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Here is a list of all class members with links to the classes they belong to:

### - s -

- S : BALL::Element
- s : boost::hash< RTpieCpp::InstanceHandle >::conv, boost::hash< RTpieCpp::MeshHandle >::conv
- safeBufferSwap() : BALL::VIEW::GLRenderWindow
- salt_bridge_atom : BALL::PDB::RecordCONECT
- saltbridges : BALL::PDB::Structure::ConectAtomList, BALL::PDB::Structure
- SAMARIUM : BALL::Element
- same_energy_counter_ : BALL::EnergyMinimizer
- Sample() : BALL::NMRStarFile::Sample
- SampleCondition() : BALL::NMRStarFile::SampleCondition
- SAMPLES : BALL::Pair6_12RDFIntegrator::Default, BALL::Pair6_12RDFIntegrator::Option, BALL::PairExpRDFIntegrator::Default, BALL::PairExpRDFIntegrator::Option
- samples : BALL::NMRStarFile::NMRAtomDataSet
- sampling_rate_ : BALL::CCP4File, BALL::DSN6File
- sas_ : BALL::TriangulatedSAS
- SAS_grid : BALL::FDPB
- SASEdge : BALL::RSEdge, BALL::RSFace, BALL::RSVertex, BALL::SASEdge, BALL::SASFace, BALL::SASVertex
- SASFace : BALL::RSEdge, BALL::RSFace, BALL::RSVertex, BALL::SASEdge, BALL::SASFace, BALL::SASVertex
- SASTriangulator : BALL::RSEdge, BALL::RSFace, BALL::RSVertex, BALL::SASEdge, BALL::SASFace, BALL::SASTriangulator, BALL::SASVertex, BALL::SolventAccessibleSurface, BALL::Triangle, BALL::TriangleEdge, BALL::TrianglePoint, BALL::TriangulatedSAS
- SASVertex : BALL::RSEdge, BALL::RSFace, BALL::RSVertex, BALL::SASEdge, BALL::SASFace, BALL::SASVertex
- saturate() : BALL::StructurePreparer
- saturateWithHydrogens() : BALL::VIEW::Scene
- save() : BALL::ResourceFile
- save_file : BALL::VIEW::TestFramework
- save_id_ : BALL::VIEW::MolecularFileDialog
- save_images_ : BALL::VIEW::MDSimulationThread
- SAVE_ONLY_SUMS : BALL::MolecularInteractions
- saveAs() : BALL::ResourceFile
- saveBALLViewProjectFile() : BALL::VIEW::MainControl
- saveClassInformationToFile() : BALL::QSAR::ClassificationModel
- saved_position_ : BALL::AtomVector
- saveDescriptorInformationToFile() : BALL::QSAR::Model, BALL::QSAR::RegressionModel
- saveDockTrajectory() : BALL::VIEW::DockResultController
- saveFile() : BALL::VIEW::TestFramework
- saveframe : BALL::CIFFile::Datacontent
- saveframe_categories : BALL::CIFFile::Datablock
- saveframe_names : BALL::CIFFile::Datablock
- saveGridSetsToFile() : BALL::GridBasedScoring
- saveKernelParametersToFile() : BALL::QSAR::KernelModel
- saveModel() : BALL::Rescoring
- saveModelParametersToFile() : BALL::QSAR::Model
- savePositions() : BALL::AtomVector
- saveResponseTransformationToFile() : BALL::QSAR::Model
- saveScript() : BALL::VIEW::PyWidget
- saveSettingsToLight_() : BALL::VIEW::LightSettings
- saveSurface() : BALL::VIEW::GeometricControl
- saveToFile() : BALL::QSAR::ALLModel, BALL::QSAR::ClassificationValidation, BALL::QSAR::KernelModel, BALL::QSAR::LDAModel, BALL::QSAR::LogitModel, BALL::QSAR::Model, BALL::QSAR::NBModel, BALL::QSAR::QSARData, BALL::QSAR::RegressionModel, BALL::QSAR::RegressionValidation, BALL::QSAR::SNBModel, BALL::QSAR::Validation, BALL::ScoreGridSet
- saveTrainingResult() : BALL::QSAR::KernelModel
- Sb : BALL::Element
- sbmb : BALL::MMFF94AtomType, BALL::MMFF94StretchBend::Stretch
- sbmb_exists : BALL::MMFF94StretchParameters::BondData
- sbtijk : BALL::MMFF94StretchBend::StretchBend
- Sc : BALL::Element
- scalarProduct() : BALL::QSAR::Statistics
- scale() : BALL::PeakList< PT >, BALL::TMatrix4x4< T >
- scale_() : BALL::VIEW::GLRenderer
- scaleAllDescriptors() : BALL::QSAR::QSARData
- scaleScore() : BALL::ScoringComponent
- scaleVector3_() : BALL::VIEW::GLRenderer
- scaling() : BALL::QSAR::Statistics
- scaling_ : BALL::VIEW::ForceModel
- SCALING_ELECTROSTATIC_1_4 : BALL::AmberFF::Default, BALL::AmberFF::Option, BALL::CharmmFF::Default, BALL::CharmmFF::Option
- SCALING_VDW_1_4 : BALL::AmberFF::Default, BALL::AmberFF::Option, BALL::CharmmFF::Default, BALL::CharmmFF::Option
- scalingUsed : BALL::VIEW::VRMLRenderer
- SCANDIUM : BALL::Element
- Scene : BALL::VIEW::GLRenderer, BALL::VIEW::Scene
- scene_ : BALL::VIEW::AnimationThread, BALL::VIEW::InteractionMode, BALL::VIEW::InteractionModeManager, BALL::VIEW::LightSettings, BALL::VIEW::Renderer, BALL::VIEW::RenderSetup
- SceneMessage() : BALL::VIEW::SceneMessage
- SceneMessageType : BALL::VIEW::SceneMessage
- scheduleDelete_() : BALL::VIEW::PropertyEditor
- scheduleDuplicate_() : BALL::VIEW::PropertyEditor
- score_ : BALL::ScoringComponent, BALL::ScoringFunction
- score_contribution_names : BALL::ScoringOptimizer::Result
- score_contributions : BALL::ScoringOptimizer::Result
- SCOREGRID_INTERPOLATION : BALL::GridBasedScoring::Default, BALL::GridBasedScoring::Option
- scoregrid_interpolation_ : BALL::GridBasedScoring
- SCOREGRID_RESOLUTION : BALL::GridBasedScoring::Default, BALL::GridBasedScoring::Option
- scoregrid_resolution_ : BALL::GridBasedScoring
- ScoreGridSet : BALL::GridBasedScoring, BALL::ScoreGridSet
- scores_ : BALL::DockResult::Scoring_
- Scoring_() : BALL::DockResult::Scoring_
- scoring_components_ : BALL::ScoringFunction
- scoring_function_ : BALL::Constraint, BALL::DockingAlgorithm, BALL::DockProblem, BALL::GridAnalysis, BALL::Rescoring, BALL::ScoringComponent
- SCORING_TOLERANCE : BALL::AromaticRingStacking::Default, BALL::AromaticRingStacking::Option
- SCORING_TYPE : BALL::EvolutionaryDocking::Default, BALL::EvolutionaryDocking::Option, BALL::IMGDock::Default, BALL::IMGDock::Option
- scoring_type_ : BALL::DockingAlgorithm
- scoringAdvancedPressed() : BALL::VIEW::DockDialog
- ScoringBaseFunction() : BALL::ScoringBaseFunction
- scoringClicked() : BALL::VIEW::DockResultDialog
- ScoringComponent() : BALL::ScoringComponent
- scoringFuncChosen() : BALL::VIEW::DockDialog, BALL::VIEW::DockResultDialog
- ScoringFunction() : BALL::ScoringFunction, BALL::VIEW::DockingController
- ScoringOptimizer() : BALL::ScoringOptimizer
- scorings_ : BALL::DockResult
- screenCountChanged() : BALL::VIEW::StageSettings
- screenshot_nr_ : BALL::VIEW::Scene
- script_edit_ : BALL::VIEW::PyWidget
- script_mode_ : BALL::VIEW::PyWidget
- script_output_ : BALL::VIEW::PyWidget
- scriptDialog() : BALL::VIEW::PyWidget
- SCWRL_4_0 : BALL::SideChainPlacementProcessor::Method
- SCWRL_BINARY_PATH : BALL::SideChainPlacementProcessor::Default, BALL::SideChainPlacementProcessor::Option
- SCWRL_INPUT_FILE : BALL::SideChainPlacementProcessor::Default, BALL::SideChainPlacementProcessor::Option
- SCWRL_OUTPUT_FILE : BALL::SideChainPlacementProcessor::Default, BALL::SideChainPlacementProcessor::Option
- SCWRL_SEQUENCE_FILE : BALL::SideChainPlacementProcessor::Default, BALL::SideChainPlacementProcessor::Option
- SCWRLRotamerFile() : BALL::SCWRLRotamerFile
- SD_FILE : BALL::VIEW::MolecularFileDialog
- sd_file : BALL::QSAR::InputConfiguration
- sd_systems_ : BALL::VIEW::AssignBondOrderResultsDialog, BALL::VIEW::PubChemDialog
- SDFile() : BALL::SDFile
- SDGenerator() : BALL::SDGenerator
- SDWidget() : BALL::VIEW::SDWidget
- sdwidget_ : BALL::VIEW::AssignBondOrderResultsDialog
- Se : BALL::Element
- search() : BALL::LineBasedFile
- searchPattern() : BALL::StructureMapper
- searchTextChanged() : BALL::VIEW::ShortcutDialog
- sec_axis_ : BALL::CCP4File
- sec_struct : BALL::PDB::Structure::AtomEntry
- sec_structs : BALL::PDB::Structure
- second : BALL::Quadruple< T1, T2, T3, T4 >, BALL::Triple< T1, T2, T3 >
- second_ : BALL::Addition< First, Second, DataType >, BALL::Bond, BALL::Division< First, Second, DataType >, BALL::Product< First, Second, DataType >, BALL::SmartsParser::SPEdge, BALL::Subtraction< First, Second, DataType >
- second_argument_pointer : BALL::BinaryFunctor< FirstArgumentType, SecondArgumentType, ResultType >
- second_argument_reference : BALL::BinaryFunctor< FirstArgumentType, SecondArgumentType, ResultType >
- second_argument_type : BALL::BinaryFunctor< FirstArgumentType, SecondArgumentType, ResultType >
- second_atom : BALL::MOLFile::BondStruct, BALL::PDB::RecordLINK, BALL::PDB::RecordSLTBRG
- second_atom_expressions_ : BALL::EFShiftProcessor
- second_edge_ : BALL::SmartsParser::SPEdge, BALL::SmartsParser::SPNode
- second_non_hydrogen_atom : BALL::PDB::RecordHYDBND
- second_type : BALL::MolmecSupport::pair< T1, T2 >
- SecondaryStructure() : BALL::SecondaryStructure
- SecondaryStructureColorProcessor() : BALL::VIEW::SecondaryStructureColorProcessor
- SecondaryStructureIteratorTraits() : BALL::SecondaryStructureIteratorTraits
- SecondaryStructureProcessor() : BALL::SecondaryStructureProcessor
- secondToFirst() : BALL::NucleotideMapping
- secs_ : BALL::PreciseTime
- SecStructList : BALL::PDBFile
- section_entries_ : BALL::ParameterSection
- section_index_ : BALL::INIFile
- section_name_ : BALL::ParameterSection
- SectionIterator : BALL::INIFile
- sections_ : BALL::INIFile
- seekAndWriteHeader() : BALL::DCDFile
- segment_ID : BALL::PDB::RecordANISOU, BALL::PDB::RecordATOM, BALL::PDB::RecordHETATM, BALL::PDB::RecordSIGATM, BALL::PDB::RecordSIGUIJ
- select() : BALL::Composite, BALL::GeneticAlgorithm, BALL::Selectable, BALL::VIEW::MolecularControl
- select_action_ : BALL::VIEW::MolecularControl
- select_id_ : BALL::VIEW::MolecularControl
- Selectable() : BALL::Selectable
- selectAllModels() : BALL::PDBFile
- selectAllResultsForInput() : BALL::DockResultFile
- selectAltLocationIndicator() : BALL::PDBFile
- selectAtoms() : BALL::VIEW::GeometricControl
- selectBaseFunction() : BALL::ScoringComponent
- selectClipRepresentations() : BALL::VIEW::GeometricControl
- selectColoringMethod() : BALL::VIEW::DisplayProperties
- selectCompositeRecursive() : BALL::VIEW::MainControl
- selectComposites_() : BALL::VIEW::MainControl
- SELECTED : BALL::VIEW::DatasetMessage, BALL::VIEW::RepresentationMessage
- selected_ : BALL::GeneticAlgorithm, BALL::Selectable, BALL::VIEW::MolecularControl
- selected_atoms_ : BALL::Selector
- selected_color : BALL::VIEW::ModifyRepresentationDialog
- selected_coloring_method_ : BALL::VIEW::MolecularControl
- SELECTED_COMPOSITE : BALL::VIEW::CompositeMessage
- SELECTED_FF : BALL::VIEW::DockingController
- selected_model_ : BALL::PDBFile, BALL::VIEW::MolecularControl
- selectedForceField() : BALL::VIEW::MinimizationDialog, BALL::VIEW::MolecularDynamicsDialog
- selectedRepresentation() : BALL::VIEW::GeometricControl
- selectFile_() : BALL::VIEW::DockDialog, BALL::VIEW::FDPBDialog
- selectFont() : BALL::VIEW::MainControlPreferences, BALL::VIEW::PythonSettings
- selectForceField() : BALL::VIEW::MinimizationDialog, BALL::VIEW::MolecularDynamicsDialog
- selectHeavyAtoms() : BALL::StructurePreparer
- SELECTION : BALL::Composite
- selection_ : BALL::ResidueChecker, BALL::VIEW::MainControl
- selection_color_ : BALL::VIEW::ColorProcessor
- selection_enabled_ : BALL::ForceField
- selection_name : BALL::QSAR::FeatureSelectionConfiguration
- selectionChanged_() : BALL::VIEW::DockResultDialog
- selectionPressed_() : BALL::VIEW::Scene
- selectionPressedMoved_() : BALL::VIEW::PickingMode, BALL::VIEW::Scene
- selectItems() : BALL::VIEW::TreeWidget
- selectMode() : BALL::VIEW::DisplayProperties
- selectModel() : BALL::PDBFile, BALL::VIEW::DisplayProperties
- selectObjects_() : BALL::VIEW::PickingMode, BALL::VIEW::Scene
- Selector() : BALL::Selector
- selector_edit_ : BALL::VIEW::MolecularControl
- selectStat() : BALL::QSAR::ClassificationValidation, BALL::QSAR::FeatureSelection, BALL::QSAR::RegressionValidation, BALL::QSAR::Validation
- SELENIUM : BALL::Element
- send() : BALL::RingPerceptionProcessor::TNode_
- send_buffer : BALL::RingPerceptionProcessor::TNode_
- sendMessage() : BALL::VIEW::MainControl
- sendMessage_() : BALL::VIEW::BALLThread
- sendObject() : BALL::VIEW::ServerWidget::BALLViewServer
- sendOptions() : BALL::MPISupport
- sendPersistenceStream_() : BALL::MPISupport
- sendSystem() : BALL::MPISupport
- sense_of_strand : BALL::PDB::RecordSHEET
- separate_activity_file : BALL::QSAR::InputConfiguration
- SEPARATOR : BALL::ResourceFile
- seq_identity : BALL::NMRStarFile::MonomericPolymer::HomologDB
- seq_positive : BALL::NMRStarFile::MonomericPolymer::HomologDB
- seq_to_submitted_percentage : BALL::NMRStarFile::MonomericPolymer::HomologDB
- seqres_records : BALL::PDB::BookKeeping
- sequence_ : BALL::Peptides::PeptideBuilder
- sequence_database_accession_code : BALL::PDB::RecordDBREF
- sequence_database_ID_code : BALL::PDB::RecordDBREF
- sequence_database_name : BALL::PDB::RecordDBREF
- sequence_number : BALL::PDB::RecordSITE, BALL::PDB::RecordTURN, BALL::PDB::Residue
- sequence_number_ : BALL::PDBFile
- sequenceRing() : BALL::RingAnalyser
- sequenceSubstituents_() : BALL::SDGenerator
- ser_pressed() : BALL::VIEW::PeptideDialog
- serial_number : BALL::PDB::RecordANISOU, BALL::PDB::RecordATOM, BALL::PDB::RecordHELIX, BALL::PDB::RecordHETATM, BALL::PDB::RecordMTRIX1, BALL::PDB::RecordMTRIX2, BALL::PDB::RecordMTRIX3, BALL::PDB::RecordSEQRES, BALL::PDB::RecordSIGATM, BALL::PDB::RecordSIGUIJ, BALL::PDB::RecordSSBOND, BALL::PDB::RecordTER, BALL::PDB::RecordTVECT, BALL::PDB::Structure::ConectAtomList
- serialize() : BALL::PoseClustering::ClusterProperties
- serializeWardClusterTree() : BALL::PoseClustering
- server_ : BALL::PyInterpreter
- serverChanged() : BALL::VIEW::DownloadElectronDensity
- serverIsRunning() : BALL::PyInterpreter
- ServerPreferences() : BALL::VIEW::ServerPreferences
- ServerWidget() : BALL::VIEW::ServerWidget
- ses_ : BALL::SESComputer, BALL::SESSingularityCleaner, BALL::TriangulatedSES
- SESComputer : BALL::ReducedSurface, BALL::RSEdge, BALL::RSFace, BALL::RSVertex, BALL::SESComputer, BALL::SESEdge, BALL::SESFace, BALL::SESSingularityCleaner, BALL::SESVertex, BALL::SolventExcludedSurface
- SESEdge : BALL::RSEdge, BALL::RSFace, BALL::RSVertex, BALL::SESEdge, BALL::SESFace, BALL::SESVertex
- SESFace : BALL::RSEdge, BALL::RSFace, BALL::RSVertex, BALL::SESEdge, BALL::SESFace, BALL::SESVertex
- SESSingularityCleaner : BALL::ReducedSurface, BALL::RSEdge, BALL::RSFace, BALL::RSVertex, BALL::SESEdge, BALL::SESFace, BALL::SESSingularityCleaner, BALL::SESVertex, BALL::SolventExcludedSurface
- SESTriangulator : BALL::ReducedSurface, BALL::RSEdge, BALL::RSFace, BALL::RSVertex, BALL::SESEdge, BALL::SESFace, BALL::SESTriangulator, BALL::SESVertex, BALL::SolventExcludedSurface, BALL::Triangle, BALL::TriangleEdge, BALL::TrianglePoint, BALL::TriangulatedSES
- SESVertex : BALL::RSEdge, BALL::RSFace, BALL::RSVertex, BALL::SESEdge, BALL::SESFace, BALL::SESVertex
- set() : BALL::Atom, BALL::AtomContainer, BALL::AtomVector, BALL::BitVector, BALL::Chain, BALL::Composite, BALL::CosineTorsion::Values, BALL::Directory, BALL::Exception::GlobalExceptionHandler, BALL::Gradient, BALL::GraphEdge< Vertex, Edge, Face >, BALL::GraphFace< Vertex, Edge, Face >, BALL::GraphTriangle< Vertex, Edge, Face >, BALL::GraphVertex< Vertex, Edge, Face >, BALL::HashGrid3< Item >, BALL::HashSet< Key >, BALL::List< Value >, BALL::MolecularDynamics, BALL::Molecule, BALL::NucleicAcid, BALL::Nucleotide, BALL::Options, BALL::PDB::Residue, BALL::PDBAtom, BALL::PiecewiseFunction, BALL::PiecewisePolynomial, BALL::PreciseTime, BALL::PropertyManager, BALL::Protein, BALL::Quadruple< T1, T2, T3, T4 >, BALL::ReducedSurface, BALL::RegularExpression, BALL::Residue, BALL::ResourceEntry, BALL::RSEdge, BALL::RSFace, BALL::RSVertex, BALL::RuleProcessor, BALL::SASEdge, BALL::SASFace, BALL::SASVertex, BALL::SecondaryStructure, BALL::Selectable, BALL::SESEdge, BALL::SESFace, BALL::SESVertex, BALL::String, BALL::StringHashMap< Value >, BALL::StructureMapper, BALL::Substring, BALL::System, BALL::TAngle< T >, BALL::TBox3< T >, BALL::TCircle3< T >, BALL::TLine3< T >, BALL::TMatrix4x4< T >, BALL::TPlane3< T >, BALL::TQuaternion< T >, BALL::Triangle, BALL::TrianglePoint, BALL::TriangulatedSAS, BALL::TriangulatedSES, BALL::TriangulatedSphere, BALL::TriangulatedSurface, BALL::Triple< T1, T2, T3 >, BALL::TSimpleBox3< T >, BALL::TSphere3< T >, BALL::TSurface< T >, BALL::TVector2< T >, BALL::TVector3< T >, BALL::TVector4< T >, BALL::VIEW::AddBallAndStickModel, BALL::VIEW::AtomBondModelBaseProcessor, BALL::VIEW::Box, BALL::VIEW::ColorExtension2, BALL::VIEW::ColorHSV, BALL::VIEW::ColorProcessor, BALL::VIEW::ColorRGBA, BALL::VIEW::ColorUnit, BALL::VIEW::ColorUnitHue, BALL::VIEW::Dataset, BALL::VIEW::Disc, BALL::VIEW::GeometricObject, BALL::VIEW::HBondModelProcessor, BALL::VIEW::Hotkey, BALL::VIEW::Label, BALL::VIEW::Line, BALL::VIEW::Mesh, BALL::VIEW::MultiColorExtension, BALL::VIEW::MultiLine, BALL::VIEW::Point, BALL::VIEW::SimpleBox, BALL::VIEW::Sphere, BALL::VIEW::Tube, BALL::VIEW::TwoColoredLine, BALL::VIEW::TwoColoredTube, BALL::VIEW::Vertex2, BALL::VIEW::Vertex
- setAcidicColor() : BALL::VIEW::ResidueTypeColorProcessor
- setActive() : BALL::VIEW::ClippingPlane
- setAdditionalGridDistance() : BALL::VIEW::ColorProcessor
- setAdvancedElectrostatic() : BALL::AmberNonBonded
- setAlpha() : BALL::LineSearch, BALL::VIEW::ColorRGBA
- setAlphaBlending() : BALL::VIEW::ColorMap
- setAlphas() : BALL::VIEW::MultiColorExtension
- setAltered() : BALL::GeneticIndividual
- setAlternateLocationIndicator() : BALL::PDBAtom
- setAmberDialog() : BALL::VIEW::MinimizationDialog, BALL::VIEW::MolecularDynamicsDialog
- setAmberFF() : BALL::VIEW::AmberConfigurationDialog
- setAminoAcidType() : BALL::Peptides::AminoAcidDescriptor
- setAngle() : BALL::RSEdge, BALL::SASEdge, BALL::VIEW::LightSource
- setAnimationSmoothness() : BALL::VIEW::Scene
- setAntialiasing() : BALL::VIEW::GLRenderer
- setApplyEnabled() : BALL::VIEW::Preferences
- setArgument() : BALL::ConnectedToPredicate, BALL::ExpressionPredicate
- setAromatic() : BALL::SmilesParser::SPAtom
- setAromaticColor() : BALL::VIEW::ResidueTypeColorProcessor
- setAromaticRings() : BALL::AtomTyper, BALL::Kekuliser, BALL::MMFF94ChargeProcessor
- setArrowWidth() : BALL::VIEW::AddCartoonModel
- setAtom() : BALL::Peak< PositionType >, BALL::RSVertex, BALL::SESVertex
- setAtomAveraging() : BALL::CreateSpectrumProcessor
- setAtomForces() : BALL::SnapShot
- setAtomicNumber() : BALL::Element
- setAtomicRadius() : BALL::Element
- setAtomicWeight() : BALL::Element
- setAtomIgnoring() : BALL::CreateSpectrumProcessor
- setAtomPositions() : BALL::Conformation, BALL::SnapShot
- setAtoms() : BALL::CHPI::CHGroup, BALL::CHPISlick::CHGroup
- setAtomType() : BALL::GridBasedScoring, BALL::GridedPLP, BALL::PLPScoring
- setAtomTypeNames() : BALL::GridBasedScoring
- setAtomTypeSmarts() : BALL::HybridisationProcessor
- setAtomVelocities() : BALL::SnapShot
- setAtomVelocitites() : BALL::SnapShot
- setAttenuation() : BALL::VIEW::LightSource
- setAttenuation_() : BALL::VIEW::LightSettings
- setAutoActivatePlugins() : BALL::PluginManager
- setAutoDeletable() : BALL::AutoDeletable
- setBackboneDependent() : BALL::RotamerLibrary
- setBackgroundColor() : BALL::VIEW::Stage
- setBallAndStickStickDashedBondsEnabled() : BALL::VIEW::ModelSettingsDialog
- setBallAndStickStickRadius() : BALL::VIEW::ModelSettingsDialog
- setBallRadius() : BALL::VIEW::AddBallAndStickModel, BALL::VIEW::ModelSettingsDialog
- setBarrier() : BALL::MPISupport
- setBaseColors() : BALL::VIEW::ColorMap
- setBaseDirectory() : BALL::VIEW::HelpViewer
- setBaseFunction() : BALL::ScoringFunction
- setBaseSize() : BALL::VIEW::ForceModel
- setBaseSystemAndPoses() : BALL::PoseClustering
- setBaseSystemAndTransformations() : BALL::PoseClustering
- setBasicColor() : BALL::VIEW::ResidueTypeColorProcessor
- setBathRelaxationTime() : BALL::CanonicalMD
- setBeta() : BALL::LineSearch
- setBit() : BALL::BitVector
- setBlue() : BALL::VIEW::ColorRGBA
- setBondLengths() : BALL::BuildBondsProcessor
- setBondOrder() : BALL::SmartsParser::SPBond
- setBondType() : BALL::ConnectedToPredicate::CTPNode
- setBool() : BALL::Options
- setBoudaryDerivatives() : BALL::CubicSpline1D
- setBoundingBox() : BALL::TRRFile
- setBox() : BALL::PeriodicBoundary
- setBracketedFlag() : BALL::LineSearch
- setBranchDesignator() : BALL::PDBAtom
- setBreakpoints() : BALL::VIEW::ColorByGridProcessor
- setBufferReady() : BALL::VIEW::RenderSetup
- setBusyMode_() : BALL::VIEW::MainControl
- SetCamera() : BALL::VIEW::SetCamera
- setCamera() : BALL::VIEW::Scene, BALL::VIEW::Stage
- setCappingEnabled() : BALL::VIEW::ClippingPlane
- setCartoonArrowWidth() : BALL::VIEW::ModelSettingsDialog
- setCartoonDNABaseRadius() : BALL::VIEW::ModelSettingsDialog
- setCartoonDNAHelixRadius() : BALL::VIEW::ModelSettingsDialog
- setCartoonDNALadderRadius() : BALL::VIEW::ModelSettingsDialog
- setCartoonHelixRadius() : BALL::VIEW::ModelSettingsDialog
- setCartoonStrandHeight() : BALL::VIEW::ModelSettingsDialog
- setCartoonStrandWidth() : BALL::VIEW::ModelSettingsDialog
- setCartoonTubeRadius() : BALL::VIEW::ModelSettingsDialog
- setCategory() : BALL::CIFFile::SaveFrame
- setCAtom() : BALL::CHPI::CHGroup, BALL::CHPISlick::CHGroup
- setCellAngleAlpha() : BALL::CrystalInfo
- setCellAngleBeta() : BALL::CrystalInfo
- setCellAngleGamma() : BALL::CrystalInfo
- setCellAngles() : BALL::CrystalInfo
- setCellDimensions() : BALL::CrystalInfo
- setCellEdgeLengthA() : BALL::CrystalInfo
- setCellEdgeLengthB() : BALL::CrystalInfo
- setCellEdgeLengthC() : BALL::CrystalInfo
- setCenter() : BALL::RSFace
- setCenterOfTorus() : BALL::RSEdge
- setCFS_() : BALL::SDGenerator
- setChain() : BALL::NMRStarFile::BALLToBMRBMapper
- setChainName() : BALL::Peptides::PeptideBuilder
- setCharge() : BALL::Atom
- setCharmmDialog() : BALL::VIEW::MinimizationDialog, BALL::VIEW::MolecularDynamicsDialog
- setCharmmFF() : BALL::VIEW::CharmmConfigurationDialog
- setChirality() : BALL::SmilesParser::SPAtom
- setCircle() : BALL::SASEdge, BALL::SESEdge, BALL::VIEW::Disc
- SetClippingPlane() : BALL::VIEW::SetClippingPlane
- setClippingPlane() : BALL::VIEW::ClippingDialog
- setClippingPlane_() : BALL::VIEW::GeometricControl
- setClippingPlaneX() : BALL::VIEW::GeometricControl
- setClippingPlaneY() : BALL::VIEW::GeometricControl
- setClippingPlaneZ() : BALL::VIEW::GeometricControl
- setClippingPosition() : BALL::VIEW::GeometricControl
- setCoefficient() : BALL::ScoringComponent, BALL::ScoringFunction
- setCoefficients() : BALL::PiecewiseFunction
- setCoefficientStdErrors() : BALL::QSAR::RegressionValidation
- setCoilColor() : BALL::VIEW::SecondaryStructureColorProcessor
- setColor() : BALL::VIEW::ColorButton, BALL::VIEW::GeometricObject, BALL::VIEW::LabelModel, BALL::VIEW::LightSource
- setColor2() : BALL::VIEW::ColorExtension2
- setColor4ub_() : BALL::VIEW::GLRenderer
- setColoringMethod() : BALL::VIEW::Representation
- setColoringSettingsDialog() : BALL::VIEW::DisplayProperties
- setColorProcessor() : BALL::VIEW::Representation
- setColorRGBA_() : BALL::VIEW::GLRenderer
- setColors() : BALL::VIEW::ColorByGridProcessor, BALL::VIEW::ColorTable, BALL::VIEW::InterpolateColorProcessor, BALL::VIEW::MultiColorExtension, BALL::VIEW::PositionColorProcessor
- setColumn() : BALL::TMatrix4x4< T >
- setCombineOperation() : BALL::GridBasedScoring
- setCompareMode() : BALL::String
- setComponentGrouping() : BALL::SmartsParser
- setComponentNumber() : BALL::SmartsParser::SPNode
- setComposite() : BALL::FragmentDistanceCollector, BALL::VIEW::BALLThread, BALL::VIEW::CompositeMessage, BALL::VIEW::Dataset, BALL::VIEW::GeometricObject, BALL::VIEW::Representation
- setCompositeName() : BALL::VIEW::CompositeMessage
- setComposites() : BALL::VIEW::ColorProcessor, BALL::VIEW::Representation
- setConformation() : BALL::Result::ResultData
- setConformationSet() : BALL::DockResult, BALL::PoseClustering, BALL::VIEW::DockingFinishedMessage
- setConstant() : BALL::MutableConstant< DataType >
- setConstants() : BALL::Pair6_12RDFIntegrator, BALL::PairExpRDFIntegrator
- setContactCircle() : BALL::RSEdge
- setContent() : BALL::INIFile, BALL::VIEW::ColorTable, BALL::VIEW::HotkeyTable, BALL::VIEW::PythonSettings
- setContentSize() : BALL::VIEW::MainControl
- setController() : BALL::VIEW::ContourSurfaceDialog, BALL::VIEW::GridVisualizationDialog
- setControlsEnabled_() : BALL::VIEW::LightSettings
- setCorrectionParameter() : BALL::ShiftedLVMMMinimizer
- setCovalentRadius() : BALL::Element
- setCrystalDialog() : BALL::VIEW::GenerateCrystalThread
- setCrystalInfo() : BALL::CrystalGenerator
- setCurrent() : BALL::Directory, BALL::VIEW::InteractionMode
- setCurrentAtom() : BALL::VIEW::Scene
- setCurrentBond() : BALL::VIEW::Scene
- setCurrentCharge() : BALL::GAMESSLogFile
- setCurrentModel() : BALL::PDBInfo
- setCurrentRepresentation() : BALL::VIEW::MaterialSettings
- setCurrentTime() : BALL::MolecularDynamics
- setCursor() : BALL::VIEW::Scene
- setCurvature() : BALL::CubicSpline1D
- setCustomColor() : BALL::VIEW::DisplayProperties
- setCVRes() : BALL::QSAR::ClassificationValidation, BALL::QSAR::RegressionValidation, BALL::QSAR::Validation
- setData() : BALL::BinaryFileAdaptor< T >, BALL::EdgeItem< Node, Edge >, BALL::NodeItem< Node, Edge >, BALL::QSAR::AutomaticModelCreator, BALL::TFFT1D< ComplexTraits >, BALL::TFFT2D< ComplexTraits >, BALL::TFFT3D< ComplexTraits >, BALL::VIEW::FrameBuffer, BALL::VIEW::ShortcutTableModel
- setDataFolder() : BALL::PartialChargeBase, BALL::PartialChargeProcessor, BALL::QSAR::QSARData, BALL::SimpleBase
- setDataPath() : BALL::Path
- setDataset() : BALL::VIEW::DatasetMessage
- setDatasetControl() : BALL::VIEW::DatasetController
- setDataSource() : BALL::QSAR::Model
- setDCDFile() : BALL::VIEW::MolecularDynamicsDialog
- setDefault() : BALL::Options
- setDefaultBool() : BALL::Options
- setDefaultColor() : BALL::VIEW::ColorButton, BALL::VIEW::ColorProcessor
- setDefaultCommunicator() : BALL::MPISupport
- setDefaultInteger() : BALL::Options
- setDefaultLighting() : BALL::VIEW::Scene
- setDefaultOptions() : BALL::AromaticityProcessor, BALL::AssignBondOrderProcessor, BALL::AStarBondOrderStrategy, BALL::BondOrderAssignmentStrategy, BALL::BranchAndBoundBondOrderStrategy, BALL::BuildBondsProcessor, BALL::CrystalInfo, BALL::EmpiricalHSShiftProcessor, BALL::FPTBondOrderStrategy, BALL::HBondProcessor, BALL::HybridisationProcessor, BALL::ILPBondOrderStrategy, BALL::KGreedyBondOrderStrategy, BALL::Peptides::NameConverter, BALL::PoseClustering, BALL::SDGenerator, BALL::SideChainPlacementProcessor, BALL::VIEW::SDWidget
- setDefaultOptions_() : BALL::NumericalSAS
- setDefaultPage() : BALL::VIEW::HelpViewer
- setDefaultPeak() : BALL::Experiment< PeakListType >
- setDefaultPluginDirectory() : BALL::VIEW::PluginDialog
- setDefaultPositionAddress() : BALL::VIEW::Sphere
- setDefaultRangeValues_() : BALL::VIEW::RaytraceableContourSurfaceDialog
- setDefaultReal() : BALL::Options
- setDefaultValue() : BALL::CubicSpline1D
- setDefaultValues() : BALL::VIEW::Preferences
- setDefaultValues_() : BALL::VIEW::ColoringSettingsDialog, BALL::VIEW::ModelSettingsDialog
- setDefaultVertex1Address() : BALL::VIEW::Vertex2
- setDefaultVertex2Address() : BALL::VIEW::Vertex2
- setDefaultVertexAddress() : BALL::VIEW::Vertex
- setDefaultVertexAddresses() : BALL::VIEW::Vertex2
- setDegree() : BALL::PiecewisePolynomial
- setDeletable() : BALL::VIEW::Message
- setDeleteEntryEnabled() : BALL::VIEW::MainControl
- setDensity() : BALL::SurfaceProcessor, BALL::TriangulatedSAS, BALL::TriangulatedSES, BALL::TriangulatedSurface
- setDepth() : BALL::TBox3< T >
- setDepthVector() : BALL::TBox3< T >
- setDescription() : BALL::Result
- setDescriptorIDs() : BALL::QSAR::Model
- setDescriptorNames() : BALL::QSAR::QSARData
- setDihedral() : BALL::RotateBond
- setDimension() : BALL::ShiftModel1D, BALL::ShiftModel2D, BALL::TRegularData1D< ValueType >, BALL::TRegularData2D< ValueType >, BALL::TRegularData3D< ValueType >
- setDirection() : BALL::VIEW::LightSource
- setDirection_() : BALL::VIEW::LightSettings
- setDisplayMode() : BALL::DockingAlgorithm
- setDistance() : BALL::FragmentDistanceCollector, BALL::VIEW::AtomDistanceColorProcessor
- setDNABaseRadius() : BALL::VIEW::AddCartoonModel
- setDNAHelixRadius() : BALL::VIEW::AddCartoonModel
- setDNALadderRadius() : BALL::VIEW::AddCartoonModel
- setDockedSystem() : BALL::VIEW::DockResultDialog
- setDockingAlgorithm() : BALL::VIEW::DockingThread, BALL::VIEW::DockProgressDialog
- setDockResult() : BALL::VIEW::DockResultDialog
- setDoNotResize() : BALL::VIEW::TRenderWindow< taPixelDatatype >
- setDotSize() : BALL::VIEW::GridVisualisation
- setDownsamplingFactor() : BALL::VIEW::GLRenderWindow, BALL::VIEW::Scene
- setDrawDNAAsLadderModel() : BALL::VIEW::AddCartoonModel
- setDrawingMode() : BALL::VIEW::Representation
- setDrawingPrecision() : BALL::VIEW::DisplayProperties, BALL::VIEW::ModelProcessor, BALL::VIEW::Representation
- setDuplicateKeyCheck() : BALL::INIFile
- setEdge() : BALL::GraphTriangle< Vertex, Edge, Face >, BALL::SolventAccessibleSurface
- setEditable() : BALL::VIEW::PropEditorWidget, BALL::VIEW::PropertyEditor
- setEditElementType() : BALL::VIEW::Scene
- setEditorData() : BALL::VIEW::ComboBoxDelegate
- setEDSPrefix() : BALL::VIEW::DownloadElectronDensity
- setEDSSuffix() : BALL::VIEW::DownloadElectronDensity
- setElectronegativity() : BALL::Element
- setElement() : BALL::Atom
- setElementCursor() : BALL::VIEW::Scene
- setElementName() : BALL::GAFFCESParser::CESelementConnectionPredicate, BALL::GAFFCESParser::CESelementPredicate
- setEMDBPrefix() : BALL::VIEW::DownloadElectronDensity
- setEMDBSuffix() : BALL::VIEW::DownloadElectronDensity
- setEnableAlpha() : BALL::VIEW::ColorButton
- setEnabled() : BALL::ForceFieldComponent, BALL::VIEW::FakeDriver, BALL::VIEW::InputDeviceDriver
- setEnergy() : BALL::Result::ResultData
- setEnergyDifference() : BALL::VIEW::MinimizationDialog
- setEnergyDifferenceBound() : BALL::EnergyMinimizer
- setEnergyMinimizer() : BALL::VIEW::EnergyMinimizerThread
- setEnergyOutputFrequency() : BALL::EnergyMinimizer, BALL::MolecularDynamics
- setEnergyToAbort() : BALL::EnergyMinimizer, BALL::MolecularDynamics
- setEpsilon() : BALL::RombergIntegrator< Function, DataType >
- setEquivalences() : BALL::MMFF94ParametersBase
- setError_() : BALL::VIEW::PyWidget
- setErrorText() : BALL::VIEW::EditSingleShortcut
- setESParameters() : BALL::MMFF94ChargeProcessor
- setExponent() : BALL::MutablePower< Function, DataType >
- setExpression() : BALL::CreateSpectrumProcessor, BALL::Expression, BALL::NumberOfHydrogenBondAcceptors, BALL::NumberOfHydrogenBondDonors, BALL::NumberOfHydrophobicAtoms, BALL::Selector, BALL::SimpleExperiment1D
- setEyeDistance() : BALL::VIEW::Stage
- setFace() : BALL::GraphEdge< Vertex, Edge, Face >, BALL::SolventAccessibleSurface
- setFDPBDialog() : BALL::VIEW::CalculateFDPBThread
- setFile() : BALL::Exception::GlobalExceptionHandler
- setFileName() : BALL::VIEW::FileObserver, BALL::VIEW::POVRenderer, BALL::VIEW::STLRenderer, BALL::VIEW::VRMLRenderer, BALL::VIEW::XML3DRenderer
- setFilename() : BALL::AssignRadiusProcessor, BALL::FragmentDB, BALL::INIFile, BALL::Parameters, BALL::PDBInfo, BALL::ShiftModel1D, BALL::ShiftModel2D, BALL::ShiftModel, BALL::VIEW::ExportGeometryDialog, BALL::VIEW::PythonSettings, BALL::VIEW::TestFramework
- setFilter() : BALL::VIEW::ShortcutTableView
- setFinalizeOnDestruct() : BALL::MPISupport
- setFinished() : BALL::ConnectedToPredicate::CTPNode
- setFirst() : BALL::Addition< First, Second, DataType >, BALL::Division< First, Second, DataType >, BALL::Product< First, Second, DataType >, BALL::Subtraction< First, Second, DataType >
- setFirstAtom() : BALL::Bond
- setFirstColor() : BALL::VIEW::ResidueNumberColorProcessor
- setFirstEdge() : BALL::SmartsParser::SPNode
- setFirstMolecule() : BALL::ScoringFunction
- setFirstSPEdge() : BALL::SmartsParser::SPEdge
- setFirstSPNode() : BALL::SmartsParser::SPEdge
- setFirstStrand() : BALL::DNAMutator
- setFitnessValue() : BALL::GeneticIndividual
- setFlags() : BALL::VIEW::PixelFormat
- setFlexDefinition() : BALL::Receptor
- setFlexibleResidues() : BALL::ScoringFunction, BALL::SideChainOptimizer
- setFlushToDiskFrequency() : BALL::SnapShotManager
- setFocalDistance() : BALL::VIEW::Stage
- setFogIntensity() : BALL::VIEW::GLRenderer, BALL::VIEW::Stage
- setFont() : BALL::VIEW::Label, BALL::VIEW::LabelModel, BALL::VIEW::MainControlPreferences
- setFontSize() : BALL::VIEW::Label
- setForce() : BALL::Atom
- setForceBase() : BALL::VIEW::ModelSettingsDialog
- setForceField() : BALL::AmberEvaluation, BALL::DNAMutator, BALL::ForceFieldComponent, BALL::ForceFieldEvaluation, BALL::SnapShotManager
- setForceMaxLenght() : BALL::VIEW::ModelSettingsDialog
- setForceOffset() : BALL::VIEW::ModelSettingsDialog
- setForceScaling() : BALL::VIEW::ModelSettingsDialog
- setForceStorage() : BALL::TRRFile
- setFormalCharge() : BALL::Atom, BALL::SmilesParser::SPAtom
- setFormalCharge_() : BALL::VIEW::EditMode, BALL::VIEW::Scene
- setFormat() : BALL::VIEW::FrameBuffer
- setFPSEnabled() : BALL::VIEW::Scene
- setFracVar() : BALL::QSAR::KPCRModel, BALL::QSAR::PCRModel
- setFragmentDB() : BALL::ElectrostaticPotentialCalculator, BALL::FragmentDB::BuildBondsProcessor, BALL::FragmentDB::NormalizeNamesProcessor, BALL::Mutator, BALL::Peptides::PeptideBuilder, BALL::ReconstructFragmentProcessor
- setFrameBufferFormat() : BALL::VIEW::BufferedRenderer
- setFrustum() : BALL::VIEW::RTfactRenderer
- setFullScreen() : BALL::VIEW::Scene
- setFunction() : BALL::CubicFunction< Function, DataType >, BALL::MutablePower< Function, DataType >, BALL::NumericalIntegrator< Function, DataType >, BALL::Reciprocal< Function, DataType >, BALL::SquareFunction< Function, DataType >
- setGeometricObjects() : BALL::VIEW::Representation
- setGLRenderer() : BALL::VIEW::MeshBuffer, BALL::VIEW::Scene
- setGreen() : BALL::VIEW::ColorRGBA
- setGrid() : BALL::VIEW::ContourSurfaceDialog, BALL::VIEW::GridVisualisation, BALL::VIEW::GridVisualizationDialog, BALL::VIEW::ModifyRepresentationDialog, BALL::VIEW::RaytraceableContourSurfaceDialog
- setGroup() : BALL::Element
- setGuest() : BALL::VIEW::DockWidget
- setHandleStreamsExternally() : BALL::XDRPersistenceManager
- setHashGrid() : BALL::ScoreGridSet
- setHAtom() : BALL::CHPI::CHGroup, BALL::CHPISlick::CHGroup
- setHBondRadius() : BALL::VIEW::ModelSettingsDialog
- setHeight() : BALL::TBox3< T >, BALL::VIEW::FrameBufferFormat
- setHeightVector() : BALL::TBox3< T >
- setHelixColor() : BALL::VIEW::SecondaryStructureColorProcessor
- setHelixRadius() : BALL::VIEW::AddCartoonModel
- setHidden() : BALL::VIEW::ClippingPlane, BALL::VIEW::Representation
- setHTMLView() : BALL::VIEW::HTMLViewDock
- setHue() : BALL::VIEW::ColorHSV
- setHumanReadable() : BALL::VIEW::POVRenderer, BALL::VIEW::XML3DRenderer
- setHydrophobicColor() : BALL::VIEW::ResidueTypeColorProcessor
- setIcon() : BALL::VIEW::ModularWidget
- setID() : BALL::Conformation, BALL::NucleicAcid, BALL::Nucleotide, BALL::PDBInfo, BALL::Protein, BALL::Residue
- setId() : BALL::FlexibleMolecule
- setIdentifier() : BALL::Embeddable
- setIdentity() : BALL::TMatrix4x4< T >, BALL::TQuaternion< T >
- setImportant() : BALL::VIEW::LogEvent
- setImprovedFlag() : BALL::StrangLBFGSMinimizer
- setInBrackets() : BALL::SmilesParser::SPAtom
- setIndex() : BALL::GraphEdge< Vertex, Edge, Face >, BALL::GraphFace< Vertex, Edge, Face >, BALL::GraphTriangle< Vertex, Edge, Face >, BALL::GraphVertex< Vertex, Edge, Face >, BALL::SnapShot, BALL::VIEW::EditSingleShortcut
- setIndices() : BALL::TriangulatedSurface
- setInfo() : BALL::VIEW::Scene
- setInfoColor() : BALL::VIEW::Stage
- setINIFileSectionName() : BALL::VIEW::PreferencesEntry
- setInputParameters() : BALL::DockResultFile
- setInsertionCode() : BALL::Nucleotide, BALL::Residue
- setInteger() : BALL::Options
- setIntensity() : BALL::Peak< PositionType >, BALL::VIEW::LightSource
- setIntercept() : BALL::ScoringFunction
- setInternal() : BALL::SmartsParser::SPEdge, BALL::SmartsParser::SPNode
- setInterpolationBoundaries() : BALL::VIEW::ColorMap
- setIntersectionPoint() : BALL::RSEdge
- setIntervals() : BALL::PiecewiseFunction
- setIsotope() : BALL::SmilesParser::SPAtom
- setIstream() : BALL::PersistenceManager
- setKineticEnergy() : BALL::SnapShot
- setKw() : BALL::QSAR::ALLModel
- setLabelText_() : BALL::VIEW::ModelSettingsDialog
- setLastColor() : BALL::VIEW::ResidueNumberColorProcessor
- setLevel() : BALL::LogStream
- setLibraryFeatures() : BALL::BinaryFingerprintMethods
- setLigand() : BALL::DiffGridBasedScoring, BALL::DockingAlgorithm, BALL::GridedPLP, BALL::PLPScoring, BALL::ScoringFunction
- setLigandConformation() : BALL::Result::ResultData
- setLigandConformationId() : BALL::Result::ResultData
- setLigandIntraMolecular() : BALL::RotationalEntropy, BALL::ScoringComponent
- setLights() : BALL::VIEW::GLRenderer, BALL::VIEW::Renderer, BALL::VIEW::RenderSetup, BALL::VIEW::RTfactRenderer, BALL::VIEW::TilingRenderer
- setLine() : BALL::Exception::GlobalExceptionHandler, BALL::INIFile
- setLine_() : BALL::INIFile::IteratorTraits_
- setLinked() : BALL::ConnectedToPredicate::CTPNode
- setLocked() : BALL::VIEW::ServerWidget::BALLViewServer
- setLoggingFilename() : BALL::VIEW::MainControl
- setLogicalOperator() : BALL::SmartsParser::SPEdge, BALL::SmartsParser::SPNode
- setLookAtPosition() : BALL::VIEW::Camera
- setLookUpVector() : BALL::VIEW::Camera
- setLower() : BALL::FermiBaseFunction, BALL::ScoringBaseFunction
- setLowerBound() : BALL::CubicSpline1D, BALL::LineSearch
- setLowerDerivative() : BALL::CubicSpline1D
- setMainControl() : BALL::VIEW::AtomOverview::ApplyProcessor, BALL::VIEW::BALLThread, BALL::VIEW::ModularWidgetPlugin
- setMajorRadiusOfTorus() : BALL::RSEdge
- setMatchingMode() : BALL::DNAMutator
- setMaterial_() : BALL::VIEW::GLRenderer
- setMatrix() : BALL::VIEW::TransformationMessage
- setMaxColor() : BALL::VIEW::InterpolateColorProcessor
- setMaxDistanceColor() : BALL::VIEW::AtomDistanceColorProcessor
- setMaxFps() : BALL::DockingAlgorithm
- setMaxGradient() : BALL::EnergyMinimizer, BALL::VIEW::MinimizationDialog
- setMaximalNumberOfIterations() : BALL::MolecularDynamics
- setMaximalSimulationTime() : BALL::MolecularDynamics
- setMaximumDisplacement() : BALL::EnergyMinimizer
- setMaximumNumberOfErrors() : BALL::ForceField, BALL::ScoringFunction
- setMaximumUnassignedAtoms() : BALL::AssignBaseProcessor, BALL::Templates
- setMaxIterations() : BALL::VIEW::MinimizationDialog
- setMaxLength() : BALL::VIEW::ForceModel
- setMaxLevel() : BALL::LogStream
- setMaxNumberOfIterations() : BALL::EnergyMinimizer
- setMaxNumOfColumns() : BALL::ShiftedLVMMMinimizer
- setMaxNumOfStoredVectPairs() : BALL::StrangLBFGSMinimizer
- setMaxNumSteps() : BALL::RombergIntegrator< Function, DataType >
- setMaxOptimizationSteps() : BALL::DNAMutator
- setMaxSameEnergy() : BALL::EnergyMinimizer
- setMaxSteps() : BALL::LineSearch
- setMaxValue() : BALL::VIEW::GridColorWidget, BALL::VIEW::GridVisualizationDialog, BALL::VIEW::InterpolateColorProcessor, BALL::VIEW::ModifyRepresentationDialog
- setMenuHelp() : BALL::VIEW::ModularWidget
- setMenuHint() : BALL::VIEW::MainControl
- setMesh() : BALL::VIEW::MeshBuffer
- setMessage() : BALL::Exception::GeneralException, BALL::Exception::GlobalExceptionHandler, BALL::VIEW::LogEvent, BALL::VIEW::MessageEvent
- setMethod() : BALL::Result
- setMicroCanonical() : BALL::VIEW::MolecularDynamicsDialog
- setMiddleColor() : BALL::VIEW::ResidueNumberColorProcessor
- setMidValue() : BALL::VIEW::GridColorWidget, BALL::VIEW::GridVisualizationDialog, BALL::VIEW::ModifyRepresentationDialog
- setMinColor() : BALL::VIEW::InterpolateColorProcessor
- setMinGridSpacing() : BALL::VIEW::ColorProcessor
- setMinimizer() : BALL::DNAMutator, BALL::LineSearch
- setMinLevel() : BALL::LogStream
- setMinMaxColors() : BALL::VIEW::ColorMap
- setMinQuality() : BALL::QSAR::AutomaticModelCreator
- setMinValue() : BALL::VIEW::GridColorWidget, BALL::VIEW::GridVisualizationDialog, BALL::VIEW::InterpolateColorProcessor, BALL::VIEW::ModifyRepresentationDialog
- setMMFF94() : BALL::VIEW::MMFF94ConfigurationDialog
- setMMFF94Dialog() : BALL::VIEW::MinimizationDialog, BALL::VIEW::MolecularDynamicsDialog
- setMode() : BALL::VIEW::InterpolateColorProcessor, BALL::VIEW::LabelModel, BALL::VIEW::ModifyRepresentationDialog, BALL::VIEW::UIOperationMode
- setMode_() : BALL::VIEW::InteractionModeManager
- setModel() : BALL::QSAR::FeatureSelection
- setModelData() : BALL::VIEW::ComboBoxDelegate
- setModelInformation() : BALL::VIEW::MainControl, BALL::VIEW::Representation
- setModelProcessor() : BALL::VIEW::Representation
- setModelSettingsDialog() : BALL::VIEW::DisplayProperties
- setModelType() : BALL::VIEW::ColorProcessor, BALL::VIEW::Representation
- setMolecularDynamics() : BALL::VIEW::MDSimulationThread
- setMolecule() : BALL::CIFFile
- setMoleculeName() : BALL::GAMESSDatFile, BALL::GAMESSLogFile
- setMouseSensitivity() : BALL::VIEW::InteractionMode, BALL::VIEW::InteractionModeManager, BALL::VIEW::Scene
- setMouseWheelSensitivity() : BALL::VIEW::InteractionMode, BALL::VIEW::InteractionModeManager, BALL::VIEW::Scene
- setMpiInfo() : BALL::MPISupport
- setMultithreading() : BALL::VIEW::MainControl
- setMutated() : BALL::GeneticIndividual
- setMutations() : BALL::SideChainPlacementProcessor
- setName() : BALL::Atom, BALL::AtomContainer, BALL::Bond, BALL::CIFFile::Datablock, BALL::Constraint, BALL::Descriptor, BALL::Element, BALL::Exception::GlobalExceptionHandler, BALL::File, BALL::ForceField, BALL::ForceFieldComponent, BALL::Options, BALL::PDBInfo, BALL::ReferenceArea, BALL::ResidueRotamerSet, BALL::ScoringComponent, BALL::ScoringFunction, BALL::ShiftModule, BALL::SolventDescriptor, BALL::VIEW::Dataset, BALL::VIEW::Representation
- setNamesTitle() : BALL::VIEW::ColorTable
- setNamingStandard() : BALL::FragmentDB::NormalizeNamesProcessor
- setNeedsSSSR() : BALL::SmartsParser
- setNeedsUpdate() : BALL::VIEW::Representation
- setNegate() : BALL::ExpressionTree
- setNextComponentNumberToSubTree() : BALL::SmartsParser
- setNMRAtomDataSet() : BALL::NMRStarFile::BALLToBMRBMapper
- setNMRAtomDataSetByName() : BALL::NMRStarFile::BALLToBMRBMapper
- setNMRStarFile() : BALL::NMRStarFile::BALLToBMRBMapper
- setNoComponents() : BALL::QSAR::KPLSModel, BALL::QSAR::PLSModel
- setNoOrthoComponents() : BALL::QSAR::OPLSModel
- setNormal() : BALL::RSFace, BALL::SESVertex, BALL::TrianglePoint, BALL::VIEW::ClippingPlane, BALL::VIEW::GridVisualisation
- setNormalizationEnabled() : BALL::VIEW::ColorByGridProcessor, BALL::VIEW::GridColorWidget
- setNormalizationParameters() : BALL::ScoringComponent, BALL::ScoringFunction
- setNot() : BALL::SmartsParser::SPBond, BALL::SmartsParser::SPEdge, BALL::SmartsParser::SPNode
- setNotProperty() : BALL::SmartsParser::SPAtom
- setNucleotideMapping() : BALL::DNAMutator
- setNullDistanceColor() : BALL::VIEW::AtomDistanceColorProcessor
- setNumberDensity() : BALL::SolventDescriptor
- setNumberDesiredAtoms() : BALL::ReferenceArea
- setNumberOfATOMRecords() : BALL::PDBInfo
- setNumberOfAtoms() : BALL::SnapShot
- setNumberOfColors() : BALL::VIEW::ColorMap
- setNumberOfFFTTransforms() : BALL::TFFT1D< ComplexTraits >, BALL::TFFT2D< ComplexTraits >, BALL::TFFT3D< ComplexTraits >
- setNumberOfHETATMRecords() : BALL::PDBInfo
- setNumberOfiFFTTransforms() : BALL::TFFT1D< ComplexTraits >, BALL::TFFT2D< ComplexTraits >, BALL::TFFT3D< ComplexTraits >
- setNumberOfIteration() : BALL::MolecularDynamics
- setNumberOfIterations() : BALL::EnergyMinimizer
- setNumberOfModels() : BALL::PDBInfo
- setNumberOfPartners() : BALL::GAFFCESParser::CESelementConnectionPredicate, BALL::GAFFCESParser::CESwildcardsConnectionPredicate
- setNumberOfRecords() : BALL::PDBInfo
- setNumberOfSteps() : BALL::VIEW::MDSimulationThread, BALL::VIEW::MolecularDynamicsDialog
- setNumberOfStepsBetweenUpdates() : BALL::VIEW::SimulationThread
- setNumberOfTorsions() : BALL::ResidueRotamerSet
- setNumLevels() : BALL::VIEW::ColorByGridProcessor
- setObject() : BALL::VIEW::RegisterHelpSystemMessage
- setOccupancy() : BALL::PDBAtom
- setOffScreenRendering() : BALL::VIEW::Scene
- setOffset() : BALL::VIEW::BufferedRenderer, BALL::VIEW::ForceModel, BALL::VIEW::RenderSetup
- setOmega() : BALL::Peptides::AminoAcidDescriptor
- setOmega_() : BALL::Peptides::PeptideBuilder
- setOpenItems() : BALL::VIEW::NewSelectionMessage
- setOptions() : BALL::AmberEvaluation, BALL::ForceFieldEvaluation
- setOrder() : BALL::Bond
- setOrigin() : BALL::ShiftModel1D, BALL::ShiftModel2D, BALL::TRegularData1D< ValueType >, BALL::TRegularData2D< ValueType >, BALL::TRegularData3D< ValueType >
- setOrthographicZoom() : BALL::VIEW::GLRenderer
- setOstream() : BALL::PersistenceManager, BALL::VIEW::POVRenderer, BALL::VIEW::XML3DRenderer
- setOtherColor() : BALL::VIEW::ResidueTypeColorProcessor
- setOutputParameters() : BALL::DockResultFile
- setParameterAsAdvanced() : BALL::CommandlineParser
- setParameterAsHidden() : BALL::CommandlineParser
- setParameterRestrictions() : BALL::CommandlineParser
- setParameters() : BALL::QSAR::ALLModel, BALL::QSAR::GPModel, BALL::QSAR::KNNModel, BALL::QSAR::KPCRModel, BALL::QSAR::KPLSModel, BALL::QSAR::LDAModel, BALL::QSAR::LibsvmModel, BALL::QSAR::Model, BALL::QSAR::NBModel, BALL::QSAR::OPLSModel, BALL::QSAR::PCRModel, BALL::QSAR::PLSModel, BALL::QSAR::RRModel, BALL::QSAR::SNBModel, BALL::ScoreGridSet, BALL::ShiftModule
- setParent() : BALL::Conformation, BALL::ConformationSet, BALL::ConnectedToPredicate::CTPNode, BALL::HashGridBox3< Item >, BALL::VIEW::AtomOverview
- setPeaks() : BALL::ShiftModel1D, BALL::ShiftModel2D
- setPeriod() : BALL::Element
- setPharmacophoreConstraint() : BALL::ScoreGridSet
- setPhi() : BALL::Peptides::AminoAcidDescriptor
- setPhysStepWidth() : BALL::TFFT1D< ComplexTraits >, BALL::TFFT2D< ComplexTraits >, BALL::TFFT3D< ComplexTraits >
- setPitch() : BALL::VIEW::FrameBufferFormat
- setPixelFormat() : BALL::VIEW::FrameBufferFormat
- setPluginDirectories() : BALL::PluginManager
- setPoint() : BALL::SASVertex, BALL::SESVertex, BALL::TBox3< T >, BALL::Triangle, BALL::TriangleEdge, BALL::TrianglePoint, BALL::VIEW::ClippingPlane, BALL::VIEW::GridVisualisation
- setPolarColor() : BALL::VIEW::ResidueTypeColorProcessor
- setPort() : BALL::TCPServer, BALL::VIEW::ServerWidget
- setPosition() : BALL::Atom, BALL::Composite::CompositeIteratorTraits, BALL::Peak< PositionType >, BALL::VIEW::LightSource, BALL::VIEW::Sphere
- setPosition_() : BALL::VIEW::LightSettings
- setPositionAddress() : BALL::VIEW::Sphere
- setPositions() : BALL::CubicSpline1D
- setPotentialEnergy() : BALL::SnapShot
- setPOVNumber() : BALL::VIEW::Scene
- setPrecision() : BALL::TRRFile
- setPredicate() : BALL::CompositeIteratorTraits, BALL::ExpressionTree
- setPreferencesEnabled_() : BALL::VIEW::MainControl
- setPrefix() : BALL::LogStream, BALL::RuleEvaluator, BALL::VIEW::DownloadPDBFile
- setPreview() : BALL::VIEW::Scene
- setPreviewMode() : BALL::VIEW::Renderer
- setProbeRadius() : BALL::SurfaceProcessor, BALL::VIEW::AddSurfaceModel
- setProcessor() : BALL::VIEW::AssignBondOrderResultsDialog
- setProject() : BALL::VIEW::HelpViewer
- setProjection() : BALL::VIEW::GLRenderer
- setProjectionMode() : BALL::VIEW::Camera
- setProperty() : BALL::PropertyManager, BALL::SmartsParser::SPAtom
- setPropertyManager() : BALL::VIEW::PropertyEditor
- setProteinName() : BALL::Peptides::PeptideBuilder
- setPsi() : BALL::Peptides::AminoAcidDescriptor
- setQ2() : BALL::QSAR::RegressionValidation
- setQualityIncreaseCutoff() : BALL::QSAR::FeatureSelection
- setQueryFeatures() : BALL::BinaryFingerprintMethods
- setRadius() : BALL::Atom, BALL::VIEW::HBondModelProcessor, BALL::VIEW::Sphere, BALL::VIEW::Tube, BALL::VIEW::TwoColoredTube
- setRange() : BALL::VIEW::ColorMap
- setRDF() : BALL::RDFIntegrator
- setRDFIntegrator() : BALL::Pair6_12InteractionEnergyProcessor
- setRDFParameters() : BALL::Pair6_12InteractionEnergyProcessor
- setReadPDBModels() : BALL::VIEW::MolecularFileDialog
- setReal() : BALL::Options
- setReceiveBufferUpdates() : BALL::VIEW::RenderSetup
- setReceiver() : BALL::VIEW::InputDeviceDriver, BALL::VIEW::InputPlugin
- setReceptor() : BALL::ScoringFunction
- setReceptorConformation() : BALL::Result::ResultData
- setReceptorConformationId() : BALL::Result::ResultData
- setRecursive() : BALL::SmartsParser, BALL::SmartsParser::SPNode
- setRed() : BALL::VIEW::ColorRGBA
- setReferenceTemperature() : BALL::MolecularDynamics
- setRefresh() : BALL::VIEW::MinimizationDialog
- setRegisterMode() : BALL::VIEW::RegisterHelpSystemMessage
- setRelativeToCamera() : BALL::VIEW::LightSource
- setRemotenessIndicator() : BALL::PDBAtom
- setRenderMode() : BALL::VIEW::GLRenderer
- setRepresentation() : BALL::RadialDistributionFunction, BALL::VIEW::ModifyRepresentationDialog, BALL::VIEW::RepresentationMessage, BALL::VIEW::UpdateRepresentationThread
- setResolution() : BALL::GridAnalysis
- setRibbonMode() : BALL::VIEW::AddBackboneModel
- setRightVector() : BALL::TBox3< T >
- setRing() : BALL::CHPI::AromaticRing, BALL::CHPISlick::AromaticRing
- setRings() : BALL::AddHydrogenProcessor, BALL::AtomTyper, BALL::Kekuliser
- setRingSize() : BALL::RingFinder
- setRoot() : BALL::SmartsParser
- setRotamer() : BALL::ResidueRotamerSet
- setRotatableBonds() : BALL::PLP
- setRotation() : BALL::TMatrix4x4< T >
- setRotationX() : BALL::TMatrix4x4< T >
- setRotationY() : BALL::TMatrix4x4< T >
- setRotationZ() : BALL::TMatrix4x4< T >
- setRow() : BALL::TMatrix4x4< T >
- setRS() : BALL::SolventAccessibleSurface
- setRSEdge() : BALL::SESEdge, BALL::SESFace
- setRSFace() : BALL::SESFace
- setRSVertex() : BALL::SESFace
- setRubberBandGeometry() : BALL::VIEW::Scene
- setRubberBandVisible() : BALL::VIEW::Scene
- sets_ : BALL::MOL2File
- setSaturation() : BALL::VIEW::ColorHSV
- setSaveImages() : BALL::VIEW::MDSimulationThread
- setScale() : BALL::TMatrix4x4< T >
- setScaling() : BALL::VIEW::ForceModel
- setScalingFactorFile() : BALL::GeneralizedBornModel
- setScalingFactors() : BALL::GeneralizedBornModel
- setScene() : BALL::VIEW::AnimationThread
- setScoring() : BALL::ConformationSet
- setScoringFunction() : BALL::Constraint, BALL::DockingAlgorithm, BALL::PharmacophoreConstraint, BALL::ReferenceArea, BALL::ScoringComponent
- setScoringMethod() : BALL::Result::ResultData
- setScoringType() : BALL::StructurePreparer
- setScreenShotNumber() : BALL::VIEW::Scene
- setSecond() : BALL::Addition< First, Second, DataType >, BALL::Division< First, Second, DataType >, BALL::Product< First, Second, DataType >, BALL::Subtraction< First, Second, DataType >
- setSecondaryStructureType_() : BALL::SecondaryStructureProcessor
- setSecondAtom() : BALL::Bond
- setSecondEdge() : BALL::SmartsParser::SPNode
- setSecondMolecule() : BALL::ScoringFunction
- setSecondSPEdge() : BALL::SmartsParser::SPEdge
- setSecondSPNode() : BALL::SmartsParser::SPEdge
- setSecondStrand() : BALL::DNAMutator
- setSelected() : BALL::Selectable, BALL::VIEW::GeometricObjectSelectionMessage
- setSelection() : BALL::VIEW::GenericSelectionMessage, BALL::VIEW::GeometricObjectSelectionMessage
- setSelection_() : BALL::VIEW::MolecularControl
- setSender() : BALL::VIEW::Message
- setShiftRange() : BALL::Bruker2DFile
- setShortcutText() : BALL::VIEW::EditSingleShortcut
- setShowLightSources() : BALL::VIEW::Scene
- setShowOnlyInLogView() : BALL::VIEW::LogEvent
- setShowSelected() : BALL::VIEW::AtomDistanceColorProcessor
- setShowSelectionInfos() : BALL::VIEW::CompositeMessage
- setSimpleAtomTypes() : BALL::StructurePreparer
- setSimulationThread() : BALL::VIEW::MainControl
- setSingular() : BALL::RSEdge, BALL::RSFace
- setSize() : BALL::BitVector, BALL::VIEW::GLRenderer, BALL::VIEW::Renderer, BALL::VIEW::RTfactRenderer, BALL::VIEW::TilingRenderer, BALL::VIEW::XML3DRenderer
- setSmoothLines() : BALL::VIEW::GLRenderer
- setSnapShotFrequency() : BALL::EnergyMinimizer, BALL::MolecularDynamics
- setSnapShotManager() : BALL::VIEW::SnapshotVisualisationDialog
- setSoluteDC() : BALL::GeneralizedBornModel
- setSolventAtomDescriptorList() : BALL::SolventDescriptor
- setSolventDC() : BALL::GeneralizedBornModel
- setSolventDescriptor() : BALL::Pair6_12InteractionEnergyProcessor
- setSource() : BALL::VIEW::DragLogView
- setSpaceGroup() : BALL::CrystalInfo
- setSpaceGroupFilename() : BALL::CrystalGenerator
- setSpacing() : BALL::Spectrum< DataT, PeakT, PositionT >
- setSPAtom() : BALL::SmartsParser::SPNode
- setSPBond() : BALL::SmartsParser::SPEdge
- setSphere() : BALL::SASFace
- setSplitRadius() : BALL::VIEW::ModifyRepresentationDialog
- setSSSR() : BALL::SmartsMatcher, BALL::SmartsParser
- setStage() : BALL::VIEW::Renderer, BALL::VIEW::SceneMessage
- setStateAssignment() : BALL::FPTBondOrderStrategy::DPBackTracking_
- setStatusbarText() : BALL::VIEW::DatasetController, BALL::VIEW::MainControl, BALL::VIEW::ModularWidget
- setStereoDelta() : BALL::VIEW::GLRenderWindow
- setStereoFrustumConversion() : BALL::VIEW::Renderer
- setStereoMode() : BALL::VIEW::InteractionModeManager, BALL::VIEW::Renderer, BALL::VIEW::RenderSetup
- setStickRadius() : BALL::VIEW::AddBallAndStickModel
- setSticks() : BALL::Spectrum< DataT, PeakT, PositionT >
- setStickStickRadius() : BALL::VIEW::ModelSettingsDialog
- setStrandColor() : BALL::VIEW::SecondaryStructureColorProcessor
- setStrandHeight() : BALL::VIEW::AddCartoonModel
- setStrands() : BALL::DNAMutator
- setStrandWidth() : BALL::VIEW::AddCartoonModel
- setStride() : BALL::VIEW::BufferedRenderer
- setStyle() : BALL::VIEW::MainControlPreferences
- setSuffix() : BALL::VIEW::DownloadPDBFile
- setSupportedFormats() : BALL::CommandlineParser
- setSurfaceDrawingPrecision() : BALL::VIEW::DisplayProperties, BALL::VIEW::ModelProcessor, BALL::VIEW::Representation
- setSurfaceProbeRadius() : BALL::VIEW::ModelSettingsDialog
- setSwapEndian() : BALL::BinaryFileAdaptor< T >
- setSwapSideBySideStereo() : BALL::VIEW::Stage
- setSymbol() : BALL::ConnectedToPredicate::CTPNode, BALL::Element
- setSysPath() : BALL::PyInterpreter
- setSystem() : BALL::CrystalGenerator, BALL::ShiftModel1D, BALL::ShiftModel2D, BALL::SnapShotManager, BALL::VIEW::FDPBDialog, BALL::VIEW::SDWidget
- setSystems() : BALL::VIEW::DockDialog
- setTable() : BALL::VIEW::AtomOverview::ApplyProcessor, BALL::VIEW::AtomOverview::OverviewProcessor
- setTemperature() : BALL::VIEW::MolecularDynamicsDialog
- setTemperatureFactor() : BALL::PDBAtom
- setTemplateResidue() : BALL::ResidueRotamerSet
- setTestLine() : BALL::QSAR::Validation
- setText() : BALL::VIEW::Label, BALL::VIEW::LabelModel
- setTexture() : BALL::VIEW::GridVisualisation
- setThreshold() : BALL::MolecularInteractions
- setTimeout() : BALL::SimpleDownloader
- setTimestamp() : BALL::Result
- setTimeStep() : BALL::CanonicalMD, BALL::MicroCanonicalMD, BALL::MolecularDynamics, BALL::VIEW::MolecularDynamicsDialog
- setTimestep() : BALL::TRRFile
- setTimeToLive() : BALL::VIEW::RenderSetup
- setTo() : BALL::TContourSurface< T >::Cube
- setToolInfo() : BALL::DockResultFile, BALL::Result
- setToolManual() : BALL::CommandlineParser
- setTorsionAngle_() : BALL::ResidueRotamerSet
- setTorsionPhi() : BALL::ResidueRotamerSet
- setTorsionPsi() : BALL::ResidueRotamerSet
- setTrainingLine() : BALL::QSAR::Validation
- setTraits() : BALL::BaseIterator< Container, DataType, Position, Traits >
- setTrajectoryFile() : BALL::SnapShotManager, BALL::VIEW::SimulationThread
- setTransformation() : BALL::TransformationProcessor
- setTranslation() : BALL::TMatrix4x4< T >, BALL::TranslationProcessor
- setTransparency() : BALL::VIEW::ColorProcessor, BALL::VIEW::DisplayProperties, BALL::VIEW::ElementColorProcessor, BALL::VIEW::Representation, BALL::VIEW::ResidueNameColorProcessor, BALL::VIEW::ResidueTypeColorProcessor, BALL::VIEW::SecondaryStructureColorProcessor
- setTransparency_() : BALL::VIEW::GridColorWidget
- setTransparencyEnabled() : BALL::VIEW::GridColorWidget
- setTriangle() : BALL::TriangleEdge
- setTubeRadius() : BALL::VIEW::AddBackboneModel, BALL::VIEW::ModelSettingsDialog
- setTurnColor() : BALL::VIEW::SecondaryStructureColorProcessor
- setTurnPoint() : BALL::VIEW::Scene
- setType() : BALL::Atom, BALL::Bond, BALL::ExpressionTree, BALL::SecondaryStructure, BALL::SESEdge, BALL::SESFace, BALL::SurfaceProcessor, BALL::VIEW::AddSurfaceModel, BALL::VIEW::CompositeMessage, BALL::VIEW::Dataset, BALL::VIEW::DatasetMessage, BALL::VIEW::LightSource, BALL::VIEW::MolecularTaskMessage, BALL::VIEW::RepresentationMessage, BALL::VIEW::SceneMessage
- setTypeName() : BALL::Atom
- setUnit() : BALL::Descriptor
- setUnitConversionFactor() : BALL::GAMESSLogFile
- setUnsignedChar() : BALL::BitVector
- setUnsignedInt() : BALL::BitVector
- setUnsignedLong() : BALL::BitVector
- setUnsignedShort() : BALL::BitVector
- setUp() : BALL::VIEW::FakeDriver, BALL::VIEW::InputDeviceDriver
- setup() : BALL::AmberBend, BALL::AmberNonBonded, BALL::AmberStretch, BALL::AmberTorsion, BALL::AromaticRingStacking, BALL::AtomTyper, BALL::BuriedPolar, BALL::CanonicalMD, BALL::CharmmBend, BALL::CharmmImproperTorsion, BALL::CharmmNonBonded, BALL::CharmmStretch, BALL::CharmmTorsion, BALL::CHPI, BALL::CHPISlick, BALL::ConformationSet, BALL::DNAMutator, BALL::DockingAlgorithm, BALL::DockProblem, BALL::EnergyMinimizer, BALL::EvolutionaryDocking, BALL::FDPB, BALL::ForceField, BALL::ForceFieldComponent, BALL::FresnoTypes, BALL::GeneralizedBornModel, BALL::GeneticAlgorithm, BALL::GeometricFit, BALL::GridBasedScoring::GridSetsResult, BALL::GridBasedScoring, BALL::GridedMM, BALL::GridedPLP, BALL::HydrogenBond, BALL::HydrogenBondSlick, BALL::IMGDock, BALL::Kekuliser, BALL::Lipophilic, BALL::MicroCanonicalMD, BALL::MMFF94ChargeProcessor, BALL::MMFF94NonBonded, BALL::MMFF94OutOfPlaneBend, BALL::MMFF94StretchBend, BALL::MMFF94Torsion, BALL::MMScoring, BALL::MolecularDynamics, BALL::Mutator, BALL::NonpolarSolvation, BALL::PBScoring, BALL::PeriodicBoundary, BALL::PLP, BALL::PLPScoring, BALL::Polarity, BALL::PolarSolvation, BALL::ScoringComponent, BALL::ScoringFunction, BALL::SLICKEnergy, BALL::SLICKScore, BALL::SnapShotManager, BALL::VanDerWaalsSlick, BALL::VIEW::EditSingleShortcut, BALL::VIEW::SnapshotManagerInterface
- setup_() : BALL::MMFF94AtomTypeEquivalences, BALL::MMFF94AtomTypes, BALL::MMFF94BendParameters, BALL::MMFF94ESParameters, BALL::MMFF94ParametersBase, BALL::MMFF94PlaneParameters, BALL::MMFF94StretchBendParameters, BALL::MMFF94StretchParameters, BALL::MMFF94TorsionParameters, BALL::MMFF94VDWParameters, BALL::Rescoring1D, BALL::Rescoring3D, BALL::Rescoring, BALL::VIEW::MainControl, BALL::VIEW::SDWidget
- setup_time_stamp_ : BALL::ForceField
- setupAromaticTypes() : BALL::MMFF94AtomTyper
- setupAtomArray() : BALL::FDPB
- setupBoundary() : BALL::FDPB
- setUpdateInterval() : BALL::VIEW::FileObserver
- setUpdateMethod() : BALL::ConjugateGradientMinimizer, BALL::ShiftedLVMMMinimizer
- setUpdateRepresentations() : BALL::VIEW::CompositeMessage
- setupEnvironmentMap() : BALL::VIEW::Renderer, BALL::VIEW::RenderSetup, BALL::VIEW::RTfactRenderer, BALL::VIEW::Scene
- setupEpsGrid() : BALL::FDPB
- setupFlexibleResidues_() : BALL::ScoringFunction
- setupForceField() : BALL::VIEW::MolecularStructure
- setupGridClipPlanes_() : BALL::VIEW::GLRenderer
- setupHydrogenTypes() : BALL::MMFF94AtomTyper
- setupKappaGrid() : BALL::FDPB
- setupLigand() : BALL::AromaticRingStacking, BALL::BuriedPolar, BALL::CHPI, BALL::HydrogenBond, BALL::Lipophilic, BALL::PB, BALL::Polarity, BALL::ScoringComponent
- setUpper() : BALL::FermiBaseFunction, BALL::ScoringBaseFunction
- setUpperBound() : BALL::CubicSpline1D
- setUpperDerivative() : BALL::CubicSpline1D
- setupPhiGrid() : BALL::FDPB
- setupProximityLight() : BALL::VIEW::GeometricControl
- setupQGrid() : BALL::FDPB
- setupReferenceLigand() : BALL::GridBasedScoring, BALL::ScoringFunction
- setupSASGrid() : BALL::FDPB
- setupStereo() : BALL::VIEW::GLRenderer, BALL::VIEW::GLRenderWindow, BALL::VIEW::Renderer, BALL::VIEW::RenderTarget, BALL::VIEW::RTfactRenderer
- setupSymbolsToTypes() : BALL::MMFF94AtomTyper
- setupUi_() : BALL::VIEW::PropEditorWidget, BALL::VIEW::PropertyEditor
- setupViewVolume() : BALL::VIEW::Scene
- setURL() : BALL::SimpleDownloader, BALL::VIEW::RegisterHelpSystemMessage
- setUseConjugateGradient() : BALL::VIEW::MinimizationDialog
- setUsedProperty() : BALL::DNAMutator
- setUseFormalCharges() : BALL::Kekuliser
- setUsePotentialGrid() : BALL::VIEW::FieldLineCreator
- setUseShiftedLVMM() : BALL::VIEW::MinimizationDialog
- setUseStrangLBFGS() : BALL::VIEW::MinimizationDialog
- setValue() : BALL::DoubleGene, BALL::INIFile, BALL::PreferencesObject, BALL::ResourceEntry, BALL::VIEW::ColorHSV, BALL::VIEW::ColorTable, BALL::VIEW::HotkeyTable, BALL::VIEW::PreferencesEntry::ExtendedPreferencesObject, BALL::VIEW::ShortcutRegistry
- setValue_() : BALL::VIEW::ModelSettingsDialog, BALL::VIEW::PreferencesEntry
- setValueAllowed() : BALL::VIEW::PreferencesEntry, BALL::VIEW::StageSettings
- setValues() : BALL::CubicSpline1D
- setVanDerWaalsRadius() : BALL::Element
- setVDWRadiusFactor() : BALL::VIEW::AddVanDerWaalsModel, BALL::VIEW::ModelSettingsDialog
- setVector() : BALL::Options
- setVelocity() : BALL::Atom
- setVelocityStorage() : BALL::TRRFile
- setVerbosity() : BALL::CubicSpline1D, BALL::CubicSpline2D
- setVerbosityLevel() : BALL::BinaryFingerprintMethods
- setVertex() : BALL::GraphEdge< Vertex, Edge, Face >, BALL::GraphTriangle< Vertex, Edge, Face >, BALL::SolventAccessibleSurface, BALL::VIEW::Vertex
- setVertex1() : BALL::VIEW::Vertex2
- setVertex1Address() : BALL::VIEW::Vertex2
- setVertex2() : BALL::VIEW::Vertex2
- setVertex2Address() : BALL::VIEW::Vertex2
- setVertexAddress() : BALL::VIEW::Vertex
- setVertexAddresses() : BALL::VIEW::Vertex2
- setVertices() : BALL::VIEW::Vertex2
- setViewPoint() : BALL::VIEW::Camera
- setViewPoint_() : BALL::VIEW::Scene
- setVisualizationPose() : BALL::DockingAlgorithm
- setVRMLNumber() : BALL::VIEW::Scene
- setWhatsThisEnabled() : BALL::VIEW::HelpViewer
- setWidgetStack() : BALL::VIEW::PreferencesEntry
- setWidgetStackName() : BALL::VIEW::PreferencesEntry
- setWidgetVisible() : BALL::VIEW::DockWidget, BALL::VIEW::Scene
- setWidth() : BALL::CreateSpectrumProcessor, BALL::Peak< PositionType >, BALL::TBox3< T >, BALL::VIEW::FrameBufferFormat
- setWildcards() : BALL::GAFFCESParser::CESwildcardsConnectionPredicate, BALL::GAFFCESParser::CESwildcardsPredicate
- setWorkingDir() : BALL::VIEW::MainControl, BALL::VIEW::ModularWidget
- setWorkingDirFromFilename_() : BALL::VIEW::ModularWidget
- setXDefaultValues() : BALL::CubicSpline2D
- setXLowerBounds() : BALL::CubicSpline2D
- setXLowerDerivatives() : BALL::CubicSpline2D
- setXTol() : BALL::LineSearch
- setXUpperBounds() : BALL::CubicSpline2D
- setXUpperDerivatives() : BALL::CubicSpline2D
- setYDefaultValue() : BALL::CubicSpline2D
- setYLowerBound() : BALL::CubicSpline2D
- setYLowerDerivative() : BALL::CubicSpline2D
- setYUpperBound() : BALL::CubicSpline2D
- setYUpperDerivative() : BALL::CubicSpline2D
- setZEType() : BALL::SmartsParser::SPBond, BALL::SmilesParser::SPBond
- setZScore() : BALL::CrystalInfo
- sg_entry_ : BALL::VIEW::GenerateCrystalDialog
- sg_list_ : BALL::VIEW::GenerateCrystalDialog
- sg_symops_ : BALL::CrystalInfo
- SHANNO : BALL::ConjugateGradientMinimizer
- share_from_ : BALL::VIEW::GLOffscreenTarget
- shared_bonds : BALL::RingAnalyser::Ring
- shared_handlers_ : BALL::PluginManager
- sheet_ : BALL::SecondaryStructureProcessor
- sheet_ID : BALL::PDB::RecordSHEET
- sheet_list_ : BALL::PDBFile
- sheet_records : BALL::PDB::BookKeeping
- SHIFT : BALL::VIEW::HotkeyTable
- shift() : BALL::TContourSurface< T >::Cube, BALL::TriangulatedSurface
- shift_map_ : BALL::RandomCoilShiftProcessor
- shift_s_ : BALL::ShiftedLVMMMinimizer
- shift_units : BALL::NMRStarFile::ShiftReferenceElement
- shift_value : BALL::NMRStarFile::NMRAtomData, BALL::NMRStarFile::ShiftReferenceElement
- shifted_direction_ : BALL::ShiftedLVMMMinimizer
- ShiftedLVMMMinimizer() : BALL::ShiftedLVMMMinimizer
- ShiftHyperSurface_() : BALL::EmpiricalHSShiftProcessor::ShiftHyperSurface_
- ShiftModel() : BALL::ShiftModel
- ShiftModel1D() : BALL::ShiftModel1D
- ShiftModel2D() : BALL::ShiftModel2D
- ShiftModule() : BALL::ShiftModule
- ShiftReferenceElement() : BALL::NMRStarFile::ShiftReferenceElement
- ShiftReferenceSet() : BALL::NMRStarFile::ShiftReferenceSet
- shifts : BALL::NMRStarFile::MolecularSystem::ChemicalUnit
- ShiftXwise_hydrogen_bonds_computation_ : BALL::HBondShiftProcessor
- shininess : BALL::VIEW::Stage::Material
- shininessFactorChanged() : BALL::VIEW::MaterialSettings
- SHORT : BALL::VIEW::PubChemDialog
- shortcut_ : BALL::VIEW::TestFramework
- shortcut_keys_ : BALL::VIEW::ShortcutRegistry
- shortcut_registry_ : BALL::VIEW::MainControl
- shortcutChanged() : BALL::VIEW::ShortcutRegistry, BALL::VIEW::ShortcutTableView
- shortcutChanged_() : BALL::VIEW::ShortcutDialog
- ShortcutDialog() : BALL::VIEW::ShortcutDialog
- ShortcutRegistry() : BALL::VIEW::ShortcutRegistry
- shortcuts_ : BALL::VIEW::ShortcutRegistry
- ShortcutTableModel() : BALL::VIEW::ShortcutTableModel
- ShortcutTableView() : BALL::VIEW::ShortcutTableView
- show() : BALL::QSAR::RegressionModel, BALL::VIEW::AssignBondOrderResultsDialog, BALL::VIEW::DisplayProperties, BALL::VIEW::DockProgressDialog, BALL::VIEW::DockResultDialog, BALL::VIEW::GeometricFitDialog, BALL::VIEW::LabelDialog, BALL::VIEW::MainControl, BALL::VIEW::ModifyRepresentationDialog, BALL::VIEW::Preferences, BALL::VIEW::PubChemDialog, BALL::VIEW::SnapshotVisualisationDialog, BALL::VIEW::StereoSettingsDialog, BALL::VIEW::UndoManagerDialog
- show_coordinate_system_ : BALL::VIEW::Stage
- show_error_ : BALL::VIEW::HTMLViewDock
- show_fps_ : BALL::VIEW::Scene
- SHOW_HYDROGENS : BALL::SDGenerator::Default, BALL::SDGenerator::Option, BALL::VIEW::SDWidget::Default, BALL::VIEW::SDWidget::Option
- SHOW_IDENTICAL_LIGANDS_WARNING : BALL::DockResultFile
- show_light_sources_ : BALL::VIEW::Renderer, BALL::VIEW::Scene
- show_preview_ : BALL::VIEW::Renderer
- show_ruler_ : BALL::VIEW::RenderSetup
- show_selection_infos_ : BALL::VIEW::CompositeMessage
- show_ss_ : BALL::VIEW::MolecularControl
- show_ss_id_ : BALL::VIEW::MolecularControl
- show_window_enty_ : BALL::VIEW::ModularWidget
- showAmberForceFieldOptions() : BALL::VIEW::MolecularStructure
- showAngle() : BALL::VIEW::MolecularControl
- showAtomOverview() : BALL::VIEW::MolecularControl
- showAtomOverviewForSelection() : BALL::VIEW::MolecularControl
- showBondOrderAssignmentResults() : BALL::VIEW::MolecularStructure
- showCharmmForceFieldOptions() : BALL::VIEW::MolecularStructure
- showClassDocu() : BALL::VIEW::PyWidget
- showCompletion() : BALL::VIEW::PyWidget
- showContextMenu() : BALL::VIEW::PyWidget, BALL::VIEW::Scene
- showCoordinateSystem() : BALL::VIEW::Stage
- ShowDisplayPropertiesMessage() : BALL::VIEW::ShowDisplayPropertiesMessage
- showDistance() : BALL::VIEW::MolecularControl
- showDockingOptions() : BALL::VIEW::DockResultDialog
- showDockResult() : BALL::VIEW::DockResultController
- showDocumentation() : BALL::VIEW::PyWidget
- showDocumentationFor() : BALL::VIEW::HelpViewer
- showDocumentationForObject() : BALL::VIEW::HelpViewer
- showEditContextMenu() : BALL::VIEW::PyWidget
- showEntry() : BALL::VIEW::Preferences
- showExportPNGDialog() : BALL::VIEW::Scene
- showExportVRMLDialog() : BALL::VIEW::Scene
- showFilename() : BALL::VIEW::MolecularControl
- showGuestContextMenu() : BALL::VIEW::DatasetControl, BALL::VIEW::DockWidget, BALL::VIEW::GeometricControl, BALL::VIEW::LogView, BALL::VIEW::MolecularControl
- showHelp() : BALL::VIEW::HelpViewer, BALL::VIEW::ModularWidget, BALL::VIEW::Preferences
- showHelp_() : BALL::VIEW::PyWidget
- showHelpFor() : BALL::VIEW::HelpViewer
- ShowHelpMessage() : BALL::VIEW::ShowHelpMessage
- showInfos() : BALL::VIEW::Scene
- showLightSources() : BALL::VIEW::Renderer
- showLightSourcesEnabled() : BALL::VIEW::Scene
- showMMFF94ForceFieldOptions() : BALL::VIEW::MolecularStructure
- showOnlyInLogView() : BALL::VIEW::LogEvent
- showOnlySelection() : BALL::VIEW::AtomOverview::ApplyProcessor, BALL::VIEW::AtomOverview::OverviewProcessor, BALL::VIEW::AtomOverview
- showRuler() : BALL::VIEW::RenderSetup
- showScoringOptions_() : BALL::VIEW::DockResultDialog
- showSelected() : BALL::VIEW::AtomDistanceColorProcessor
- showSelectionInfos() : BALL::VIEW::CompositeMessage
- showSelectorHelp() : BALL::VIEW::MolecularControl
- showSnapshot() : BALL::VIEW::DockResultDialog
- showStackPage() : BALL::VIEW::PreferencesEntry
- showText() : BALL::VIEW::Scene
- showViewPoint_() : BALL::VIEW::Scene
- shrink() : BALL::TriangulatedSurface
- shrink_to_fit() : BALL::String
- Si : BALL::Element
- SideChainOptimizer : BALL::ScoringFunction, BALL::SideChainOptimizer
- SideChainPlacementProcessor() : BALL::SideChainPlacementProcessor
- sig11 : BALL::PDB::RecordSIGUIJ
- sig12 : BALL::PDB::RecordSIGUIJ
- sig13 : BALL::PDB::RecordSIGUIJ
- sig22 : BALL::PDB::RecordSIGUIJ
- sig23 : BALL::PDB::RecordSIGUIJ
- sig33 : BALL::PDB::RecordSIGUIJ
- sig_w : BALL::CharmmEEF1::Values
- sig_w_ : BALL::CharmmEEF1
- SIGNED_INT_CHANNEL : BALL::VIEW::ChannelFormat
- silent_ : BALL::VIEW::PyWidget
- SILICIUM : BALL::Element
- SILICON : BALL::Element
- SILVER : BALL::Element
- SIM_CUTOFF : BALL::BinaryFingerprintMethods::Default, BALL::BinaryFingerprintMethods::Option
- SIMPLE : BALL::AStarBondOrderStrategy::Heuristic, BALL::PartialBondOrderAssignment
- SimpleBase() : BALL::SimpleBase
- SimpleBox() : BALL::VIEW::SimpleBox
- SimpleDownloader() : BALL::SimpleDownloader
- SimpleExperiment1D() : BALL::SimpleExperiment1D
- SIMPLICIAL_TYPE : BALL::TreeWidthImplementation< UndirectedGraph >::QuickBB< Lowerbound, Upperbound >
- simulate() : BALL::MolecularDynamics
- simulateIterations() : BALL::CanonicalMD, BALL::MicroCanonicalMD, BALL::MolecularDynamics
- simulateTime() : BALL::MolecularDynamics
- simulation_icon_ : BALL::VIEW::MainControl
- simulation_running_xpm_ : BALL::VIEW::MainControl
- simulation_stoped_xpm_ : BALL::VIEW::MainControl
- simulation_thread_ : BALL::VIEW::MainControl
- SimulationThread : BALL::VIEW::MainControl, BALL::VIEW::SimulationThread
- SINGLE : BALL::SmartsParser::SPBond
- SINGLE__CHI : BALL::EmpiricalHSShiftProcessor::ShiftHyperSurface_
- SINGLE__DISCRETE : BALL::EmpiricalHSShiftProcessor::ShiftHyperSurface_
- SINGLE__REAL : BALL::EmpiricalHSShiftProcessor::ShiftHyperSurface_
- SINGLE_BOND : BALL::GAFFCESParser::APSMatcher
- SINGLE_BOND_TO_PARENT : BALL::GAFFCESParser::APSMatcher
- SINGLE_DOWN : BALL::SmartsParser::SPBond
- SINGLE_DOWN_OR_ANY : BALL::SmartsParser::SPBond
- SINGLE_OR_AROMATIC : BALL::SmartsParser::SPBond
- single_pick_ : BALL::VIEW::GLRenderer
- SINGLE_UP : BALL::SmartsParser::SPBond
- SINGLE_UP_OR_ANY : BALL::SmartsParser::SPBond
- SingleAmberTorsion() : BALL::AmberTorsion::SingleAmberTorsion
- SingleCharmmTorsion() : BALL::CharmmTorsion::SingleCharmmTorsion
- SingleValues() : BALL::CosineTorsion::SingleValues
- singular_ : BALL::RSEdge, BALL::RSFace
- singular_edges_ : BALL::SolventExcludedSurface
- SingularEdgeIterator : BALL::SolventExcludedSurface
- SingularMatrixError() : BALL::QSAR::Exception::SingularMatrixError
- Site : BALL::Enumerator< Container, SiteIterator, Variant >
- site_records : BALL::PDB::BookKeeping
- SiteList : BALL::Enumerator< Container, SiteIterator, Variant >
- size() : BALL::ConformationSet, BALL::FPTBondOrderStrategy::DPTable_, BALL::HashMap< Key, T >, BALL::HashSet< Key >, BALL::PDBRecords, BALL::PoseClustering::ClusterProperties, BALL::String, BALL::Substring, BALL::TRegularData1D< ValueType >, BALL::TRegularData2D< ValueType >, BALL::TRegularData3D< ValueType >, BALL::VIEW::ShortcutRegistry
- size_ : BALL::Exception::IndexOverflow, BALL::Exception::IndexUnderflow, BALL::Exception::InvalidSize, BALL::Exception::OutOfMemory, BALL::Exception::SizeUnderflow, BALL::TRegularData2D< ValueType >, BALL::TRegularData3D< ValueType >
- size_type : BALL::HashSet< Key >, BALL::PDBRecords, BALL::String, BALL::TRegularData1D< ValueType >, BALL::TRegularData2D< ValueType >, BALL::TRegularData3D< ValueType >, BALL::VIEW::CompositeManager
- sizeHint() : BALL::VIEW::ColorButton, BALL::VIEW::SDWidget, BALL::VIEW::TextEditorWidget::LineNumbers
- SizeOfSSSR() : BALL::SizeOfSSSR
- SizeType : BALL::PDBRecords
- SizeUnderflow() : BALL::Exception::SizeUnderflow
- SizeVector : BALL::UCK
- sizeX() : BALL::ScoreGridSet
- sizeX_ : BALL::Rescoring3D
- sizeY() : BALL::ScoreGridSet
- sizeY_ : BALL::Rescoring3D
- sizeZ() : BALL::ScoreGridSet
- sizeZ_ : BALL::Rescoring3D
- skip_checks_ : BALL::VIEW::HTMLViewDock
- skipCurrentRecord() : BALL::PDBFile
- skipFrame() : BALL::TRRFile
- skipLines() : BALL::LineBasedFile
- skipped_records_ : BALL::PDBInfo
- SLATER_KIRKWOOD_FORMAT : BALL::LennardJones
- SLAVE_PATH : BALL::GeometricFit::Default, BALL::GeometricFit::Option
- SLICES : BALL::VIEW::GridVisualisation
- slices : BALL::VIEW::GridVisualisation
- SLICKEnergy() : BALL::SLICKEnergy
- SLICKScore() : BALL::SLICKScore
- sliderDragEnded_() : BALL::VIEW::SnapshotVisualisationDialog
- sliderDragStarted_() : BALL::VIEW::SnapshotVisualisationDialog
- sliderMovedToPos() : BALL::VIEW::SnapshotVisualisationDialog
- slides_ : BALL::VIEW::AddBackboneModel
- slides_angle_ : BALL::VIEW::AddBackboneModel
- slinkInner_() : BALL::PoseClustering
- slotCancel() : BALL::VIEW::GenerateCrystalDialog
- slotDownload() : BALL::VIEW::DownloadElectronDensity, BALL::VIEW::DownloadPDBFile
- slotOk() : BALL::VIEW::GenerateCrystalDialog
- Sm : BALL::Element
- smallX : BALL::VIEW::VRMLRenderer
- smallY : BALL::VIEW::VRMLRenderer
- smallZ : BALL::VIEW::VRMLRenderer
- SMART_MATCHING : BALL::HybridisationProcessor::Method
- smart_names_ : BALL::MolecularSimilarity
- SMART_OBJECT : BALL::NamedProperty
- smart_pointer_list_ : BALL::PersistenceManager
- SmartPointerList : BALL::PersistenceManager
- smarts_ : BALL::MolecularSimilarity
- smarts_edit_ : BALL::VIEW::MolecularControl
- SmartsMatcher() : BALL::SmartsMatcher
- SmartsParser() : BALL::SmartsParser
- SMARTSPredicate() : BALL::SMARTSPredicate
- smiles : BALL::VIEW::PubChemDialog::ParsedResult_
- smiles_parser_ : BALL::VIEW::PubChemDialog
- SmilesParser() : BALL::SmilesParser
- smooth_lines_ : BALL::VIEW::GLRenderer
- smoothCFSAngle_() : BALL::SDGenerator
- Sn : BALL::Element
- snap : BALL::PoseClustering::PosePointer
- snap_shot_manager_ : BALL::VIEW::SnapshotVisualisationDialog
- SnapShot() : BALL::SnapShot
- snapshot_ : BALL::EnergyMinimizer
- snapshot_buffer_ : BALL::SnapShotManager
- SNAPSHOT_FREQUENCY : BALL::EnergyMinimizer::Default, BALL::EnergyMinimizer::Option, BALL::MolecularDynamics::Default, BALL::MolecularDynamics::Option
- snapshot_frequency_ : BALL::EnergyMinimizer, BALL::MolecularDynamics
- snapshot_interface_ : BALL::VIEW::UndoManagerDialog
- snapshot_manager_ptr_ : BALL::MolecularDynamics
- snapshot_order_ : BALL::ConformationSet, BALL::DockResult::Scoring_
- snapShotInputTest() : BALL::VIEW::SnapshotVisualisationDialog
- SnapShotManager() : BALL::SnapShotManager
- SnapshotManagerInterface() : BALL::VIEW::SnapshotManagerInterface
- SnapshotVisualisationDialog() : BALL::VIEW::SnapshotVisualisationDialog
- SNBModel() : BALL::QSAR::SNBModel
- SODIUM : BALL::Element
- soffsetf1_ : BALL::Bruker2DFile
- soffsetf2_ : BALL::Bruker2DFile
- SOLUTE_DC : BALL::FDPB::Default, BALL::FDPB::Option
- solution_number_ : BALL::FPTBondOrderStrategy::DPBackTrackingCombiner_, BALL::VIEW::AssignBondOrderResultsDialog
- solution_systems_ : BALL::VIEW::AssignBondOrderResultsDialog
- solutions_ : BALL::AssignBondOrderProcessor, BALL::Kekuliser
- Solvation() : BALL::Solvation
- SOLVATION_CUTOFF : BALL::CharmmFF::Default, BALL::CharmmFF::Option
- SOLVATION_CUTON : BALL::CharmmFF::Default, BALL::CharmmFF::Option
- solvation_energy_ : BALL::CharmmNonBonded
- solvation_parameters : BALL::Solvation
- solvation_volumes : BALL::Solvation
- solve() : BALL::FDPB
- solvent_ : BALL::Pair6_12InteractionEnergyProcessor, BALL::PairExpInteractionEnergyProcessor
- SOLVENT_ACCESSIBLE_SURFACE : BALL::SurfaceProcessor
- solvent_atoms_ : BALL::SolventDescriptor, BALL::SolventParameter
- SOLVENT_DC : BALL::FDPB::Default, BALL::FDPB::Option
- solvent_descriptor_ : BALL::SolventParameter
- SOLVENT_DESCRIPTOR_FILE : BALL::NonpolarSolvation::Default, BALL::NonpolarSolvation::Option
- SOLVENT_EXCLUDED_SURFACE : BALL::SurfaceProcessor
- SOLVENT_FILENAME : BALL::Pair6_12InteractionEnergyProcessor::Default, BALL::Pair6_12InteractionEnergyProcessor::Option, BALL::PairExpInteractionEnergyProcessor::Default, BALL::PairExpInteractionEnergyProcessor::Option
- SOLVENT_NUMBER_DENSITY : BALL::NonpolarSolvation::Default, BALL::NonpolarSolvation::Option, BALL::Pair6_12InteractionEnergyProcessor::Default, BALL::Pair6_12InteractionEnergyProcessor::Option, BALL::PCMCavFreeEnergyProcessor::Default, BALL::PCMCavFreeEnergyProcessor::Option, BALL::PierottiCavFreeEnergyProcessor::Default, BALL::PierottiCavFreeEnergyProcessor::Option, BALL::ReissCavFreeEnergyProcessor::Default, BALL::ReissCavFreeEnergyProcessor::Option
- SolventAccessibleSurface : BALL::ReducedSurface, BALL::RSEdge, BALL::RSFace, BALL::RSVertex, BALL::SASEdge, BALL::SASFace, BALL::SASVertex, BALL::SolventAccessibleSurface
- SolventAtomDescriptor() : BALL::SolventAtomDescriptor
- SolventDescriptor() : BALL::SolventDescriptor
- SolventExcludedSurface : BALL::ReducedSurface, BALL::RSEdge, BALL::RSFace, BALL::RSVertex, BALL::SESEdge, BALL::SESFace, BALL::SESVertex, BALL::SolventExcludedSurface
- SolventParameter() : BALL::SolventParameter
- sort() : BALL::ResidueRotamerSet, BALL::Result, BALL::RotamerLibrary
- sortBy() : BALL::DockResult
- sorted_by_ : BALL::DockResult
- sorted_edges : BALL::FPTBondOrderStrategy::DPBackTrackingCombiner_
- SortedPosition2() : BALL::SortedPosition2
- SortedPosition3() : BALL::SortedPosition3
- sortSelectedAtomVector_() : BALL::ForceField
- sortTable() : BALL::VIEW::DockResultDialog
- source_ : BALL::EdgeItem< Node, Edge >
- sources : BALL::PDB::RecordSOURCE
- SP : BALL::SmilesParser
- sp_atom_ : BALL::SmartsParser::SPNode
- space_group : BALL::PDB::RecordCRYST1::UnitCell, BALL::PDB::Structure::UnitCellInfo
- space_group_ : BALL::CCP4File, BALL::CrystalInfo
- SPACE_GROUP_FILE : BALL::CrystalGenerator::Default, BALL::CrystalGenerator::Option, BALL::CrystalInfo::Default, BALL::CrystalInfo::Option
- SpaceGroupParameters() : BALL::SpaceGroupParameters
- SPACING : BALL::FDPB::Default, BALL::FDPB::Option
- spacing_ : BALL::FDPB, BALL::ShiftModel1D, BALL::ShiftModel2D, BALL::Spectrum< DataT, PeakT, PositionT >, BALL::TContourSurface< T >::Cube, BALL::TRegularData1D< ValueType >, BALL::TRegularData2D< ValueType >, BALL::TRegularData3D< ValueType >
- SPAtom : BALL::SmartsMatcher, BALL::SmartsParser::SPAtom, BALL::SmilesParser::SPAtom
- SPBond : BALL::SmartsMatcher, BALL::SmartsParser::SPBond, BALL::SmilesParser::SPBond
- SPBondOrder : BALL::SmartsParser::SPBond
- specific_model_ID : BALL::PDB::RecordCISPEP
- specificSetup() : BALL::AmberFF, BALL::CanonicalMD, BALL::CharmmFF, BALL::ConjugateGradientMinimizer, BALL::EnergyMinimizer, BALL::ForceField, BALL::MicroCanonicalMD, BALL::MMFF94, BALL::MolecularDynamics, BALL::ShiftedLVMMMinimizer, BALL::SteepestDescentMinimizer, BALL::StrangLBFGSMinimizer
- specificSetup_() : BALL::AtomTyper, BALL::PluginHandler, BALL::VIEW::InputDevPluginHandler, BALL::VIEW::ModularWidgetPluginHandler, BALL::VIEW::PluginDialog
- specificShutdown_() : BALL::PluginHandler, BALL::VIEW::InputDevPluginHandler, BALL::VIEW::ModularWidgetPluginHandler, BALL::VIEW::PluginDialog
- Spectrum() : BALL::Spectrum< DataT, PeakT, PositionT >
- spectrum_ : BALL::Bruker1DFile, BALL::Bruker2DFile
- SPECTRUM_TYPE : BALL::ShiftModel1D, BALL::ShiftModel2D
- specular_color : BALL::VIEW::Stage::Material
- specular_intensity : BALL::VIEW::Stage::Material
- specularityFactorChanged() : BALL::VIEW::MaterialSettings
- SPEdge : BALL::SmartsMatcher, BALL::SmartsParser::SPEdge
- SPEED_OF_LIGHT : BALL::Constant
- Sphere() : BALL::VIEW::Sphere
- sphere_ : BALL::SASFace
- sphere_list_ : BALL::VIEW::GLRenderer
- sphere_template_ : BALL::VIEW::XML3DRenderer
- spheres_ : BALL::SurfaceProcessor
- spheric_faces_ : BALL::SolventExcludedSurface
- SphericFaceIterator : BALL::SolventExcludedSurface
- SPIRO : BALL::RingAnalyser
- splice() : BALL::AtomContainer, BALL::Chain, BALL::Composite, BALL::Molecule, BALL::NucleicAcid, BALL::Nucleotide, BALL::Protein, BALL::Residue, BALL::SecondaryStructure, BALL::System
- spliceAfter() : BALL::AtomContainer, BALL::Chain, BALL::Composite, BALL::Molecule, BALL::NucleicAcid, BALL::Nucleotide, BALL::Protein, BALL::Residue, BALL::SecondaryStructure, BALL::System
- spliceBefore() : BALL::AtomContainer, BALL::Chain, BALL::Composite, BALL::Molecule, BALL::NucleicAcid, BALL::Nucleotide, BALL::Protein, BALL::Residue, BALL::SecondaryStructure, BALL::System
- split() : BALL::String, BALL::VIEW::ExportGeometryDialog
- splitMethodChanged() : BALL::VIEW::ModifyRepresentationDialog
- splitQuoted() : BALL::String
- splitSphericFaces() : BALL::SolventExcludedSurface
- SPNode : BALL::SmartsMatcher, BALL::SmartsParser::SPNode
- spointnumf1_ : BALL::Bruker2DFile
- spointnumf2_ : BALL::Bruker2DFile
- sq() : BALL::QSAR::Statistics
- sqrt_density_ : BALL::SASTriangulator, BALL::SESTriangulator
- square_distance_ : BALL::VIEW::ModifyRepresentationDialog
- SQUARE_ROOT : BALL::ShiftedLVMMMinimizer
- squared_distance_ : BALL::FragmentDistanceCollector
- SquareFunction() : BALL::SquareFunction< Function, DataType >
- Sr : BALL::Element
- ss_ : BALL::VIEW::AddBackboneModel
- ssbond_correction_ : BALL::EmpiricalHSShiftProcessor
- ssbond_list_ : BALL::PDBFile
- ssbonds : BALL::PDB::Structure
- sslErrors() : BALL::SimpleDownloaderHelper::BasicHelper
- sssr_ : BALL::GAFFTypeProcessor, BALL::SmartsMatcher, BALL::SmartsParser
- STABLE : BALL::VersionInfo
- stack_pages_ : BALL::VIEW::PreferencesEntry
- StackPages : BALL::VIEW::PreferencesEntry
- Stage() : BALL::VIEW::Stage
- stage_ : BALL::VIEW::LightSettings, BALL::VIEW::Renderer, BALL::VIEW::RenderSetup, BALL::VIEW::Scene
- stage_settings_ : BALL::VIEW::Scene
- StageSettings() : BALL::VIEW::StageSettings
- stamp() : BALL::Composite, BALL::TimeStamp
- StampType : BALL::Composite
- standard_bond_exists : BALL::MMFF94StretchParameters::BondData
- STANDARD_BOND_LENGTH : BALL::SDGenerator::Default, BALL::SDGenerator::Option
- standard_occupancy_deviation : BALL::PDB::RecordSIGATM
- standard_residue_name : BALL::PDB::RecordMODRES
- standard_temperature_deviation : BALL::PDB::RecordSIGATM
- standard_vector_deviation : BALL::PDB::RecordSIGATM
- standardized_moments : BALL::Spectrum< DataT, PeakT, PositionT >
- STANNUM : BALL::Element
- start() : BALL::AddHydrogenProcessor, BALL::AromaticityProcessor, BALL::AssignBondOrderProcessor, BALL::AssignChargeProcessor, BALL::AssignRadiusProcessor, BALL::BinaryProcessor< T1, T2 >, BALL::BoundingBoxProcessor, BALL::BuildBondsProcessor, BALL::CIFFile::Datablock, BALL::CIFFile::SaveFrame, BALL::ConnectedComponentsProcessor, BALL::ConstBinaryProcessor< T1, T2 >, BALL::ConstUnaryProcessor< T >, BALL::CreateSpectrumProcessor, BALL::DisulfidBondProcessor, BALL::DockingAlgorithm, BALL::EFShiftProcessor, BALL::EmpiricalHSShiftProcessor, BALL::EnergyProcessor, BALL::EvolutionaryDocking, BALL::FragmentDB::BuildBondsProcessor, BALL::FragmentDB::NormalizeNamesProcessor, BALL::FragmentDistanceCollector, BALL::GeneticAlgorithm, BALL::GeometricCenterProcessor, BALL::GeometricFit, BALL::HaighMallionShiftProcessor, BALL::HBondProcessor, BALL::HBondShiftProcessor, BALL::HybridisationProcessor, BALL::IMGDock, BALL::JohnsonBoveyShiftProcessor, BALL::MMFF94ChargeProcessor, BALL::ReconstructFragmentProcessor, BALL::ResidueChecker, BALL::RingAnalyser, BALL::RuleProcessor, BALL::Selector, BALL::ShiftModel1D, BALL::ShiftModel2D, BALL::ShiftModel, BALL::ShiftModule, BALL::SideChainPlacementProcessor, BALL::SimpleExperiment1D, BALL::SurfaceProcessor, BALL::Timer, BALL::UnaryProcessor< T >, BALL::VIEW::AddBackboneModel, BALL::VIEW::ColorByGridProcessor, BALL::VIEW::ColorProcessor, BALL::VIEW::FileObserver, BALL::VIEW::InterpolateColorProcessor, BALL::VIEW::PositionColorProcessor, BALL::VIEW::ResidueNumberColorProcessor
- start_ : BALL::CCP4File, BALL::DSN6File, BALL::TContour< T >
- start_action_ : BALL::VIEW::FileObserver
- start_animation_action_ : BALL::VIEW::Scene
- start_recording : BALL::VIEW::TestFramework
- startAccepting() : BALL::TCPServer
- startAnimation() : BALL::VIEW::Scene
- startChildPredicates() : BALL::GAFFCESParser
- startContinuousLoop() : BALL::VIEW::Scene
- startDefinition() : BALL::VIEW::GLDisplayList
- startDock() : BALL::IMGDock
- startDocking() : BALL::VIEW::DockingController
- startDriver() : BALL::VIEW::InputPlugin
- started_startup_script_ : BALL::VIEW::PyWidget
- STARTED_UPDATE : BALL::VIEW::RepresentationMessage
- startEditorDialog() : BALL::VIEW::PDBInfoEditorWidget
- starting_configuration_ : BALL::AssignBondOrderProcessor
- startInterpreter() : BALL::VIEW::PyWidget
- startLoop() : BALL::CIFFile::Item
- startOutput() : BALL::PersistenceManager
- startPlugin() : BALL::PluginHandler, BALL::PluginManager
- startRecording_() : BALL::VIEW::EditSingleShortcut
- startRendering() : BALL::VIEW::RenderSetup, BALL::VIEW::RepresentationManager
- startServer() : BALL::PyInterpreter
- startsWith() : BALL::LineBasedFile
- startTest() : BALL::VIEW::TestFramework
- startup_script_ : BALL::VIEW::PyWidget
- state : BALL::CIFFile, BALL::ExpressionParser, BALL::GAFFCESParser, BALL::GAMESSDatFile, BALL::GAMESSLogFile, BALL::SmartsParser, BALL::SmilesParser, BALL::TreeWidthImplementation< UndirectedGraph >::QuickBB< Lowerbound, Upperbound >, BALL::VIEW::RunPythonThread
- static_ligand_energy_ : BALL::ScoringFunction
- static_ligand_fragments_ : BALL::ScoringFunction
- static_members : BALL::MOL2File::SetStruct
- static_residues_hashgrid_ : BALL::ScoringFunction
- statistic : BALL::QSAR::FeatureSelectionConfiguration, BALL::QSAR::PredictionConfiguration, BALL::QSAR::ValidationConfiguration
- statistic_name : BALL::QSAR::FeatureSelectionConfiguration, BALL::QSAR::PredictionConfiguration, BALL::QSAR::ValidationConfiguration
- Statistics() : BALL::QSAR::Statistics
- status : BALL::MOL2File::SetStruct, BALL::RSComputer::ProbePosition
- status_ : BALL::ResidueChecker
- STATUS_INSIDE : BALL::RSComputer
- STATUS_NOT_OK : BALL::RSComputer
- STATUS_NOT_TESTED : BALL::RSComputer
- STATUS_OK : BALL::RSComputer
- STATUS_ON_SURFACE : BALL::RSComputer
- STATUS_UNKNOWN : BALL::RSComputer
- stddev_ : BALL::ScoringComponent
- stddev_out_ : BALL::Rescoring
- SteepestDescentMinimizer() : BALL::SteepestDescentMinimizer
- step_ : BALL::AStarBondOrderStrategy, BALL::EnergyMinimizer
- step_number_of_starting_time_ : BALL::DCDFile
- STEP_WIDTH : BALL::IMGDock::Default, BALL::IMGDock::Option
- step_width_ : BALL::RotamerLibrary
- stepFourier_ : BALL::TFFT1D< ComplexTraits >
- stepFourierX_ : BALL::TFFT2D< ComplexTraits >, BALL::TFFT3D< ComplexTraits >
- stepFourierY_ : BALL::TFFT2D< ComplexTraits >, BALL::TFFT3D< ComplexTraits >
- stepFourierZ_ : BALL::TFFT3D< ComplexTraits >
- stepPhys_ : BALL::TFFT1D< ComplexTraits >
- stepPhysX_ : BALL::TFFT2D< ComplexTraits >, BALL::TFFT3D< ComplexTraits >
- stepPhysY_ : BALL::TFFT2D< ComplexTraits >, BALL::TFFT3D< ComplexTraits >
- stepPhysZ_ : BALL::TFFT3D< ComplexTraits >
- steps() : BALL::IMGDock
- steps_ : BALL::VIEW::MDSimulationThread
- steps_between_saves_ : BALL::DCDFile
- steps_between_updates_ : BALL::VIEW::SimulationThread
- stepwiseSelection() : BALL::QSAR::FeatureSelection
- stereo : BALL::MOLFile::BondStruct
- stereo_ : BALL::VIEW::Renderer
- stereo_camera_ : BALL::VIEW::Scene
- stereo_care_box : BALL::MOLFile::AtomStruct
- stereo_delta_ : BALL::VIEW::GLRenderWindow
- stereo_frustum_conversion_height_ : BALL::VIEW::Renderer
- stereo_frustum_conversion_width_ : BALL::VIEW::Renderer
- stereo_left_eye_ : BALL::VIEW::Scene
- stereo_mode_ : BALL::VIEW::InteractionModeManager
- stereo_right_eye_ : BALL::VIEW::Scene
- STEREO_SETUP : BALL::VIEW::RenderSetup
- stereo_setup_ : BALL::VIEW::RenderSetup
- stereoBufferSupportTest() : BALL::VIEW::Scene
- StereoMode : BALL::VIEW::Renderer
- stereoModeChanged() : BALL::VIEW::StageSettings
- stereoScreenChanged() : BALL::VIEW::StageSettings
- StereoSettingsDialog() : BALL::VIEW::StereoSettingsDialog
- steric : BALL::PLP::NonBondedPairData
- STIBIUM : BALL::Element
- stickRadiusChanged() : BALL::VIEW::ModelSettingsDialog
- sticks_ : BALL::Spectrum< DataT, PeakT, PositionT >
- still_to_notify_ : BALL::VIEW::RepresentationManager
- STL_RENDERER : BALL::VIEW::RenderSetup
- STLRenderer() : BALL::VIEW::STLRenderer
- stop() : BALL::Timer, BALL::VIEW::FileObserver, BALL::VIEW::RenderSetup
- stop_() : BALL::VIEW::SnapshotVisualisationDialog
- stop_action_ : BALL::VIEW::FileObserver
- stop_animation_ : BALL::VIEW::Scene
- stop_recording : BALL::VIEW::TestFramework
- stop_script_ : BALL::VIEW::PyWidget
- stop_simulation_ : BALL::VIEW::MainControl
- stop_simulation_action_ : BALL::VIEW::MainControl
- stopAnimation() : BALL::VIEW::Scene
- stopContinuousLoop() : BALL::VIEW::Scene
- stopedSimulation() : BALL::VIEW::MainControl
- stopedSimulation_() : BALL::VIEW::MainControl
- stopPlugin() : BALL::PluginHandler, BALL::PluginManager
- stopRecording_() : BALL::VIEW::EditSingleShortcut
- stopServer() : BALL::PyInterpreter
- stopSimulation() : BALL::VIEW::MainControl
- stopTest() : BALL::VIEW::TestFramework
- store_interactions_ : BALL::ScoringFunction
- store_interactions_disabled_ : BALL::Atom
- store_interactions_phC_only_ : BALL::ScoringFunction
- STORE_NN : BALL::BinaryFingerprintMethods::Default, BALL::BinaryFingerprintMethods::Option
- STORE_SKIPPED_RECORDS : BALL::PDBFile::Default, BALL::PDBFile::Option
- store_skipped_records_ : BALL::PDBFile
- storeColor_() : BALL::VIEW::POVRenderer, BALL::VIEW::XML3DRenderer
- storeConnections_() : BALL::FragmentDB::BuildBondsProcessor
- stored_camera_ : BALL::VIEW::Scene
- stored_s_ : BALL::StrangLBFGSMinimizer
- stored_y_ : BALL::StrangLBFGSMinimizer
- storeEvent() : BALL::VIEW::TestFramework
- storeGradientEnergy() : BALL::EnergyMinimizer
- storeInteractionsEnabled() : BALL::ScoringFunction
- storeOriginalConfiguration_() : BALL::AssignBondOrderProcessor
- storeRepresentations() : BALL::VIEW::RepresentationManager
- storeScript_() : BALL::VIEW::PyWidget
- storeSnapShotReferences_() : BALL::PoseClustering
- storeValues() : BALL::VIEW::OpenSavePreferences, BALL::VIEW::PreferencesEntry
- storeViewPoint() : BALL::VIEW::Scene
- stptol_ : BALL::LineSearch
- STRAND : BALL::SecondaryStructure, BALL::VIEW::AddCartoonModel
- strand_height_ : BALL::VIEW::AddCartoonModel
- strand_number : BALL::PDB::RecordSHEET
- strand_width_ : BALL::VIEW::AddCartoonModel
- StrangLBFGSMinimizer() : BALL::StrangLBFGSMinimizer
- strategies_ : BALL::AssignBondOrderProcessor
- stream : BALL::LogStreamBuf::StreamStruct
- stream_ : BALL::LogStreamNotifier
- STREAM_HEADER : BALL::XDRPersistenceManager
- stream_list_ : BALL::LogStreamBuf
- STREAM_TRAILER : BALL::XDRPersistenceManager
- StreamStruct() : BALL::LogStreamBuf::StreamStruct
- Stretch() : BALL::MMFF94StretchBend::Stretch
- stretch_ : BALL::StretchComponent
- stretch_i_j : BALL::MMFF94StretchBend::StretchBend
- stretch_j_k : BALL::MMFF94StretchBend::StretchBend
- stretch_parameters_ : BALL::StretchComponent
- StretchBendMap : BALL::MMFF94StretchBendParameters
- StretchComponent() : BALL::StretchComponent
- StretchMap : BALL::MMFF94StretchParameters
- STRICT_LINE_CHECKING : BALL::PDBFile::Default, BALL::PDBFile::Option
- strict_line_checking_ : BALL::PDBFile
- stride_ : BALL::VIEW::BufferedRenderer
- STRING : BALL::JCAMPFile, BALL::NamedProperty, BALL::ParamFile
- String() : BALL::String, BALL::Substring
- string : BALL::PDB::RecordTypeFormat
- string_format : BALL::VIEW::PythonHighlighter
- string_pattern : BALL::VIEW::PythonHighlighter
- string_value : BALL::JCAMPFile::JCAMPValue
- StringEditorWidget() : BALL::VIEW::StringEditorWidget
- StringHashMap() : BALL::StringHashMap< Value >
- STRINGLIST : BALL::ParamFile
- stringToWildcard_ : BALL::GAFFCESParser::CESPredicate
- STRONGLY_OVERLAPPING_ATOMS : BALL::ResidueChecker
- STRONTIUM : BALL::Element
- STRUCTURE_BASED : BALL::HybridisationProcessor::Method
- StructureMapper() : BALL::StructureMapper
- StructurePreparer() : BALL::StructurePreparer
- structures_ : BALL::ConformationSet
- sub_type : BALL::MOL2File::SetStruct, BALL::MOL2File::SubstructureStruct
- subcategories_ : BALL::Options
- SUBCATEGORY_NAME : BALL::ScoringFunction
- subdivideTriangle_() : BALL::VIEW::GLRenderer
- subject_length : BALL::NMRStarFile::MonomericPolymer::HomologDB
- submission_date : BALL::NMRStarFile::EntryInformation
- substance_names_ : BALL::QSAR::Model, BALL::QSAR::QSARData
- substances_names_ : BALL::QSAR::Validation
- substitute() : BALL::GraphEdge< Vertex, Edge, Face >, BALL::GraphFace< Vertex, Edge, Face >, BALL::GraphTriangle< Vertex, Edge, Face >, BALL::GraphVertex< Vertex, Edge, Face >, BALL::String
- substituteAll() : BALL::String
- substr() : BALL::String
- Substring : BALL::String, BALL::Substring
- substructure : BALL::MOL2File::AtomStruct
- substructure_name : BALL::MOL2File::AtomStruct
- substructure_type : BALL::MOL2File::SubstructureStruct
- substructures_ : BALL::MOL2File
- Subtraction() : BALL::Subtraction< First, Second, DataType >
- successor() : BALL::RingAnalyser::Ring
- suffix_ : BALL::VIEW::DownloadPDBFile
- SULFUR : BALL::Element
- sulfur_bridges_ : BALL::DisulfidBondProcessor
- SULPHUR : BALL::Element
- summary_ : BALL::SecondaryStructureProcessor
- SUPERPOSE_LIGAND : BALL::IMGDock::Default, BALL::IMGDock::Option
- supported_formats : BALL::ParamFile::ParameterDescription
- supports() : BALL::VIEW::BufferedRenderer, BALL::VIEW::RaytracingRenderer
- supportsNamingScheme() : BALL::Peptides::NameConverter
- supportsPseudoAtomNamingScheme() : BALL::Peptides::NameConverter
- surface_ : BALL::NumericalSAS, BALL::SurfaceProcessor
- SURFACE__EXTERNAL : BALL::Pair6_12InteractionEnergyProcessor, BALL::PairExpInteractionEnergyProcessor
- SURFACE__SAS : BALL::Pair6_12InteractionEnergyProcessor, BALL::PairExpInteractionEnergyProcessor
- SURFACE__SES : BALL::Pair6_12InteractionEnergyProcessor, BALL::PairExpInteractionEnergyProcessor
- SURFACE__UNKNOWN : BALL::Pair6_12InteractionEnergyProcessor, BALL::PairExpInteractionEnergyProcessor
- surface_drawing_precision_ : BALL::VIEW::ModelProcessor, BALL::VIEW::Representation
- SURFACE_FILENAME : BALL::Pair6_12InteractionEnergyProcessor::Default, BALL::Pair6_12InteractionEnergyProcessor::Option, BALL::PairExpInteractionEnergyProcessor::Default, BALL::PairExpInteractionEnergyProcessor::Option
- SURFACE_TENSION : BALL::NonpolarSolvation::Default, BALL::NonpolarSolvation::Option, BALL::UhligCavFreeEnergyProcessor::Default, BALL::UhligCavFreeEnergyProcessor::Option
- SURFACE_THICKNESS : BALL::GeometricFit::Default, BALL::GeometricFit::Option
- SURFACE_TYPE : BALL::GeometricFit::Default, BALL::GeometricFit::Option, BALL::Pair6_12InteractionEnergyProcessor::Default, BALL::Pair6_12InteractionEnergyProcessor::Option, BALL::PairExpInteractionEnergyProcessor::Default, BALL::PairExpInteractionEnergyProcessor::Option
- surface_type_ : BALL::SurfaceProcessor
- SurfaceBase() : BALL::SurfaceBase
- SurfaceProcessor() : BALL::SurfaceProcessor
- SurfaceType : BALL::GeometricFit, BALL::Pair6_12InteractionEnergyProcessor, BALL::PairExpInteractionEnergyProcessor, BALL::SurfaceProcessor
- SURVIVORS : BALL::EvolutionaryDocking::Default, BALL::EvolutionaryDocking::Option
- survivors_ : BALL::GeneticAlgorithm
- SUSPECT_BOND_LENGTHS : BALL::ResidueChecker
- SVMModel() : BALL::QSAR::SVMModel
- SVRModel() : BALL::QSAR::SVRModel
- swap() : BALL::Atom, BALL::AtomContainer, BALL::BaseIterator< Container, DataType, Position, Traits >, BALL::Bond, BALL::Chain, BALL::Composite, BALL::ConstForwardIterator< Container, DataType, Position, Traits >, BALL::ForwardIterator< Container, DataType, Position, Traits >, BALL::HashSet< Key >, BALL::List< Value >, BALL::Molecule, BALL::NucleicAcid, BALL::Nucleotide, BALL::PDBAtom, BALL::PDBRecords, BALL::PropertyManager, BALL::Protein, BALL::Residue, BALL::SecondaryStructure, BALL::Selectable, BALL::String, BALL::StringHashMap< Value >, BALL::TAngle< T >, BALL::TBox3< T >, BALL::TCircle3< T >, BALL::TLine3< T >, BALL::TMatrix4x4< T >, BALL::TPlane3< T >, BALL::TQuaternion< T >, BALL::TRegularData1D< ValueType >, BALL::TRegularData2D< ValueType >, BALL::TRegularData3D< ValueType >, BALL::TSimpleBox3< T >, BALL::TSphere3< T >, BALL::TVector3< T >, BALL::TVector4< T >, BALL::VIEW::ColorExtension2, BALL::VIEW::ColorHSV, BALL::VIEW::ColorRGBA, BALL::VIEW::ColorUnit, BALL::VIEW::ColorUnitHue, BALL::VIEW::Disc, BALL::VIEW::GeometricObject, BALL::VIEW::Label, BALL::VIEW::Line, BALL::VIEW::Mesh, BALL::VIEW::MultiColorExtension, BALL::VIEW::Point, BALL::VIEW::Sphere, BALL::VIEW::Tube, BALL::VIEW::TwoColoredLine, BALL::VIEW::TwoColoredTube, BALL::VIEW::Vertex2, BALL::VIEW::Vertex
- swap_bytes_ : BALL::CCP4File, BALL::DCDFile, BALL::DSN6File
- swap_endian_ : BALL::BinaryFileAdaptor< T >
- swap_side_by_side_stereo_ : BALL::VIEW::Stage
- swapSideBySideStereo() : BALL::VIEW::Stage
- swapValues_() : BALL::VIEW::DockDialog, BALL::VIEW::GeometricFitDialog
- swidthf1_ : BALL::Bruker2DFile
- swidthf2_ : BALL::Bruker2DFile
- switch_grid_ : BALL::VIEW::Scene
- switch_move : BALL::VIEW::TestFramework
- switchRecordMove() : BALL::VIEW::TestFramework
- switchRenderer() : BALL::VIEW::Scene
- switchShowGrid() : BALL::VIEW::Scene
- switchShowSecondaryStructure() : BALL::VIEW::MolecularControl
- switchShowWidget() : BALL::VIEW::Scene
- switchString() : BALL::LineBasedFile
- switchToLastMode() : BALL::VIEW::InteractionModeManager, BALL::VIEW::Scene
- switchView() : BALL::VIEW::AssignBondOrderResultsDialog, BALL::VIEW::PubChemDialog
- sym_size : BALL::TRRFile::TRRHeader
- SYMBOL : BALL::SmartsParser::SPAtom
- Symbol : BALL::Element
- symbol : BALL::MOLFile::AtomStruct, BALL::PTE_::SymbolToElement
- symmetry_group_ : BALL::GAMESSDatFile
- symmetry_operator : BALL::PDB::RecordSSBOND
- symops_ : BALL::SpaceGroupParameters
- sync() : BALL::LogStreamBuf
- SyncClippingPlanesMessage() : BALL::VIEW::SyncClippingPlanesMessage
- syntax_tree_ : BALL::ExpressionParser
- SyntaxTree() : BALL::ExpressionParser::SyntaxTree
- sys_path_ : BALL::PyInterpreter
- System() : BALL::System
- system : BALL::GAMESSLogFile
- system1_ : BALL::DockingAlgorithm
- system2_ : BALL::DockingAlgorithm
- system_ : BALL::ConformationSet, BALL::CrystalGenerator, BALL::ForceField, BALL::SDGenerator, BALL::ShiftModel1D, BALL::ShiftModel2D, BALL::SmilesParser, BALL::VIEW::FDPBDialog, BALL::VIEW::GenerateCrystalDialog, BALL::VIEW::SDWidget
- system_backup_a_ : BALL::GeometricFit
- system_backup_b_ : BALL::GeometricFit
- system_i_ : BALL::PoseClustering
- system_j_ : BALL::PoseClustering
- system_molecular_weight : BALL::NMRStarFile::MolecularSystem
- system_name : BALL::NMRStarFile::MolecularSystem
- system_oligomer_state : BALL::NMRStarFile::MolecularSystem
- system_origin_ : BALL::VIEW::Scene
- system_paramagnetic : BALL::NMRStarFile::MolecularSystem
- system_physical_state : BALL::NMRStarFile::MolecularSystem
- system_ptr_ : BALL::MolecularDynamics, BALL::SnapShotManager
- system_thiol_state : BALL::NMRStarFile::MolecularSystem