AddSurfaceModel
• addToolBarEntries() : VIEW::Scene, VIEW::EditableScene, VIEW::ModularWidget
• AddVanDerWaalsModel() : VIEW::AddVanDerWaalsModel
• addVariants() : Enumerator< Container, SiteIterator, Variant >
• advancedClicked() : VIEW::DockResultDialog
• advancedOptions() : VIEW::MinimizationDialog
• after() : String
• algAdvancedPressed() : VIEW::DockDialog
• Algorithm : VIEW::DockingController
• ALGORITHM_NAME : RingPerceptionProcessor::Default, RingPerceptionProcessor::Option
• algorithmChosen() : VIEW::DockDialog
• all_small_beers_ : RingPerceptionProcessor
• all_small_rings_ : RingPerceptionProcessor
• ALPHA : PairExpInteractionEnergyProcessor::Default, PairExpInteractionEnergyProcessor::Option, RegularExpression
• alpha_ : DSN6File
• ALPHANUMERIC : RegularExpression
• AmberBend() : AmberBend
• AmberConfigurationDialog() : VIEW::AmberConfigurationDialog
• AmberFF() : AmberFF
• AmberNonBonded() : AmberNonBonded
• AmberStretch() : AmberStretch
• AmberTorsion() : AmberTorsion
• AMBIENT : VIEW::LightSource
• AminoAcidDescriptor() : Peptides::AminoAcidDescriptor
• analyseRings() : RingAnalyser
• AND : ExpressionTree
• angle : TQuaternion< T >
• animateClicked() : VIEW::SnapshotVisualisationDialog
• AnisotropyShiftProcessor() : AnisotropyShiftProcessor
• ANY_TYPE : Atom
• append() : System, SecondaryStructure, Residue, Nucleotide, Molecule, Chain, AtomContainer, TRRFile, TrajectoryFile, DCDFile
• appendChild() : ExpressionTree, Composite
• appendHotkey() : VIEW::HotkeyTable
• appendLine() : INIFile
• appendSection() : INIFile
• apply() : VIEW::StageSettings, VIEW::MaterialSettings, VIEW::LightSettings, VIEW::DisplayProperties, ElectrostaticPotentialCalculator, PTE_, INIFile, List< Value >, HashSet< Key >, HashMap< Key, T >, Composite
• applyAncestor() : Composite
• applyBonds() : Atom
• applyChild() : Composite
• applyDescendant() : Composite
• applyDescendantPostorder() : Composite
• applyDescendantPreorder() : Composite
• applyFirstSnapShot() : SnapShotManager
• applyInterBond() : AtomContainer
• applyIntraBond() : AtomContainer
• applyLastSnapShot() : SnapShotManager
• applyLevel() : Composite
• applyNextSnapShot() : SnapShotManager
• applyPostorder() : Composite
• applyPreferences() : VIEW::Scene, VIEW::PyWidget, VIEW::EditableScene, VIEW::Server, VIEW::ModularWidget, VIEW::MainControl, VIEW::Preferences, VIEW::DisplayProperties
• applyPreorder() : Composite
• applyProcessors_() : VIEW::DockDialog
• applySelector() : VIEW::MolecularControl
• applySnapShot() : SnapShotManager, SnapShot
• applyTo() : VIEW::MMFF94ConfigurationDialog, VIEW::CharmmConfigurationDialog, VIEW::AmberConfigurationDialog
• applyValues_() : VIEW::DockDialog
• argument : ExpressionParser::SyntaxTree
• arom : MMFF94AtomType
• AromaticityProcessor() : AromaticityProcessor
• aromatize() : AromaticityProcessor
• aromatizeSimple() : AromaticityProcessor
• aspec : MMFF94AtomType
• assembleMolecule() : MoleculeAssembler
• assign() : Templates
• ASSIGN_CHARGES : MMFF94::Default, MMFF94::Option, CharmmFF::Default, CharmmFF::Option, AmberFF::Default, AmberFF::Option
• ASSIGN_TYPENAMES : MMFF94::Default, MMFF94::Option, CharmmFF::Default, CharmmFF::Option, AmberFF::Default, AmberFF::Option
• ASSIGN_TYPES : MMFF94::Default, MMFF94::Option, CharmmFF::Default, CharmmFF::Option, AmberFF::Default, AmberFF::Option
• assignBackboneAtoms() : AtomBijection
• assignByName() : AtomBijection
• assignCAlphaAtoms() : AtomBijection
• AssignChargeProcessor() : AssignChargeProcessor
• assignCharges() : Templates
• assignParameters() : QuadraticImproperTorsion, QuadraticBondStretch, QuadraticAngleBend, Potential1210, LennardJones, CosineTorsion, CharmmEEF1
• AssignRadiusProcessor() : AssignRadiusProcessor
• AssignShiftProcessor() : AssignShiftProcessor
• assignSpecificValues_() : AtomTyper
• assignTorsion() : ResidueTorsions
• assignTrivial() : AtomBijection
• assignTypeNames() : Templates
• atom : CharmmEEF1::Data
• Atom() : Atom
• atom_ : SmartsParser::SPAtom
• atom_array : FDPB
• atom_format_ : MOLFile
• AtomBijection() : AtomBijection
• AtomBondModelBaseProcessor() : VIEW::AtomBondModelBaseProcessor
• AtomBox : VIEW::ColorProcessor
• AtomChargeColorProcessor() : VIEW::AtomChargeColorProcessor
• AtomContainer() : AtomContainer
• AtomDistanceColorProcessor() : VIEW::AtomDistanceColorProcessor
• AtomGrid : VIEW::ColorProcessor
• AtomicNumber : Element
• AtomicPolarizabilities() : AtomicPolarizabilities
• AtomInformationContent() : AtomInformationContent
• AtomOverview() : VIEW::AtomOverview
• AtomPair : AtomBijection
• AtomStatus : RSComputer
• AtomTypes() : AtomTypes
• AtomVector() : AtomVector
• attributes_changed_time_ : Atom
• AVERAGE_SECTION_NAME : CreateSpectrumProcessor
• AVERAGING__NONE : PolarSolvation
• AVERAGING__RANDOM : PolarSolvation
• AVERAGING__RANDOM_FACTOR : PolarSolvation
• AVERAGING__STATIC : PolarSolvation
• AveragingMethod : PolarSolvation
• AVOGADRO : Constant

- b -

• b : TSimpleBox3< T >
• b_ : HBondShiftProcessor
• b_i_ : ConjugateGradientMinimizer
• backbone_dependent_ : RotamerLibrary
• backward() : CompositeIteratorTraits
• BalabanIndexJ() : BalabanIndexJ
• BALANCING_VALUE : ShiftedLVMMMinimizer
• BaseIterator() : BaseIterator< Container, DataType, Position, Traits >
• baseName() : FileSystem
• BATH_RELAXATION_TIME : MolecularDynamics::Option
• bath_relaxation_time_ : CanonicalMD
• bb_dep_sets_ : RotamerLibrary
• bb_indep_sets_ : RotamerLibrary
• before() : String
• begin() : VIEW::RepresentationManager, SmartsParser::SPNode, Gradient, AtomVector, ExpressionParser::SyntaxTree, PDBRecords, RandomAccessIterator< Container, DataType, Position, Traits >, ForwardIterator< Container, DataType, Position, Traits >, ConstForwardIterator< Container, DataType, Position, Traits >, BidirectionalIterator< Container, DataType, Position, Traits >, ConstBidirectionalIterator< Container, DataType, Position, Traits >
• beginBond() : Atom
• beginBox() : HashGridBox3< Item >
• BendMap : MMFF94BendParameters
• beta_ : DSN6File
• BidirectionalIterator() : BidirectionalIterator< Container, DataType, Position, Traits >
• BinaryFileAdaptor() : BinaryFileAdaptor< T >
• BinaryProcessor() : BinaryProcessor< T1, T2 >
• binaryRead() : TRegularData3D< ValueType >, TRegularData2D< ValueType >, TRegularData1D< ValueType >
• binaryWrite() : TRegularData3D< ValueType >, TRegularData2D< ValueType >, TRegularData1D< ValueType >
• bind() : Substring
• Bit() : Bit
• BitVector() : BitVector
• bitwiseAnd() : BitVector
• bitwiseOr() : BitVector
• bitwiseXor() : BitVector
• blockname : GAMESSDatFile::block
• blowUp() : TriangulatedSurface
• BOHR_RADIUS : Constant
• BOLTZMANN : Constant
• Bond() : Bond
• bond_ : SmartsParser::SPEdge
• bond_format_ : MOLFile
• bond_lengths_ : BuildBondsProcessor
• bond_order_ : SmartsParser::SPBond
• bond_to_index_ : RingPerceptionProcessor
• BondConstIterator : Atom
• BondConstReverseIterator : Atom
• BondIterator : Atom
• BONDLENGTHS_FILENAME : BuildBondsProcessor::Default, BuildBondsProcessor::Option
• BondOrder : Bond
• BondPolarizabilities() : BondPolarizabilities
• bondProperties() : VIEW::MolecularControl
• BondReverseIterator : Atom
• BondType : Bond
• book_keeping_ : PDBFile
• BOOL : NamedProperty
• BORDER : FDPB::Default, FDPB::Option
• bound_ : CompositeIteratorTraits
• BOUNDARY : FDPB::Default, FDPB::Option
• bounding_box_data_size : TRRFile::TRRHeader
• BOUNDING_BOX_LOWER : FDPB::Option
• BOUNDING_BOX_UPPER : FDPB::Option
• Box() : VIEW::Box
• BoxIterator : HashGridBox3< Item >
• BREAK : Processor
• browseChargesData() : VIEW::DockDialog
• browseChargesRules() : VIEW::DockDialog
• browseRadiiData() : VIEW::DockDialog
• browseRadiiRules() : VIEW::DockDialog
• Bruker1DFile() : Bruker1DFile
• Bruker2DFile() : Bruker2DFile
• bucket_ : HashMap< Key, T >
• bufferRepresentation() : VIEW::GLRenderer
• BUILD : VIEW::MainControl
• build_bonds : FragmentDB
• buildBondModels_() : VIEW::AtomBondModelBaseProcessor
• buildBonds() : VIEW::MolecularStructure, VIEW::MolecularControl
• buildBondsHashGrid3_() : BuildBondsProcessor
• BuildBondsProcessor() : BuildBondsProcessor
• buildChains() : ChainBuilder
• buildConnection_() : FragmentDB::BuildBondsProcessor
• buildContextMenu() : VIEW::GeometricControl, VIEW::VectorGridController, VIEW::DockResultController, VIEW::TrajectoryController, VIEW::RegularData3DController, VIEW::DatasetController
• buildFragmentBonds() : FragmentDB::BuildBondsProcessor
• buildInterFragmentBonds() : FragmentDB::BuildBondsProcessor
• buildPeptide() : VIEW::MolecularStructure
• buildVectorOfNonBondedAtomPairs() : CharmmNonBonded, AmberNonBonded
• BuriedPolar() : BuriedPolar

- c -

• c : Constant
• c_str() : Substring
• CAL_PER_JOULE : Constant
• calculate() : VIEW::FDPBDialog
• calculateAbsoluteCoordinates() : VIEW::Stage
• calculateBendEmpericalForceConstant() : MMFF94StretchBend
• calculateBendEmpericalReferenceAngle() : MMFF94StretchBend
• calculateDefaultBijection() : StructureMapper
• calculateDistances() : VIEW::AtomDistanceColorProcessor
• calculateEnergy() : GeneralizedBornModel
• calculateFactors_() : CanonicalMD
• calculateForceFieldEnergy() : VIEW::MolecularStructure
• calculateFragmentBijection() : StructureMapper
• calculateHBonds() : VIEW::MolecularStructure
• calculateMinSpacing() : HashGrid3< Item >
• calculatePEOE() : PartialChargeProcessor
• calculatePotential() : GeneralizedBornModel
• calculateRamachandranPlot() : VIEW::MolecularStructure
• calculateReactionFieldEnergy() : FDPB
• calculateRelativeCoordinates() : VIEW::Stage
• calculateRMSD() : VIEW::MolecularStructure, StructureMapper, AtomBijection
• calculateScore() : RotationalEntropyLoss, PolarSolvation, NonpolarSolvation, Lipophilic, BuriedPolar
• calculateSecondaryStructure() : VIEW::MolecularStructure
• calculateSolvationEnergy() : GeneralizedBornModel
• calculateSSSR() : RingPerceptionProcessor
• calculateStretchR0() : MMFF94StretchBend
• calculateTransformation() : StructureMapper
• CALCULATION__BOEHM : RotationalEntropyLoss
• CALCULATION__FROZEN_GLYCOSIDIC_BONDS : RotationalEntropyLoss
• CALCULATION__FULL_LJ_POTENTIAL : VanDerWaals
• CALCULATION__GLYCOSIDIC_BONDS : RotationalEntropyLoss
• CALCULATION__GLYCOSIDIC_CONTRIBUTION : RotationalEntropyLoss
• CALCULATION__ORIGINAL : RotationalEntropyLoss
• CALCULATION__SOFTENED_LJ_POTENTIAL_LOG : VanDerWaals
• CALCULATION__SOFTENED_LJ_POTENTIAL_SIMPLE : VanDerWaals
• CalculationMethod : VanDerWaals, RotationalEntropyLoss
• Camera() : VIEW::Camera
• cancelPressed() : VIEW::DockDialog
• canHandle() : VIEW::TestFramework, VIEW::PyWidget, VIEW::DatasetControl, VIEW::ModularWidget, VIEW::MolecularFileDialog
• CanonicalMD() : CanonicalMD
• canonizePath() : FileSystem
• capacity_ : HashMap< Key, T >
• CASE_INSENSITIVE : String
• CASE_SENSITIVE : String
• cell_scaling_ : DSN6File
• CENTER_CAMERA : VIEW::CompositeMessage
• centerCamera() : VIEW::MolecularStructure, VIEW::MolecularControl
• Chain() : Chain
• ChainBuilder() : ChainBuilder
• CHANGED_COMPOSITE : VIEW::CompositeMessage
• CHANGED_COMPOSITE_HIERARCHY : VIEW::CompositeMessage
• changeToUserHomeDir() : Directory
• CHARACTER_CLASS__ASCII_ALPHA : String
• CHARACTER_CLASS__ASCII_ALPHANUMERIC : String
• CHARACTER_CLASS__ASCII_FLOAT : String
• CHARACTER_CLASS__ASCII_LOWER : String
• CHARACTER_CLASS__ASCII_NUMERIC : String
• CHARACTER_CLASS__ASCII_UPPER : String
• CHARACTER_CLASS__QUOTES : String
• CHARACTER_CLASS__WHITESPACE : String
• CHARGE_DISTRIBUTION : FDPB::Default, FDPB::Option
• ChargeRuleProcessor() : ChargeRuleProcessor
• CharmmBend() : CharmmBend
• CharmmConfigurationDialog() : VIEW::CharmmConfigurationDialog
• CharmmEEF1() : CharmmEEF1
• CharmmFF() : CharmmFF
• CharmmImproperTorsion() : CharmmImproperTorsion
• CharmmNonBonded() : CharmmNonBonded
• CharmmStretch() : CharmmStretch
• CharmmTorsion() : CharmmTorsion
• CHECK_AFTER_ITERATIONS : FDPB::Default, FDPB::Option
• checkAtomType() : MMFF94
• checkHeader() : XDRPersistenceManager, TextPersistenceManager, PersistenceManager
• checkMenu() : VIEW::TestFramework, VIEW::Scene, VIEW::PyWidget, VIEW::MolecularStructure, VIEW::MolecularControl, VIEW::GeometricControl, VIEW::FileObserver, VIEW::EditableScene, VIEW::DockingController, VIEW::DatasetControl, VIEW::ModularWidget, VIEW::PubChemDialog, VIEW::MolecularFileDialog, VIEW::LabelDialog, VIEW::DownloadPDBFile, VIEW::DisplayProperties, VIEW::DatasetController
• checkMenus() : VIEW::MainControl
• checkName() : XDRPersistenceManager, TextPersistenceManager, PersistenceManager
• checkObjectHeader() : PersistenceManager
• checkObjectPointerArrayHeader() : XDRPersistenceManager, TextPersistenceManager, PersistenceManager
• checkObjectPointerArrayTrailer() : XDRPersistenceManager, TextPersistenceManager, PersistenceManager
• checkObjectPointerHeader() : XDRPersistenceManager, TextPersistenceManager, PersistenceManager
• checkObjectReferenceHeader() : XDRPersistenceManager, TextPersistenceManager, PersistenceManager
• checkObjectTrailer() : PersistenceManager
• checkPrimitiveHeader() : XDRPersistenceManager, TextPersistenceManager, PersistenceManager
• checkPrimitiveTrailer() : XDRPersistenceManager, TextPersistenceManager, PersistenceManager
• checkResidue() : VIEW::MolecularStructure, VIEW::MolecularControl
• checkStorableHeader() : XDRPersistenceManager, TextPersistenceManager, PersistenceManager
• checkStorableTrailer() : XDRPersistenceManager, TextPersistenceManager, PersistenceManager
• checkStreamHeader() : XDRPersistenceManager, TextPersistenceManager, PersistenceManager
• checkStreamTrailer() : XDRPersistenceManager, TextPersistenceManager, PersistenceManager
• checkTrailer() : XDRPersistenceManager, TextPersistenceManager, PersistenceManager
• ChemScoreMetal() : ChemScoreMetal
• chi1 : Rotamer
• chi2 : Rotamer
• chi3 : Rotamer
• chi4 : Rotamer
• children : ExpressionParser::SyntaxTree
• ChiralClass : SmartsParser
• CHOOSE_FF : VIEW::MainControl
• CHOOSE_MODEL : PDBFile::Default, PDBFile::Option
• chooseAmberFF() : VIEW::MolecularStructure
• chooseCharmmFF() : VIEW::MolecularStructure
• chooseFile() : VIEW::FileObserver
• chooseMMFF94() : VIEW::MolecularStructure
• ClaverieParameter() : ClaverieParameter
• clean() : ReducedSurface
• clear() : VIEW::Scene, VIEW::PyWidget, VIEW::GeometricControl, VIEW::VRMLRenderer, VIEW::MeshBuffer, VIEW::Renderer, VIEW::POVRenderer, VIEW::GLRenderer, VIEW::GLDisplayList, VIEW::TwoColoredTube, VIEW::TwoColoredLine, VIEW::Tube, VIEW::Sphere, VIEW::SimpleBox, VIEW::Point, VIEW::MultiLine, VIEW::Mesh, VIEW::Line, VIEW::Label, VIEW::Disc, VIEW::Box, VIEW::AddSurfaceModel, VIEW::ModelProcessor, VIEW::HBondModelProcessor, VIEW::ColorProcessor, VIEW::AddBallAndStickModel, VIEW::AddBackboneModel, VIEW::AtomBondModelBaseProcessor, VIEW::Stage, VIEW::Camera, VIEW::Server, VIEW::RepresentationManager, VIEW::Representation, VIEW::ModularWidget, VIEW::MainControl, VIEW::GeometricObject, VIEW::ConnectionObject, VIEW::CompositeManager, VIEW::Vertex2, VIEW::Vertex, VIEW::Dataset, VIEW::ColorUnitHue, VIEW::ColorUnit, VIEW::ColorRGBA, VIEW::ColorHSV, VIEW::MultiColorExtension, VIEW::ColorExtension2, Timer, TCPTransfer, File, Directory, TriangulatedSurface, SmartsParser, SmartsMatcher::RecStruct_, SmartsMatcher::RecStructCore_, RotamerLibrary, ReducedSurface, RDFSection, RDFParameter, RDFIntegrator, RadialDistributionFunction, UhligCavFreeEnergyProcessor, SolventParameter, SolventDescriptor, ReissCavFreeEnergyProcessor, PierottiCavFreeEnergyProcessor, PCMCavFreeEnergyProcessor, PairExpRDFIntegrator, PairExpInteractionEnergyProcessor, Pair6_12RDFIntegrator, Pair6_12InteractionEnergyProcessor, ClaverieParameter, SLICKScore, SLICKEnergy, RotationalEntropyLoss, PolarSolvation, NonpolarSolvation, ChemScoreMetal, Lipophilic, HydrogenBond, CHPI, BuriedPolar, Spectrum< DataT, PeakT, PositionT >, ShiftModule, ShiftModel, Templates, ResidueTorsions, QuadraticImproperTorsion, QuadraticBondStretch, QuadraticAngleBend, Potential1210, LennardJones, ForceFieldParameters, CosineTorsion, CharmmEEF1, AtomTypes, MMFF94ESParameters, MMFF94VDWParameters, MMFF94PlaneParameters, MMFF94TorsionParameters, MMFF94StretchBendParameters, MMFF94BendParameters, MMFF94StretchParameters, MMFF94AtomTypeEquivalences, MMFF94ParametersBase, MMFF94NonBonded, MMFF94, SnapShotManager, SnapShot, RuleEvaluator, PeriodicBoundary, ForceField, CharmmNonBonded, CharmmFF, AmberNonBonded, AmberFF, TVector4< T >, TVector3< T >, TVector2< T >, TSphere3< T >, TSimpleBox3< T >, RombergIntegrator< Function, DataType >, TQuaternion< T >, TPlane3< T >, PiecewisePolynomial, PiecewiseFunction, TMatrix4x4< T >, TLine3< T >, TFFT3D< ComplexTraits >, TFFT2D< ComplexTraits >, TFFT1D< ComplexTraits >, TCircle3< T >, TBox3< T >, TAngle< T >, ConnectedToPredicate, Selector, SecondaryStructure, Residue, PTE_, Element, Protein, PDBAtom, Nucleotide, NucleicAcid, ExpressionTree, ExpressionPredicate, ExpressionParser::SyntaxTree, Expression, Bond, AtomContainer, Atom, TRRFile, TrajectoryFile, ResourceFile, PDBInfo, PDBFile, ParameterSection, Parameters, NMRStarFile, LineBasedFile, INIFile, DSN6File, DCDFile, EnergyProcessor, ComposedEnergyProcessor, Triple< T1, T2, T3 >, Substring, String, RegularExpression, TRegularData3D< ValueType >, TRegularData2D< ValueType >, TRegularData1D< ValueType >, Quadruple< T1, T2, T3, T4 >, Options, HashSet< Key >, HashMap< Key, T >, HashGrid3< Item >, HashGridBox3< Item >, TContourSurface< T >, TContourLine< T >, TContour< T >, BitVector, Bit, TimeStamp, PreciseTime, Selectable, PropertyManager, NamedProperty, ObjectCreator, Object, MoleculeObjectCreator, MolecularInformation, Composite, Client, LogStream
• clearBuffer() : VIEW::MeshBuffer, SnapShotManager
• clearClipboard() : VIEW::MolecularControl
• clearComposites() : VIEW::AddSurfaceModel, VIEW::ModelProcessor, VIEW::AtomBondModelBaseProcessor
• clearData() : VIEW::MainControl
• clearGeometricObjects() : VIEW::Representation
• clearNormals() : TSurface< T >
• clearProperty() : PropertyManager
• clearSelection() : VIEW::MainControl
• clearSelector() : VIEW::MolecularControl
• ClearShiftProcessor() : ClearShiftProcessor
• clearTriangles() : TSurface< T >
• clearUsedAtoms_() : VIEW::AtomBondModelBaseProcessor
• clearVertices() : TSurface< T >
• Client() : Client
• ClippingDialog() : VIEW::ClippingDialog
• clone() : Composite
• cloneBond() : Atom
• close() : File, ResourceFile
• closeClicked() : VIEW::DockResultDialog
• clusterRings() : RingClusterer
• collapseAll() : VIEW::MolecularControl
• ColorExtension2() : VIEW::ColorExtension2
• ColorHSV() : VIEW::ColorHSV
• coloringMuteableByDisplayProperties() : VIEW::ModelInformation
• ColoringSettingsDialog() : VIEW::ColoringSettingsDialog
• ColorMap() : VIEW::ColorMap
• colorPressed() : VIEW::StageSettings, VIEW::LightSettings
• ColorProcessor() : VIEW::ColorProcessor
• ColorRGBA() : VIEW::ColorRGBA
• ColorUnit() : VIEW::ColorUnit
• ColorUnitHue() : VIEW::ColorUnitHue
• Command : Client
• COMMAND__SEND_OBJECT : Client
• COMMAND__UNKOWN : Client
• compact() : Atom
• Comparator() : Comparator< T >
• compare() : Object
• Compare_() : VIEW::DockResultDialog::Compare_, DockResult::Compare_
• compareChains() : ChainBuilder
• CompareMode : String
• compareRingsystems() : MoleculeAssembler
• component_grouping_ : SmartsParser
• component_no_ : SmartsParser, SmartsParser::SPNode
• ComposedEnergyProcessor() : ComposedEnergyProcessor
• Composite() : Composite
• composite_iterator_ : CompositeIteratorTraits
• CompositeIteratorTraits() : CompositeIteratorTraits
• CompositeManager() : VIEW::CompositeManager
• CompositeMessage() : VIEW::CompositeMessage
• CompositeMessageType : VIEW::CompositeMessage
• compositeProperties() : VIEW::MolecularControl
• compositesAreLocked() : VIEW::MainControl
• CompositeSet : VIEW::ColorProcessor
• compute() : TriangulatedSAS, SolventExcludedSurface, SolventAccessibleSurface, ReducedSurface
• compute_() : SecondaryStructureProcessor
• computeTopology() : TContourSurface< T >::Cube
• Conformation : ConformationSet
• conformation_set_ : VIEW::DockingFinishedMessage, DockResult
• ConjugateGradientMinimizer() : ConjugateGradientMinimizer
• connect() : Client
• ConnectionObject() : VIEW::ConnectionObject
• ConnectivityBase() : ConnectivityBase
• CONST : SLICKScore::Default, SLICKScore::Option, SLICKEnergy::Default, SLICKEnergy::Option
• CONSTANT : UhligCavFreeEnergyProcessor::Default, UhligCavFreeEnergyProcessor::Option
• constants_ : ParsedFunction< arg >
• ConstBidirectionalIterator() : ConstBidirectionalIterator< Container, DataType, Position, Traits >
• ConstBoxIterator : HashGridBox3< Item >
• ConstDataIterator : HashGridBox3< Item >
• ConstForwardIterator() : ConstForwardIterator< Container, DataType, Position, Traits >
• ConstIterator : PyIndexList, PyDatasetVector, PyCompositeList, PyColorRGBAVector, Spectrum< DataT, PeakT, PositionT >, PeakList< PT >, Gradient, AtomVector, ExpressionParser::SyntaxTree, StringHashMap< Value >, TRegularData3D< ValueType >, TRegularData2D< ValueType >, TRegularData1D< ValueType >, List< Value >, Enumerator< Container, SiteIterator, Variant >
• ConstReverseIterator : Gradient
• construct() : Peptides::PeptideBuilder
• constructRS() : RSConstructor
• containsSelection() : Composite
• CONTINUE : Processor
• convertObject() : ObjectCreator, MoleculeObjectCreator
• coordinateSystemEnabled() : VIEW::Stage
• CoordinateType : TRegularData3D< ValueType >, TRegularData2D< ValueType >, TRegularData1D< ValueType >
• copy() : VIEW::MolecularControl, File
• copyTo() : File
• corr_par_ : ShiftedLVMMMinimizer
• CORRECTION_PARAMETER : ShiftedLVMMMinimizer::Option
• CorrectionParameter : ShiftedLVMMMinimizer
• CosineTorsion() : CosineTorsion
• COULOMB : FDPB::Boundary
• count() : Composite
• countAtomContainers() : AtomContainer
• countAtoms() : System, AtomContainer
• countBonds() : AtomContainer, Atom
• countChains() : System, Protein
• countChildren() : ResourceEntry
• countComponents() : ForceField
• countDescendants() : ResourceEntry, Composite
• countDirectories() : Directory
• countEdges() : SmartsParser::SPNode
• countFields() : String
• countFieldsQuoted() : String
• countFiles() : Directory
• countFragments() : System
• countInstances_() : Embeddable
• countInterBonds() : AtomContainer
• countIntraBonds() : AtomContainer
• countItems() : VIEW::MolecularControl, Directory
• countMolecules() : System
• countNamedProperties() : PropertyManager
• countNonEmptyBoxes() : HashGrid3< Item >
• countNucleicAcids() : System
• countNucleotides() : System, NucleicAcid
• countPDBAtoms() : SecondaryStructure, Residue, Protein, Chain
• countProperties() : SmartsParser::SPAtom, PropertyManager
• countProteins() : System
• countRealValences() : SmartsParser::SPAtom
• countRecord() : PDBFile
• countRecordFields() : PDBFile
• countRecords() : PDBFile
• countResidues() : System, SecondaryStructure, Protein, Chain
• counts_format_ : MOLFile
• countSecondaryStructures() : System, Protein, Chain
• countSubexpressions() : RegularExpression
• countValue() : BitVector
• countVariants() : Enumerator< Container, SiteIterator, Variant >
• Cp_ref : CharmmEEF1::Values
• crd : MMFF94AtomType
• create() : Directory, Factory< T >
• createAtom() : SmartsParser
• createBond() : Bond, Atom
• createCombination() : Enumerator< Container, SiteIterator, Variant >
• createContourLine() : TContourLine< T >
• createCoordinateSystem() : VIEW::Scene
• createCoordinateSystemAtOrigin() : VIEW::Scene
• createGeometricObjects() : VIEW::AddSurfaceModel, VIEW::ModelProcessor, VIEW::LabelModel, VIEW::AddBallAndStickModel, VIEW::AddBackboneModel, VIEW::AtomBondModelBaseProcessor
• createGridFromDistance() : VIEW::MolecularStructure
• createMap() : VIEW::ColorMap
• createMapJet() : VIEW::ColorMap
• createMenuEntries() : VIEW::VectorGridController, VIEW::DockResultController, VIEW::TrajectoryController, VIEW::RegularData3DController, VIEW::DatasetController
• CreateMethod : ShiftModel, PersistenceManager
• CreateMethodMap : ShiftModel
• createObject() : PersistenceManager
• createPlot() : VIEW::RegularData2DWidget, VIEW::RegularData1DWidget
• createRepresentation() : VIEW::MolecularControl, VIEW::RepresentationManager
• createRepresentationMode() : VIEW::DisplayProperties
• createResidue_() : Peptides::PeptideBuilder
• CreateSpectrumProcessor() : CreateSpectrumProcessor
• createTemporaryFilename() : File
• createVoid() : Factory< T >
• CreationMethod : Expression
• crystal_dimension_ : DSN6File
• CubicFunction() : CubicFunction< Function, DataType >
• curr_num_of_vect_pairs_ : StrangLBFGSMinimizer
• curr_number_of_cols_ : ShiftedLVMMMinimizer
• CURRENT_DIRECTORY : FileSystem
• current_energy_ : EnergyMinimizer
• current_grad_ : EnergyMinimizer
• current_parser_ : SmartsParser
• CURRENT_TIME : MolecularDynamics::Option
• currentStackPage() : VIEW::PreferencesEntry
• cut() : VIEW::MolecularControl, TriangulatedSurface
• cutlo_ : EnergyMinimizer

- d -

• d : TLine3< T >
• D_1_ : ConjugateGradientMinimizer
• D_4_ : ConjugateGradientMinimizer
• data : GAMESSDatFile::block
• data_ : TRegularData3D< ValueType >, TRegularData2D< ValueType >, TRegularData1D< ValueType >
• DataIterator : HashGridBox3< Item >
• Dataset() : VIEW::Dataset
• DatasetControl() : VIEW::DatasetControl
• DataType : Spectrum< DataT, PeakT, PositionT >
• DCDFile() : DCDFile
• deactivate() : VIEW::Server
• DEBYE : FDPB::Boundary
• decodeBase64() : String
• DEFAULT_FRAGMENT_DB : RotamerLibrary
• DEFAULT_LIBRARY : RotamerLibrary
• defaultsPressed() : VIEW::LightSettings
• DEG_PER_RAD : Constant
• DELETE_EXISTING_BONDS : BuildBondsProcessor::Default, BuildBondsProcessor::Option
• DELETE_OVERESTIMATED_BONDS : BuildBondsProcessor::Default, BuildBondsProcessor::Option
• deleteColumn_() : VIEW::DockResultDialog
• deleteCurrentItems() : VIEW::MolecularControl, VIEW::GeometricControl, VIEW::GenericControl
• deleteDataset() : VIEW::DatasetController
• deleteDataset_() : VIEW::VectorGridController, VIEW::DockResultController, VIEW::TrajectoryController, VIEW::RegularData3DController, VIEW::DatasetController
• deleteDatasets() : VIEW::DatasetController
• deleteIsolatedEdges() : TriangulatedSurface
• deleteIsolatedPoints() : TriangulatedSurface
• deleteLine() : INIFile
• deleteOverestimatedBonds_() : BuildBondsProcessor
• deleteRotamer() : ResidueRotamerSet
• deleteRotamers() : ResidueRotamerSet
• deleteScoring() : DockResult
• deleteSection() : INIFile
• deleteSimilarFaces() : ReducedSurface
• deleteVariants() : Enumerator< Container, SiteIterator, Variant >
• Density() : Density
• Descriptor() : Descriptor
• deselect() : VIEW::MolecularControl, Selectable, Composite
• deselectCompositeRecursive() : VIEW::MainControl
• DESELECTED_COMPOSITE : VIEW::CompositeMessage
• destroy() : VIEW::ModularWidget, VIEW::ConnectionObject, Directory, SmartsMatcher::RecStructPool_, FDPB, TFFT3D< ComplexTraits >, TFFT2D< ComplexTraits >, TFFT1D< ComplexTraits >, SecondaryStructure, Residue, Protein, PDBAtom, Nucleotide, NucleicAcid, Bond, AtomContainer, Atom, ResourceFile, StringHashMap< Value >, Substring, String, RegularExpression, List< Value >, HashSet< Key >, HashMap< Key, T >, HashGrid3< Item >, HashGridBox3< Item >, PropertyManager, Composite
• destroyBond() : Atom
• destroyBonds() : AtomContainer, Atom
• destroyGrids() : FDPB
• determineMethodOfAtomPairGeneration() : MMFF94NonBonded, CharmmNonBonded, AmberNonBonded
• dfs() : RingFinder
• dG_free : CharmmEEF1::Values
• dG_ref : CharmmEEF1::Values
• dH_ref : CharmmEEF1::Values
• DIELECTRIC_SMOOTHING : FDPB::Default, FDPB::Option
• difference() : Spectrum< DataT, PeakT, PositionT >
• dimension_ : TRegularData3D< ValueType >, TRegularData2D< ValueType >, TRegularData1D< ValueType >
• DIPOLE : FDPB::Boundary
• DIRECT_RENDERING : VIEW::Scene
• direction_ : EnergyMinimizer
• Directory() : Directory
• disable() : ResidueChecker, PeriodicBoundary
• disableAtoms() : SDFile
• disableLoggingToFile() : VIEW::MainControl
• disableOutput() : LogStream
• disableSelection() : ResidueChecker, ForceField
• Disc() : VIEW::Disc
• DISPLAY : VIEW::MainControl
• DISPLAY_ANIMATION : VIEW::MainControl
• DISPLAY_CREATE : VIEW::MainControl
• DISPLAY_LISTS_RENDERING : VIEW::Scene
• DISPLAY_STEREO : VIEW::MainControl
• DISPLAY_VIEWPOINT : VIEW::MainControl
• DISPLAYLIST_NOT_DEFINED : VIEW::GLDisplayList
• DisplayProperties() : VIEW::DisplayProperties
• DISTANCE_DEPENDENT_DIELECTRIC : MMFF94::Default, CharmmFF::Default, CharmmFF::Option, AmberFF::Default, AmberFF::Option
• Division() : Division< First, Second, DataType >
• DockDialog() : VIEW::DockDialog
• docking_algorithm_ : DockResult
• docking_options_ : DockResult
• DockingController() : VIEW::DockingController
• DockingThread() : VIEW::DockingThread
• DockProgressDialog() : VIEW::DockProgressDialog
• DockResult() : DockResult
• DockResultDialog() : VIEW::DockResultDialog
• DockWidget() : VIEW::DockWidget
• doFFT() : TFFT3D< ComplexTraits >, TFFT2D< ComplexTraits >, TFFT1D< ComplexTraits >
• doiFFT() : TFFT3D< ComplexTraits >, TFFT2D< ComplexTraits >, TFFT1D< ComplexTraits >
• donor_list_ : HBondShiftProcessor
• DOUBLE : NamedProperty
• downwardClicked() : VIEW::DockResultDialog
• draw() : VIEW::MeshBuffer, VIEW::GLDisplayList
• drawBuffered() : VIEW::GLRenderer
• DSN6File() : DSN6File
• DUAL_VIEW_STEREO : VIEW::GLRenderer
• dump() : VIEW::Scene, VIEW::PyWidget, VIEW::GLDisplayList, VIEW::TwoColoredTube, VIEW::TwoColoredLine, VIEW::Tube, VIEW::Sphere, VIEW::SimpleBox, VIEW::Point, VIEW::MultiLine, VIEW::Mesh, VIEW::Line, VIEW::Label, VIEW::Disc, VIEW::Box, VIEW::AddVanDerWaalsModel, VIEW::AddSurfaceModel, VIEW::ModelProcessor, VIEW::AddLineModel, VIEW::ColorProcessor, VIEW::AddBallAndStickModel, VIEW::AddBackboneModel, VIEW::AtomBondModelBaseProcessor, VIEW::Stage, VIEW::Camera, VIEW::LightSource, VIEW::Server, VIEW::RepresentationManager, VIEW::Representation, VIEW::PreferencesEntry, VIEW::ModularWidget, VIEW::MainControl, VIEW::GeometricObject, VIEW::ConnectionObject, VIEW::CompositeManager, VIEW::Vertex2, VIEW::Vertex, VIEW::ColorUnitHue, VIEW::ColorUnit, VIEW::ColorRGBA, VIEW::ColorMap, VIEW::ColorHSV, VIEW::MultiColorExtension, VIEW::ColorExtension2, Timer, TCPTransfer, SmartsMatcher::RecStruct_, RadialDistributionFunction, PairExpRDFIntegrator, Pair6_12RDFIntegrator, TVector4< T >, TVector3< T >, TVector2< T >, TSphere3< T >, TSimpleBox3< T >, TQuaternion< T >, TPlane3< T >, PiecewisePolynomial, PiecewiseFunction, TMatrix4x4< T >, TLine3< T >, TCircle3< T >, TBox3< T >, TAngle< T >, SecondaryStructure, Residue, Protein, PDBAtom, Nucleotide, NucleicAcid, Molecule, Fragment, Chain, Bond, AtomContainer, Atom, Substring, RegularExpression, Options, HashSet< Key >, HashMap< Key, T >, HashGrid3< Item >, PropertyManager, Embeddable, Composite, Client, LogStreamBuf
• dumpTree() : SmartsParser
• dumpTreeRecursive_() : SmartsParser
• duplicateKeyCheckEnabled() : INIFile

- e -

• E : Constant
• e0 : Constant
• e_size : TRRFile::TRRHeader
• EdgeConstIterator : SmartsParser::SPNode
• EdgeIterator : SmartsParser::SPNode
• edges_ : SmartsParser, SmartsParser::SPNode
• EDIT : VIEW::MainControl
• EditableScene() : VIEW::EditableScene
• editColor() : VIEW::LabelDialog, VIEW::DisplayProperties
• editSelectionColor() : VIEW::DisplayProperties
• EFShiftProcessor() : EFShiftProcessor
• ELECTRON_MASS : Constant
• ELECTROSTATIC_CUTOFF : MMFF94::Default, MMFF94::Option, CharmmFF::Default, CharmmFF::Option, AmberFF::Default, AmberFF::Option
• ELECTROSTATIC_CUTON : MMFF94::Default, MMFF94::Option, CharmmFF::Default, CharmmFF::Option, AmberFF::Default, AmberFF::Option
• ElectrostaticPotentialCalculator() : ElectrostaticPotentialCalculator
• Element() : Element
• element_symbol : SolventAtomDescriptor
• ELEMENTARY_CHARGE : Constant
• ElementColorProcessor() : VIEW::ElementColorProcessor
• Embeddable() : Embeddable
• empty() : TRegularData3D< ValueType >, TRegularData2D< ValueType >, TRegularData1D< ValueType >
• EMPTY : String
• enable() : ResidueChecker, PeriodicBoundary
• enableAtoms() : SDFile
• enableBallAndStickModel() : VIEW::AddBallAndStickModel
• enableCreationForNewMolecules() : VIEW::DisplayProperties
• enableEnergyAbortCondition() : EnergyMinimizer, MolecularDynamics
• enableLoggingToFile() : VIEW::MainControl, VIEW::MainControlPreferences
• enableOutput() : LogStream
• enableSelection() : ResidueChecker, ForceField
• enableStickModel() : VIEW::AddBallAndStickModel
• enableTrimWhitespaces() : LineBasedFile
• encodeBase64() : String
• end() : VIEW::RepresentationManager, SmartsParser::SPNode, Gradient, AtomVector, ExpressionParser::SyntaxTree, RandomAccessIterator< Container, DataType, Position, Traits >, ForwardIterator< Container, DataType, Position, Traits >, ConstForwardIterator< Container, DataType, Position, Traits >, BidirectionalIterator< Container, DataType, Position, Traits >, ConstBidirectionalIterator< Container, DataType, Position, Traits >
• endBond() : Atom
• endBox() : HashGridBox3< Item >
• endDefinition() : VIEW::GLDisplayList
• endOutput() : PersistenceManager
• EndPos : String
• ENERGY_DIFFERENCE_BOUND : EnergyMinimizer::Option
• energy_difference_bound_ : EnergyMinimizer
• ENERGY_OUTPUT_FREQUENCY : EnergyMinimizer::Option, MolecularDynamics::Option
• energy_output_frequency_ : EnergyMinimizer
• energy_update_counter_ : EnergyMinimizer
• energyAbortConditionEnabled() : EnergyMinimizer, MolecularDynamics
• EnergyMinimizer() : EnergyMinimizer
• EnergyProcessor() : EnergyProcessor
• ENTER_MOVE_MODE : VIEW::SceneMessage
• entries_ : JCAMPFile
• EntryMap : JCAMPFile
• Enumerator() : Enumerator< Container, SiteIterator, Variant >
• EnumeratorIndex() : EnumeratorIndex
• eps_grid : FDPB
• EPSILON : Constant
• equals() : SmartsParser::SPAtom
• erase() : HashSet< Key >, HashMap< Key, T >
• error() : LogStream
• ERROR__ATOM_ARRAY_REQUIRED : FDPB
• ERROR__CANNOT_CREATE_ATOM_ARRAY : FDPB
• ERROR__CANNOT_CREATE_CHARGE_GRID : FDPB
• ERROR__CANNOT_CREATE_EPSILON_GRID : FDPB
• ERROR__CANNOT_CREATE_KAPPA_GRID : FDPB
• ERROR__CANNOT_CREATE_PHI_GRID : FDPB
• ERROR__CANNOT_CREATE_SAS_GRID : FDPB
• ERROR__EPSILON_GRID_REQUIRED : FDPB
• ERROR__ILLEGAL_VALUE_FOR_LOWER_UPPER : FDPB
• ERROR__NONE : FDPB
• ERROR__NOT_A_VECTOR_IN_UPPER_LOWER : FDPB
• ERROR__NOT_IMPLEMENTED : FDPB
• ERROR__OUT_OF_MEMORY : FDPB
• ERROR__PHI_GRID_REQUIRED : FDPB
• ERROR__SAS_GRID_REQUIRED : FDPB
• ERROR__SETUP_REQUIRED : FDPB
• ERROR__UNKNOWN : FDPB
• ERROR__UNKNOWN_BOUNDARY_CONDITION_TYPE : FDPB
• ERROR__UNKNOWN_CHARGE_DISTRIBUTION_METHOD : FDPB
• ERROR__UNKNOWN_DIELECTRIC_SMOOTHING_METHOD : FDPB
• ERROR_LEVEL : LogStream
• ErrorCode : FDPB
• estimateBondOrders_() : BuildBondsProcessor
• evaluated : ExpressionParser::SyntaxTree
• event() : VIEW::MainControl
• eventFilter() : VIEW::LogView, VIEW::HelpViewer
• exec() : VIEW::DockDialog, VIEW::ClippingDialog
• expandAll() : VIEW::MolecularControl
• expect() : TextPersistenceManager
• Experiment() : Experiment< PeakListType >
• EXPORT_PNG : VIEW::SceneMessage
• EXPORT_POVRAY : VIEW::SceneMessage
• exportNextPOVRay() : VIEW::Scene
• exportPNG() : VIEW::Scene
• exportScene() : VIEW::Scene
• exportSceneToPNG_() : VIEW::SimulationThread
• exportSurface() : TriangulatedSurface
• Expression() : Expression
• ExpressionPredicate() : ExpressionPredicate
• ExpressionTree() : ExpressionTree
• extent_ : DSN6File
• extractSection() : RDFSection, RDFParameter, SolventParameter, ClaverieParameter, Templates, ResidueTorsions, QuadraticImproperTorsion, QuadraticBondStretch, QuadraticAngleBend, Potential1210, LennardJones, CosineTorsion, CharmmEEF1, AtomTypes, ParameterSection
• extractStructure_() : PDBFile

- f -

• F : Constant
• FARADAY : Constant
• FDPB() : FDPB
• FDPBDialog() : VIEW::FDPBDialog
• FermiBaseFunction() : FermiBaseFunction
• fetchPreferences() : VIEW::Scene, VIEW::PyWidget, VIEW::MolecularStructure, VIEW::MolecularControl, VIEW::DockWidget, VIEW::DockingController, VIEW::ModularWidget, VIEW::MainControl, VIEW::Preferences, VIEW::LabelDialog, VIEW::GeometricFitDialog, VIEW::DownloadPDBFile, VIEW::DockDialog
• fetchPreferences_() : VIEW::GeometricFitDialog, VIEW::DockDialog
• FieldLineCreator() : VIEW::FieldLineCreator
• FieldLinesDialog() : VIEW::FieldLinesDialog
• FILE : VIEW::MainControl
• File() : File
• FILE_EXPORT : VIEW::MainControl
• FILE_IMPORT : VIEW::MainControl
• FILE_OPEN : VIEW::MainControl
• FILE_OPEN_GRID : VIEW::MainControl
• FILENAME : CharmmFF::Default, CharmmFF::Option, AmberFF::Default, AmberFF::Option
• filename_ : PDBInfo
• fileSelected() : VIEW::PythonSettings
• fill() : BitVector
• fillDialog() : VIEW::DockProgressDialog
• fillSystemComboboxes_() : VIEW::DockDialog
• filterLines() : LogStream
• finalize() : PyInterpreter, Bond, PersistentObject
• finalizeInputStream() : XDRPersistenceManager, PersistenceManager
• finalizeOutputStream() : XDRPersistenceManager, PersistenceManager
• finalizePreferencesTab() : VIEW::Scene, VIEW::PyWidget, VIEW::EditableScene, VIEW::Server, VIEW::ModularWidget, VIEW::DisplayProperties
• finalizeWidget() : VIEW::PyWidget, VIEW::LogView, VIEW::EditFunctions, VIEW::Server, VIEW::ModularWidget
• find() : Path, Directory, RegularExpression, HashSet< Key >, HashMap< Key, T >, HashGridBox3< Item >
• findAllBCC() : RingPerceptionProcessor
• findStep() : StrangLBFGSMinimizer, SteepestDescentMinimizer, ShiftedLVMMMinimizer, EnergyMinimizer, ConjugateGradientMinimizer
• findStrict() : Path
• findTransformation() : TransformationManager
• FINE_STRUCTURE_CONSTANT : Constant
• finish() : VIEW::VRMLRenderer, VIEW::POVRenderer, VIEW::AtomDistanceColorProcessor, SurfaceProcessor, ResidueChecker, ReconstructFragmentProcessor, HBondProcessor, FragmentDistanceCollector, GeometricCenterProcessor, BoundingBoxProcessor, FragmentDB::BuildBondsProcessor, FragmentDB::NormalizeNamesProcessor, AssignRadiusProcessor, UhligCavFreeEnergyProcessor, ReissCavFreeEnergyProcessor, PierottiCavFreeEnergyProcessor, PCMCavFreeEnergyProcessor, PairExpInteractionEnergyProcessor, Pair6_12InteractionEnergyProcessor, ShiftModule, ShiftModel, JohnsonBoveyShiftProcessor, HBondShiftProcessor, HaighMallionShiftProcessor, EFShiftProcessor, AnisotropyShiftProcessor, MMFF94ChargeProcessor, RuleProcessor, ComposedEnergyProcessor, BinaryProcessor< T1, T2 >, UnaryProcessor< T >
• finish_() : VIEW::SimulationThread
• FINISHED_UPDATE : VIEW::RepresentationMessage
• finishIteration() : EnergyMinimizer
• first : Triple< T1, T2, T3 >, Quadruple< T1, T2, T3, T4 >
• first_ : SmartsParser::SPEdge
• first_edge_ : SmartsParser::SPNode, SmartsParser::SPEdge
• first_iter_ : StrangLBFGSMinimizer, ShiftedLVMMMinimizer, ConjugateGradientMinimizer
• first_matches : SmartsMatcher::RecStruct_, SmartsMatcher::RecStructCore_
• firstSnapshotClicked() : VIEW::SnapshotVisualisationDialog
• FLETCHER_REEVES : ConjugateGradientMinimizer
• FLOAT : NamedProperty
• FLUSH_TO_DISK_FREQUENCY : SnapShotManager::Default, SnapShotManager::Option
• flushToDisk() : SnapShotManager, TRRFile, TrajectoryFile, DCDFile
• FOCUSING : FDPB::Boundary
• FOLDER : MMFF94::Default, MMFF94::Option
• force_data_size : TRRFile::TRRHeader
• force_field_ : EnergyMinimizer
• force_update_counter_ : EnergyMinimizer
• ForceField() : ForceField
• ForceFieldComponent() : ForceFieldComponent
• ForceFieldEvaluation() : ForceFieldEvaluation
• ForceFieldParameters() : ForceFieldParameters
• ForceModel() : VIEW::ForceModel
• Form : TLine3< T >
• FormalCharge() : FormalCharge
• forward() : CompositeIteratorTraits
• forwarded_rings_ : RingPerceptionProcessor
• fourth : Quadruple< T1, T2, T3, T4 >
• Fragment() : Fragment
• fragment_db_ : RotamerLibrary, FragmentDB::BuildBondsProcessor
• fragment_list_ : FragmentDB::BuildBondsProcessor
• FragmentDB() : FragmentDB
• FragmentDistanceCollector() : FragmentDistanceCollector
• fragments : FragmentDistanceCollector
• FragmentTypes : FragmentDB
• from() : String
• FullNameType : Residue, Atom
• functions_ : ParsedFunction< arg >

- g -

• GAMESSDatFile() : GAMESSDatFile
• GAMESSLogFile() : GAMESSLogFile
• gamma_ : DSN6File
• GAS_CONSTANT : Constant
• GeneralException() : Exception::GeneralException
• generateButtonClicked() : VIEW::PubChemDialog
• generateFromSMILES() : VIEW::PubChemDialog
• generateListViewItem_() : VIEW::MolecularControl, VIEW::GeometricControl
• generateMoleculesVector() : PeriodicBoundary
• generateSD() : SDGenerator
• GenericControl() : VIEW::GenericControl
• GenericMolFile() : GenericMolFile
• GenericSelectionMessage() : VIEW::GenericSelectionMessage
• GEOMETRIC_MEAN : ShiftedLVMMMinimizer
• GeometricControl() : VIEW::GeometricControl
• GeometricFit() : GeometricFit
• GeometricFitDialog() : VIEW::GeometricFitDialog
• GeometricObject() : VIEW::GeometricObject
• GeometricObjectSelectionMessage() : VIEW::GeometricObjectSelectionMessage
• get() : VIEW::ColorUnitHue, VIEW::ColorUnit, VIEW::ColorRGBA, VIEW::ColorHSV, Directory, TVector4< T >, TVector3< T >, TSphere3< T >, TSimpleBox3< T >, TQuaternion< T >, TPlane3< T >, TMatrix4x4< T >, TLine3< T >, TCircle3< T >, TAngle< T >, System, SecondaryStructure, Residue, Protein, PDBAtom, Nucleotide, NucleicAcid, Molecule, Chain, AtomContainer, Atom, ResourceEntry, StringHashMap< Value >, String, RegularExpression, Options, List< Value >, HashSet< Key >, HashMap< Key, T >, BitVector, XDRPersistenceManager, TextPersistenceManager, Selectable, PropertyManager, PersistenceManager, Composite
• get3DPosition_() : VIEW::Scene
• get3Prime() : NucleicAcid
• get5Prime() : NucleicAcid
• getAddr() : SockInetAddr, SockAddr
• getAlgorithmOptions() : VIEW::DockDialog
• getAllSmallRings() : RingPerceptionProcessor
• getAlpha() : VIEW::ColorRGBA, LineSearch
• getAlphaBlending() : VIEW::ColorMap
• getAlternateLocationIndicator() : PDBAtom
• getAmberConfigurationDialog() : VIEW::MolecularStructure
• getAmberFF() : VIEW::MolecularStructure
• getAncestor() : Composite
• getAngle() : VIEW::LightSource, SASEdge, RSEdge, ReducedSurface, TVector3< T >, TQuaternion< T >
• getArea() : TSurface< T >
• getArgument() : ExpressionPredicate
• getAtom() : SESVertex, RSVertex, Peak< PositionType >, AtomContainer
• getAtomBranchDesignator() : PDBFile
• getAtomContainer() : AtomContainer
• getAtomDescriptor() : SolventDescriptor
• getAtomElementSymbol() : PDBFile
• getAtomForces() : SnapShot
• getAtomicNumber() : Element
• getAtomicRadius() : Element
• getAtomicWeight() : Element
• getAtomList_() : VIEW::AtomBondModelBaseProcessor
• getAtomName() : PDBFile
• getAtomPositions() : SnapShot
• getAtomRemotenessIndicator() : PDBFile
• getAtoms() : ForceField
• getAtomSet_() : VIEW::AtomBondModelBaseProcessor
• getAtomTypes() : ForceFieldParameters
• getAtomVelocities() : SnapShot
• getAttributes() : Atom
• getAttributesModificationTime() : Atom
• getAxis() : TQuaternion< T >
• getBackgroundColor() : VIEW::Stage
• getBallRadius() : VIEW::AddBallAndStickModel
• getBathRelaxationTime() : CanonicalMD
• getBendEnergy() : MMFF94, CharmmFF, AmberFF
• getBeta() : LineSearch
• getBijection() : StructureMapper
• getBit() : BitVector
• getBitSet() : BitVector
• getBitVector() : PropertyManager
• getBlue() : VIEW::ColorRGBA
• getBond() : Atom
• getBondOrder() : SmartsParser::SPBond
• getBool() : Options, NamedProperty
• getBorder() : TriangulatedSurface
• getBoundAtom() : Bond
• getBoundingBox() : ReducedSurface
• getBoundString() : Substring
• getBox() : BoundingBoxProcessor, PeriodicBoundary, HashGrid3< Item >
• getBranchDesignator() : PDBAtom
• getBucketSize() : HashSet< Key >, HashMap< Key, T >
• getBuffer() : TCPTransfer
• getCamera() : VIEW::Stage
• getCapacity() : HashSet< Key >, HashMap< Key, T >
• getCenter() : RSFace, GeometricCenterProcessor
• getCenterOfTorus() : RSEdge
• getChain() : SecondaryStructure, Residue, Protein, PDBAtom, Atom
• getChainName() : Peptides::PeptideBuilder
• getCharge() : Templates, Atom
• getCharmmConfigurationDialog() : VIEW::MolecularStructure
• getCharmmFF() : VIEW::MolecularStructure
• getChild() : ResourceEntry, Composite
• getChildren() : ExpressionTree
• getCircle() : SESEdge, SASEdge
• getClockTime() : Timer
• getClosestIndex() : TRegularData3D< ValueType >, TRegularData2D< ValueType >, TRegularData1D< ValueType >
• getClosestItem() : HashGrid3< Item >
• getClosestValue() : TRegularData3D< ValueType >, TRegularData2D< ValueType >, TRegularData1D< ValueType >
• getCoefficients() : PiecewiseFunction
• getColor() : VIEW::ResidueTypeColorProcessor, VIEW::SecondaryStructureColorProcessor, VIEW::ForceColorProcessor, VIEW::OccupancyColorProcessor, VIEW::TemperatureFactorColorProcessor, VIEW::AtomDistanceColorProcessor, VIEW::AtomChargeColorProcessor, VIEW::ResidueNameColorProcessor, VIEW::ResidueNumberColorProcessor, VIEW::ElementColorProcessor, VIEW::ColorProcessor, VIEW::LightSource
• getColor2() : VIEW::ColorExtension2
• getColoringName() : VIEW::ModelInformation
• getColors() : VIEW::GeometricObject, VIEW::MultiColorExtension
• getColumn() : TMatrix4x4< T >
• getColumnIndex() : ParameterSection
• getCompareMode() : String
• getComponent() : ForceField
• getComponentNumber() : SmartsParser::SPNode
• getComposite() : VIEW::CompositeMessage, FragmentDistanceCollector
• getCompositeManager() : VIEW::MainControl
• getCompositeName() : VIEW::CompositeMessage
• getComposites() : VIEW::ColorProcessor
• getConformationSet() : GeometricFit, DockResult, DockingAlgorithm
• getConjugate() : TQuaternion< T >
• getConstant() : MutableConstant< DataType >
• getConstants() : PairExpRDFIntegrator, Pair6_12RDFIntegrator
• getContactCircle() : RSEdge
• getContainer() : CompositeIteratorTraits, BaseIterator< Container, DataType, Position, Traits >
• getController() : VIEW::DatasetControl
• getCoordinates() : TRegularData3D< ValueType >, TRegularData2D< ValueType >, TRegularData1D< ValueType >
• getCorrectionParameter() : ShiftedLVMMMinimizer
• getCovalentRadius() : Element
• getCPUTime() : Timer
• getCreationMethods() : Expression
• getCTerminal() : SecondaryStructure, Protein, Chain
• getCurentModel() : PDBInfo
• getCurrent() : Enumerator< Container, SiteIterator, Variant >
• getCurrentModel() : PDBInfo, PDBFile
• getData() : BinaryFileAdaptor< T >, TFFT3D< ComplexTraits >, TFFT2D< ComplexTraits >, TFFT1D< ComplexTraits >, CompositeIteratorTraits, NMRStarFile, Bruker2DFile, Bruker1DFile, TRegularData3D< ValueType >, TRegularData2D< ValueType >, TRegularData1D< ValueType >
• getDataPath() : Path
• getDataset() : VIEW::DatasetController
• getDatasets() : VIEW::DatasetControl, VIEW::DatasetController
• getDefault() : Factory< T >
• getDefaultColor() : VIEW::ColorProcessor
• getDefaultDataPath() : Path
• getDefaultNamingStandard() : FragmentDB
• getDefaultPeak() : Experiment< PeakListType >
• getDefaultValence() : SmartsParser::SPAtom
• getDegree() : PiecewisePolynomial, Composite
• getDensity() : TriangulatedSES, TriangulatedSAS
• getDepth() : TSimpleBox3< T >, TBox3< T >, ResourceEntry, Composite
• getDeterminant() : TMatrix4x4< T >
• getDiagonal() : TMatrix4x4< T >
• getDimension() : TRegularData3D< ValueType >, TRegularData2D< ValueType >, TRegularData1D< ValueType >
• getDirection() : VIEW::LightSource, EnergyMinimizer
• getDistance() : VIEW::AtomDistanceColorProcessor, VIEW::Camera, FragmentDistanceCollector, TVector4< T >, TVector3< T >, TVector2< T >
• getDockDialog() : VIEW::DockingController
• getDockingAlgorithm() : VIEW::DockProgressDialog, DockResult
• getDockingOptions() : DockResult
• getDouble() : NamedProperty
• getEdge() : ReducedSurface, GraphTriangle< Vertex, Edge, Face >, GraphFace< Vertex, Edge, Face >
• getEdges() : SmartsParser, GraphTriangle< Vertex, Edge, Face >, GraphFace< Vertex, Edge, Face >
• getElectronegativity() : Element
• getElectrostaticEnergy() : CharmmNonBonded, AmberNonBonded
• getElement() : PTE_, Atom
• getEnclosingIndices() : TRegularData3D< ValueType >, TRegularData2D< ValueType >, TRegularData1D< ValueType >
• getEnclosingValues() : TRegularData3D< ValueType >, TRegularData2D< ValueType >, TRegularData1D< ValueType >
• getEnergy() : FDPB, EnergyMinimizer, ForceFieldComponent, ForceField, EnergyProcessor
• getEnergyDifferenceBound() : EnergyMinimizer
• getEnergyOutputFrequency() : EnergyMinimizer, MolecularDynamics
• getEnergyToAbort() : MolecularDynamics
• getEnergyUpdateCounter() : EnergyMinimizer
• getEntry() : ResourceEntry
• getEquivalence() : MMFF94AtomTypeEquivalences
• getErrorCode() : FDPB
• getErrorMessage() : FDPB
• getESEnergy() : MMFF94, CharmmFF, AmberFF
• getExpandedText() : VIEW::Label
• getExponent() : MutablePower< Function, DataType >
• getExpression() : Selector
• getExpressionString() : Expression
• getExpressionTree() : Expression
• getEyeDistance() : VIEW::Stage
• getFace() : ReducedSurface, GraphEdge< Vertex, Edge, Face >
• getFamily() : SockInetAddr, SockAddr
• getFDPBSolver() : VIEW::FDPBDialog
• getField() : LineBasedFile, String
• getFieldQuoted() : String
• getFile() : Exception::GeneralException
• getFileAddress() : TCPTransfer
• getFilename() : VIEW::PythonSettings, FragmentDB, AssignRadiusProcessor, ShiftModel, PDBInfo, Parameters, INIFile
• getFileStream() : File
• getFirst() : Division< First, Second, DataType >, Product< First, Second, DataType >, Subtraction< First, Second, DataType >, Addition< First, Second, DataType >
• getFirstAtom() : Bond
• getFirstChild() : Composite
• getFirstEdge() : SmartsParser::SPNode
• getFirstEntry() : Directory
• getFirstIndex() : Substring
• getFirstSPEdge() : SmartsParser::SPEdge
• getFirstSPNode() : SmartsParser::SPEdge
• getFloat() : NamedProperty
• getFlushToDiskFrequency() : SnapShotManager
• getFocalDistance() : VIEW::Stage
• getForce() : Atom
• getForceField() : VIEW::MolecularStructure, EnergyMinimizer, MolecularDynamics, SnapShotManager, ForceFieldComponent
• getForceUpdateCounter() : EnergyMinimizer
• getFormalCharge() : Atom
• getFourierSpaceMax() : TFFT1D< ComplexTraits >
• getFourierSpaceMaxX() : TFFT3D< ComplexTraits >, TFFT2D< ComplexTraits >
• getFourierSpaceMaxY() : TFFT3D< ComplexTraits >, TFFT2D< ComplexTraits >
• getFourierSpaceMaxZ() : TFFT3D< ComplexTraits >
• getFourierSpaceMin() : TFFT1D< ComplexTraits >
• getFourierSpaceMinX() : TFFT3D< ComplexTraits >, TFFT2D< ComplexTraits >
• getFourierSpaceMinY() : TFFT3D< ComplexTraits >, TFFT2D< ComplexTraits >
• getFourierSpaceMinZ() : TFFT3D< ComplexTraits >
• getFourierStepWidth() : TFFT1D< ComplexTraits >
• getFourierStepWidthX() : TFFT3D< ComplexTraits >, TFFT2D< ComplexTraits >
• getFourierStepWidthY() : TFFT3D< ComplexTraits >, TFFT2D< ComplexTraits >
• getFourierStepWidthZ() : TFFT3D< ComplexTraits >
• getFragment() : FragmentDB, Atom
• getFragmentCopy() : FragmentDB
• getFragmentDB() : VIEW::ModularWidget, VIEW::MainControl, ReconstructFragmentProcessor
• getFragmentType() : FragmentDB
• getFullName() : Residue, Atom
• getFunction() : NumericalIntegrator< Function, DataType >, MutablePower< Function, DataType >, CubicFunction< Function, DataType >, SquareFunction< Function, DataType >, Reciprocal< Function, DataType >
• getGeometricObjects() : VIEW::ModelProcessor
• getGradient() : EnergyMinimizer
• getGreen() : VIEW::ColorRGBA
• getGridCoordinates() : TFFT3D< ComplexTraits >, TFFT2D< ComplexTraits >, TFFT1D< ComplexTraits >
• getGroup() : Element
• getHandle() : Object
• getHeight() : TSimpleBox3< T >, TBox3< T >, Composite
• getHeightVector() : TBox3< T >
• getHelpEntryFor() : VIEW::HelpViewer
• getHighlightedRepresentations() : VIEW::GeometricControl
• getHostAddress() : TCPTransfer
• getHue() : VIEW::ColorHSV
• getID() : Residue, Protein, Nucleotide, NucleicAcid, PDBInfo
• getIdentifier() : Embeddable
• getIdentity() : TMatrix4x4< T >
• getImproperTorsionEnergy() : CharmmFF
• getImprovedFlag() : StrangLBFGSMinimizer
• getIndex() : RDFParameter, GraphVertex< Vertex, Edge, Face >, GraphTriangle< Vertex, Edge, Face >, GraphFace< Vertex, Edge, Face >, GraphEdge< Vertex, Edge, Face >, SnapShot, Atom, TContourSurface< T >::Cube
• getIndices() : ClaverieParameter, HashGrid3< Item >
• getInfoColor() : VIEW::Stage
• getInformationVisitor_() : VIEW::MolecularControl
• getINIFile() : VIEW::MainControl
• getINIFileSectionName() : VIEW::PreferencesEntry
• getInitialEnergy() : EnergyMinimizer
• getInitialGradient() : EnergyMinimizer
• getInsertedAtoms() : ReconstructFragmentProcessor
• getInsertionCode() : Residue, Nucleotide
• getInstance_() : Embeddable
• getInt() : NamedProperty
• getInteger() : Options
• getIntensity() : VIEW::LightSource, Peak< PositionType >
• getInterpolatedValue() : TFFT3D< ComplexTraits >, TFFT2D< ComplexTraits >, TFFT1D< ComplexTraits >, TRegularData3D< ValueType >, TRegularData2D< ValueType >, TRegularData1D< ValueType >
• getIntersectionPoint() : RSEdge
• getInterval() : PiecewiseFunction
• getIntervalIndex() : PiecewiseFunction
• getIntervals() : PiecewiseFunction
• getInvalidRecords() : PDBInfo
• getInverse() : TQuaternion< T >
• getKey() : ResourceEntry, ParameterSection
• getKineticEnergy() : MolecularDynamics, SnapShot
• getLastChild() : Composite
• getLastHighLightedMenuEntry() : VIEW::MainControl
• getLastIndex() : Substring
• getLastPosition() : SmartsMatcher::RecStructPool_
• getLength() : VIEW::TwoColoredTube, VIEW::Tube, TVector4< T >, TVector3< T >, TVector2< T >, Bond
• getLevel() : LogStream
• getLightSources() : VIEW::Stage
• getLine() : LineBasedFile, INIFile, Exception::GeneralException
• getLineLevel() : LogStream
• getLineNumber() : LineBasedFile
• getLineText() : LogStream
• getLineTime() : LogStream
• getLoadFactor() : StringHashMap< Value >
• getLockingWidget() : VIEW::MainControl
• getLoggingFilename() : VIEW::MainControl
• getLogicalOperator() : SmartsParser::SPNode, SmartsParser::SPEdge
• getLogin() : TCPTransfer
• getLookAtPosition() : VIEW::Camera
• getLookUpVector() : VIEW::Camera
• getLower() : BoundingBoxProcessor
• getLowerBound() : LineSearch
• getLowerIndex() : TRegularData3D< ValueType >, TRegularData2D< ValueType >, TRegularData1D< ValueType >
• getLowestCommonAncestor() : Composite
• getMainControl() : VIEW::ModularWidget, VIEW::MainControl
• getMajorRadiusOfTorus() : RSEdge
• getMajorRevision() : VersionInfo
• getMassCenter_() : GeometricFit
• getMaxDistanceColor() : VIEW::AtomDistanceColorProcessor
• getMaxGradient() : EnergyMinimizer
• getMaximalNumberOfIterations() : MolecularDynamics
• getMaximalRadius() : ReducedSurface
• getMaximalSimulationTime() : MolecularDynamics
• getMaximumDisplacement() : EnergyMinimizer
• getMaximumNumberOfErrors() : ForceField
• getMaximumUnassignedAtoms() : Templates, AssignBaseProcessor
• getMaxIndex() : TFFT1D< ComplexTraits >
• getMaxIntensity() : PeakList< PT >
• getMaxIterations() : VIEW::MinimizationDialog
• getMaxNumberOfIterations() : EnergyMinimizer
• getMaxNumOfColumns() : ShiftedLVMMMinimizer
• getMaxNumOfStoredVectPairs() : StrangLBFGSMinimizer
• getMaxSameEnergy() : EnergyMinimizer
• getMaxSteps() : LineSearch
• getMaxXIndex() : TFFT3D< ComplexTraits >, TFFT2D< ComplexTraits >
• getMaxYIndex() : TFFT3D< ComplexTraits >, TFFT2D< ComplexTraits >
• getMaxZIndex() : TFFT3D< ComplexTraits >
• getMenuHint() : VIEW::MainControl
• getMesh() : VIEW::MeshBuffer
• getMessage() : Exception::GeneralException
• getMicroSeconds() : PreciseTime
• getMiddleVertex() : VIEW::TwoColoredTube, VIEW::TwoColoredLine
• getMinIntensity() : PeakList< PT >
• getMinorRevision() : VersionInfo
• getModelBuildTime() : VIEW::Representation
• getModelName() : VIEW::ModelInformation
• getModificationTime() : Composite
• getModuleList() : ShiftModel
• getModulus() : EnumeratorIndex
• getMolecularControlSelection() : VIEW::MainControl
• getMolecule() : System, Atom
• getMoleculeCopy() : FragmentDB
• getName() : File, ResidueRotamerSet, SolventDescriptor, ShiftModule, ForceFieldComponent, ForceField, Element, Bond, AtomContainer, Atom, PDBInfo, Options, NamedProperty, Exception::GeneralException
• getNamedProperty() : PropertyManager
• getNamingStandard() : FragmentDB::NormalizeNamesProcessor
• getNamingStandards() : FragmentDB
• getNeedsSSSR() : SmartsParser
• getNegate() : ExpressionTree
• getNeighbours() : SDGenerator
• getNewHandle() : Object
• getNext() : Composite
• getNextContourLine() : TContour< T >
• getNextEntry() : Directory
• getNextFree() : SmartsMatcher::RecStructPool_
• getNextHandle() : Object
• getNextPoint() : TContourLine< T >
• getNodes() : SmartsParser
• getNonbondedEnergy() : MMFF94, CharmmFF, AmberFF
• getNormal() : TrianglePoint, SESVertex, RSFace, TSurface< T >
• getNot() : SmartsParser::SPNode
• getNTerminal() : SecondaryStructure, Protein, Chain
• getNucleicAcid() : Nucleotide
• getNucleotide() : NucleicAcid
• getNullDistanceColor() : VIEW::AtomDistanceColorProcessor
• getNumberDensity() : SolventDescriptor
• getNumberOfAssignments() : AssignRadiusProcessor
• getNumberOfATOMRecords() : PDBInfo
• getNumberOfAtoms() : SnapShot, ForceField, TrajectoryFile, NMRStarFile
• getNumberOfAtomTypes() : SolventDescriptor
• getNumberOfBondsBuilt() : FragmentDB::BuildBondsProcessor, BuildBondsProcessor
• getNumberOfClasses() : PersistenceManager
• getNumberOfColors() : VIEW::ColorMap
• getNumberOfComposites() : VIEW::CompositeManager
• getNumberOfEnergyProcessors() : ComposedEnergyProcessor
• getNumberOfErrors() : AssignRadiusProcessor
• getNumberOfFragments() : FragmentDistanceCollector
• getNumberOfHETATMRecords() : PDBInfo
• getNumberOfImplicitHydrogens() : SmartsParser::SPAtom
• getNumberOfInsertedAtoms() : ReconstructFragmentProcessor
• getNumberOfInverseTransforms() : TFFT3D< ComplexTraits >, TFFT2D< ComplexTraits >, TFFT1D< ComplexTraits >
• getNumberOfIterations() : FDPB, EnergyMinimizer, MolecularDynamics
• getNumberOfKeys() : ParameterSection
• getNumberOfLines() : INIFile, LogStream
• getNumberOfModels() : PDBInfo
• getNumberOfMovableAtoms() : ForceField
• getNumberOfNormals() : TSurface< T >
• getNumberOfRecords() : PDBInfo
• getNumberOfRepresentations() : VIEW::RepresentationManager
• getNumberOfResidueTorsions() : ResidueTorsions
• getNumberOfRotamers() : RotamerLibrary, ResidueRotamerSet
• getNumberOfRotamerSets() : RotamerLibrary
• getNumberOfSections() : INIFile
• getNumberOfSelectedAtoms() : Selector
• getNumberOfSnapShots() : TrajectoryFile
• getNumberOfTorsions() : ResidueRotamerSet
• getNumberOfTriangles() : TSurface< T >
• getNumberOfUnassignedAtoms() : Templates, AssignBaseProcessor
• getNumberOfVariables() : ParameterSection
• getNumberOfVertices() : TSurface< T >
• getObject() : NamedProperty
• getObjectHeader() : XDRPersistenceManager, TextPersistenceManager, PersistenceManager
• getOccupancy() : PDBAtom
• getOmega() : Peptides::AminoAcidDescriptor
• getOpenMode() : File
• getOppositeEdge() : GraphTriangle< Vertex, Edge, Face >
• getOppositeVertex() : GraphTriangle< Vertex, Edge, Face >
• getOptions() : VIEW::GeometricFitDialog
• getOrder() : Bond
• getOrientation() : GeometricFit
• getOrigin() : TRegularData3D< ValueType >, TRegularData2D< ValueType >, TRegularData1D< ValueType >, HashGrid3< Item >
• getOrthogonalProjection() : TVector3< T >
• getParameterFile() : Parameters
• getParameters() : ClaverieParameter, ShiftModule, QuadraticImproperTorsion, QuadraticBondStretch, QuadraticAngleBend, Potential1210, LennardJones, CosineTorsion, CharmmEEF1, ForceField
• getParent() : VIEW::ConnectionObject, Composite
• getPartialCharge() : MMFF94ESParameters
• getPartner() : Bond
• getPartnerSPNode() : SmartsParser::SPEdge
• getPassword() : TCPTransfer
• getPath() : Directory, ResourceEntry
• getPathLength() : Composite
• getPattern() : RegularExpression
• getPDBAtom() : SecondaryStructure, Residue, Protein, Chain
• getPeakList() : Experiment< PeakListType >, CreateSpectrumProcessor, Bruker2DFile
• getPeriod() : Element
• getPeriodicBoundary() : HINFile
• getPerpendicularNormalization() : TVector3< T >
• getPhi() : Peptides::AminoAcidDescriptor
• getPhysSpaceMax() : TFFT1D< ComplexTraits >
• getPhysSpaceMaxX() : TFFT3D< ComplexTraits >, TFFT2D< ComplexTraits >
• getPhysSpaceMaxY() : TFFT3D< ComplexTraits >, TFFT2D< ComplexTraits >
• getPhysSpaceMaxZ() : TFFT3D< ComplexTraits >
• getPhysSpaceMin() : TFFT1D< ComplexTraits >
• getPhysSpaceMinX() : TFFT3D< ComplexTraits >, TFFT2D< ComplexTraits >
• getPhysSpaceMinY() : TFFT3D< ComplexTraits >, TFFT2D< ComplexTraits >
• getPhysSpaceMinZ() : TFFT3D< ComplexTraits >
• getPhysStepWidth() : TFFT1D< ComplexTraits >
• getPhysStepWidthX() : TFFT3D< ComplexTraits >, TFFT2D< ComplexTraits >
• getPhysStepWidthY() : TFFT3D< ComplexTraits >, TFFT2D< ComplexTraits >
• getPhysStepWidthZ() : TFFT3D< ComplexTraits >
• getPoint() : TrianglePoint, TriangleEdge, Triangle, SESVertex, SASVertex, TBox3< T >
• getPort() : VIEW::Server, VIEW::ServerPreferences, TCPTransfer
• getPosition() : VIEW::LightSource, Peak< PositionType >, CompositeIteratorTraits, Atom, Bruker2DFile
• getPotentialEnergy() : MolecularDynamics, SnapShot
• getPredicate() : CompositeIteratorTraits, ExpressionTree, Expression
• getPreferences() : VIEW::MainControl
• getPrefix() : RuleEvaluator
• getPrevious() : Composite
• getProbeRadius() : ReducedSurface
• getProperties() : VIEW::Representation
• getProperTorsionEnergy() : CharmmFF
• getProperty() : SmartsParser::SPAtom, PropertyManager
• getProtein() : SecondaryStructure, Residue, PDBAtom, Chain
• getProteinName() : Peptides::PeptideBuilder
• getProtocol() : TCPTransfer
• getProxy() : VIEW::MainControl
• getProxyPort() : VIEW::MainControl
• getPsi() : Peptides::AminoAcidDescriptor
• getQColor() : VIEW::ColorRGBA
• getRadius() : VIEW::TwoColoredTube, VIEW::Tube, Atom
• getRadius_() : GeometricFit
• getRange() : RadialDistributionFunction, PiecewiseFunction
• getRDF() : RDFSection, RDFParameter, RDFIntegrator
• getRDFIntegrator() : Pair6_12InteractionEnergyProcessor
• getRDFParameter() : Pair6_12InteractionEnergyProcessor
• getReactionFieldEnergy() : FDPB
• getReal() : Options
• getReceivedBytes() : TCPTransfer
• getRecordIndices() : PDBInfo
• getRecordNumber() : PDBFile
• getRecordString() : PDBFile
• getRecordType() : PDBFile
• getRed() : VIEW::ColorRGBA
• getReferenceFragment() : FragmentDB
• getRefresh() : VIEW::MinimizationDialog
• getRelativeIndex() : GraphTriangle< Vertex, Edge, Face >
• getRemotenessIndicator() : PDBAtom
• getRepresentation() : VIEW::DisplayProperties, RadialDistributionFunction
• getRepresentationManager() : VIEW::MainControl
• getRepresentations() : VIEW::RepresentationManager
• getRepresentationsOf() : VIEW::RepresentationManager
• getResidue() : FragmentDB, SecondaryStructure, Protein, PDBAtom, Chain, Atom
• getResidueCopy() : FragmentDB
• getResults() : MMFF94, ForceField, CharmmFF, AmberFF
• getRightVector() : VIEW::Camera, TBox3< T >
• getRingAtoms() : RingFinder
• getRingConnections() : SmartsParser
• getRMSGradient() : ForceField
• getRoot() : VIEW::ConnectionObject, SmartsParser, Composite
• getRotamer() : ResidueRotamerSet
• getRotamerSet() : RotamerLibrary
• getRotationMatrix() : TQuaternion< T >
• getRow() : TMatrix4x4< T >
• getRSEdge() : SESFace, SESEdge
• getRSFace() : SESFace
• getRSVertex() : SESFace
• getSaturation() : VIEW::ColorHSV
• getScores() : DockResult
• getScoring() : ConformationSet
• getScoringName() : DockResult
• getScoringOptions() : VIEW::DockDialog, DockResult
• getScreenPosition_() : VIEW::EditableScene
• getSecond() : Division< First, Second, DataType >, Product< First, Second, DataType >, Subtraction< First, Second, DataType >, Addition< First, Second, DataType >
• getSecondaryStructure() : Residue, Protein, Chain, Atom
• getSecondAtom() : Bond
• getSecondEdge() : SmartsParser::SPNode
• getSeconds() : PreciseTime
• getSecondSPEdge() : SmartsParser::SPEdge
• getSecondSPNode() : SmartsParser::SPEdge
• getSection() : INIFile
• getSectionFirstLine() : INIFile
• getSectionLastLine() : INIFile
• getSectionLength() : INIFile
• getSectionName() : ParameterSection
• getSelectedAtoms() : Selector
• getSelectedDataset() : VIEW::DatasetController
• getSelectedDatasets() : VIEW::DatasetController
• getSelectedModel() : PDBFile
• getSelectedSystem() : VIEW::MainControl
• getSelection() : VIEW::MolecularControl, VIEW::GeometricObjectSelectionMessage, VIEW::GenericSelectionMessage, VIEW::MainControl
• getSelectionSize() : VIEW::DatasetControl
• getSelectionTime() : Composite
• getSender() : VIEW::Message
• getServerStatus() : VIEW::ServerPreferences
• getSettingsFromString() : VIEW::DisplayProperties
• getSetupTime() : ForceField
• getShift() : Bruker2DFile
• getSibling() : Composite
• getSimilarEdge() : GraphTriangle< Vertex, Edge, Face >, GraphFace< Vertex, Edge, Face >
• getSimulationThread() : VIEW::MainControl
• getSize() : SockInetAddr, SockAddr, File, ResourceEntry, StringHashMap< Value >, TRegularData3D< ValueType >, TRegularData2D< ValueType >, TRegularData1D< ValueType >, List< Value >, HashSet< Key >, HashMap< Key, T >, HashGrid3< Item >, HashGridBox3< Item >, BitVector, EnumeratorIndex
• getSizeX() : HashGrid3< Item >
• getSizeY() : HashGrid3< Item >
• getSizeZ() : HashGrid3< Item >
• getSkippedRecords() : PDBInfo
• getSnapShotFrequency() : EnergyMinimizer, MolecularDynamics
• getSnapShotManager() : VIEW::SnapshotVisualisationDialog
• getSolvationEnergy() : CharmmNonBonded, CharmmFF
• getSolventAtomDescriptorList() : SolventDescriptor
• getSolventDensity() : SolventParameter
• getSolventDescription() : SolventParameter
• getSolventDescriptor() : SolventParameter, Pair6_12InteractionEnergyProcessor
• getSolventName() : SolventParameter
• getSpacing() : Spectrum< DataT, PeakT, PositionT >, TRegularData3D< ValueType >, TRegularData2D< ValueType >, TRegularData1D< ValueType >
• getSPAtom() : SmartsParser::SPNode
• getSPBond() : SmartsParser::SPEdge
• getSphere() : SASFace, ReducedSurface
• getSquareDistance() : TVector4< T >, TVector3< T >, TVector2< T >
• getSquareLength() : VIEW::Tube, TVector4< T >, TVector3< T >, TVector2< T >
• getStackPages() : VIEW::PreferencesEntry
• getStage() : VIEW::Renderer, VIEW::SceneMessage
• getStatus() : ResidueChecker
• getStatusCode() : TCPTransfer
• getStickRadius() : VIEW::AddBallAndStickModel
• getStream() : TCPTransfer
• getStretchEnergy() : MMFF94, CharmmFF, AmberFF
• getString() : NamedProperty
• getStyle() : VIEW::MainControlPreferences
• getSubstring() : String
• getSuperAtomContainer() : Molecule, AtomContainer
• getSupportedFileFormats() : VIEW::DatasetController
• getSurface() : TSimpleBox3< T >, TBox3< T >
• getSymbol() : Element
• getSyntaxTree() : ExpressionParser
• getSysPath() : PyInterpreter
• getSystem() : VIEW::FDPBDialog, SnapShotManager, ForceField, Molecule
• getSystem1() : VIEW::DockDialog
• getSystem2() : VIEW::DockDialog
• getSystemTime() : Timer
• getTemperature() : MolecularDynamics, HINFile
• getTemperatureFactor() : PDBAtom
• getText() : VIEW::Label
• getTime() : MolecularDynamics, TimeStamp
• getTimeStep() : MolecularDynamics
• getTorsionEnergy() : MMFF94, CharmmFF, AmberFF
• getTorsionPhi() : Residue
• getTorsionPsi() : Residue
• getTotalCharge() : AssignChargeProcessor
• getTotalEnergy() : MolecularDynamics
• getTrace() : TMatrix4x4< T >
• getTraits() : BaseIterator< Container, DataType, Position, Traits >
• getTrajectoryFile() : SnapShotManager
• getTransformation() : TransformationProcessor
• getTransformationManager() : File
• getTranslation() : TranslationProcessor, GeometricFit
• getTransparency() : VIEW::Representation
• getTriangle() : TriangleEdge, TSurface< T >
• getTripleProduct() : TVector3< T >
• getTwoReferenceAtoms() : ReconstructFragmentProcessor
• getType() : VIEW::DatasetControl, VIEW::AddSurfaceModel, VIEW::LightSource, VIEW::SceneMessage, VIEW::DatasetController, File, SurfaceProcessor, SmartsParser::SPAtom::Property, SESFace, SESEdge, Peptides::AminoAcidDescriptor, AtomTypes, SecondaryStructure, ExpressionTree, Bond, Atom, NamedProperty, MolecularInformation, VersionInfo
• getTypeName() : Templates, AtomTypes, Atom
• getUnassignedAtoms() : Templates, ForceField, AssignBaseProcessor
• getUnit() : TVector4< T >, TVector3< T >, TVector2< T >, HashGrid3< Item >
• getUnscoredConformations() : ConformationSet
• getUnsignedChar() : BitVector
• getUnsignedInt() : BitVector, NamedProperty
• getUnsignedLong() : BitVector
• getUnsignedShort() : BitVector
• getUpdateFrequency() : MMFF94, ForceField, AmberFF
• getUpdateMethod() : ShiftedLVMMMinimizer, ConjugateGradientMinimizer
• getUpdateTime() : ForceField
• getUpper() : BoundingBoxProcessor
• getUserHomeDir() : Directory
• getUserTime() : Timer
• getUseSelection() : ForceField
• getValue() : VIEW::PreferencesEntry::ExtendedPreferencesObject, VIEW::HotkeyTable, VIEW::QColorTable, VIEW::ColorHSV, SmartsParser::SPAtom::Property, NumericalIntegrator< Function, DataType >, ResourceEntry, ParameterSection, INIFile
• getVanDerWaalsRadius() : Element
• getVariantNames() : FragmentDB
• getVdWEnergy() : MMFF94, CharmmFF, AmberFF
• getVdwEnergy() : CharmmNonBonded, AmberNonBonded
• getVector() : Options
• getVelocity() : Atom
• getVersion() : PDBFile, VersionInfo
• getVertex() : VIEW::Vertex, ReducedSurface, GraphTriangle< Vertex, Edge, Face >, GraphEdge< Vertex, Edge, Face >, TSurface< T >
• getVertex1() : VIEW::Vertex2
• getVertex1Address() : VIEW::Vertex2
• getVertex2() : VIEW::Vertex2
• getVertex2Address() : VIEW::Vertex2
• getVertexAddress() : VIEW::Vertex
• getVertices() : VIEW::Vertex2
• getViewPoint() : VIEW::Camera
• getViewVector() : VIEW::Camera
• getVisitedBonds() : RingFinder
• getVolume() : TSimpleBox3< T >, TBox3< T >
• getWidth() : Peak< PositionType >, TSimpleBox3< T >, TBox3< T >
• getWorkingDir() : VIEW::ModularWidget, VIEW::MainControl
• getXTol() : LineSearch
• getZero() : TVector4< T >, TVector3< T >, TVector2< T >, TMatrix4x4< T >
• getZEType() : SmartsParser::SPBond
• GLDisplayList() : VIEW::GLDisplayList
• GLList : VIEW::GLDisplayList
• GlobalExceptionHandler() : Exception::GlobalExceptionHandler
• GLRenderer() : VIEW::GLRenderer
• gotoLine() : LineBasedFile
• grad_diff_ : ShiftedLVMMMinimizer
• Gradient() : Gradient
• GraphEdge() : GraphEdge< Vertex, Edge, Face >
• GraphFace() : GraphFace< Vertex, Edge, Face >
• GraphTriangle() : GraphTriangle< Vertex, Edge, Face >
• GraphVertex() : GraphVertex< Vertex, Edge, Face >
• GRAVITATIONAL_CONSTANT : Constant
• Group : Element

- h -

• h : Constant, TVector4< T >
• h_bond_pairs_ : HBondProcessor
• HaighMallionShiftProcessor() : HaighMallionShiftProcessor
• handle() : VIEW::DatasetController
• HARMONIC : FDPB::DielectricSmoothing
• has() : VIEW::RepresentationManager, VIEW::CompositeManager, Directory, GraphVertex< Vertex, Edge, Face >, GraphTriangle< Vertex, Edge, Face >, GraphFace< Vertex, Edge, Face >, FragmentDB, Templates, TSphere3< T >, TSimpleBox3< T >, TPlane3< T >, TLine3< T >, TCircle3< T >, ParameterSection, LineBasedFile, StringHashMap< Value >, String, HashSet< Key >, HashMap< Key, T >, HashGridBox3< Item >
• has_torsion_phi_ : ResidueRotamerSet
• has_torsion_psi_ : ResidueRotamerSet
• hasAncestor() : Composite
• hasBond() : Atom
• hasChild() : Composite
• hasComponentGrouping() : SmartsParser
• hasDataset() : VIEW::DatasetController
• hasDisplayListFor() : VIEW::GLRenderer
• hasEdges() : GraphVertex< Vertex, Edge, Face >
• hasEntry() : INIFile
• hasFaces() : GraphVertex< Vertex, Edge, Face >
• hasFormat() : PDBFile
• hasHelpFor() : VIEW::HelpViewer
• HashGrid3() : HashGrid3< Item >
• HashGridBox3() : HashGridBox3< Item >
• HashMap() : HashMap< Key, T >
• HashSet() : HashSet< Key >
• hasInitializedParameters() : MMFF94, CharmmFF, AmberFF
• hasItem() : VIEW::DatasetController
• hasNextSibling() : Composite
• hasPages() : VIEW::Preferences
• hasParameters() : RDFParameter, ClaverieParameter, QuadraticImproperTorsion, QuadraticBondStretch, QuadraticAngleBend, Potential1210, LennardJones, CosineTorsion, CharmmEEF1
• hasParent() : Composite
• hasPeriodicBoundary() : HINFile
• hasPrefix() : String
• hasPreviousSibling() : Composite
• hasProperty() : SmartsParser::SPAtom, PropertyManager
• hasRDF() : RDFParameter
• hasRecursiveEdge() : SmartsParser
• hasRoot() : VIEW::CompositeManager
• hasRotamers() : RotamerLibrary
• hasSection() : INIFile
• hasSibling() : Composite
• hasSingularEdges() : SESFace
• hasStage() : VIEW::Renderer
• hasSubstring() : String
• hasSuffix() : String
• hasTorsion() : ResidueTorsions
• hasTorsionPhi() : Residue
• hasTorsionPsi() : Residue
• hasType() : AtomTypes
• hasVariable() : ParameterSection
• HBondModelProcessor() : VIEW::HBondModelProcessor
• HBondShiftProcessor() : HBondShiftProcessor
• HEADER : INIFile
• header_ : JCAMPFile
• HeaderMap : JCAMPFile
• HELP : VIEW::MainControl
• hess_factor_ : ShiftedLVMMMinimizer
• hessify() : TPlane3< T >
• HEXADECIMAL_INTEGER : RegularExpression
• HINFile() : HINFile
• host() : StringHashMap< Value >, List< Value >, HashSet< Key >, HashMap< Key, T >, HashGridBox3< Item >, Composite
• hundredBackwardClicked() : VIEW::SnapshotVisualisationDialog
• hundredForwardClicked() : VIEW::SnapshotVisualisationDialog
• HydrogenBond() : HydrogenBond
• HydrophobicVdWSurface() : HydrophobicVdWSurface

- i -

• i : TQuaternion< T >
• icosaeder() : TriangulatedSphere
• id_ : PDBInfo
• IDENTIFIER : RegularExpression
• IGNORE_SECTION_NAME : CreateSpectrumProcessor
• IGNORE_XPLOR_PSEUDO_ATOMS : PDBFile::Default, PDBFile::Option
• ignore_xplor_pseudo_atoms_ : PDBFile
• importModule() : PyInterpreter
• IMPROVED : StrangLBFGSMinimizer::Option
• improved_ : StrangLBFGSMinimizer
• indent() : TextPersistenceManager
• index_ : VIEW::DockResultDialog::Compare_
• index_of_free_vect_ : StrangLBFGSMinimizer
• IndexType : TRegularData1D< ValueType >
• info : LogStream, PDBFile
• INFORMATION_LEVEL : LogStream
• INIFile() : INIFile
• init() : VIEW::VRMLRenderer, VIEW::Renderer, VIEW::POVRenderer, VIEW::GLRenderer, FragmentDB, ShiftModule, RandomCoilShiftProcessor, JohnsonBoveyShiftProcessor, HBondShiftProcessor, HaighMallionShiftProcessor, EFShiftProcessor, CreateSpectrumProcessor, AnisotropyShiftProcessor, ForceFieldParameters, TRRFile, Parameters, DCDFile
• initFFTGrid_() : GeometricFit
• initGL() : VIEW::MeshBuffer
• initial_atoms_ : StrangLBFGSMinimizer, ShiftedLVMMMinimizer
• INITIAL_CAPACITY : HashSet< Key >, HashMap< Key, T >
• initial_energy_ : EnergyMinimizer
• initial_grad_ : EnergyMinimizer
• INITIAL_NUMBER_OF_BUCKETS : HashSet< Key >, HashMap< Key, T >
• initialize() : VIEW::MeshBuffer, PyInterpreter
• initializeGL() : VIEW::Scene
• initializeInputStream() : XDRPersistenceManager, PersistenceManager
• initializeOutputStream() : XDRPersistenceManager, PersistenceManager
• initializePreferencesTab() : VIEW::Scene, VIEW::PyWidget, VIEW::EditableScene, VIEW::Server, VIEW::ModularWidget, VIEW::DisplayProperties
• initializeWidget() : VIEW::TestFramework, VIEW::Scene, VIEW::PyWidget, VIEW::MolecularStructure, VIEW::MolecularControl, VIEW::LogView, VIEW::HelpViewer, VIEW::GeometricControl, VIEW::GenericControl, VIEW::FileObserver, VIEW::EditFunctions, VIEW::EditableScene, VIEW::DockWidget, VIEW::DockingController, VIEW::DatasetControl, VIEW::Server, VIEW::ModularWidget, VIEW::PubChemDialog, VIEW::OpenBruker2DFile, VIEW::OpenBruker1DFile, VIEW::MolecularFileDialog, VIEW::LabelDialog, VIEW::DockDialog, VIEW::DisplayProperties
• initPersistenceManager() : ObjectCreator, MoleculeObjectCreator
• initPopupMenu() : VIEW::MainControl
• initRead_() : HINFile, GenericMolFile, GAMESSLogFile, GAMESSDatFile
• initTable() : ParsedFunction< arg >
• initWrite_() : GenericMolFile
• InRingPredicate() : InRingPredicate
• insert() : VIEW::RepresentationManager, VIEW::MainControl, VIEW::CompositeManager, TriangulatedSurface, ReducedSurface, GraphVertex< Vertex, Edge, Face >, GraphFace< Vertex, Edge, Face >, System, SecondaryStructure, Residue, Nucleotide, Molecule, Chain, AtomContainer, ResourceEntry, StringHashMap< Value >, HashSet< Key >, HashMap< Key, T >, HashGrid3< Item >, HashGridBox3< Item >, Client, LogStream
• insert_() : VIEW::EditableScene
• insertAfter() : System, SecondaryStructure, Residue, Nucleotide, Molecule, Chain, AtomContainer, Composite
• insertAtom_() : VIEW::AtomBondModelBaseProcessor
• insertBefore() : System, SecondaryStructure, Residue, Nucleotide, Molecule, Chain, AtomContainer, Composite
• insertChild() : ResourceEntry
• insertComponent() : ForceField
• insertDeleteEntry() : VIEW::MainControl
• insertEntry() : VIEW::Preferences
• insertLine() : INIFile
• insertMenuEntry() : VIEW::MainControl
• insertNotification() : LogStream
• insertParent() : Composite
• insertPopupMenuSeparator() : VIEW::MainControl
• insertSibling() : ResourceEntry
• insertValue() : INIFile
• instr() : String
• INT : NamedProperty
• INTEGER : RegularExpression
• integrate() : PairExpRDFIntegrator, Pair6_12RDFIntegrator, RombergIntegrator< Function, DataType >, NumericalIntegrator< Function, DataType >
• integrateToInf() : PairExpRDFIntegrator, Pair6_12RDFIntegrator
• IntegrationMethod : Pair6_12RDFIntegrator
• intensityChanged() : VIEW::LightSettings
• internal_ : SmartsParser::SPNode, SmartsParser::SPEdge
• interpol12() : TContourLine< T >
• interpolateColor() : VIEW::InterpolateColorProcessor
• interpretRecord() : PDBFile
• inv_norm : Gradient
• INVALID : ExpressionTree
• invalid_records_ : PDBInfo
• invalidate() : Gradient, CompositeIteratorTraits, BaseIterator< Container, DataType, Position, Traits >
• invert() : TMatrix4x4< T >
• ION_RADIUS : FDPB::Default, FDPB::Option
• IONIC_STRENGTH : FDPB::Default, FDPB::Option
• IOSockStream() : IOSockStream
• ir_size : TRRFile::TRRHeader
• is3Prime() : Nucleotide
• is5Prime() : Nucleotide
• is_not_ : SmartsParser::SPNode, SmartsParser::SPEdge
• is_orthogonal_ : TRegularData3D< ValueType >
• is_proline_ : Peptides::PeptideBuilder
• isAccessible() : File
• isAlnum() : String
• isAlpha() : String
• isAminoAcid() : Residue
• isAncestorOf() : Composite
• isAnyBit() : BitVector
• isAutoDeletable() : AutoDeletable
• isBackboneDependent() : RotamerLibrary
• isBallAndStickModel() : VIEW::AddBallAndStickModel
• isBeeingRendered() : VIEW::RepresentationManager
• isBegin() : CompositeIteratorTraits, ConstForwardIterator< Container, DataType, Position, Traits >, ConstBidirectionalIterator< Container, DataType, Position, Traits >
• isBondOf() : Bond
• isBool() : Options
• isBound() : Bond, Atom, Substring
• isBoundTo() : Atom
• isBracketed() : LineSearch
• isBusy() : VIEW::MeshBuffer
• isCanonized() : File
• isChildOf() : Composite
• isClosed() : File
• isCompileAndExecuteMode() : VIEW::GLDisplayList
• isCompileMode() : VIEW::GLDisplayList
• isConnectionObjectRegistered() : VIEW::ConnectionObject
• isConverged() : EnergyMinimizer
• isCTerminal() : Residue
• isCurrent() : Directory
• isDefaultVertex1Address() : VIEW::Vertex2
• isDefaultVertex2Address() : VIEW::Vertex2
• isDefaultVertexAddress() : VIEW::Vertex
• isDefaultVertexAddresses() : VIEW::Vertex2
• isDeletable() : VIEW::Message
• isDescendantOf() : Composite
• isDiagonal() : TMatrix4x4< T >
• isDigit() : String
• isEmpty() : Directory, TSphere3< T >, StringHashMap< Value >, Substring, String, RegularExpression, List< Value >, HashSet< Key >, HashMap< Key, T >, HashGrid3< Item >, HashGridBox3< Item >, Composite
• isEnabled() : ResidueChecker, PeriodicBoundary
• isEnd() : CompositeIteratorTraits, ConstForwardIterator< Container, DataType, Position, Traits >, ConstBidirectionalIterator< Container, DataType, Position, Traits >
• isEqual() : TMatrix4x4< T >, Comparator< T >
• isEquivalent() : TAngle< T >
• isEveryBit() : BitVector
• isExecutable() : File
• isExtensionSupported() : VIEW::GLRenderer
• isFirstChild() : Composite
• isFirstChildOf() : Composite
• isFloat() : String
• isFree() : SESFace, SESEdge, SASEdge, RSEdge
• isGeminal() : Atom
• isGreater() : Comparator< T >
• isGreaterOrEqual() : Comparator< T >
• isHeteroAtom_() : PDBFile
• isHomomorph() : Composite
• isIdentity() : TMatrix4x4< T >
• isImportant() : VIEW::LogEvent
• isInFourierSpace() : TFFT3D< ComplexTraits >, TFFT2D< ComplexTraits >, TFFT1D< ComplexTraits >
• isInitialized() : PyInterpreter
• isInRange() : RadialDistributionFunction, PiecewiseFunction
• isInRing() : RingAnalyser
• isInside() : TRegularData3D< ValueType >, TRegularData2D< ValueType >, TRegularData1D< ValueType >
• isInteger() : Options
• isInterBond() : Bond
• isInterBondOf() : Bond
• isInterior() : Composite
• isInternal() : SmartsParser::SPNode, SmartsParser::SPEdge
• isIntersecting() : TSimpleBox3< T >
• isIntraBond() : Bond
• isIntraBondOf() : Bond
• isLastChild() : Composite
• isLastChildOf() : Composite
• isLess() : Comparator< T >
• isLessOrEqual() : Comparator< T >
• isLowerTriangular() : TMatrix4x4< T >
• isNeighbouredTo() : SESFace
• isNewerThan() : TimeStamp
• isNextSiblingOf() : Composite
• isNot() : SmartsParser::SPEdge, SmartsParser::SPBond
• isNotEqual() : Comparator< T >
• isNTerminal() : Residue
• ISockStream() : ISockStream
• isOlderThan() : TimeStamp
• isOpen() : File
• isOrthogonalTo() : TVector4< T >, TVector3< T >, TVector2< T >
• isParentOf() : Composite
• isPreviousSiblingOf() : Composite
• isRBegin() : CompositeIteratorTraits, ConstBidirectionalIterator< Container, DataType, Position, Traits >
• isReadable() : File
• isReal() : Options
• isRecursive() : SmartsParser, SmartsParser::SPNode
• isRedock() : VIEW::GeometricFitDialog, VIEW::DockDialog
• isRegistered() : ShiftModel
• isRegular() : TMatrix4x4< T >
• isRelatedWith() : Composite
• isRelativeToCamera() : VIEW::LightSource
• isREnd() : CompositeIteratorTraits, ConstBidirectionalIterator< Container, DataType, Position, Traits >
• isRoot() : Composite
• isRootOf() : Composite
• isRunning() : Timer
• isSelected() : VIEW::GeometricObjectSelectionMessage, Selectable
• isSelectionEnabled() : ResidueChecker, ForceField
• isSet() : Options
• isSiblingOf() : Composite
• isSingular() : RSFace, RSEdge, TMatrix4x4< T >, CompositeIteratorTraits, BaseIterator< Container, DataType, Position, Traits >
• isSpace() : String
• isStickModel() : VIEW::AddBallAndStickModel
• isSubAtomContainerOf() : Molecule, AtomContainer
• isSuperAtomContainerOf() : AtomContainer
• isSurfaceModel() : VIEW::ModelInformation
• isSymmetric() : TMatrix4x4< T >
• isTerminal() : Residue, Nucleotide
• isUnknown() : Element
• isUpperTriangular() : TMatrix4x4< T >
• isValid() : VIEW::Scene, VIEW::PyWidget, VIEW::GLDisplayList, VIEW::TwoColoredTube, VIEW::TwoColoredLine, VIEW::Tube, VIEW::Sphere, VIEW::SimpleBox, VIEW::Point, VIEW::MultiLine, VIEW::Mesh, VIEW::Line, VIEW::Label, VIEW::Disc, VIEW::Box, VIEW::ModelProcessor, VIEW::Server, VIEW::Representation, VIEW::GeometricObject, VIEW::ConnectionObject, VIEW::Vertex2, VIEW::Vertex, Timer, File, Directory, ResidueRotamerSet, RDFIntegrator, RadialDistributionFunction, SolventDescriptor, ShiftModule, ShiftModel, AssignShiftProcessor, ForceFieldParameters, EnergyMinimizer, MolecularDynamics, SnapShotManager, SnapShot, Gradient, ForceField, TVector4< T >, TVector3< T >, TVector2< T >, TSphere3< T >, TSimpleBox3< T >, TPlane3< T >, PiecewiseFunction, TMatrix4x4< T >, TLine3< T >, TCircle3< T >, TBox3< T >, TAngle< T >, SecondaryStructure, Residue, Protein, Nucleotide, NucleicAcid, CompositeIteratorTraits, Bond, AtomContainer, Atom, ResourceFile, ParameterSection, Parameters, INIFile, EnergyProcessor, Substring, RegularExpression, HashSet< Key >, HashMap< Key, T >, HashGrid3< Item >, BitVector, PropertyManager, Composite, Client, BaseIterator< Container, DataType, Position, Traits >
• isVector() : Options
• isVicinal() : Atom
• isWhitespace() : String
• isWritable() : File
• isZero() : TVector3< T >, TVector2< T >
• ItemList : VIEW::GenericControl
• Iterator : PyIndexList, PyDatasetVector, PyCompositeList, PyColorRGBAVector, Spectrum< DataT, PeakT, PositionT >, PeakList< PT >, Gradient, AtomVector, ExpressionParser::SyntaxTree, StringHashMap< Value >, TRegularData3D< ValueType >, TRegularData2D< ValueType >, TRegularData1D< ValueType >, List< Value >, Enumerator< Container, SiteIterator, Variant >

- j -

• j : TQuaternion< T >
• JCAMPFile() : JCAMPFile
• JohnsonBoveyShiftProcessor() : JohnsonBoveyShiftProcessor
• join() : TriangulatedSurface, GraphVertex< Vertex, Edge, Face >, TSimpleBox3< T >
• JOULE_PER_CAL : Constant

- k -

• k : Constant, TQuaternion< T >
• kappa_grid : FDPB
• KernelPredicateType : Composite
• keyPressEvent() : VIEW::Scene, VIEW::EditableScene
• KeyValuePair : JCAMPFile

- l -

• Label() : VIEW::Label
• LabelDialog() : VIEW::LabelDialog
• LabelModel() : VIEW::LabelModel
• lambda : TRRFile::TRRHeader
• last_restart_iter_ : ConjugateGradientMinimizer
• lastSnapshotClicked() : VIEW::SnapshotVisualisationDialog
• LEAF : ExpressionTree
• left() : String
• LennardJones() : LennardJones
• level() : LogStream
• lightSelected() : VIEW::LightSettings
• LightSettings() : VIEW::LightSettings
• LightSource() : VIEW::LightSource
• lin : MMFF94AtomType
• Line() : VIEW::Line
• line_ : MOL2File, LineBasedFile
• line_number_ : LineBasedFile
• line_search_ : StrangLBFGSMinimizer, SteepestDescentMinimizer, ShiftedLVMMMinimizer, ConjugateGradientMinimizer
• LinearBaseFunction() : LinearBaseFunction
• LineBasedFile() : LineBasedFile
• LineIterator : INIFile
• LineSearch() : LineSearch
• Lipophilic() : Lipophilic
• List() : List< Value >
• LJ_FILENAME : Pair6_12InteractionEnergyProcessor::Option
• loadBALLViewProjectFile() : VIEW::MainControl
• LOCALITY : ElectrostaticPotentialCalculator::Default, ElectrostaticPotentialCalculator::Option
• lockComposites() : VIEW::ModularWidget
• lockCompositesFor() : VIEW::MainControl
• log_op_ : SmartsParser::SPNode, SmartsParser::SPEdge
• LogicalOperator : SmartsParser
• logNotify() : VIEW::LogView
• LogStream() : LogStream
• LogStreamBuf() : LogStreamBuf
• LogStreamLevel : LogStream
• LogView() : VIEW::LogView
• LOWER : FDPB::Option
• LOWERCASE : RegularExpression

- m -

• m11 : TMatrix4x4< T >
• m12 : TMatrix4x4< T >
• m13 : TMatrix4x4< T >
• m14 : TMatrix4x4< T >
• m21 : TMatrix4x4< T >
• m22 : TMatrix4x4< T >
• m23 : TMatrix4x4< T >
• m24 : TMatrix4x4< T >
• m31 : TMatrix4x4< T >
• m32 : TMatrix4x4< T >
• m33 : TMatrix4x4< T >
• m34 : TMatrix4x4< T >
• m41 : TMatrix4x4< T >
• m42 : TMatrix4x4< T >
• m43 : TMatrix4x4< T >
• m44 : TMatrix4x4< T >
• M_PER_FOOT : Constant
• MACRO : VIEW::MainControl
• MAGIC : TRRFile::TRRHeader
• MainControl() : VIEW::MainControl
• MainControlPreferences() : VIEW::MainControlPreferences
• map() : VIEW::PyWidget, VIEW::ColorMap
• mapFragments() : StructureMapper
• mapInverse_() : TRegularData3D< ValueType >
• mapped_atoms : SmartsMatcher::RecStruct_, SmartsMatcher::RecStructCore_
• mapping_ : TRegularData3D< ValueType >
• mapProteins() : VIEW::MolecularStructure, StructureMapper
• mapThreeVectors() : ReconstructFragmentProcessor
• mapToCartesian_() : TRegularData3D< ValueType >
• mapViewplaneToScreen_() : VIEW::Scene
• mass_factor_ : CanonicalMD
• match() : RegularExpression
• matched_atoms : SmartsMatcher::RecStruct_, SmartsMatcher::RecStructCore_
• matchName() : FragmentDB::NormalizeNamesProcessor
• matchPoints() : StructureMapper
• MaterialSettings() : VIEW::MaterialSettings
• matrix_ : RingPerceptionProcessor
• max_bond_lengths_ : BuildBondsProcessor
• MAX_CRITERION : FDPB::Default, FDPB::Option
• MAX_ENTRY_LENGTH : Options
• MAX_FILENAME_LENGTH : FileSystem
• MAX_GRADIENT : EnergyMinimizer::Option
• max_gradient_ : EnergyMinimizer
• MAX_ITERATIONS : FDPB::Default, FDPB::Option
• max_length_ : BuildBondsProcessor
• MAX_LINE_LENGTH : INIFile
• max_num_of_vect_pairs_ : StrangLBFGSMinimizer
• MAX_NUMBER_OF_BONDS : Atom
• max_number_of_cols_ : ShiftedLVMMMinimizer
• MAX_PATH_LENGTH : FileSystem, Directory
• MAX_SAME_ENERGY : EnergyMinimizer::Option
• max_same_energy_ : EnergyMinimizer
• MAXIMAL_NUMBER_OF_ITERATIONS : EnergyMinimizer::Option, MolecularDynamics::Option
• maximal_number_of_iterations_ : EnergyMinimizer
• MAXIMAL_SIMULATION_TIME : MolecularDynamics::Option
• maximum_bond_length_ : HBondShiftProcessor
• MAXIMUM_DISPLACEMENT : EnergyMinimizer::Option
• maximum_displacement_ : EnergyMinimizer
• MDSimulation() : VIEW::MolecularStructure
• MeanAtomInformationContent() : MeanAtomInformationContent
• menuItemHighlighted() : VIEW::MainControl
• mergeChildrenOf() : ResourceEntry
• Mesh() : VIEW::Mesh
• Message() : VIEW::Message
• METHOD : Pair6_12RDFIntegrator::Option
• MicroCanonicalMD() : MicroCanonicalMD
• min_bond_lengths_ : BuildBondsProcessor
• MinimizationDialog() : VIEW::MinimizationDialog
• minimize() : StrangLBFGSMinimizer, SteepestDescentMinimizer, ShiftedLVMMMinimizer, LineSearch, EnergyMinimizer, ConjugateGradientMinimizer
• minimum_bond_length_ : HBondShiftProcessor
• mltb : MMFF94AtomType
• MM_PER_INCH : Constant
• MMFF94() : MMFF94
• MMFF94BendParameters() : MMFF94BendParameters
• MMFF94ConfigurationDialog() : VIEW::MMFF94ConfigurationDialog
• MMFF94ESParameters() : MMFF94ESParameters
• MMFF94NonBonded() : MMFF94NonBonded
• MMFF94OutOfPlaneBend() : MMFF94OutOfPlaneBend
• MMFF94ParametersBase() : MMFF94ParametersBase
• MMFF94PlaneParameters() : MMFF94PlaneParameters
• MMFF94StretchBend() : MMFF94StretchBend
• MMFF94StretchBendParameters() : MMFF94StretchBendParameters
• MMFF94StretchParameters() : MMFF94StretchParameters
• MMFF94Torsion() : MMFF94Torsion
• MMFF94TorsionParameters() : MMFF94TorsionParameters
• MMFF94VDWParameters() : MMFF94VDWParameters
• MODE_APP : File
• MODE_ATE : File
• MODE_BINARY : File
• MODE_IN : File
• MODE_OUT : File
• MODE_TRUNC : File
• ModeAction : VIEW::Scene
• model_read_ : PDBInfo
• ModelInformation() : VIEW::ModelInformation
• modelMustBeRebuild() : VIEW::ModelInformation
• modelMuteableByDisplayProperties() : VIEW::ModelInformation
• ModelSettingsDialog() : VIEW::ModelSettingsDialog
• ModeType : VIEW::Scene
• modifyRepresentationMode() : VIEW::DisplayProperties
• ModularWidget() : VIEW::ModularWidget
• MODULE_LIST_SECTION : ShiftModel
• ModuleList : ShiftModel
• MOL : Constant
• MOL2File() : MOL2File
• MolecularControl() : VIEW::MolecularControl
• MolecularDynamics() : MolecularDynamics
• MolecularFileDialog() : VIEW::MolecularFileDialog
• MolecularInformation() : MolecularInformation
• MOLECULARMECHANICS : VIEW::MainControl
• MolecularStructure() : VIEW::MolecularStructure
• MolecularTaskMessageType : VIEW::MolecularTaskMessage
• MolecularWeight() : MolecularWeight
• Molecule() : Molecule
• MoleculeAssembler() : MoleculeAssembler
• MoleculeObjectCreator() : MoleculeObjectCreator
• MOLFile() : MOLFile
• mouseMoveEvent() : VIEW::Scene, VIEW::EditableScene
• mousePressEvent() : VIEW::Scene, VIEW::EditableScene
• mouseReleaseEvent() : VIEW::Scene, VIEW::EditableScene
• movable_atoms_chi1_ : ResidueRotamerSet
• move() : VIEW::Scene, File
• MOVE__MODE : VIEW::Scene
• moveComposites() : VIEW::Scene
• moveItems() : VIEW::MolecularControl
• moveTo() : File, AtomVector
• MultiColorExtension() : VIEW::MultiColorExtension
• MultiLine() : VIEW::MultiLine
• MutableConstant() : MutableConstant< DataType >
• MutablePower() : MutablePower< Function, DataType >
• MutatorFunction : Enumerator< Container, SiteIterator, Variant >

- n -

• n : TPlane3< T >, TCircle3< T >
• NA : Constant
• Name : Element, VIEW::GLRenderer
• name_ : ResidueRotamerSet, DockResult::Scoring_, PDBInfo
• NamedProperty() : NamedProperty
• NameMap : FragmentDB
• needs_SSSR_ : SmartsParser
• needsUpdate() : VIEW::Representation
• negate : Gradient, TVector3< T >, TVector2< T >, TAngle< T >, ExpressionParser::SyntaxTree
• NegativePolarVdWSurface() : NegativePolarVdWSurface
• NegativeVdWSurface() : NegativeVdWSurface
• NetworkPreferences() : VIEW::NetworkPreferences
• NEUTRON_MASS : Constant
• NEW_COMPOSITE : VIEW::CompositeMessage
• NEW_MOLECULE : VIEW::CompositeMessage
• newHandler() : Exception::GlobalExceptionHandler
• newPrompt_() : VIEW::PyWidget
• NMRStarFile() : NMRStarFile
• NO_VARIANT_EXTENSIONS : Residue
• nodes_ : SmartsParser
• NON_ALPHA : RegularExpression
• NON_ALPHANUMERIC : RegularExpression
• NON_NUMERIC : RegularExpression
• NON_WHITESPACE : RegularExpression
• NONBONDED_CUTOFF : MMFF94::Default, MMFF94::Option, CharmmFF::Default, CharmmFF::Option, AmberFF::Default, AmberFF::Option
• NONE : FDPB::DielectricSmoothing, NamedProperty
• NonpolarSolvation() : NonpolarSolvation
• norm : Gradient
• Normal : TSurface< T >
• normal : TSurface< T >
• normalize() : SESFace, Gradient, TVector4< T >, TVector3< T >, TVector2< T >, TPlane3< T >, TLine3< T >, TAngle< T >
• normalize_names : FragmentDB
• NormalizeNamesProcessor() : FragmentDB::NormalizeNamesProcessor
• not_ : SmartsParser::SPBond
• not_properties_ : SmartsParser::SPAtom
• notify_() : VIEW::ConnectionObject
• now() : PreciseTime
• nre : TRRFile::TRRHeader
• NucleicAcid() : NucleicAcid
• Nucleotide() : Nucleotide
• num_bonds_ : BuildBondsProcessor
• NUM_OF_COLUMNS : ShiftedLVMMMinimizer::Option
• NUM_OF_STORED_VECT_PAIRS : StrangLBFGSMinimizer::Option
• number_of_atom_records_ : PDBInfo
• number_of_atoms : SolventAtomDescriptor, TRRFile::TRRHeader
• number_of_atoms_ : StrangLBFGSMinimizer, ShiftedLVMMMinimizer, ConjugateGradientMinimizer
• NUMBER_OF_BOND_ORDERS : Bond
• NUMBER_OF_COMMANDS : Client
• NUMBER_OF_ERRORS : FDPB
• number_of_hetatm_records_ : PDBInfo
• NUMBER_OF_ITERATION : EnergyMinimizer::Option, MolecularDynamics::Option
• number_of_iterations_ : EnergyMinimizer
• number_of_models_ : PDBInfo
• number_of_records_ : PDBInfo
• number_of_torsions_ : ResidueRotamerSet
• NumberOfAromaticAtoms() : NumberOfAromaticAtoms
• NumberOfAromaticBonds() : NumberOfAromaticBonds
• numberOfAtoms() : ReducedSurface
• NumberOfAtoms() : NumberOfAtoms
• NumberOfBonds() : NumberOfBonds
• NumberOfBondsPredicate() : NumberOfBondsPredicate
• NumberOfBoron() : NumberOfBoron
• NumberOfBromine() : NumberOfBromine
• NumberOfCarbon() : NumberOfCarbon
• NumberOfChlorine() : NumberOfChlorine
• NumberOfDoubleBonds() : NumberOfDoubleBonds
• numberOfEdges() : TriangulatedSurface, ReducedSurface, GraphVertex< Vertex, Edge, Face >, GraphFace< Vertex, Edge, Face >
• numberOfFaces() : ReducedSurface, GraphVertex< Vertex, Edge, Face >
• NumberOfFlourine() : NumberOfFlourine
• NumberOfHeavyAtoms() : NumberOfHeavyAtoms
• NumberOfHeavyBonds() : NumberOfHeavyBonds
• NumberOfHydrogen() : NumberOfHydrogen
• NumberOfHydrogenBondAcceptors() : NumberOfHydrogenBondAcceptors
• NumberOfHydrogenBondDonors() : NumberOfHydrogenBondDonors
• NumberOfHydrophobicAtoms() : NumberOfHydrophobicAtoms
• NumberOfIodine() : NumberOfIodine
• NumberOfNitrogen() : NumberOfNitrogen
• NumberOfOxygen() : NumberOfOxygen
• NumberOfPhosphorus() : NumberOfPhosphorus
• numberOfPoints() : TriangulatedSurface
• NumberOfRotatableBonds() : NumberOfRotatableBonds
• NumberOfRotatableSingleBonds() : NumberOfRotatableSingleBonds
• numberOfScorings() : DockResult
• NumberOfSingleBonds() : NumberOfSingleBonds
• NumberOfSulfur() : NumberOfSulfur
• numberOfTriangles() : TriangulatedSurface
• NumberOfTripleBonds() : NumberOfTripleBonds
• numberOfVertices() : ReducedSurface, GraphFace< Vertex, Edge, Face >
• NumericalIntegrator() : NumericalIntegrator< Function, DataType >

- o -

• Object() : Object
• OBJECT : NamedProperty
• OBJECT_HEADER : XDRPersistenceManager
• OBJECT_TRAILER : XDRPersistenceManager
• ObjectCreator() : ObjectCreator
• OFFSET : FDPB::Option
• okPressed() : VIEW::DockDialog
• old_energy_ : EnergyMinimizer
• old_grad_ : EnergyMinimizer
• old_gtg_ : ConjugateGradientMinimizer
• oneBackwardClicked() : VIEW::SnapshotVisualisationDialog
• oneForwardClicked() : VIEW::SnapshotVisualisationDialog
• onNotify() : VIEW::Scene, VIEW::RegularData2DWidget, VIEW::RegularData1DWidget, VIEW::MolecularStructure, VIEW::MolecularControl, VIEW::HelpViewer, VIEW::GeometricControl, VIEW::GenericControl, VIEW::EditableScene, VIEW::DockingController, VIEW::DatasetControl, VIEW::MainControl, VIEW::ConnectionObject, VIEW::MolecularFileDialog, VIEW::ModifyRepresentationDialog, VIEW::LabelDialog, VIEW::DisplayProperties, NotificationTarget< NotificationSource >
• open() : VIEW::DatasetController, File, DSN6File, DCDFile
• OpenBruker1DFile() : VIEW::OpenBruker1DFile
• OpenBruker2DFile() : VIEW::OpenBruker2DFile
• openFile() : VIEW::TestFramework, VIEW::PyWidget, VIEW::DatasetControl, VIEW::ModularWidget, VIEW::MainControl, VIEW::OpenBruker2DFile, VIEW::OpenBruker1DFile, VIEW::MolecularFileDialog
• openItems() : VIEW::NewSelectionMessage
• OpenMode : File
• openMolecularFile() : VIEW::MolecularFileDialog
• operator &() : HashSet< Key >, BitVector
• operator &=() : HashSet< Key >, BitVector
• operator *() : Gradient, TVector4< T >, TVector3< T >, TVector2< T >, TMatrix4x4< T >, ForwardIterator< Container, DataType, Position, Traits >, BidirectionalIterator< Container, DataType, Position, Traits >, BaseIterator< Container, DataType, Position, Traits >
• operator *=() : TrianglePoint, TriangleEdge, Triangle, SESVertex, SESFace, SESEdge, SASVertex, SASFace, SASEdge, RSVertex, RSFace, RSEdge, GraphVertex< Vertex, Edge, Face >, GraphTriangle< Vertex, Edge, Face >, GraphFace< Vertex, Edge, Face >, GraphEdge< Vertex, Edge, Face >, TVector4< T >, TVector3< T >, TVector2< T >, TMatrix4x4< T >, TAngle< T >
• operator BitVector &() : PropertyManager
• operator bool() : Bit
• operator char() : VIEW::ColorUnit
• operator const Position &() : BaseIterator< Container, DataType, Position, Traits >
• operator delete() : AutoDeletable
• operator double() : VIEW::ColorUnitHue, VIEW::ColorUnit
• operator float() : VIEW::ColorUnitHue, VIEW::ColorUnit
• operator int() : VIEW::ColorUnitHue, VIEW::ColorUnit, SocketBuf
• operator long() : VIEW::ColorUnitHue, VIEW::ColorUnit
• operator long double() : VIEW::ColorUnitHue
• operator new() : AutoDeletable
• operator short() : VIEW::ColorUnitHue, VIEW::ColorUnit
• operator sockaddr *() : SockAddr
• operator String() : VIEW::ColorUnitHue, VIEW::ColorUnit, VIEW::ColorRGBA, VIEW::ColorHSV, Substring
• operator T() : TAngle< T >
• operator unsigned char() : VIEW::ColorUnit
• operator unsigned int() : VIEW::ColorUnitHue, VIEW::ColorUnit
• operator unsigned long() : VIEW::ColorUnitHue, VIEW::ColorUnit
• operator unsigned short() : VIEW::ColorUnitHue, VIEW::ColorUnit
• operator void *() : SockInetAddr, SockAddr
• operator!=() : VIEW::ColorUnitHue, VIEW::ColorUnit, VIEW::ColorRGBA, VIEW::ColorHSV, Timer, File, Directory, TrianglePoint, TriangleEdge, Triangle, SESVertex, SESFace, SESEdge, SASVertex, SASFace, SASEdge, RSVertex, RSFace, RSEdge, GraphVertex< Vertex, Edge, Face >, GraphTriangle< Vertex, Edge, Face >, GraphFace< Vertex, Edge, Face >, GraphEdge< Vertex, Edge, Face >, TVector4< T >, TVector3< T >, TVector2< T >, TSphere3< T >, TSimpleBox3< T >, TQuaternion< T >, TPlane3< T >, TMatrix4x4< T >, TLine3< T >, TCircle3< T >, TBox3< T >, TAngle< T >, System, SecondaryStructure, Residue, Element, Protein, PDBAtom, Nucleotide, NucleicAcid, Molecule, CompositeIteratorTraits, Fragment, ExpressionTree, Chain, Bond, AtomContainer, Atom, ResourceFile, ResourceEntry, PDBInfo, NMRStarFile, LineBasedFile, JCAMPFile, Triple< T1, T2, T3 >, StringHashMap< Value >, Substring, RegularExpression, TRegularData3D< ValueType >, TRegularData2D< ValueType >, TRegularData1D< ValueType >, Quadruple< T1, T2, T3, T4 >, Options, List< Value >, HashSet< Key >, HashMap< Key, T >, HashGrid3< Item >, HashGridBox3< Item >, BitVector, Bit, Selectable, PropertyManager, NamedProperty, Object, EnumeratorIndex, Composite, BaseIterator< Container, DataType, Position, Traits >
• operator%() : TVector3< T >
• operator%=() : TVector3< T >
• operator()() : VIEW::AddVanDerWaalsModel, VIEW::AddSurfaceModel, VIEW::AtomDistanceColorProcessor, VIEW::AddLineModel, VIEW::LabelModel, VIEW::HBondModelProcessor, VIEW::ForceModel, VIEW::ColorProcessor, VIEW::AddBallAndStickModel, VIEW::AddBackboneModel, VIEW::AtomBondModelBaseProcessor, VIEW::DockResultDialog::Compare_, SurfaceProcessor, SecondaryStructureProcessor, ResidueChecker, ReconstructFragmentProcessor, RDFIntegrator, RadialDistributionFunction, HBondProcessor, TransformationProcessor, TranslationProcessor, FragmentDistanceCollector, GeometricCenterProcessor, BoundingBoxProcessor, FragmentDB::BuildBondsProcessor, FragmentDB::NormalizeNamesProcessor, RandomEvaluation, ForceFieldEvaluation, EnergeticEvaluation, DockResult::Compare_, DockResult, AssignChargeProcessor, AssignRadiusProcessor, ClearRadiusProcessor, ClearChargeProcessor, BuildBondsProcessor, AddHydrogenProcessor, PairExpRDFIntegrator, Pair6_12RDFIntegrator, ElectrostaticPotentialCalculator, RingPerceptionProcessor, PartialChargeProcessor, Descriptor, AromaticityProcessor, ShiftModel, RandomCoilShiftProcessor, JohnsonBoveyShiftProcessor, HBondShiftProcessor, HaighMallionShiftProcessor, SimpleExperiment1D, EFShiftProcessor, CreateSpectrumProcessor, ClearShiftProcessor, AssignShiftProcessor, AnisotropyShiftProcessor, MMFF94ChargeProcessor, TypeRuleProcessor, TypenameRuleProcessor, RuleEvaluator, RadiusRuleProcessor, ChargeRuleProcessor, AssignTypeNameProcessor, AssignTypeProcessor, PiecewisePolynomial, PiecewiseFunction, ParsedFunction< arg >, TMatrix4x4< T >, MutablePower< Function, DataType >, CubicFunction< Function, DataType >, SquareFunction< Function, DataType >, Reciprocal< Function, DataType >, Division< First, Second, DataType >, Product< First, Second, DataType >, Subtraction< First, Second, DataType >, Addition< First, Second, DataType >, MutableConstant< DataType >, ConstantFunction< constant_template >, SMARTSPredicate, RingFinder, Conformation4C1Predicate, AxialPredicate, ChargePredicate, Sp3HybridizedPredicate, Sp2HybridizedPredicate, SpHybridizedPredicate, ConnectedToPredicate, AromaticBondsPredicate, TripleBondsPredicate, DoubleBondsPredicate, SingleBondsPredicate, NumberOfBondsPredicate, InRingPredicate, NucleotidePredicate, BackBonePredicate, MoleculePredicate, SolventPredicate, SecondaryStructurePredicate, ChainPredicate, ProteinPredicate, ResidueIDPredicate, ResiduePredicate, ElementPredicate, AtomTypePredicate, AtomNamePredicate, SelectedPredicate, FalsePredicate, TruePredicate, Selector, KernelPredicate< T >, ExpressionTree, ExpressionPredicate, Expression, EnergyProcessor, String, TRegularData3D< ValueType >, TRegularData2D< ValueType >, TRegularData1D< ValueType >, BitVector, BinaryProcessor< T1, T2 >, UnaryProcessor< T >, ObjectCreator, Comparator< T >
• operator+() : TVector4< T >, TVector3< T >, TVector2< T >, TMatrix4x4< T >, TAngle< T >, String, HashSet< Key >, BaseIterator< Container, DataType, Position, Traits >
• operator++() : ForwardIterator< Container, DataType, Position, Traits >, ConstForwardIterator< Container, DataType, Position, Traits >, EnumeratorIndex, BidirectionalIterator< Container, DataType, Position, Traits >, ConstBidirectionalIterator< Container, DataType, Position, Traits >
• operator+=() : TriangulatedSurface, TVector4< T >, TVector3< T >, TVector2< T >, TQuaternion< T >, TMatrix4x4< T >, TAngle< T >, HashSet< Key >
• operator-() : TVector4< T >, TVector3< T >, TVector2< T >, TQuaternion< T >, TMatrix4x4< T >, TAngle< T >, HashSet< Key >, BaseIterator< Container, DataType, Position, Traits >
• operator--() : EnumeratorIndex, BidirectionalIterator< Container, DataType, Position, Traits >, ConstBidirectionalIterator< Container, DataType, Position, Traits >
• operator-=() : TVector4< T >, TVector3< T >, TVector2< T >, TQuaternion< T >, TMatrix4x4< T >, TAngle< T >, HashSet< Key >
• operator->() : ForwardIterator< Container, DataType, Position, Traits >, BidirectionalIterator< Container, DataType, Position, Traits >, BaseIterator< Container, DataType, Position, Traits >, LogStream
• operator/() : TVector4< T >, TVector3< T >, TVector2< T >, TMatrix4x4< T >, TAngle< T >
• operator/=() : TVector4< T >, TVector3< T >, TVector2< T >, TMatrix4x4< T >, TAngle< T >
• operator<() : VIEW::Camera, VIEW::LightSource, VIEW::Representation, VIEW::GeometricObject, VIEW::ColorUnitHue, VIEW::ColorUnit, VIEW::ColorRGBA, VIEW::ColorHSV, Timer, Peak< PositionType >, TVector3< T >, TAngle< T >, Element, INIFile::Section, Triple< T1, T2, T3 >, RegularExpression, Quadruple< T1, T2, T3, T4 >, PreciseTime, Object, EnumeratorIndex
• operator<<() : VIEW::ColorUnitHue, VIEW::ColorUnit, VIEW::ColorRGBA, VIEW::ColorHSV, DockResult, Element, XYZFile, PDBFile, GenericMolFile, Substring, RegularExpression, TContourSurface< T >, BitVector, PersistenceManager, EnumeratorIndex
• operator<=() : VIEW::ColorUnitHue, VIEW::ColorUnit, VIEW::ColorRGBA, VIEW::ColorHSV, Timer, TAngle< T >, Element, Triple< T1, T2, T3 >, RegularExpression, Quadruple< T1, T2, T3, T4 >, Object, EnumeratorIndex
• operator=() : VIEW::Scene, VIEW::DockingController, VIEW::TwoColoredTube, VIEW::TwoColoredLine, VIEW::Tube, VIEW::Sphere, VIEW::SimpleBox, VIEW::Point, VIEW::MultiLine, VIEW::Mesh, VIEW::Line, VIEW::Label, VIEW::Disc, VIEW::Box, VIEW::HBondModelProcessor, VIEW::ColorProcessor, VIEW::AddBallAndStickModel, VIEW::AtomBondModelBaseProcessor, VIEW::DockingThread, VIEW::GeometricObject, VIEW::GeometricFitDialog, VIEW::DockResultDialog, VIEW::DockDialog, VIEW::Vertex2, VIEW::Vertex, VIEW::Dataset, VIEW::ColorUnitHue, VIEW::ColorUnit, VIEW::ColorRGBA, VIEW::ColorHSV, VIEW::MultiColorExtension, VIEW::ColorExtension2, Timer, SockInetBuf, SocketBuf, File, Directory, TriangulatedSphere, TriangulatedSurface, TriangulatedSES, TriangulatedSAS, TrianglePoint, Triangle, SmartsParser::SPAtom::Property, SmartsMatcher::RecStruct_, SmartsMatcher::RecStructCore_, SESVertex, SESFace, SESEdge, SASVertex, SASFace, SASEdge, RSVertex, RSFace, RSEdge, RotamerLibrary, ResidueRotamerSet, ReducedSurface, RDFParameter, RDFIntegrator, RadialDistributionFunction, GraphVertex< Vertex, Edge, Face >, GraphTriangle< Vertex, Edge, Face >, GraphFace< Vertex, Edge, Face >, GraphEdge< Vertex, Edge, Face >, FragmentDB, DockResult::Scoring_, DockResult, BuildBondsProcessor, UhligCavFreeEnergyProcessor, SolventParameter, SolventDescriptor, ReissCavFreeEnergyProcessor, PierottiCavFreeEnergyProcessor, PCMCavFreeEnergyProcessor, PairExpRDFIntegrator, PairExpInteractionEnergyProcessor, Pair6_12RDFIntegrator, Pair6_12InteractionEnergyProcessor, ClaverieParameter, SLICKScore, SLICKEnergy, RotationalEntropyLoss, PolarSolvation, NonpolarSolvation, ChemScoreMetal, Lipophilic, HydrogenBond, CHPI, BuriedPolar, VdWSurface, Density, VdWVolume, RelPolarVdWSurface, RelHydrophobicVdWSurface, RelNegativePolarVdWSurface, RelPositivePolarVdWSurface, RelNegativeVdWSurface, RelPositiveVdWSurface, PolarVdWSurface, HydrophobicVdWSurface, NegativePolarVdWSurface, PositivePolarVdWSurface, NegativeVdWSurface, PositiveVdWSurface, SurfaceBase, PrincipalMomentOfInertiaZ, PrincipalMomentOfInertiaY, PrincipalMomentOfInertiaX, PrincipalMomentOfInertia, SizeOfSSSR, AtomicPolarizabilities, BondPolarizabilities, NumberOfHydrophobicAtoms, NumberOfHydrogenBondDonors, NumberOfHydrogenBondAcceptors, VertexAdjacencyEquality, VertexAdjacency, RelNumberOfRotatableBonds, NumberOfRotatableBonds, NumberOfHeavyBonds, NumberOfAromaticAtoms, RelNumberOfRotatableSingleBonds, NumberOfRotatableSingleBonds, AtomInformationContent, MeanAtomInformationContent, NumberOfHeavyAtoms, FormalCharge, NumberOfHydrogen, NumberOfIodine, NumberOfBromine, NumberOfChlorine, NumberOfSulfur, NumberOfPhosphorus, NumberOfFlourine, NumberOfOxygen, NumberOfNitrogen, NumberOfCarbon, NumberOfBoron, NumberOfAtoms, NumberOfAromaticBonds, NumberOfTripleBonds, NumberOfDoubleBonds, NumberOfSingleBonds, NumberOfBonds, MolecularWeight, SimpleBase, RingPerceptionProcessor, PartialChargeProcessor, RelNegativePartialCharge, RelPositivePartialCharge, TotalNegativePartialCharge, TotalPositivePartialCharge, PartialChargeBase, Descriptor, BalabanIndexJ, ZagrebIndex, ConnectivityBase, AromaticityProcessor, PyDatasetVector, PyCompositeList, ShiftModule, ShiftModel, Peak< PositionType >, Templates, QuadraticImproperTorsion, Potential1210, LennardJones, ForceFieldParameters, CosineTorsion, CharmmEEF1, AtomTypes, MMFF94ESParameters, MMFF94VDWParameters, MMFF94PlaneParameters, MMFF94TorsionParameters, MMFF94StretchBendParameters, MMFF94BendParameters, MMFF94StretchParameters, MMFF94ParametersBase, MMFF94NonBonded, MMFF94, StrangLBFGSMinimizer, SteepestDescentMinimizer, ShiftedLVMMMinimizer, LineSearch, EnergyMinimizer, ConjugateGradientMinimizer, MolecularDynamics, MicroCanonicalMD, CanonicalMD, SnapShotManager, SnapShot, RuleEvaluator, PeriodicBoundary, Gradient, ForceField, AtomVector, CharmmNonBonded, CharmmFF, AmberNonBonded, AmberFF, TVector4< T >, TVector3< T >, TVector2< T >, TSphere3< T >, TSimpleBox3< T >, RombergIntegrator< Function, DataType >, TQuaternion< T >, TPlane3< T >, PiecewisePolynomial, PiecewiseFunction, NumericalIntegrator< Function, DataType >, TMatrix4x4< T >, TLine3< T >, MutablePower< Function, DataType >, CubicFunction< Function, DataType >, SquareFunction< Function, DataType >, Reciprocal< Function, DataType >, Division< First, Second, DataType >, Product< First, Second, DataType >, Subtraction< First, Second, DataType >, Addition< First, Second, DataType >, MutableConstant< DataType >, TFFT3D< ComplexTraits >, TFFT2D< ComplexTraits >, TFFT1D< ComplexTraits >, TCircle3< T >, TBox3< T >, TAngle< T >, System, Selector, SecondaryStructure, Residue, PTE_, Element, Protein, PDBAtom, Nucleotide, NucleicAcid, Molecule, CompositeIteratorTraits, Fragment, ExpressionTree, ExpressionPredicate, Expression, Chain, Bond, AtomContainer, Atom, TRRFile, TrajectoryFile, SCWRLRotamerFile, ResourceEntry, ParameterSection, Parameters, NMRStarFile, LineBasedFile, HINFile, GenericMolFile, GAMESSLogFile, GAMESSDatFile, DSN6File, DCDFile, EnergyProcessor, ComposedEnergyProcessor, Triple< T1, T2, T3 >, StringHashMap< Value >, Substring, String, RegularExpression, TRegularData3D< ValueType >, TRegularData2D< ValueType >, TRegularData1D< ValueType >, Quadruple< T1, T2, T3, T4 >, Options, List< Value >, HashSet< Key >, HashMap< Key, T >, HashGrid3< Item >, TContourSurface< T >, TContourLine< T >, TContour< T >, BitVector, Bit, TimeStamp, PreciseTime, Selectable, PropertyManager, Object, EnumeratorIndex, Composite, BaseIterator< Container, DataType, Position, Traits >
• operator==() : VIEW::GeometricObject, VIEW::ColorUnitHue, VIEW::ColorUnit, VIEW::ColorRGBA, VIEW::ColorHSV, Timer, File, Directory, TrianglePoint, TriangleEdge, Triangle, SESVertex, SESFace, SESEdge, SASVertex, SASFace, SASEdge, RSVertex, RSFace, RSEdge, RDFSection, RDFIntegrator, RadialDistributionFunction, GraphVertex< Vertex, Edge, Face >, GraphTriangle< Vertex, Edge, Face >, GraphFace< Vertex, Edge, Face >, GraphEdge< Vertex, Edge, Face >, UhligCavFreeEnergyProcessor, SolventParameter, SolventDescriptor, ReissCavFreeEnergyProcessor, PierottiCavFreeEnergyProcessor, PCMCavFreeEnergyProcessor, PairExpRDFIntegrator, Pair6_12RDFIntegrator, Pair6_12InteractionEnergyProcessor, ClaverieParameter, Peak< PositionType >, QuadraticImproperTorsion, Potential1210, LennardJones, ForceFieldParameters, CosineTorsion, CharmmEEF1, AtomTypes, MMFF94NonBonded, EnergyMinimizer, SnapShot, RuleEvaluator, CharmmNonBonded, AmberNonBonded, TVector4< T >, TVector3< T >, TVector2< T >, TSphere3< T >, TSimpleBox3< T >, RombergIntegrator< Function, DataType >, TQuaternion< T >, TPlane3< T >, PiecewisePolynomial, PiecewiseFunction, NumericalIntegrator< Function, DataType >, TMatrix4x4< T >, TLine3< T >, MutablePower< Function, DataType >, CubicFunction< Function, DataType >, SquareFunction< Function, DataType >, Reciprocal< Function, DataType >, Division< First, Second, DataType >, Product< First, Second, DataType >, Subtraction< First, Second, DataType >, Addition< First, Second, DataType >, MutableConstant< DataType >, TFFT3D< ComplexTraits >, TFFT2D< ComplexTraits >, TFFT1D< ComplexTraits >, TCircle3< T >, TBox3< T >, TAngle< T >, System, Selector, SecondaryStructure, Residue, PTE_, Element, Protein, PDBAtom, Nucleotide, NucleicAcid, Molecule, CompositeIteratorTraits, Fragment, ExpressionTree, ExpressionPredicate, Expression, Chain, Bond, AtomContainer, Atom, TRRFile, TrajectoryFile, ResourceFile, ResourceEntry, PDBInfo, ParameterSection, Parameters, NMRStarFile, LineBasedFile, JCAMPFile, INIFile, DSN6File, DCDFile, EnergyProcessor, ComposedEnergyProcessor, Triple< T1, T2, T3 >, StringHashMap< Value >, Substring, RegularExpression, TRegularData3D< ValueType >, TRegularData2D< ValueType >, TRegularData1D< ValueType >, Quadruple< T1, T2, T3, T4 >, Options, List< Value >, HashSet< Key >, HashMap< Key, T >, HashGrid3< Item >, HashGridBox3< Item >, TContourSurface< T >, TContourLine< T >, TContour< T >, BitVector, Bit, TimeStamp, PreciseTime, Selectable, PropertyManager, NamedProperty, Object, EnumeratorIndex, Composite, BaseIterator< Container, DataType, Position, Traits >
• operator>() : VIEW::ColorUnitHue, VIEW::ColorUnit, VIEW::ColorRGBA, VIEW::ColorHSV, Timer, Peak< PositionType >, TAngle< T >, Element, INIFile::Section, Triple< T1, T2, T3 >, RegularExpression, Quadruple< T1, T2, T3, T4 >, PreciseTime, Object, EnumeratorIndex
• operator>=() : VIEW::ColorUnitHue, VIEW::ColorUnit, VIEW::ColorRGBA, VIEW::ColorHSV, Timer, TAngle< T >, Element, Triple< T1, T2, T3 >, RegularExpression, Quadruple< T1, T2, T3, T4 >, Object, EnumeratorIndex
• operator>>() : VIEW::ColorUnitHue, VIEW::ColorUnit, VIEW::ColorRGBA, VIEW::ColorHSV, DockResult, XYZFile, TRRFile, SCWRLRotamerFile, PDBFile, GenericMolFile, RegularExpression, BitVector, PersistentObject, PersistenceManager
• operator[]() : ResidueRotamerSet, ConformationSet, AtomVector, TVector4< T >, TVector3< T >, TVector2< T >, TMatrix4x4< T >, TFFT3D< ComplexTraits >, TFFT2D< ComplexTraits >, TFFT1D< ComplexTraits >, PTE_, Substring, TRegularData3D< ValueType >, TRegularData2D< ValueType >, TRegularData1D< ValueType >, HashMap< Key, T >, BitVector, EnumeratorIndex
• operator^() : BitVector
• operator^=() : BitVector
• operator|() : HashSet< Key >, BitVector
• operator|=() : HashSet< Key >, BitVector
• operator~() : BitVector
• optimizeGridSize_() : GeometricFit
• Options() : Options
• options : GeometricFit, DockingAlgorithm, BuildBondsProcessor, UhligCavFreeEnergyProcessor, ReissCavFreeEnergyProcessor, FDPB, PierottiCavFreeEnergyProcessor, PCMCavFreeEnergyProcessor, PairExpInteractionEnergyProcessor, Pair6_12RDFIntegrator, Pair6_12InteractionEnergyProcessor, ElectrostaticPotentialCalculator, ShiftModel, EnergyMinimizer, MolecularDynamics, SnapShotManager, PeriodicBoundary, ForceField, PDBFile, ParameterSection
• options_ : DockResult::Scoring_
• OR : ExpressionTree
• Order : Bond
• ORDER__ANY : Bond
• ORDER__AROMATIC : Bond
• ORDER__DOUBLE : Bond
• ORDER__QUADRUPLE : Bond
• ORDER__SINGLE : Bond
• ORDER__TRIPLE : Bond
• ORDER__UNKNOWN : Bond
• origin_ : TFFT3D< ComplexTraits >, TFFT2D< ComplexTraits >, TFFT1D< ComplexTraits >, DSN6File, TRegularData3D< ValueType >, TRegularData2D< ValueType >, TRegularData1D< ValueType >
• original_coordinates_ : ResidueRotamerSet
• OSockStream() : OSockStream
• other() : GraphEdge< Vertex, Edge, Face >
• output_() : VIEW::BALLThread
• outputEnabled() : LogStream
• overflow() : LogStreamBuf
• OVERWRITE_CHARGES : MMFF94::Default, MMFF94::Option, CharmmFF::Default, CharmmFF::Option, AmberFF::Default, AmberFF::Option
• OVERWRITE_TYPENAMES : MMFF94::Default, MMFF94::Option, CharmmFF::Default, CharmmFF::Option, AmberFF::Default, AmberFF::Option

- p -

• P : Rotamer
• p : TSphere3< T >, TPlane3< T >, TLine3< T >, TCircle3< T >
• p_i_ : ConjugateGradientMinimizer
• p_t_ : ConjugateGradientMinimizer
• paintGL() : VIEW::Scene, VIEW::EditableScene
• Pair6_12InteractionEnergyProcessor() : Pair6_12InteractionEnergyProcessor
• Pair6_12RDFIntegrator() : Pair6_12RDFIntegrator
• PairExpInteractionEnergyProcessor() : PairExpInteractionEnergyProcessor
• PairExpRDFIntegrator() : PairExpRDFIntegrator
• PairVector : ForceField
• Parameters() : Parameters
• parameters_ : MMFF94ESParameters, MMFF94VDWParameters, MMFF94PlaneParameters, MMFF94TorsionParameters, MMFF94StretchBendParameters, MMFF94BendParameters, MMFF94StretchParameters
• ParameterSection() : ParameterSection
• PARENT_DIRECTORY : FileSystem
• pars_ : Bruker1DFile
• parse() : SmartsParser, ExpressionParser
• PARSE_PARTIAL_CHARGES : PDBFile::Default, PDBFile::Option
• parse_partial_charges_ : PDBFile
• parseColumnFormat() : LineBasedFile
• ParsedFunction() : ParsedFunction< arg >
• parseLine() : PDBFile
• parseLine_() : VIEW::PyWidget
• parsf1_ : Bruker2DFile
• PartialChargeBase() : PartialChargeBase
• PartialChargeProcessor() : PartialChargeProcessor
• partner1Chosen() : VIEW::DockDialog
• partner2Chosen() : VIEW::DockDialog
• paste() : VIEW::MolecularControl
• path() : FileSystem
• Path() : Path
• PATH_SEPARATOR : FileSystem
• PathStrings : PyInterpreter
• pauseClicked() : VIEW::DockProgressDialog
• pbcis_ : MMFF94ESParameters
• PCMCavFreeEnergyProcessor() : PCMCavFreeEnergyProcessor
• PDBAtom() : PDBAtom
• PDBFile() : PDBFile
• Peak() : Peak< PositionType >
• PeakList() : PeakList< PT >
• PeakType : Spectrum< DataT, PeakT, PositionT >, PeakList< PT >, Experiment< PeakListType >
• PeptideBuilder() : Peptides::PeptideBuilder
• PeptideDialog() : VIEW::PeptideDialog
• Period : Element
• periodic_boundary : ForceField
• PERIODIC_BOX_ADD_SOLVENT : PeriodicBoundary::Default
• PERIODIC_BOX_DISTANCE : PeriodicBoundary::Default
• PERIODIC_BOX_ENABLED : PeriodicBoundary::Default
• PERIODIC_BOX_LOWER : PeriodicBoundary::Default
• PERIODIC_BOX_SOLVENT_FILE : PeriodicBoundary::Default
• PERIODIC_BOX_SOLVENT_SOLUTE_DISTANCE : PeriodicBoundary::Default
• PERIODIC_BOX_UPPER : PeriodicBoundary::Default
• PERIODIC_WATER_FILE : PeriodicBoundary::Default
• PeriodicBoundary() : PeriodicBoundary
• PersistenceManager() : PersistenceManager
• PersistentObject() : PersistentObject
• persistentRead() : TVector2< T >, System, SecondaryStructure, Residue, Protein, PDBAtom, Nucleotide, NucleicAcid, Molecule, Fragment, Chain, Bond, AtomContainer, Atom, NamedProperty, PersistentObject, Composite
• persistentWrite() : TVector2< T >, System, SecondaryStructure, Residue, Protein, PDBAtom, Nucleotide, NucleicAcid, Molecule, Fragment, Chain, Bond, AtomContainer, Atom, NamedProperty, PersistentObject, Composite
• phase() : TFFT3D< ComplexTraits >, TFFT2D< ComplexTraits >, TFFT1D< ComplexTraits >
• phi_ : ResidueRotamerSet
• phi_grid : FDPB
• phis_ : MMFF94ESParameters
• PICKING__MODE : VIEW::Scene
• pickingMode_() : VIEW::Scene
• pickObjects1() : VIEW::GLRenderer
• pickObjects2() : VIEW::GLRenderer
• PiecewiseFunction() : PiecewiseFunction
• PiecewisePolynomial() : PiecewisePolynomial
• PierottiCavFreeEnergyProcessor() : PierottiCavFreeEnergyProcessor
• pilp : MMFF94AtomType
• PLANCK : Constant
• PlaneMap : MMFF94PlaneParameters
• Point() : VIEW::Point
• PointerType : PyIndexList, PyDatasetVector, PyCompositeList, PyColorRGBAVector
• PointType : TContourSurface< T >, TContourLine< T >
• POLAK_RIBIERE : ConjugateGradientMinimizer
• PolarSolvation() : PolarSolvation
• PolarVdWSurface() : PolarVdWSurface
• PopUpID : VIEW::MainControl
• Position : PeakList< PT >
• position_data_size : TRRFile::TRRHeader
• POSITIONAL : VIEW::LightSource
• PositionType : Spectrum< DataT, PeakT, PositionT >
• PositivePolarVdWSurface() : PositivePolarVdWSurface
• PositiveVdWSurface() : PositiveVdWSurface
• Potential1210() : Potential1210
• POVColorRGBA() : VIEW::POVRenderer
• POVFinish() : VIEW::POVRenderer
• POVRenderer() : VIEW::POVRenderer
• POVVector3() : VIEW::POVRenderer
• PreciseTime() : PreciseTime
• predicate : ExpressionParser::SyntaxTree
• predicate_ : CompositeIteratorTraits
• Preferences() : VIEW::Preferences
• prepend() : System, SecondaryStructure, Residue, Nucleotide, Molecule, Chain, AtomContainer
• prependChild() : Composite
• pres_size : TRRFile::TRRHeader
• PRESSURE : ReissCavFreeEnergyProcessor::Default, ReissCavFreeEnergyProcessor::Option, PierottiCavFreeEnergyProcessor::Default, PierottiCavFreeEnergyProcessor::Option
• prev_shift_val_ : ShiftedLVMMMinimizer
• PrincipalMomentOfInertia() : PrincipalMomentOfInertia
• PrincipalMomentOfInertiaX() : PrincipalMomentOfInertiaX
• PrincipalMomentOfInertiaY() : PrincipalMomentOfInertiaY
• PrincipalMomentOfInertiaZ() : PrincipalMomentOfInertiaZ
• PRINT_TIMING : FDPB::Default, FDPB::Option
• printEnergy() : EnergyMinimizer
• printSelectionInfos() : VIEW::MainControl
• PROBE_RADIUS : UhligCavFreeEnergyProcessor::Default, UhligCavFreeEnergyProcessor::Option, ReissCavFreeEnergyProcessor::Default, ReissCavFreeEnergyProcessor::Option, FDPB::Default, FDPB::Option, PierottiCavFreeEnergyProcessor::Default, PierottiCavFreeEnergyProcessor::Option, PCMCavFreeEnergyProcessor::Default, PCMCavFreeEnergyProcessor::Option
• ProbeStatus : RSComputer
• processEvents() : VIEW::MainControl
• prod_ : DSN6File
• Product() : Product< First, Second, DataType >
• Properties : VIEW::Representation
• properties_ : SmartsParser::SPAtom
• Property() : SDGenerator, Residue, Protein, PDBAtom, Nucleotide, NucleicAcid, Molecule, Fragment, Chain, Bond, AtomContainer, Atom, SmartsParser::SPAtom::Property
• PROPERTY__ANISOTROPY_SHIFT : AnisotropyShiftProcessor
• PROPERTY__CYCLIC : Residue
• PROPERTY__EF_SHIFT : EFShiftProcessor
• PROPERTY__RANDOM_COIL_SHIFT : RandomCoilShiftProcessor
• PROPERTY__RING_CURRENT_SHIFT : JohnsonBoveyShiftProcessor, HaighMallionShiftProcessor
• PROPERTY__SHIFT : ShiftModule
• PropertyManager() : PropertyManager
• PropertyType : SmartsParser::SPAtom
• Protein() : Protein
• Protocol : TCPTransfer
• PROTON_MASS : Constant
• psi_ : ResidueRotamerSet
• PubChemDialog() : VIEW::PubChemDialog
• pushBackNormal() : TSurface< T >
• pushBackTriangle() : TSurface< T >
• pushBackVertex() : TSurface< T >
• put() : XDRPersistenceManager, TextPersistenceManager, PersistenceManager
• PyColorRGBAVector() : PyColorRGBAVector
• PyCompositeList() : PyCompositeList
• PyDatasetVector() : PyDatasetVector
• PyIndexList() : PyIndexList
• PythonSettings() : VIEW::PythonSettings
• PyWidget() : VIEW::PyWidget

- q -

• q_grid : FDPB
• QuadMesh() : VIEW::QuadMesh
• QuadraticAngleBend() : QuadraticAngleBend
• QuadraticBondStretch() : QuadraticBondStretch
• QuadraticImproperTorsion() : QuadraticImproperTorsion
• Quadruple() : Quadruple< T1, T2, T3, T4 >
• queryPubChem() : VIEW::PubChemDialog
• quickLoad() : VIEW::MainControl
• quickSave() : VIEW::MainControl
• quit() : VIEW::MainControl

- r -

• R : Constant
• r_min : CharmmEEF1::Values
• RAD_PER_DEG : Constant
• RadialDistributionFunction() : RadialDistributionFunction
• radius : SolventAtomDescriptor, TSphere3< T >, TCircle3< T >
• RadiusRuleProcessor() : RadiusRuleProcessor
• RandomCoilShiftProcessor() : RandomCoilShiftProcessor
• randomDouble() : RandomNumberGenerator
• randomGaussian() : RandomNumberGenerator
• randomInteger() : RandomNumberGenerator
• randomUniform() : RandomNumberGenerator
• Range : TAngle< T >
• RANK_1 : ShiftedLVMMMinimizer
• RANK_2 : ShiftedLVMMMinimizer
• RATIO_OF_SHIFT_PARAMS : ShiftedLVMMMinimizer
• rbegin() : Gradient, RandomAccessIterator< Container, DataType, Position, Traits >, BidirectionalIterator< Container, DataType, Position, Traits >, ConstBidirectionalIterator< Container, DataType, Position, Traits >
• rbeginBond() : Atom
• rdbuf() : LogStream
• RDF_FILENAME : PairExpInteractionEnergyProcessor::Option, Pair6_12InteractionEnergyProcessor::Option
• RDFIntegrator() : RDFIntegrator
• RDFParameter() : RDFParameter
• RDFSection() : RDFSection
• reactToMessages_() : VIEW::MolecularControl
• read() : TVector3< T >, XYZFile, TRRFile, TrajectoryFile, SDFile, PDBFile, MOLFile, MOL2File, KCFFile, JCAMPFile, INIFile, HINFile, GenericMolFile, GAMESSLogFile, GAMESSDatFile, DSN6File, DCDFile, Bruker2DFile, Bruker1DFile, Options, BitVector, TimeStamp, PreciseTime, Selectable, PropertyManager
• read_atoms_ : SDFile
• readAtomLine_() : MOLFile
• readBondLengthsFromFile_() : BuildBondsProcessor
• readBondLine_() : MOLFile
• readCountsLine_() : MOLFile
• readCTAB_() : MOLFile
• readDockResult() : DockResult
• readEmpericalParameters() : MMFF94StretchBendParameters
• readFiles() : VIEW::MolecularFileDialog
• readFirstRecord() : PDBFile
• readFromFile() : SnapShotManager
• readHeader() : TrajectoryFile, DSN6File, DCDFile
• readHINFile() : VIEW::MolecularFileDialog
• readInvalidRecord() : PDBFile
• readLine() : PDBFile, LineBasedFile
• readMOL2File() : VIEW::MolecularFileDialog
• readMOLFile() : VIEW::MolecularFileDialog
• readMSMSFile() : TSurface< T >
• readNextHeader() : TRRFile
• readNextRecord() : PDBFile
• readObject() : PersistenceManager
• readObjectArray() : PersistenceManager
• readObjectPointer() : PersistenceManager
• readObjectPointerArray() : PersistenceManager
• readObjectReference() : PersistenceManager
• readOptionFile() : Options
• readPDBFile() : VIEW::MolecularFileDialog
• readPreferenceEntries() : VIEW::PreferencesEntry, VIEW::PythonSettings, VIEW::MainControlPreferences
• readPrimitive() : PersistenceManager
• readPropertyBlock_() : SDFile
• readRecords() : PDBFile
• readSDFile() : VIEW::MolecularFileDialog
• readStorableObject() : PersistenceManager
• readUnknownRecord() : PDBFile
• readXYZFile() : VIEW::MolecularFileDialog
• REAL : RegularExpression
• REBUILD_DISPLAY_LISTS : VIEW::Scene, VIEW::SceneMessage
• rec_edges_ : SmartsParser
• Reciprocal() : Reciprocal< Function, DataType >
• ReconstructFragmentProcessor() : ReconstructFragmentProcessor
• records_ : PDBRecords
• RecStruct_() : SmartsMatcher::RecStruct_
• RecStructCore_() : SmartsMatcher::RecStructCore_
• RecStructPool_() : SmartsMatcher::RecStructPool_
• recurseGeneration_() : VIEW::MolecularControl
• recursive_ : SmartsParser, SmartsParser::SPNode
• redock_() : VIEW::DockResultDialog
• REDRAW : VIEW::SceneMessage
• redrawAllRepresentations() : VIEW::MainControl
• ReducedSurface() : ReducedSurface
• REESTIMATE_BONDORDERS_RINGS : BuildBondsProcessor::Default, BuildBondsProcessor::Option
• reestimateBondOrdersRings_() : BuildBondsProcessor
• REFERENCE_TEMPERATURE : MolecularDynamics::Option
• refine() : TriangulatedSphere
• registerClass() : PersistenceManager
• registerConnectionObject() : VIEW::ConnectionObject
• registerController() : VIEW::DatasetControl
• registerForHelpSystem() : VIEW::HelpViewer, VIEW::DockWidget, VIEW::ModularWidget
• registerModule() : ShiftModel
• registerObjectCreator() : VIEW::Server
• registerPredicate() : Expression
• registerThis() : Embeddable
• registerTransformation() : TransformationManager
• registerWidget() : VIEW::ModularWidget
• registerWidgetForHelpSystem_() : VIEW::PreferencesEntry
• registerWidgets_() : VIEW::PreferencesEntry
• RegularData1DWidget() : VIEW::RegularData1DWidget
• RegularExpression() : RegularExpression
• ReissCavFreeEnergyProcessor() : ReissCavFreeEnergyProcessor
• reject() : VIEW::GeometricFitDialog
• RelHydrophobicVdWSurface() : RelHydrophobicVdWSurface
• RelNegativePartialCharge() : RelNegativePartialCharge
• RelNegativePolarVdWSurface() : RelNegativePolarVdWSurface
• RelNegativeVdWSurface() : RelNegativeVdWSurface
• RelNumberOfRotatableBonds() : RelNumberOfRotatableBonds
• RelNumberOfRotatableSingleBonds() : RelNumberOfRotatableSingleBonds
• RelPolarVdWSurface() : RelPolarVdWSurface
• RelPositivePartialCharge() : RelPositivePartialCharge
• RelPositivePolarVdWSurface() : RelPositivePolarVdWSurface
• RelPositiveVdWSurface() : RelPositiveVdWSurface
• RemotenessIndicator : PDBAtom
• remove() : VIEW::RepresentationManager, VIEW::MainControl, VIEW::CompositeManager, File, Directory, TriangulatedSurface, Triangle, RSFace, GraphVertex< Vertex, Edge, Face >, GraphFace< Vertex, Edge, Face >, GraphEdge< Vertex, Edge, Face >, System, SecondaryStructure, Residue, Nucleotide, Molecule, Chain, AtomContainer, StringHashMap< Value >, List< Value >, HashGrid3< Item >, HashGridBox3< Item >, LogStream
• REMOVE : VIEW::RepresentationMessage, VIEW::DatasetMessage
• REMOVE_COORDINATE_SYSTEM : VIEW::SceneMessage
• removeAll() : HashGridBox3< Item >
• removeChild() : ResourceEntry, Composite
• removeComponent() : ForceField, ComposedEnergyProcessor
• removeComposite() : VIEW::MolecularControl
• REMOVED_COMPOSITE : VIEW::CompositeMessage
• removedComposite() : VIEW::RepresentationManager
• removeEntry() : VIEW::Preferences
• removeLightPressed() : VIEW::LightSettings
• removeLightSource() : VIEW::Stage
• removeModularWidget() : VIEW::MainControl
• removeRepresentation() : VIEW::GeometricControl, VIEW::GLRenderer
• removeSelected() : Composite
• removeSolvent() : PeriodicBoundary
• rename() : File, Directory
• renameTo() : File, Directory
• rend() : Gradient, RandomAccessIterator< Container, DataType, Position, Traits >, BidirectionalIterator< Container, DataType, Position, Traits >, ConstBidirectionalIterator< Container, DataType, Position, Traits >
• rendBond() : Atom
• render() : VIEW::Renderer, VIEW::POVRenderer
• render_() : VIEW::Renderer
• renderBox_() : VIEW::Renderer, VIEW::GLRenderer
• renderDisc_() : VIEW::Renderer, VIEW::POVRenderer, VIEW::GLRenderer
• Renderer() : VIEW::Renderer
• renderGridVisualisation_() : VIEW::Renderer, VIEW::GLRenderer
• renderLine_() : VIEW::Renderer, VIEW::POVRenderer, VIEW::GLRenderer
• renderMesh_() : VIEW::VRMLRenderer, VIEW::Renderer, VIEW::POVRenderer, VIEW::GLRenderer
• RenderMode : VIEW::Scene
• renderMultiLine_() : VIEW::Renderer, VIEW::POVRenderer, VIEW::GLRenderer
• renderPoint_() : VIEW::Renderer, VIEW::POVRenderer, VIEW::GLRenderer
• renderQuadMesh_() : VIEW::Renderer, VIEW::GLRenderer
• renderSimpleBox_() : VIEW::Renderer, VIEW::GLRenderer
• renderSphere_() : VIEW::VRMLRenderer, VIEW::Renderer, VIEW::POVRenderer, VIEW::GLRenderer
• renderTube_() : VIEW::VRMLRenderer, VIEW::Renderer, VIEW::POVRenderer, VIEW::GLRenderer
• renderTwoColoredLine_() : VIEW::Renderer, VIEW::POVRenderer, VIEW::GLRenderer
• renderTwoColoredTube_() : VIEW::VRMLRenderer, VIEW::Renderer, VIEW::POVRenderer, VIEW::GLRenderer
• reopen() : File
• replace() : Composite
• Representation() : VIEW::Representation
• RepresentationManager() : VIEW::RepresentationManager
• RepresentationMessageType : VIEW::RepresentationMessage
• RepresentationsConstIterator : VIEW::RepresentationManager
• RepresentationsIterator : VIEW::RepresentationManager
• rescale() : TRegularData3D< ValueType >, TRegularData2D< ValueType >, TRegularData1D< ValueType >
• reset() : VIEW::GeometricFitDialog, VIEW::DockDialog, Timer, Path
• resetCamera_() : VIEW::Scene
• resetCounter() : TContourLine< T >, TContour< T >
• resetPositions() : AtomVector
• resetPressed() : VIEW::DockDialog
• resetScoring() : ConformationSet
• Residue() : Residue
• residue_data_ : HBondProcessor
• ResidueChecker() : ResidueChecker
• ResidueNameColorProcessor() : VIEW::ResidueNameColorProcessor
• ResidueRotamerSet() : ResidueRotamerSet
• ResidueTorsions() : ResidueTorsions
• resize() : VIEW::MainControl, AtomVector, TRegularData3D< ValueType >, TRegularData2D< ValueType >, TRegularData1D< ValueType >
• resizeGL() : VIEW::Scene
• resizeNormals() : TSurface< T >
• resizeTriangles() : TSurface< T >
• resizeVertices() : TSurface< T >
• ResourceEntry() : ResourceEntry
• ResourceFile() : ResourceFile
• restart_frequency_ : ConjugateGradientMinimizer
• restoreDefaultValues() : VIEW::PreferencesEntry, VIEW::LightSettings
• restoreValues() : VIEW::PreferencesEntry, VIEW::LightSettings
• restoreWindows() : VIEW::MainControl
• Result : Processor
• results : FDPB
• retrieveHistoryLine_() : VIEW::PyWidget
• reverse() : String
• ReverseIterator : Gradient
• rewind() : LineBasedFile
• rho_ : StrangLBFGSMinimizer
• right() : String
• ring_connections_ : SmartsParser
• RingAnalyser() : RingAnalyser
• RingClusterer() : RingClusterer
• RingFinder() : RingFinder
• RingPerceptionProcessor() : RingPerceptionProcessor
• rings_ : RingPerceptionProcessor
• rms : Gradient
• RMS_CRITERION : FDPB::Default, FDPB::Option
• RombergIntegrator() : RombergIntegrator< Function, DataType >
• root_ : SmartsParser
• Rotamer() : Rotamer
• RotamerLibrary() : RotamerLibrary
• rotamers_ : ResidueRotamerSet
• rotate() : VIEW::Camera, TMatrix4x4< T >
• ROTATE__MODE : VIEW::Scene
• rotateComposites() : VIEW::Scene
• rotateMode_() : VIEW::Scene
• rotateX() : TMatrix4x4< T >
• rotateY() : TMatrix4x4< T >
• rotateZ() : TMatrix4x4< T >
• RotationalEntropyLoss() : RotationalEntropyLoss
• RSComputer() : RSComputer
• RSConstructor() : RSConstructor
• RSEdge() : RSEdge
• RSFace() : RSFace
• RSVertex() : RSVertex
• RuleEvaluator() : RuleEvaluator
• RuleList : RuleEvaluator
• RuleMap : RuleEvaluator
• RuleProcessor() : RuleProcessor
• run() : VIEW::DockingThread, VIEW::MDSimulationThread, VIEW::EnergyMinimizerThread, VIEW::FetchHTMLThread, VIEW::BALLThread, SESSingularityCleaner, SESComputer, RSComputer, PyInterpreter
• runDocking() : VIEW::DockingController
• runFile() : PyInterpreter
• runMinimization() : VIEW::MolecularStructure
• runScoring_() : VIEW::DockingController

- s -

• same_energy_counter_ : EnergyMinimizer
• SAMPLES : PairExpRDFIntegrator::Option, Pair6_12RDFIntegrator::Option
• sampling_rate_ : DSN6File
• SAS_grid : FDPB
• SASEdge() : SASEdge
• SASFace() : SASFace
• SASTriangulator() : SASTriangulator
• SASVertex() : SASVertex
• saveBALLViewProjectFile() : VIEW::MainControl
• savePositions() : AtomVector
• sbmb : MMFF94AtomType
• scale() : PeakList< PT >, TMatrix4x4< T >
• SCALING_ELECTROSTATIC_1_4 : CharmmFF::Default, CharmmFF::Option, AmberFF::Default, AmberFF::Option
• SCALING_VDW_1_4 : CharmmFF::Default, CharmmFF::Option, AmberFF::Default, AmberFF::Option
• Scene() : VIEW::Scene
• SceneMessage() : VIEW::SceneMessage
• SceneMessageType : VIEW::SceneMessage
• scores_ : DockResult::Scoring_
• Scoring_() : DockResult::Scoring_
• scoringAdvancedPressed() : VIEW::DockDialog
• scoringClicked() : VIEW::DockResultDialog
• scoringFuncChosen() : VIEW::DockResultDialog, VIEW::DockDialog
• ScoringFunction : VIEW::DockingController
• scorings_ : DockResult
• scriptDialog() : VIEW::PyWidget
• SCWRLRotamerFile() : SCWRLRotamerFile
• SDFile() : SDFile
• SDGenerator() : SDGenerator
• search() : LineBasedFile
• second : Triple< T1, T2, T3 >, Quadruple< T1, T2, T3, T4 >
• second_ : SmartsParser::SPEdge
• second_edge_ : SmartsParser::SPNode, SmartsParser::SPEdge
• SecondaryStructure() : SecondaryStructure
• select() : VIEW::MolecularControl, Selectable, Composite
• Selectable() : Selectable
• selectAllModels() : PDBFile
• selectColoringMethod() : VIEW::DisplayProperties
• selectCompositeRecursive() : VIEW::MainControl
• SELECTED : VIEW::RepresentationMessage, VIEW::DatasetMessage
• SELECTED_COMPOSITE : VIEW::CompositeMessage
• selected_model_ : PDBFile
• selectedForceField() : VIEW::MolecularDynamicsDialog, VIEW::MinimizationDialog
• selectFile_() : VIEW::DockDialog
• selectFont() : VIEW::MainControlPreferences
• selectForceField() : VIEW::MolecularDynamicsDialog, VIEW::MinimizationDialog
• selectMode() : VIEW::DisplayProperties
• selectModel() : VIEW::DisplayProperties, PDBFile
• Selector() : Selector
• sendMessage() : VIEW::MainControl
• sendMessage_() : VIEW::BALLThread
• sequenceRings() : SDGenerator
• Server() : VIEW::Server
• ServerPreferences() : VIEW::ServerPreferences
• SESComputer() : SESComputer
• SESEdge() : SESEdge
• SESFace() : SESFace
• SESSingularityCleaner() : SESSingularityCleaner
• SESTriangulator() : SESTriangulator
• SESVertex() : SESVertex
• set() : VIEW::Scene, VIEW::TwoColoredTube, VIEW::TwoColoredLine, VIEW::Tube, VIEW::Sphere, VIEW::SimpleBox, VIEW::Point, VIEW::Mesh, VIEW::Line, VIEW::Label, VIEW::Disc, VIEW::Box, VIEW::HBondModelProcessor, VIEW::ColorProcessor, VIEW::AddBallAndStickModel, VIEW::AtomBondModelBaseProcessor, VIEW::GeometricObject, VIEW::Vertex2, VIEW::Vertex, VIEW::Dataset, VIEW::ColorUnitHue, VIEW::ColorUnit, VIEW::ColorRGBA, VIEW::ColorHSV, VIEW::MultiColorExtension, VIEW::ColorExtension2, TCPTransfer, Directory, TriangulatedSphere, TriangulatedSurface, TriangulatedSES, TriangulatedSAS, TrianglePoint, Triangle, StructureMapper, SESVertex, SESFace, SESEdge, SASVertex, SASFace, SASEdge, RSVertex, RSFace, RSEdge, ReducedSurface, GraphVertex< Vertex, Edge, Face >, GraphTriangle< Vertex, Edge, Face >, GraphFace< Vertex, Edge, Face >, GraphEdge< Vertex, Edge, Face >, MolecularDynamics, Gradient, AtomVector, TVector4< T >, TVector3< T >, TVector2< T >, TSphere3< T >, TSimpleBox3< T >, TQuaternion< T >, TPlane3< T >, PiecewisePolynomial, TMatrix4x4< T >, TLine3< T >, TCircle3< T >, TBox3< T >, TAngle< T >, System, SecondaryStructure, Residue, Protein, PDBAtom, Nucleotide, NucleicAcid, Molecule, Chain, AtomContainer, Atom, ResourceEntry, StringHashMap< Value >, Substring, String, RegularExpression, Options, List< Value >, HashSet< Key >, HashMap< Key, T >, HashGrid3< Item >, BitVector, PreciseTime, Selectable, PropertyManager, Composite, Exception::GlobalExceptionHandler
• setAlpha() : VIEW::ColorRGBA, LineSearch
• setAlphaBlending() : VIEW::ColorMap
• setAlphas() : VIEW::MultiColorExtension
• setAlternateLocationIndicator() : PDBAtom
• setAmberDialog() : VIEW::MinimizationDialog
• setAminoAcidType() : Peptides::AminoAcidDescriptor
• setAngle() : VIEW::LightSource, SASEdge, RSEdge
• setAntialiasing() : VIEW::GLRenderer
• setArgument() : ConnectedToPredicate, ExpressionPredicate
• setAtom() : SESVertex, RSVertex, Peak< PositionType >
• setAtomForces() : SnapShot
• setAtomicNumber() : Element
• setAtomicRadius() : Element
• setAtomicWeight() : Element
• setAtomPositions() : SnapShot
• setAtomVelocities() : SnapShot
• setAtomVelocitites() : SnapShot
• setAutoDeletable() : AutoDeletable
• setBackboneDependent() : RotamerLibrary
• setBackgroundColor() : VIEW::Stage
• setBallRadius() : VIEW::AddBallAndStickModel
• setBaseColors() : VIEW::ColorMap
• setBathRelaxationTime() : CanonicalMD
• setBeta() : LineSearch
• setBit() : BitVector
• setBlue() : VIEW::ColorRGBA
• setBondLengths() : BuildBondsProcessor
• setBondOrder() : SmartsParser::SPBond
• setBool() : Options
• setBox() : PeriodicBoundary
• setBracketedFlag() : LineSearch
• setBranchDesignator() : PDBAtom
• setBusyMode_() : VIEW::MainControl
• setCamera() : VIEW::Stage
• setCenter() : RSFace
• setCenterOfTorus() : RSEdge
• setChainName() : Peptides::PeptideBuilder
• setCharge() : Atom
• setCharmmDialog() : VIEW::MinimizationDialog
• setCircle() : SESEdge, SASEdge
• setCoefficients() : PiecewiseFunction
• setColor() : VIEW::LightSource
• setColor2() : VIEW::ColorExtension2
• setColors() : VIEW::MultiColorExtension
• setColumn() : TMatrix4x4< T >
• setCompareMode() : String
• setComponentGrouping() : SmartsParser
• setComponentNumber() : SmartsParser::SPNode
• setComposite() : VIEW::CompositeMessage, FragmentDistanceCollector
• setCompositeName() : VIEW::CompositeMessage
• setComposites() : VIEW::ColorProcessor
• setConformationSet() : DockResult
• setConstant() : MutableConstant< DataType >
• setConstants() : PairExpRDFIntegrator, Pair6_12RDFIntegrator
• setContactCircle() : RSEdge
• setCorrectionParameter() : ShiftedLVMMMinimizer
• setCovalentRadius() : Element
• setCurrent() : Directory
• setCurrentModel() : PDBInfo
• setCurrentTime() : MolecularDynamics
• setData() : BinaryFileAdaptor< T >, TFFT3D< ComplexTraits >, TFFT2D< ComplexTraits >, TFFT1D< ComplexTraits >
• setDataPath() : Path
• setDefault() : Options
• setDefaultBool() : Options
• setDefaultColor() : VIEW::ColorProcessor
• setDefaultInteger() : Options
• setDefaultOptions() : BuildBondsProcessor, RingPerceptionProcessor
• setDefaultPeak() : Experiment< PeakListType >
• setDefaultReal() : Options
• setDefaultVertex1Address() : VIEW::Vertex2
• setDefaultVertex2Address() : VIEW::Vertex2
• setDefaultVertexAddress() : VIEW::Vertex
• setDefaultVertexAddresses() : VIEW::Vertex2
• setDegree() : PiecewisePolynomial
• setDeletable() : VIEW::Message
• setDeleteEntryEnabled() : VIEW::MainControl
• setDensity() : TriangulatedSES, TriangulatedSAS
• setDepth() : TBox3< T >
• setDimension() : TRegularData3D< ValueType >, TRegularData2D< ValueType >, TRegularData1D< ValueType >
• setDirection() : VIEW::LightSource
• setDistance() : VIEW::AtomDistanceColorProcessor, FragmentDistanceCollector
• setDockedSystem() : VIEW::DockResultDialog
• setDockingAlgorithm() : VIEW::DockProgressDialog
• setDockResult() : VIEW::DockResultDialog
• setDuplicateKeyCheck() : INIFile
• setEdge() : GraphTriangle< Vertex, Edge, Face >
• setElectronegativity() : Element
• setElement() : Atom
• setEnergyDifferenceBound() : EnergyMinimizer
• setEnergyOutputFrequency() : EnergyMinimizer, MolecularDynamics
• setEnergyToAbort() : EnergyMinimizer, MolecularDynamics
• setEpsilon() : RombergIntegrator< Function, DataType >
• setExponent() : MutablePower< Function, DataType >
• setExpression() : Selector, Expression
• setEyeDistance() : VIEW::Stage
• setFace() : GraphEdge< Vertex, Edge, Face >
• setFile() : Exception::GlobalExceptionHandler
• setFileName() : VIEW::FileObserver, VIEW::VRMLRenderer, VIEW::POVRenderer
• setFilename() : VIEW::PythonSettings, FragmentDB, AssignRadiusProcessor, ShiftModel, PDBInfo, Parameters, INIFile
• setFirst() : Division< First, Second, DataType >, Product< First, Second, DataType >, Subtraction< First, Second, DataType >, Addition< First, Second, DataType >
• setFirstAtom() : Bond
• setFirstEdge() : SmartsParser::SPNode
• setFirstSPEdge() : SmartsParser::SPEdge
• setFirstSPNode() : SmartsParser::SPEdge
• setFlushToDiskFrequency() : SnapShotManager
• setFocalDistance() : VIEW::Stage
• setFont() : VIEW::MainControlPreferences
• setForce() : Atom
• setForceField() : ForceFieldEvaluation, AmberEvaluation, SnapShotManager, ForceFieldComponent
• setFormalCharge() : Atom
• setFragmentDB() : ReconstructFragmentProcessor, FragmentDB::BuildBondsProcessor, FragmentDB::NormalizeNamesProcessor
• setFunction() : NumericalIntegrator< Function, DataType >, MutablePower< Function, DataType >, CubicFunction< Function, DataType >, SquareFunction< Function, DataType >, Reciprocal< Function, DataType >
• setGLRenderer() : VIEW::Scene, VIEW::MeshBuffer
• setGreen() : VIEW::ColorRGBA
• setGroup() : Element
• setGuest() : VIEW::DockWidget
• setHeight() : TBox3< T >
• setHeightVector() : TBox3< T >
• setHue() : VIEW::ColorHSV
• setIcon() : VIEW::ModularWidget
• setID() : Residue, Protein, Nucleotide, NucleicAcid, PDBInfo
• setIdentifier() : Embeddable
• setIdentity() : TQuaternion< T >, TMatrix4x4< T >
• setImprovedFlag() : StrangLBFGSMinimizer
• setIndex() : GraphVertex< Vertex, Edge, Face >, GraphTriangle< Vertex, Edge, Face >, GraphFace< Vertex, Edge, Face >, GraphEdge< Vertex, Edge, Face >, SnapShot
• setIndices() : TriangulatedSurface
• setInfoColor() : VIEW::Stage
• setINIFileSectionName() : VIEW::PreferencesEntry
• setInsertionCode() : Residue, Nucleotide
• setInteger() : Options
• setIntensity() : VIEW::LightSource, Peak< PositionType >
• setInternal() : SmartsParser::SPNode, SmartsParser::SPEdge
• setInterpolationBoundaries() : VIEW::ColorMap
• setIntersectionPoint() : RSEdge
• setIntervals() : PiecewiseFunction
• setIstream() : PersistenceManager
• setKineticEnergy() : SnapShot
• setLevel() : LogStream
• setLights() : VIEW::GLRenderer
• setLine() : INIFile, Exception::GlobalExceptionHandler
• setLoggingFilename() : VIEW::MainControl
• setLogicalOperator() : SmartsParser::SPNode, SmartsParser::SPEdge
• setLookAtPosition() : VIEW::Camera
• setLookUpVector() : VIEW::Camera
• setLowerBound() : LineSearch
• setMajorRadiusOfTorus() : RSEdge
• setMaxDistanceColor() : VIEW::AtomDistanceColorProcessor
• setMaxGradient() : EnergyMinimizer
• setMaximalNumberOfIterations() : MolecularDynamics
• setMaximalSimulationTime() : MolecularDynamics
• setMaximumDisplacement() : EnergyMinimizer
• setMaximumNumberOfErrors() : ForceField
• setMaximumUnassignedAtoms() : Templates, AssignBaseProcessor
• setMaxIterations() : VIEW::MinimizationDialog
• setMaxLevel() : LogStream
• setMaxNumberOfIterations() : EnergyMinimizer
• setMaxNumOfColumns() : ShiftedLVMMMinimizer
• setMaxNumOfStoredVectPairs() : StrangLBFGSMinimizer
• setMaxNumSteps() : RombergIntegrator< Function, DataType >
• setMaxSameEnergy() : EnergyMinimizer
• setMaxSteps() : LineSearch
• setMenuHelp() : VIEW::ModularWidget
• setMenuHint() : VIEW::ModularWidget, VIEW::MainControl
• setMesh() : VIEW::MeshBuffer
• setMessage() : Exception::GlobalExceptionHandler, Exception::GeneralException
• setMinimizer() : LineSearch
• setMinLevel() : LogStream
• setMinMaxColors() : VIEW::ColorMap
• setModelInformation() : VIEW::Representation
• setMultithreading() : VIEW::MainControl
• setName() : File, ResidueRotamerSet, SolventDescriptor, ShiftModule, ForceFieldComponent, ForceField, Element, Bond, AtomContainer, Atom, PDBInfo, Options, Exception::GlobalExceptionHandler
• setNeedsSSSR() : SmartsParser
• setNegate() : ExpressionTree
• setNextComponentNumberToSubTree() : SmartsParser
• setNormal() : TrianglePoint, SESVertex, RSFace
• setNot() : SmartsParser::SPNode, SmartsParser::SPEdge, SmartsParser::SPBond
• setNotProperty() : SmartsParser::SPAtom
• setNullDistanceColor() : VIEW::AtomDistanceColorProcessor
• setNumberDensity() : SolventDescriptor
• setNumberOfATOMRecords() : PDBInfo
• setNumberOfAtoms() : SnapShot
• setNumberOfColors() : VIEW::ColorMap
• setNumberOfHETATMRecords() : PDBInfo
• setNumberOfIteration() : MolecularDynamics
• setNumberOfIterations() : EnergyMinimizer
• setNumberOfModels() : PDBInfo
• setNumberOfRecords() : PDBInfo
• setNumberOfTorsions() : ResidueRotamerSet
• setOccupancy() : PDBAtom
• setOmega() : Peptides::AminoAcidDescriptor
• setOrder() : Bond
• setOrigin() : TRegularData3D< ValueType >, TRegularData2D< ValueType >, TRegularData1D< ValueType >
• setOstream() : VIEW::POVRenderer, PersistenceManager
• setParameters() : ShiftModule
• setPeriod() : Element
• setPhi() : Peptides::AminoAcidDescriptor
• setPhysStepWidth() : TFFT3D< ComplexTraits >, TFFT2D< ComplexTraits >, TFFT1D< ComplexTraits >
• setPoint() : TrianglePoint, TriangleEdge, Triangle, SESVertex, SASVertex, TBox3< T >
• setPort() : VIEW::Server
• setPosition() : VIEW::LightSource, Peak< PositionType >, Atom
• setPotentialEnergy() : SnapShot
• setPredicate() : CompositeIteratorTraits, ExpressionTree
• setPrefix() : VIEW::DownloadPDBFile, RuleEvaluator, LogStream
• setPreview() : VIEW::Scene
• setProperty() : SmartsParser::SPAtom, PropertyManager
• setProteinName() : Peptides::PeptideBuilder
• setProxy() : VIEW::MainControl
• setPsi() : Peptides::AminoAcidDescriptor
• setRadius() : VIEW::TwoColoredTube, VIEW::Tube, Atom
• setRange() : VIEW::ColorMap
• setRDF() : RDFIntegrator
• setRDFIntegrator() : Pair6_12InteractionEnergyProcessor
• setRDFParameters() : Pair6_12InteractionEnergyProcessor
• setReal() : Options
• setRecursive() : SmartsParser, SmartsParser::SPNode
• setRed() : VIEW::ColorRGBA
• setReferenceTemperature() : MolecularDynamics
• setRefresh() : VIEW::MinimizationDialog
• setRelativeToCamera() : VIEW::LightSource
• setRemotenessIndicator() : PDBAtom
• setRepresentation() : RadialDistributionFunction
• setRightVector() : TBox3< T >
• setRingSize() : RingFinder
• setRoot() : SmartsParser
• setRotamer() : ResidueRotamerSet
• setRotation() : TMatrix4x4< T >
• setRotationX() : TMatrix4x4< T >
• setRotationY() : TMatrix4x4< T >
• setRotationZ() : TMatrix4x4< T >
• setRow() : TMatrix4x4< T >
• setRSEdge() : SESFace, SESEdge
• setRSFace() : SESFace
• setRSVertex() : SESFace
• setSaturation() : VIEW::ColorHSV
• setScale() : TMatrix4x4< T >
• setScalingFactorFile() : GeneralizedBornModel
• setScoring() : ConformationSet
• setSecond() : Division< First, Second, DataType >, Product< First, Second, DataType >, Subtraction< First, Second, DataType >, Addition< First, Second, DataType >
• setSecondAtom() : Bond
• setSecondEdge() : SmartsParser::SPNode
• setSecondSPEdge() : SmartsParser::SPEdge
• setSecondSPNode() : SmartsParser::SPEdge
• setSelected() : VIEW::GeometricObjectSelectionMessage, Selectable
• setSelection() : VIEW::GeometricObjectSelectionMessage, VIEW::GenericSelectionMessage
• setSelection_() : VIEW::MolecularControl
• setSender() : VIEW::Message
• setShiftRange() : Bruker2DFile
• setSimulationThread() : VIEW::MainControl
• setSingular() : RSFace, RSEdge
• setSize() : VIEW::Renderer, VIEW::GLRenderer, BitVector
• setSnapShotFrequency() : EnergyMinimizer, MolecularDynamics
• setSnapShotManager() : VIEW::SnapshotVisualisationDialog
• setSoluteDC() : GeneralizedBornModel
• setSolventAtomDescriptorList() : SolventDescriptor
• setSolventDC() : GeneralizedBornModel
• setSolventDescriptor() : Pair6_12InteractionEnergyProcessor
• setSPAtom() : SmartsParser::SPNode
• setSPBond() : SmartsParser::SPEdge
• setSphere() : SASFace
• setSSSR() : SmartsParser
• setStage() : VIEW::Renderer, VIEW::SceneMessage
• setStatusbarText() : VIEW::ModularWidget, VIEW::MainControl
• setStickRadius() : VIEW::AddBallAndStickModel
• setSuffix() : VIEW::DownloadPDBFile
• setSwapSideBySideStereo() : VIEW::Stage
• setSymbol() : Element
• setSysPath() : PyInterpreter
• setSystem() : VIEW::FDPBDialog, SnapShotManager
• setSystems() : VIEW::DockDialog
• setTemperatureFactor() : PDBAtom
• setTemplateResidue() : ResidueRotamerSet
• setText() : VIEW::Label
• setTimeStep() : MolecularDynamics, MicroCanonicalMD, CanonicalMD
• setTorsionAngle_() : ResidueRotamerSet
• setTraits() : BaseIterator< Container, DataType, Position, Traits >
• setTrajectoryFile() : SnapShotManager
• setTransformation() : TransformationProcessor
• setTranslation() : TranslationProcessor, TMatrix4x4< T >
• setTransparency() : VIEW::ResidueTypeColorProcessor, VIEW::SecondaryStructureColorProcessor, VIEW::ResidueNameColorProcessor, VIEW::ElementColorProcessor, VIEW::ColorProcessor, VIEW::Representation
• setTriangle() : TriangleEdge
• setType() : VIEW::AddSurfaceModel, VIEW::LightSource, VIEW::SceneMessage, SurfaceProcessor, SESFace, SESEdge, SecondaryStructure, ExpressionTree, Bond, Atom
• setTypeName() : Atom
• setUnsignedChar() : BitVector
• setUnsignedInt() : BitVector
• setUnsignedLong() : BitVector
• setUnsignedShort() : BitVector
• setup() : GeometricFit, DockingAlgorithm, ConformationSet, AtomTyper, FDPB, GeneralizedBornModel, RotationalEntropyLoss, PolarSolvation, NonpolarSolvation, ChemScoreMetal, Lipophilic, HydrogenBond, CHPI, BuriedPolar, MMFF94Torsion, MMFF94StretchBend, MMFF94OutOfPlaneBend, MMFF94NonBonded, EnergyMinimizer, MolecularDynamics, MicroCanonicalMD, CanonicalMD, SnapShotManager, PeriodicBoundary, ForceFieldComponent, ForceField, CharmmTorsion, CharmmStretch, CharmmNonBonded, CharmmImproperTorsion, CharmmBend, AmberTorsion, AmberStretch, AmberNonBonded, AmberBend
• setupAtomArray() : FDPB
• setupBoundary() : FDPB
• setUpdateInterval() : VIEW::FileObserver
• setUpdateMethod() : ShiftedLVMMMinimizer, ConjugateGradientMinimizer
• setupEpsGrid() : FDPB
• setupForceField() : VIEW::MolecularStructure
• setupKappaGrid() : FDPB
• setupPhiGrid() : FDPB
• setupQGrid() : FDPB
• setupSASGrid() : FDPB
• setUsePotentialGrid() : VIEW::FieldLineCreator
• setValue() : VIEW::PreferencesEntry::ExtendedPreferencesObject, VIEW::HotkeyTable, VIEW::QColorTable, VIEW::ColorHSV, ResourceEntry, INIFile
• setVanDerWaalsRadius() : Element
• setVDWRadiusFactor() : VIEW::AddVanDerWaalsModel
• setVector() : Options
• setVelocity() : Atom
• setVertex() : VIEW::Vertex, GraphTriangle< Vertex, Edge, Face >, GraphEdge< Vertex, Edge, Face >
• setVertex1() : VIEW::Vertex2
• setVertex1Address() : VIEW::Vertex2
• setVertex2() : VIEW::Vertex2
• setVertex2Address() : VIEW::Vertex2
• setVertexAddress() : VIEW::Vertex
• setVertexAddresses() : VIEW::Vertex2
• setVertices() : VIEW::Vertex2
• setViewPoint() : VIEW::Camera
• setViewPoint_() : VIEW::Scene
• setWidgetStack() : VIEW::PreferencesEntry
• setWidgetStackName() : VIEW::PreferencesEntry
• setWidgetVisible() : VIEW::DockWidget
• setWidth() : Peak< PositionType >, TBox3< T >
• setWorkingDir() : VIEW::ModularWidget, VIEW::MainControl
• setXTol() : LineSearch
• setZEType() : SmartsParser::SPBond
• SHANNO : ConjugateGradientMinimizer
• shift() : TriangulatedSurface
• shift_s_ : ShiftedLVMMMinimizer
• shifted_direction_ : ShiftedLVMMMinimizer
• ShiftedLVMMMinimizer() : ShiftedLVMMMinimizer
• ShiftModel() : ShiftModel
• ShiftModule() : ShiftModule
• show() : VIEW::MainControl, VIEW::PubChemDialog, VIEW::Preferences, VIEW::LabelDialog, VIEW::GeometricFitDialog, VIEW::DockResultDialog, VIEW::DockProgressDialog, VIEW::DisplayProperties
• showAmberForceFieldOptions() : VIEW::MolecularStructure
• showCharmmForceFieldOptions() : VIEW::MolecularStructure
• showCoordinateSystem() : VIEW::Stage
• showDockingOptions() : VIEW::DockResultDialog
• showDocumentationForObject() : VIEW::HelpViewer
• showEntry() : VIEW::Preferences
• showExportPNGDialog() : VIEW::Scene
• showFilename() : VIEW::MolecularControl
• showHelp() : VIEW::HelpViewer
• showHelpFor() : VIEW::HelpViewer
• showInfos() : VIEW::Scene
• showOnlyInLogView() : VIEW::LogEvent
• showScoringOptions_() : VIEW::DockResultDialog
• showSelectorHelp() : VIEW::MolecularControl
• showSnapshot() : VIEW::DockResultDialog
• showStackPage() : VIEW::PreferencesEntry
• showText() : VIEW::Scene
• showViewPoint_() : VIEW::Scene
• shrink() : TriangulatedSurface
• sig_w : CharmmEEF1::Values
• SimpleBase() : SimpleBase
• SimpleBox() : VIEW::SimpleBox
• SimpleExperiment1D() : SimpleExperiment1D
• simulate() : MolecularDynamics
• simulateIterations() : MolecularDynamics, MicroCanonicalMD, CanonicalMD
• simulateTime() : MolecularDynamics
• Site : Enumerator< Container, SiteIterator, Variant >
• SiteList : Enumerator< Container, SiteIterator, Variant >
• size() : ConformationSet, Substring, HashSet< Key >, HashMap< Key, T >
• size_ : TRegularData3D< ValueType >, TRegularData2D< ValueType >, HashMap< Key, T >
• SizeOfSSSR() : SizeOfSSSR
• skipCurrentRecord() : PDBFile
• skipLines() : LineBasedFile
• skipped_records_ : PDBInfo
• SLICKEnergy() : SLICKEnergy
• SLICKScore() : SLICKScore
• SmartsParser() : SmartsParser
• SnapShot() : SnapShot
• snapshot_ : EnergyMinimizer
• SNAPSHOT_FREQUENCY : EnergyMinimizer::Option, MolecularDynamics::Option
• snapshot_frequency_ : EnergyMinimizer
• snapshot_order_ : DockResult::Scoring_, ConformationSet
• snapShotInputTest() : VIEW::SnapshotVisualisationDialog
• SnapShotManager() : SnapShotManager
• SnapshotVisualisationDialog() : VIEW::SnapshotVisualisationDialog
• SockAddr() : SockAddr
• Socket : TCPTransfer
• SocketBuf() : SocketBuf
• SockInetAddr() : SockInetAddr
• SockInetBuf() : SockInetBuf
• SOLUTE_DC : FDPB::Default, FDPB::Option
• SOLVATION_CUTOFF : CharmmFF::Default, CharmmFF::Option
• SOLVATION_CUTON : CharmmFF::Default, CharmmFF::Option
• solve() : FDPB
• SOLVENT_DC : FDPB::Default, FDPB::Option
• SOLVENT_FILENAME : PairExpInteractionEnergyProcessor::Option, Pair6_12InteractionEnergyProcessor::Option
• SOLVENT_NUMBER_DENSITY : ReissCavFreeEnergyProcessor::Default, ReissCavFreeEnergyProcessor::Option, PierottiCavFreeEnergyProcessor::Default, PierottiCavFreeEnergyProcessor::Option, PCMCavFreeEnergyProcessor::Default, PCMCavFreeEnergyProcessor::Option, Pair6_12InteractionEnergyProcessor::Default, Pair6_12InteractionEnergyProcessor::Option
• SolventAccessibleSurface() : SolventAccessibleSurface
• SolventDescriptor() : SolventDescriptor
• SolventExcludedSurface() : SolventExcludedSurface
• SolventParameter() : SolventParameter
• sort() : RotamerLibrary, ResidueRotamerSet
• sorted_by_ : DockResult
• sortTable() : VIEW::DockResultDialog
• sp_atom_ : SmartsParser::SPNode
• SPACING : FDPB::Default, FDPB::Option
• spacing_ : TRegularData3D< ValueType >, TRegularData2D< ValueType >, TRegularData1D< ValueType >
• SPAtom() : SmartsParser::SPAtom
• SPBond() : SmartsParser::SPBond
• SPBondOrder : SmartsParser::SPBond
• specificSetup() : SLICKScore, SLICKEnergy, MMFF94, StrangLBFGSMinimizer, SteepestDescentMinimizer, ShiftedLVMMMinimizer, EnergyMinimizer, ConjugateGradientMinimizer, MolecularDynamics, MicroCanonicalMD, CanonicalMD, ForceField, CharmmFF, AmberFF
• specificSetup_() : AtomTyper
• SPEdge() : SmartsParser::SPEdge
• SPEED_OF_LIGHT : Constant
• Sphere() : VIEW::Sphere
• splice() : System, SecondaryStructure, Residue, Nucleotide, Molecule, Chain, AtomContainer, Composite
• spliceAfter() : System, SecondaryStructure, Residue, Nucleotide, Molecule, Chain, AtomContainer, Composite
• spliceBefore() : System, SecondaryStructure, Residue, Nucleotide, Molecule, Chain, AtomContainer, Composite
• split() : String
• splitQuoted() : String
• SPNode() : SmartsParser::SPNode
• SQUARE_ROOT : ShiftedLVMMMinimizer
• SquareFunction() : SquareFunction< Function, DataType >
• sssr_ : SmartsParser
• Stage() : VIEW::Stage
• StageSettings() : VIEW::StageSettings
• stamp() : TimeStamp, Composite
• StampType : Composite
• start() : VIEW::FileObserver, VIEW::ResidueNumberColorProcessor, VIEW::InterpolateColorProcessor, VIEW::ColorProcessor, VIEW::AddBackboneModel, Timer, SurfaceProcessor, ResidueChecker, ReconstructFragmentProcessor, FragmentDistanceCollector, GeometricCenterProcessor, BoundingBoxProcessor, FragmentDB::BuildBondsProcessor, FragmentDB::NormalizeNamesProcessor, GeometricFit, AssignChargeProcessor, AssignRadiusProcessor, BuildBondsProcessor, AddHydrogenProcessor, ShiftModule, ShiftModel, JohnsonBoveyShiftProcessor, HBondShiftProcessor, SimpleExperiment1D, EFShiftProcessor, CreateSpectrumProcessor, AssignShiftProcessor, MMFF94ChargeProcessor, RuleProcessor, Selector, EnergyProcessor, BinaryProcessor< T1, T2 >, UnaryProcessor< T >
• start_ : DSN6File
• startDefinition() : VIEW::GLDisplayList
• startDocking() : VIEW::DockingController
• STARTED_UPDATE : VIEW::RepresentationMessage
• startInterpreter() : VIEW::PyWidget
• startOutput() : PersistenceManager
• startsWith() : LineBasedFile
• state : SmartsParser
• Status : TCPTransfer
• SteepestDescentMinimizer() : SteepestDescentMinimizer
• step_ : EnergyMinimizer
• step_width_ : RotamerLibrary
• StereoMode : VIEW::GLRenderer
• stop() : VIEW::FileObserver, Timer
• stopedSimulation() : VIEW::MainControl
• stopSimulation() : VIEW::MainControl
• STORE_SKIPPED_RECORDS : PDBFile::Default, PDBFile::Option
• store_skipped_records_ : PDBFile
• storeConnections_() : FragmentDB::BuildBondsProcessor
• stored_s_ : StrangLBFGSMinimizer
• stored_y_ : StrangLBFGSMinimizer
• storeGradientEnergy() : EnergyMinimizer
• storeValues() : VIEW::PreferencesEntry
• StrangLBFGSMinimizer() : StrangLBFGSMinimizer
• STREAM_HEADER : XDRPersistenceManager
• STREAM_TRAILER : XDRPersistenceManager
• StretchBendMap : MMFF94StretchBendParameters
• STRICT_LINE_CHECKING : PDBFile::Default, PDBFile::Option
• String() : String
• STRING : NamedProperty
• StringHashMap() : StringHashMap< Value >
• StructureMapper() : StructureMapper
• structures_ : ConformationSet
• substitute() : GraphVertex< Vertex, Edge, Face >, GraphTriangle< Vertex, Edge, Face >, GraphFace< Vertex, Edge, Face >, GraphEdge< Vertex, Edge, Face >, String
• Substring() : Substring
• Subtraction() : Subtraction< First, Second, DataType >
• SURFACE__EXTERNAL : PairExpInteractionEnergyProcessor
• SURFACE__SAS : PairExpInteractionEnergyProcessor
• SURFACE__SES : PairExpInteractionEnergyProcessor
• SURFACE__UNKNOWN : PairExpInteractionEnergyProcessor
• SURFACE_FILENAME : PairExpInteractionEnergyProcessor::Default, PairExpInteractionEnergyProcessor::Option, Pair6_12InteractionEnergyProcessor::Default, Pair6_12InteractionEnergyProcessor::Option
• SURFACE_TENSION : UhligCavFreeEnergyProcessor::Default, UhligCavFreeEnergyProcessor::Option
• SURFACE_TYPE : GeometricFit::Option, PairExpInteractionEnergyProcessor::Default, PairExpInteractionEnergyProcessor::Option, Pair6_12InteractionEnergyProcessor::Default, Pair6_12InteractionEnergyProcessor::Option
• SurfaceBase() : SurfaceBase
• SurfaceProcessor() : SurfaceProcessor
• SurfaceType : PairExpInteractionEnergyProcessor
• swap() : VIEW::TwoColoredTube, VIEW::TwoColoredLine, VIEW::Tube, VIEW::Sphere, VIEW::Point, VIEW::Mesh, VIEW::Line, VIEW::Label, VIEW::Disc, VIEW::GeometricObject, VIEW::Vertex2, VIEW::Vertex, VIEW::ColorUnitHue, VIEW::ColorUnit, VIEW::ColorRGBA, VIEW::ColorHSV, VIEW::MultiColorExtension, VIEW::ColorExtension2, TVector4< T >, TVector3< T >, TSphere3< T >, TSimpleBox3< T >, TQuaternion< T >, TMatrix4x4< T >, TLine3< T >, TCircle3< T >, TBox3< T >, TAngle< T >, SecondaryStructure, Residue, Protein, PDBAtom, Nucleotide, NucleicAcid, Molecule, Chain, Bond, AtomContainer, Atom, StringHashMap< Value >, String, List< Value >, HashSet< Key >, HashMap< Key, T >, Selectable, PropertyManager, Composite, BaseIterator< Container, DataType, Position, Traits >
• swap_bytes_ : DSN6File
• swapSideBySideStereo() : VIEW::Stage
• swapValues_() : VIEW::GeometricFitDialog, VIEW::DockDialog
• switchShowWidget() : VIEW::Scene
• switchString() : LineBasedFile
• sym_size : TRRFile::TRRHeader
• sync() : LogStreamBuf
• SyntaxTree() : ExpressionParser::SyntaxTree
• sys_read() : SocketBuf
• sys_write() : SocketBuf
• System() : System
• system : GAMESSLogFile
• system_ : ConformationSet

- t -

• takeSnapShot() : EnergyMinimizer, SnapShotManager, SnapShot
• takeStep() : LineSearch
• TAngle() : TAngle< T >
• TBox3() : TBox3< T >
• TCircle3() : TCircle3< T >
• TContour() : TContour< T >
• TContourLine() : TContourLine< T >
• TContourSurface() : TContourSurface< T >
• TCPTransfer() : TCPTransfer
• TEMPERATURE : FDPB::Default, FDPB::Option
• Templates() : Templates
• tenBackwardClicked() : VIEW::SnapshotVisualisationDialog
• tenForwardClicked() : VIEW::SnapshotVisualisationDialog
• terminate() : Exception::GlobalExceptionHandler
• test() : LineBasedFile
• tested_beers_ : RingPerceptionProcessor
• TestType : ResidueChecker
• TextPersistenceManager() : TextPersistenceManager
• TFFT2D() : TFFT2D< ComplexTraits >
• TFFT3D() : TFFT3D< ComplexTraits >
• third : GraphTriangle< Vertex, Edge, Face >, Triple< T1, T2, T3 >, Quadruple< T1, T2, T3, T4 >
• threshold_ : TContourSurface< T >
• through() : String
• throw() : CHPI, TFFT3D< ComplexTraits >, TFFT2D< ComplexTraits >, TFFT1D< ComplexTraits >, PTE_
• time_ : TimeStamp
• TIME_STEP : MolecularDynamics::Option
• Timer() : Timer
• timer() : VIEW::Server
• TimeStamp() : TimeStamp
• timestep_index : TRRFile::TRRHeader
• timestep_time : TRRFile::TRRHeader
• title_string : TRRFile::TRRHeader
• title_string_length : TRRFile::TRRHeader
• TLine3() : TLine3< T >
• TMatrix4x4() : TMatrix4x4< T >
• tnode_to_atom_ : RingPerceptionProcessor
• toBegin() : CompositeIteratorTraits, ConstForwardIterator< Container, DataType, Position, Traits >, ConstBidirectionalIterator< Container, DataType, Position, Traits >
• toBool() : String
• toChar() : String
• toDegree() : TAngle< T >
• toDouble() : String
• toEnd() : CompositeIteratorTraits, ConstForwardIterator< Container, DataType, Position, Traits >, ConstBidirectionalIterator< Container, DataType, Position, Traits >
• toFloat() : String
• toggle() : BitVector
• toggleBit() : BitVector
• toggleProperty() : PropertyManager
• toInt() : String
• toLong() : String
• toLower() : Substring, String
• TOOLS : VIEW::MainControl
• TOOLS_GRID : VIEW::MainControl
• TOOLS_PYTHON : VIEW::MainControl
• top_size : TRRFile::TRRHeader
• toRadian() : TAngle< T >
• toRBegin() : CompositeIteratorTraits, ConstBidirectionalIterator< Container, DataType, Position, Traits >
• toREnd() : CompositeIteratorTraits, ConstBidirectionalIterator< Container, DataType, Position, Traits >
• TorsionsMap : MMFF94TorsionParameters
• toShort() : String
• toString() : VIEW::Representation, Substring
• TotalNegativePartialCharge() : TotalNegativePartialCharge
• TotalPositivePartialCharge() : TotalPositivePartialCharge
• toUnsignedChar() : String
• toUnsignedInt() : String
• toUnsignedLong() : String
• toUnsignedShort() : String
• toUpper() : Substring, String
• TPlane3() : TPlane3< T >
• TQuaternion() : TQuaternion< T >
• TrajectoryFile() : TrajectoryFile
• transfer() : TCPTransfer
• transform() : TransformationManager
• Transformation : File
• TRANSFORMATION_EXEC_PREFIX : File
• TRANSFORMATION_FILE_PREFIX : File
• TRANSFORMATION_FTP_PREFIX : File
• TRANSFORMATION_HTTP_PREFIX : File
• transformation_methods_ : TransformationManager
• TransformationManager() : TransformationManager
• TransformationProcessor() : TransformationProcessor
• translate() : VIEW::Camera, TMatrix4x4< T >, TFFT3D< ComplexTraits >, TFFT2D< ComplexTraits >, TFFT1D< ComplexTraits >
• TranslationProcessor() : TranslationProcessor
• transpose() : TMatrix4x4< T >
• trapezoid() : RombergIntegrator< Function, DataType >
• tree : FragmentDB
• TRegularData1D() : TRegularData1D< ValueType >
• TRegularData2D() : TRegularData2D< ValueType >
• TRegularData3D() : TRegularData3D< ValueType >
• Triangle() : Triangle
• triangle : TSurface< T >
• TriangleEdge() : TriangleEdge
• TrianglePoint() : TrianglePoint
• TriangulatedSAS() : TriangulatedSAS
• TriangulatedSES() : TriangulatedSES
• TriangulatedSphere() : TriangulatedSphere
• TriangulatedSurface() : TriangulatedSurface
• TRILINEAR : FDPB::ChargeDistribution
• trim() : String
• trimLeft() : String
• trimRight() : String
• Triple() : Triple< T1, T2, T3 >
• TRIPOS : MOL2File
• TRRFile() : TRRFile
• truncate() : File, String
• TSimpleBox3() : TSimpleBox3< T >
• TSphere3() : TSphere3< T >
• Tube() : VIEW::Tube
• TVector2() : TVector2< T >
• TVector3() : TVector3< T >
• TVector4() : TVector4< T >
• TwoColoredLine() : VIEW::TwoColoredLine
• TwoColoredTube() : VIEW::TwoColoredTube
• type : SolventAtomDescriptor, ExpressionParser::SyntaxTree
• Type : VIEW::DatasetMessage, File, SESFace, SESEdge, SecondaryStructure, ExpressionTree, NamedProperty, MolecularInformation, VersionInfo, FragmentDB, Atom
• type_ : SecondaryStructure
• TYPE__ATOM : MolecularInformation
• TYPE__BOND : MolecularInformation
• TYPE__CHAIN : MolecularInformation
• TYPE__FRAGMENT : MolecularInformation
• TYPE__MOLECULE : MolecularInformation
• TYPE__PROTEIN : MolecularInformation
• TYPE__RESIDUE : MolecularInformation
• TYPE__SECONDARY_STRUCTURE : MolecularInformation
• TYPE__SYSTEM : MolecularInformation
• TYPE__UNKNOWN : MolecularInformation
• TypenameRuleProcessor() : TypenameRuleProcessor
• TypeRuleProcessor() : TypeRuleProcessor
• Types : VIEW::LightSource
• typeSelected() : VIEW::LightSettings

- u -

• UhligCavFreeEnergyProcessor() : UhligCavFreeEnergyProcessor
• UnaryProcessor() : UnaryProcessor< T >
• unbind() : Substring
• UNDEFINED : VIEW::RepresentationMessage, VIEW::CompositeMessage, VIEW::DatasetMessage, ParameterSection, INIFile
• UNIFORM : FDPB::DielectricSmoothing, FDPB::ChargeDistribution
• UNIT_VALUE : ShiftedLVMMMinimizer
• UNKNOWN : Element
• UNKNOWN_TYPE : Atom
• unlockComposites() : VIEW::ModularWidget
• unlockCompositesFor() : VIEW::MainControl
• unmap() : VIEW::PyWidget
• unregisterConnectionObject() : VIEW::ConnectionObject
• unregisterForHelpSystem() : VIEW::HelpViewer
• unregisterModule() : ShiftModel
• unregisterObjectCreator() : VIEW::Server
• unregisterThis() : Embeddable
• unregisterTransformation() : TransformationManager
• unscaled_direction_ : ConjugateGradientMinimizer
• UNSIGNED_INT : NamedProperty
• UPDATE : VIEW::RepresentationMessage, VIEW::DatasetMessage
• update() : VIEW::Scene, VIEW::Representation, VIEW::MainControl, VIEW::LightSettings, MMFF94NonBonded, ForceFieldComponent, ForceField, AmberStretch, AmberNonBonded
• update_() : VIEW::Representation
• UPDATE_CAMERA : VIEW::SceneMessage
• UPDATE_METHOD : ShiftedLVMMMinimizer::Option, ConjugateGradientMinimizer::Default, ConjugateGradientMinimizer::Option
• updateAdditionalAtomInfo_() : PDBFile
• updateAlwaysNeeded() : VIEW::ColorProcessor
• updateBackgroundColor() : VIEW::GLRenderer
• updateCamera() : VIEW::GLRenderer
• updateCamera_() : VIEW::Scene
• updateContextMenu() : VIEW::MolecularControl
• updateDirection() : StrangLBFGSMinimizer, SteepestDescentMinimizer, ShiftedLVMMMinimizer, EnergyMinimizer, ConjugateGradientMinimizer
• updateEnergy() : ChemScoreMetal, MMFF94Torsion, MMFF94StretchBend, MMFF94OutOfPlaneBend, MMFF94NonBonded, EnergyMinimizer, ForceFieldComponent, ForceField, CharmmTorsion, CharmmStretch, CharmmNonBonded, CharmmImproperTorsion, CharmmBend, AmberTorsion, AmberStretch, AmberNonBonded, AmberBend
• updateFile() : VIEW::FileObserver
• updateForces() : ChemScoreMetal, MMFF94Torsion, MMFF94StretchBend, MMFF94OutOfPlaneBend, MMFF94NonBonded, EnergyMinimizer, ForceFieldComponent, ForceField, CharmmTorsion, CharmmStretch, CharmmNonBonded, CharmmImproperTorsion, CharmmBend, AmberTorsion, AmberStretch, AmberNonBonded, AmberBend
• updateFromStage() : VIEW::StageSettings, VIEW::LightSettings
• UpdateMethod : ShiftedLVMMMinimizer, ConjugateGradientMinimizer
• updateMolecules() : PeriodicBoundary
• updateOfRepresentationRunning() : VIEW::MainControl
• updateProgress_() : VIEW::DockProgressDialog
• updateRepresentation() : VIEW::GeometricControl
• updateRepresentationsOf() : VIEW::MainControl
• updateRunning() : VIEW::RepresentationManager
• updateSelection() : VIEW::MolecularControl, VIEW::DatasetControl
• updateStructure_() : VIEW::BALLThread
• updt_method_ : ShiftedLVMMMinimizer, ConjugateGradientMinimizer
• updt_u_ : ShiftedLVMMMinimizer
• updt_v_ : ShiftedLVMMMinimizer
• UPPER : FDPB::Option
• UPPERCASE : RegularExpression
• upwardClicked() : VIEW::DockResultDialog
• USE_EEF1 : CharmmFF::Default, CharmmFF::Option
• USE_RDF : PairExpInteractionEnergyProcessor::Default, PairExpInteractionEnergyProcessor::Option, Pair6_12InteractionEnergyProcessor::Default, Pair6_12InteractionEnergyProcessor::Option
• useCompileAndExecuteMode() : VIEW::GLDisplayList
• useCompileMode() : VIEW::GLDisplayList
• useMultithreading() : VIEW::MainControl
• USER : VIEW::MainControl

- v -

• V : CharmmEEF1::Values
• VACUUM_PERMEABILITY : Constant
• VACUUM_PERMITTIVITY : Constant
• val : MMFF94AtomType
• valid : MMFF94AtomType
• valid_ : ResidueRotamerSet, EnergyMinimizer
• validate() : RotamerLibrary
• value : TAngle< T >
• values : CharmmEEF1::Data
• ValueType : PyIndexList, PyDatasetVector, PyCompositeList, PyColorRGBAVector, StringHashMap< Value >
• VariantVector : Enumerator< Container, SiteIterator, Variant >
• VDW_CUTOFF : MMFF94::Default, MMFF94::Option, CharmmFF::Default, CharmmFF::Option, AmberFF::Default, AmberFF::Option
• VDW_CUTON : MMFF94::Default, MMFF94::Option, CharmmFF::Default, CharmmFF::Option, AmberFF::Default, AmberFF::Option
• VdWSurface() : VdWSurface
• VdWVolume() : VdWVolume
• VectorType : TRegularData3D< ValueType >, TRegularData2D< ValueType >, TRegularData1D< ValueType >, TContourSurface< T >, TContourLine< T >
• velocity_data_size : TRRFile::TRRHeader
• VERBOSITY : UhligCavFreeEnergyProcessor::Default, UhligCavFreeEnergyProcessor::Option, ReissCavFreeEnergyProcessor::Default, ReissCavFreeEnergyProcessor::Option, FDPB::Default, FDPB::Option, PierottiCavFreeEnergyProcessor::Default, PierottiCavFreeEnergyProcessor::Option, PCMCavFreeEnergyProcessor::Default, PCMCavFreeEnergyProcessor::Option, PairExpRDFIntegrator::Option, PairExpInteractionEnergyProcessor::Default, PairExpInteractionEnergyProcessor::Option, Pair6_12RDFIntegrator::Option, Pair6_12InteractionEnergyProcessor::Default, Pair6_12InteractionEnergyProcessor::Option, PDBFile::Default, PDBFile::Option
• verbosity_ : PDBFile
• VERSION : TRRFile::TRRHeader
• vertex : VIEW::QuadMesh, TSurface< T >
• Vertex : VIEW::Vertex, TSurface< T >
• Vertex2() : VIEW::Vertex2
• VertexAdjacency() : VertexAdjacency
• VertexAdjacencyEquality() : VertexAdjacencyEquality
• vir_size : TRRFile::TRRHeader
• visit() : Visitor< Host >, MolecularInformation
• visited_atoms : SmartsMatcher::RecStruct_, SmartsMatcher::RecStructCore_
• visited_bonds : SmartsMatcher::RecStruct_, SmartsMatcher::RecStructCore_
• visited_edges : SmartsMatcher::RecStruct_, SmartsMatcher::RecStructCore_
• Visitor() : Visitor< Host >
• VISUALIZE_END : VIEW::DatasetMessage
• VRMLColorRGBA() : VIEW::VRMLRenderer
• VRMLRenderer() : VIEW::VRMLRenderer
• VRMLVector3() : VIEW::VRMLRenderer

- w -

• wait() : VIEW::MainControl
• waitForUpdateOfRepresentations_() : VIEW::BALLThread
• warn() : LogStream
• WARNING_LEVEL : LogStream
• wasAborted() : EnergyMinimizer
• wheelEvent() : VIEW::Scene, VIEW::EditableScene
• WHITESPACE : RegularExpression
• willBeUpdated() : VIEW::RepresentationManager
• WINDOWS : VIEW::MainControl
• work_val_ : StrangLBFGSMinimizer
• write() : VIEW::DatasetController, TVector3< T >, XYZFile, SDFile, PDBFile, MOLFile, MOL2File, KCFFile, JCAMPFile, INIFile, HINFile, GenericMolFile, GAMESSLogFile, GAMESSDatFile, Options, BitVector, TimeStamp, PreciseTime, Selectable, PropertyManager
• writeAtomLine_() : MOLFile
• writeBondLine_() : MOLFile
• writeCountsLine_() : MOLFile
• writeDCDFile() : ConformationSet
• writeDockResult() : DockResult
• writeFile() : VIEW::MolecularFileDialog
• writeHeader() : TrajectoryFile, DSN6File, DCDFile, XDRPersistenceManager, TextPersistenceManager, PersistenceManager
• writeHINFile() : VIEW::MolecularFileDialog
• writeMOL2File() : VIEW::MolecularFileDialog
• writeMOLFile() : VIEW::MolecularFileDialog
• writeName() : XDRPersistenceManager, TextPersistenceManager, PersistenceManager
• writeNextHeader() : TRRFile
• writeObjectArray() : PersistenceManager
• writeObjectHeader() : PersistenceManager
• writeObjectPointer() : PersistenceManager
• writeObjectPointerArray() : PersistenceManager
• writeObjectPointerArrayHeader() : XDRPersistenceManager, TextPersistenceManager, PersistenceManager
• writeObjectPointerArrayTrailer() : XDRPersistenceManager, TextPersistenceManager, PersistenceManager
• writeObjectPointerHeader() : XDRPersistenceManager, TextPersistenceManager, PersistenceManager
• writeObjectReference() : PersistenceManager
• writeObjectReferenceHeader() : XDRPersistenceManager, TextPersistenceManager, PersistenceManager
• writeObjectTrailer() : PersistenceManager
• writeOptionFile() : Options
• writePDBFile() : VIEW::MolecularFileDialog
• writePreferenceEntries() : VIEW::PreferencesEntry, VIEW::PythonSettings, VIEW::MainControlPreferences
• writePreferences() : VIEW::Scene, VIEW::PyWidget, VIEW::MolecularStructure, VIEW::MolecularControl, VIEW::DockWidget, VIEW::DockingController, VIEW::ModularWidget, VIEW::MainControl, VIEW::Preferences, VIEW::LabelDialog, VIEW::GeometricFitDialog, VIEW::DownloadPDBFile, VIEW::DockDialog
• writePrimitive() : PersistenceManager
• writePrimitiveHeader() : XDRPersistenceManager, TextPersistenceManager, PersistenceManager
• writePrimitiveTrailer() : XDRPersistenceManager, TextPersistenceManager, PersistenceManager
• writePropertyBlock_() : SDFile
• writeRawRecord_() : PDBFile
• writeRecord_() : PDBFile
• writeSDFile() : VIEW::MolecularFileDialog
• writeStorableHeader() : XDRPersistenceManager, TextPersistenceManager, PersistenceManager
• writeStorableObject() : PersistenceManager
• writeStorableTrailer() : XDRPersistenceManager, TextPersistenceManager, PersistenceManager
• writeStreamHeader() : XDRPersistenceManager, TextPersistenceManager, PersistenceManager
• writeStreamTrailer() : XDRPersistenceManager, TextPersistenceManager, PersistenceManager
• writeTrailer() : XDRPersistenceManager, TextPersistenceManager, PersistenceManager
• writeXYZFile() : VIEW::MolecularFileDialog

- x -

• x : TVector4< T >, TVector3< T >, TVector2< T >
• xaxis_ : DSN6File
• XDRPersistenceManager() : XDRPersistenceManager
• XYZFile() : XYZFile

- y -

• y : TVector4< T >, TVector3< T >, TVector2< T >
• y_i_ : ConjugateGradientMinimizer
• y_t_ : ConjugateGradientMinimizer
• yaxis_ : DSN6File

- z -

• z : TVector4< T >, TVector3< T >
• ZagrebIndex() : ZagrebIndex
• zaxis_ : DSN6File
• ze_type_ : SmartsParser::SPBond
• ZERO : FDPB::Boundary, PreciseTime

- ~ -

• ~AddBackboneModel() : VIEW::AddBackboneModel
• ~AddBallAndStickModel() : VIEW::AddBallAndStickModel
• ~AddCartoonModel() : VIEW::AddCartoonModel
• ~Addition() : Addition< First, Second, DataType >
• ~AddLineModel() : VIEW::AddLineModel
• ~AddSurfaceModel() : VIEW::AddSurfaceModel
• ~AddVanDerWaalsModel() : VIEW::AddVanDerWaalsModel
• ~AmberBend() : AmberBend
• ~AmberConfigurationDialog() : VIEW::AmberConfigurationDialog
• ~AmberFF() : AmberFF
• ~AmberNonBonded() : AmberNonBonded
• ~AmberStretch() : AmberStretch
• ~AmberTorsion() : AmberTorsion
• ~AminoAcidDescriptor() : Peptides::AminoAcidDescriptor
• ~AnisotropyShiftProcessor() : AnisotropyShiftProcessor
• ~AromaticityProcessor() : AromaticityProcessor
• ~AssignShiftProcessor() : AssignShiftProcessor
• ~Atom() : Atom
• ~AtomBijection() : AtomBijection
• ~AtomBondModelBaseProcessor() : VIEW::AtomBondModelBaseProcessor
• ~AtomContainer() : AtomContainer
• ~AtomicPolarizabilities() : AtomicPolarizabilities
• ~AtomInformationContent() : AtomInformationContent
• ~AtomOverview() : VIEW::AtomOverview
• ~AtomTypes() : AtomTypes
• ~AtomVector() : AtomVector
• ~AutoDeletable() : AutoDeletable
• ~BalabanIndexJ() : BalabanIndexJ
• ~BaseIterator() : BaseIterator< Container, DataType, Position, Traits >
• ~BidirectionalIterator() : BidirectionalIterator< Container, DataType, Position, Traits >
• ~BinaryProcessor() : BinaryProcessor< T1, T2 >
• ~Bit() : Bit
• ~BitVector() : BitVector
• ~Bond() : Bond
• ~BondPolarizabilities() : BondPolarizabilities
• ~Box() : VIEW::Box
• ~Bruker1DFile() : Bruker1DFile
• ~Bruker2DFile() : Bruker2DFile
• ~BuildBondsProcessor() : BuildBondsProcessor
• ~BuriedPolar() : BuriedPolar
• ~Camera() : VIEW::Camera
• ~CanonicalMD() : CanonicalMD
• ~Chain() : Chain
• ~ChainBuilder() : ChainBuilder
• ~ChargeRuleProcessor() : ChargeRuleProcessor
• ~CharmmBend() : CharmmBend
• ~CharmmConfigurationDialog() : VIEW::CharmmConfigurationDialog
• ~CharmmEEF1() : CharmmEEF1
• ~CharmmFF() : CharmmFF
• ~CharmmImproperTorsion() : CharmmImproperTorsion
• ~CharmmNonBonded() : CharmmNonBonded
• ~CharmmStretch() : CharmmStretch
• ~CharmmTorsion() : CharmmTorsion
• ~ChemScoreMetal() : ChemScoreMetal
• ~CHPI() : CHPI
• ~ClaverieParameter() : ClaverieParameter
• ~ClearShiftProcessor() : ClearShiftProcessor
• ~Client() : Client
• ~ClippingDialog() : VIEW::ClippingDialog
• ~ClippingPlane() : VIEW::ClippingPlane
• ~ColorExtension2() : VIEW::ColorExtension2
• ~ColorHSV() : VIEW::ColorHSV
• ~ColoringSettingsDialog() : VIEW::ColoringSettingsDialog
• ~ColorMap() : VIEW::ColorMap
• ~ColorProcessor() : VIEW::ColorProcessor
• ~ColorRGBA() : VIEW::ColorRGBA
• ~ColorUnit() : VIEW::ColorUnit
• ~ColorUnitHue() : VIEW::ColorUnitHue
• ~Comparator() : Comparator< T >
• ~Compare_() : VIEW::DockResultDialog::Compare_, DockResult::Compare_
• ~ComposedEnergyProcessor() : ComposedEnergyProcessor
• ~Composite() : Composite
• ~CompositeIteratorTraits() : CompositeIteratorTraits
• ~CompositeManager() : VIEW::CompositeManager
• ~CompositeMessage() : VIEW::CompositeMessage
• ~ConjugateGradientMinimizer() : ConjugateGradientMinimizer
• ~ConnectionObject() : VIEW::ConnectionObject
• ~ConnectivityBase() : ConnectivityBase
• ~CosineTorsion() : CosineTorsion
• ~CreateSpectrumProcessor() : CreateSpectrumProcessor
• ~CubicFunction() : CubicFunction< Function, DataType >
• ~Dataset() : VIEW::Dataset
• ~DatasetControl() : VIEW::DatasetControl
• ~DCDFile() : DCDFile
• ~Density() : Density
• ~Descriptor() : Descriptor
• ~Directory() : Directory
• ~Disc() : VIEW::Disc
• ~DisplayProperties() : VIEW::DisplayProperties
• ~Division() : Division< First, Second, DataType >
• ~DockDialog() : VIEW::DockDialog
• ~DockingController() : VIEW::DockingController
• ~DockProgressDialog() : VIEW::DockProgressDialog
• ~DockResult() : DockResult
• ~DockResultDialog() : VIEW::DockResultDialog
• ~DSN6File() : DSN6File
• ~EditableScene() : VIEW::EditableScene
• ~EFShiftProcessor() : EFShiftProcessor
• ~ElectrostaticPotentialCalculator() : ElectrostaticPotentialCalculator
• ~Element() : Element
• ~EnergyMinimizer() : EnergyMinimizer
• ~EnergyProcessor() : EnergyProcessor
• ~Enumerator() : Enumerator< Container, SiteIterator, Variant >
• ~EnumeratorIndex() : EnumeratorIndex
• ~Experiment() : Experiment< PeakListType >
• ~Expression() : Expression
• ~ExpressionPredicate() : ExpressionPredicate
• ~ExpressionTree() : ExpressionTree
• ~FDPB() : FDPB
• ~FDPBDialog() : VIEW::FDPBDialog
• ~FieldLineCreator() : VIEW::FieldLineCreator
• ~FieldLinesDialog() : VIEW::FieldLinesDialog
• ~File() : File
• ~ForceField() : ForceField
• ~ForceFieldComponent() : ForceFieldComponent
• ~ForceFieldParameters() : ForceFieldParameters
• ~ForceModel() : VIEW::ForceModel
• ~FormalCharge() : FormalCharge
• ~Fragment() : Fragment
• ~FragmentDB() : FragmentDB
• ~GAMESSDatFile() : GAMESSDatFile
• ~GAMESSLogFile() : GAMESSLogFile
• ~GeneralException() : Exception::GeneralException
• ~GenericControl() : VIEW::GenericControl
• ~GenericMolFile() : GenericMolFile
• ~GenericSelectionMessage() : VIEW::GenericSelectionMessage
• ~GeometricControl() : VIEW::GeometricControl
• ~GeometricFitDialog() : VIEW::GeometricFitDialog
• ~GeometricObject() : VIEW::GeometricObject
• ~GeometricObjectSelectionMessage() : VIEW::GeometricObjectSelectionMessage
• ~GLDisplayList() : VIEW::GLDisplayList
• ~GLRenderer() : VIEW::GLRenderer
• ~Gradient() : Gradient
• ~GraphEdge() : GraphEdge< Vertex, Edge, Face >
• ~GraphFace() : GraphFace< Vertex, Edge, Face >
• ~GraphTriangle() : GraphTriangle< Vertex, Edge, Face >
• ~GraphVertex() : GraphVertex< Vertex, Edge, Face >
• ~GridVisualisation() : VIEW::GridVisualisation
• ~HaighMallionShiftProcessor() : HaighMallionShiftProcessor
• ~HashGrid3() : HashGrid3< Item >
• ~HashGridBox3() : HashGridBox3< Item >
• ~HashMap() : HashMap< Key, T >
• ~HashSet() : HashSet< Key >
• ~HBondModelProcessor() : VIEW::HBondModelProcessor
• ~HBondShiftProcessor() : HBondShiftProcessor
• ~HINFile() : HINFile
• ~HydrogenBond() : HydrogenBond
• ~HydrophobicVdWSurface() : HydrophobicVdWSurface
• ~INIFile() : INIFile
• ~InRingPredicate() : InRingPredicate
• ~IOSockStream() : IOSockStream
• ~IOStreamSocket() : IOStreamSocket
• ~ISockStream() : ISockStream
• ~JCAMPFile() : JCAMPFile
• ~JohnsonBoveyShiftProcessor() : JohnsonBoveyShiftProcessor
• ~Label() : VIEW::Label
• ~LabelDialog() : VIEW::LabelDialog
• ~LabelModel() : VIEW::LabelModel
• ~LennardJones() : LennardJones
• ~LightSettings() : VIEW::LightSettings
• ~LightSource() : VIEW::LightSource
• ~Line() : VIEW::Line
• ~LineSearch() : LineSearch
• ~Lipophilic() : Lipophilic
• ~List() : List< Value >
• ~LogStream() : LogStream
• ~LogStreamBuf() : LogStreamBuf
• ~LogView() : VIEW::LogView
• ~MainControl() : VIEW::MainControl
• ~MaterialSettings() : VIEW::MaterialSettings
• ~MeanAtomInformationContent() : MeanAtomInformationContent
• ~Mesh() : VIEW::Mesh
• ~Message() : VIEW::Message
• ~MicroCanonicalMD() : MicroCanonicalMD
• ~MinimizationDialog() : VIEW::MinimizationDialog
• ~MMFF94() : MMFF94
• ~MMFF94BendParameters() : MMFF94BendParameters
• ~MMFF94ConfigurationDialog() : VIEW::MMFF94ConfigurationDialog
• ~MMFF94ESParameters() : MMFF94ESParameters
• ~MMFF94NonBonded() : MMFF94NonBonded
• ~MMFF94OutOfPlaneBend() : MMFF94OutOfPlaneBend
• ~MMFF94ParametersBase() : MMFF94ParametersBase
• ~MMFF94PlaneParameters() : MMFF94PlaneParameters
• ~MMFF94StretchBend() : MMFF94StretchBend
• ~MMFF94StretchBendParameters() : MMFF94StretchBendParameters
• ~MMFF94StretchParameters() : MMFF94StretchParameters
• ~MMFF94Torsion() : MMFF94Torsion
• ~MMFF94TorsionParameters() : MMFF94TorsionParameters
• ~MMFF94VDWParameters() : MMFF94VDWParameters
• ~ModelInformation() : VIEW::ModelInformation
• ~ModelProcessor() : VIEW::ModelProcessor
• ~ModelSettingsDialog() : VIEW::ModelSettingsDialog
• ~ModularWidget() : VIEW::ModularWidget
• ~MOL2File() : MOL2File
• ~MolecularControl() : VIEW::MolecularControl
• ~MolecularDynamics() : MolecularDynamics
• ~MolecularFileDialog() : VIEW::MolecularFileDialog
• ~MolecularInformation() : MolecularInformation
• ~MolecularStructure() : VIEW::MolecularStructure
• ~MolecularWeight() : MolecularWeight
• ~Molecule() : Molecule
• ~MoleculeAssembler() : MoleculeAssembler
• ~MoleculeObjectCreator() : MoleculeObjectCreator
• ~MOLFile() : MOLFile
• ~MultiColorExtension() : VIEW::MultiColorExtension
• ~MultiLine() : VIEW::MultiLine
• ~MutableConstant() : MutableConstant< DataType >
• ~MutablePower() : MutablePower< Function, DataType >
• ~NamedProperty() : NamedProperty
• ~NegativePolarVdWSurface() : NegativePolarVdWSurface
• ~NegativeVdWSurface() : NegativeVdWSurface
• ~NetworkPreferences() : VIEW::NetworkPreferences
• ~NonpolarSolvation() : NonpolarSolvation
• ~NormalizeNamesProcessor() : FragmentDB::NormalizeNamesProcessor
• ~NucleicAcid() : NucleicAcid
• ~Nucleotide() : Nucleotide
• ~NumberOfAromaticAtoms() : NumberOfAromaticAtoms
• ~NumberOfAromaticBonds() : NumberOfAromaticBonds
• ~NumberOfAtoms() : NumberOfAtoms
• ~NumberOfBonds() : NumberOfBonds
• ~NumberOfBoron() : NumberOfBoron
• ~NumberOfBromine() : NumberOfBromine
• ~NumberOfCarbon() : NumberOfCarbon
• ~NumberOfChlorine() : NumberOfChlorine
• ~NumberOfDoubleBonds() : NumberOfDoubleBonds
• ~NumberOfFlourine() : NumberOfFlourine
• ~NumberOfHeavyAtoms() : NumberOfHeavyAtoms
• ~NumberOfHeavyBonds() : NumberOfHeavyBonds
• ~NumberOfHydrogen() : NumberOfHydrogen
• ~NumberOfHydrogenBondAcceptors() : NumberOfHydrogenBondAcceptors
• ~NumberOfHydrogenBondDonors() : NumberOfHydrogenBondDonors
• ~NumberOfHydrophobicAtoms() : NumberOfHydrophobicAtoms
• ~NumberOfIodine() : NumberOfIodine
• ~NumberOfNitrogen() : NumberOfNitrogen
• ~NumberOfOxygen() : NumberOfOxygen
• ~NumberOfPhosphorus() : NumberOfPhosphorus
• ~NumberOfRotatableBonds() : NumberOfRotatableBonds
• ~NumberOfRotatableSingleBonds() : NumberOfRotatableSingleBonds
• ~NumberOfSingleBonds() : NumberOfSingleBonds
• ~NumberOfSulfur() : NumberOfSulfur
• ~NumberOfTripleBonds() : NumberOfTripleBonds
• ~NumericalIntegrator() : NumericalIntegrator< Function, DataType >
• ~Object() : Object
• ~ObjectCreator() : ObjectCreator
• ~OpenBruker1DFile() : VIEW::OpenBruker1DFile
• ~OpenBruker2DFile() : VIEW::OpenBruker2DFile
• ~Options() : Options
• ~OSockStream() : OSockStream
• ~Pair6_12InteractionEnergyProcessor() : Pair6_12InteractionEnergyProcessor
• ~Pair6_12RDFIntegrator() : Pair6_12RDFIntegrator
• ~PairExpInteractionEnergyProcessor() : PairExpInteractionEnergyProcessor
• ~PairExpRDFIntegrator() : PairExpRDFIntegrator
• ~Parameters() : Parameters
• ~ParameterSection() : ParameterSection
• ~ParsedFunction() : ParsedFunction< arg >
• ~PartialChargeBase() : PartialChargeBase
• ~PartialChargeProcessor() : PartialChargeProcessor
• ~PCMCavFreeEnergyProcessor() : PCMCavFreeEnergyProcessor
• ~PDBAtom() : PDBAtom
• ~PDBFile() : PDBFile
• ~Peak() : Peak< PositionType >
• ~PeakList() : PeakList< PT >
• ~PeptideBuilder() : Peptides::PeptideBuilder
• ~PeptideDialog() : VIEW::PeptideDialog
• ~PeriodicBoundary() : PeriodicBoundary
• ~PersistenceManager() : PersistenceManager
• ~PersistentObject() : PersistentObject
• ~PiecewiseFunction() : PiecewiseFunction
• ~PiecewisePolynomial() : PiecewisePolynomial
• ~PierottiCavFreeEnergyProcessor() : PierottiCavFreeEnergyProcessor
• ~Point() : VIEW::Point
• ~PolarSolvation() : PolarSolvation
• ~PolarVdWSurface() : PolarVdWSurface
• ~PositivePolarVdWSurface() : PositivePolarVdWSurface
• ~PositiveVdWSurface() : PositiveVdWSurface
• ~Potential1210() : Potential1210
• ~POVRenderer() : VIEW::POVRenderer
• ~PreciseTime() : PreciseTime
• ~Preferences() : VIEW::Preferences
• ~PrincipalMomentOfInertia() : PrincipalMomentOfInertia
• ~PrincipalMomentOfInertiaX() : PrincipalMomentOfInertiaX
• ~PrincipalMomentOfInertiaY() : PrincipalMomentOfInertiaY
• ~PrincipalMomentOfInertiaZ() : PrincipalMomentOfInertiaZ
• ~Product() : Product< First, Second, DataType >
• ~Property() : SmartsParser::SPAtom::Property
• ~PropertyManager() : PropertyManager
• ~Protein() : Protein
• ~PTE_() : PTE_
• ~PubChemDialog() : VIEW::PubChemDialog
• ~PyColorRGBAVector() : PyColorRGBAVector
• ~PyCompositeList() : PyCompositeList
• ~PyDatasetVector() : PyDatasetVector
• ~PyIndexList() : PyIndexList
• ~PythonSettings() : VIEW::PythonSettings
• ~QuadraticAngleBend() : QuadraticAngleBend
• ~QuadraticBondStretch() : QuadraticBondStretch
• ~QuadraticImproperTorsion() : QuadraticImproperTorsion
• ~Quadruple() : Quadruple< T1, T2, T3, T4 >
• ~RadialDistributionFunction() : RadialDistributionFunction
• ~RadiusRuleProcessor() : RadiusRuleProcessor
• ~RandomCoilShiftProcessor() : RandomCoilShiftProcessor
• ~RDFIntegrator() : RDFIntegrator
• ~RDFParameter() : RDFParameter
• ~RDFSection() : RDFSection
• ~Reciprocal() : Reciprocal< Function, DataType >
• ~ReconstructFragmentProcessor() : ReconstructFragmentProcessor
• ~RecStruct_() : SmartsMatcher::RecStruct_
• ~RecStructCore_() : SmartsMatcher::RecStructCore_
• ~RecStructPool_() : SmartsMatcher::RecStructPool_
• ~ReducedSurface() : ReducedSurface
• ~RegularData1DWidget() : VIEW::RegularData1DWidget
• ~RegularExpression() : RegularExpression
• ~ReissCavFreeEnergyProcessor() : ReissCavFreeEnergyProcessor
• ~RelHydrophobicVdWSurface() : RelHydrophobicVdWSurface
• ~RelNegativePartialCharge() : RelNegativePartialCharge
• ~RelNegativePolarVdWSurface() : RelNegativePolarVdWSurface
• ~RelNegativeVdWSurface() : RelNegativeVdWSurface
• ~RelNumberOfRotatableBonds() : RelNumberOfRotatableBonds
• ~RelNumberOfRotatableSingleBonds() : RelNumberOfRotatableSingleBonds
• ~RelPolarVdWSurface() : RelPolarVdWSurface
• ~RelPositivePartialCharge() : RelPositivePartialCharge
• ~RelPositivePolarVdWSurface() : RelPositivePolarVdWSurface
• ~RelPositiveVdWSurface() : RelPositiveVdWSurface
• ~Renderer() : VIEW::Renderer
• ~Representation() : VIEW::Representation
• ~RepresentationManager() : VIEW::RepresentationManager
• ~Residue() : Residue
• ~ResidueChecker() : ResidueChecker
• ~ResidueRotamerSet() : ResidueRotamerSet
• ~ResidueTorsions() : ResidueTorsions
• ~ResourceFile() : ResourceFile
• ~RingAnalyser() : RingAnalyser
• ~RingClusterer() : RingClusterer
• ~RingFinder() : RingFinder
• ~RingPerceptionProcessor() : RingPerceptionProcessor
• ~RombergIntegrator() : RombergIntegrator< Function, DataType >
• ~RotamerLibrary() : RotamerLibrary
• ~RotationalEntropyLoss() : RotationalEntropyLoss
• ~RSComputer() : RSComputer
• ~RSConstructor() : RSConstructor
• ~RSEdge() : RSEdge
• ~RSFace() : RSFace
• ~RSVertex() : RSVertex
• ~RuleEvaluator() : RuleEvaluator
• ~RuleProcessor() : RuleProcessor
• ~SASEdge() : SASEdge
• ~SASFace() : SASFace
• ~SASTriangulator() : SASTriangulator
• ~SASVertex() : SASVertex
• ~Scene() : VIEW::Scene
• ~SceneMessage() : VIEW::SceneMessage
• ~Scoring_() : DockResult::Scoring_
• ~SCWRLRotamerFile() : SCWRLRotamerFile
• ~SDFile() : SDFile
• ~SDGenerator() : SDGenerator
• ~SecondaryStructure() : SecondaryStructure
• ~Selectable() : Selectable
• ~Selector() : Selector
• ~Server() : VIEW::Server
• ~ServerPreferences() : VIEW::ServerPreferences
• ~SESComputer() : SESComputer
• ~SESEdge() : SESEdge
• ~SESFace() : SESFace
• ~SESSingularityCleaner() : SESSingularityCleaner
• ~SESTriangulator() : SESTriangulator
• ~SESVertex() : SESVertex
• ~ShiftedLVMMMinimizer() : ShiftedLVMMMinimizer
• ~ShiftModel() : ShiftModel
• ~ShiftModule() : ShiftModule
• ~SimpleBase() : SimpleBase
• ~SimpleBox() : VIEW::SimpleBox
• ~SimpleExperiment1D() : SimpleExperiment1D
• ~SizeOfSSSR() : SizeOfSSSR
• ~SLICKEnergy() : SLICKEnergy
• ~SLICKScore() : SLICKScore
• ~SmartsParser() : SmartsParser
• ~SnapShot() : SnapShot
• ~SnapShotManager() : SnapShotManager
• ~SnapshotVisualisationDialog() : VIEW::SnapshotVisualisationDialog
• ~SockAddr() : SockAddr
• ~SocketBuf() : SocketBuf
• ~SockInetAddr() : SockInetAddr
• ~SockInetBuf() : SockInetBuf
• ~SolventAccessibleSurface() : SolventAccessibleSurface
• ~SolventDescriptor() : SolventDescriptor
• ~SolventExcludedSurface() : SolventExcludedSurface
• ~SolventParameter() : SolventParameter
• ~SPAtom() : SmartsParser::SPAtom
• ~SPBond() : SmartsParser::SPBond
• ~SPEdge() : SmartsParser::SPEdge
• ~Sphere() : VIEW::Sphere
• ~SPNode() : SmartsParser::SPNode
• ~SquareFunction() : SquareFunction< Function, DataType >
• ~Stage() : VIEW::Stage
• ~StageSettings() : VIEW::StageSettings
• ~SteepestDescentMinimizer() : SteepestDescentMinimizer
• ~StrangLBFGSMinimizer() : StrangLBFGSMinimizer
• ~String() : String
• ~StringHashMap() : StringHashMap< Value >
• ~StructureMapper() : StructureMapper
• ~Substring() : Substring
• ~Subtraction() : Subtraction< First, Second, DataType >
• ~SurfaceBase() : SurfaceBase
• ~SyntaxTree() : ExpressionParser::SyntaxTree
• ~System() : System
• ~TAngle() : TAngle< T >
• ~TBox3() : TBox3< T >
• ~TCircle3() : TCircle3< T >
• ~TContour() : TContour< T >
• ~TContourLine() : TContourLine< T >
• ~TContourSurface() : TContourSurface< T >
• ~TCPTransfer() : TCPTransfer
• ~Templates() : Templates
• ~TFFT1D() : TFFT1D< ComplexTraits >
• ~TFFT2D() : TFFT2D< ComplexTraits >
• ~TFFT3D() : TFFT3D< ComplexTraits >
• ~Timer() : Timer
• ~TimeStamp() : TimeStamp
• ~TLine3() : TLine3< T >
• ~TMatrix4x4() : TMatrix4x4< T >
• ~TotalNegativePartialCharge() : TotalNegativePartialCharge
• ~TotalPositivePartialCharge() : TotalPositivePartialCharge
• ~TPlane3() : TPlane3< T >
• ~TQuaternion() : TQuaternion< T >
• ~TrajectoryFile() : TrajectoryFile
• ~TransformationManager() : TransformationManager
• ~TRegularData1D() : TRegularData1D< ValueType >
• ~TRegularData2D() : TRegularData2D< ValueType >
• ~TRegularData3D() : TRegularData3D< ValueType >
• ~Triangle() : Triangle
• ~TriangleEdge() : TriangleEdge
• ~TrianglePoint() : TrianglePoint
• ~TriangulatedSAS() : TriangulatedSAS
• ~TriangulatedSES() : TriangulatedSES
• ~TriangulatedSphere() : TriangulatedSphere
• ~TriangulatedSurface() : TriangulatedSurface
• ~Triple() : Triple< T1, T2, T3 >
• ~TRRFile() : TRRFile
• ~TSimpleBox3() : TSimpleBox3< T >
• ~TSphere3() : TSphere3< T >
• ~Tube() : VIEW::Tube
• ~TVector2() : TVector2< T >
• ~TVector3() : TVector3< T >
• ~TVector4() : TVector4< T >
• ~TwoColoredLine() : VIEW::TwoColoredLine
• ~TwoColoredTube() : VIEW::TwoColoredTube
• ~TypenameRuleProcessor() : TypenameRuleProcessor
• ~TypeRuleProcessor() : TypeRuleProcessor
• ~UhligCavFreeEnergyProcessor() : UhligCavFreeEnergyProcessor
• ~UnaryProcessor() : UnaryProcessor< T >
• ~VdWSurface() : VdWSurface
• ~VdWVolume() : VdWVolume
• ~Vertex() : VIEW::Vertex
• ~Vertex2() : VIEW::Vertex2
• ~VertexAdjacency() : VertexAdjacency
• ~VertexAdjacencyEquality() : VertexAdjacencyEquality
• ~Visitor() : Visitor< Host >
• ~VRMLRenderer() : VIEW::VRMLRenderer
• ~XYZFile() : XYZFile
• ~ZagrebIndex() : ZagrebIndex