Main Page | Modules | Namespace List | Class Hierarchy | Class List | File List | Namespace Members | Class Members
a | b | c | d |
e | f | g | h |
i | j | k | l |
m | n | o | p |
q | r | s | t |
u | v | w | x |
y | z | ~
Here is a list of all documented class members with links to the class documentation for each member:
- a -
- a : BALL::TSimpleBox3< T >
- a0 : BALL::Constant
- a_ : BALL::HBondShiftProcessor
- a_i_ : BALL::ConjugateGradientMinimizer
- ABORT : BALL::Processor
- abort() : BALL::TCPTransfer
- abortClicked() : BALL::VIEW::DockProgressDialog
- aboutToExit() : BALL::VIEW::MainControl
- ABSOLUTE_TEMPERATURE : BALL::ReissCavFreeEnergyProcessor::Default, BALL::ReissCavFreeEnergyProcessor::Option, BALL::PierottiCavFreeEnergyProcessor::Default, BALL::PierottiCavFreeEnergyProcessor::Option, BALL::PCMCavFreeEnergyProcessor::Default, BALL::PCMCavFreeEnergyProcessor::Option
- ac_ : BALL::GeneralizedBornModel
- accept() : BALL::VIEW::LabelDialog, BALL::VIEW::AtomOverview
- acceptor_list_ : BALL::HBondShiftProcessor
- action_ : BALL::VIEW::DockingController
- activate() : BALL::VIEW::Server
- ACTIVE_STEREO : BALL::VIEW::GLRenderer
- ADD : BALL::VIEW::RepresentationMessage, BALL::VIEW::DatasetMessage
- add() : BALL::SmartsMatcher::RecStruct_
- add_hydrogens : BALL::FragmentDB
- ADD_TO_GEOMETRIC_CONTROL : BALL::VIEW::RepresentationMessage
- ADD_VARIANT_EXTENSIONS : BALL::Residue
- addAlgorithm() : BALL::VIEW::DockDialog
- addAllRecords_() : BALL::PDBFile
- addAminoAcid() : BALL::Peptides::PeptideBuilder
- addAtom() : BALL::VIEW::AtomDistanceColorProcessor
- AddBackboneModel() : BALL::VIEW::AddBackboneModel
- AddBallAndStickModel() : BALL::VIEW::AddBallAndStickModel
- AddCartoonModel() : BALL::VIEW::AddCartoonModel
- addComponent() : BALL::ComposedEnergyProcessor
- addComposite() : BALL::VIEW::MolecularControl
- addDataPath() : BALL::Path
- addEdge() : BALL::SmartsParser
- addHydrogens() : BALL::VIEW::MolecularStructure
- Addition() : BALL::Addition< First, Second, DataType >
- addLightPressed() : BALL::VIEW::LightSettings
- addLightSource() : BALL::VIEW::Stage
- AddLineModel() : BALL::VIEW::AddLineModel
- addModularWidget() : BALL::VIEW::MainControl
- addMovable_() : BALL::ResidueRotamerSet
- addNewFragment_() : BALL::FragmentDB
- addNode() : BALL::SmartsParser
- addPropertiesFromSPAtom() : BALL::SmartsParser::SPAtom
- addRecursiveEdge() : BALL::SmartsParser
- addRepresentation() : BALL::VIEW::GeometricControl
- addRingConnection() : BALL::SmartsParser
- addRotamer() : BALL::RotamerLibrary, BALL::ResidueRotamerSet
- addScoring() : BALL::DockResult
- addScoringFunction() : BALL::VIEW::DockResultDialog, BALL::VIEW::DockDialog
- addSolvent() : BALL::PeriodicBoundary
- addSPEdge() : BALL::SmartsParser::SPNode
- AddSurfaceModel() : BALL::VIEW::AddSurfaceModel
- addToolBarEntries() : BALL::VIEW::Scene, BALL::VIEW::EditableScene, BALL::VIEW::ModularWidget
- AddVanDerWaalsModel() : BALL::VIEW::AddVanDerWaalsModel
- addVariants() : BALL::Enumerator< Container, SiteIterator, Variant >
- advancedClicked() : BALL::VIEW::DockResultDialog
- advancedOptions() : BALL::VIEW::MinimizationDialog
- after() : BALL::String
- alg_ : BALL::VIEW::DockProgressDialog
- algAdvancedPressed() : BALL::VIEW::DockDialog
- Algorithm : BALL::VIEW::DockingController
- algorithm_dialogs_ : BALL::VIEW::DockDialog
- ALGORITHM_NAME : BALL::RingPerceptionProcessor::Default, BALL::RingPerceptionProcessor::Option
- algorithm_opt_ : BALL::VIEW::DockDialog
- algorithmChosen() : BALL::VIEW::DockDialog
- all_small_beers_ : BALL::RingPerceptionProcessor
- all_small_rings_ : BALL::RingPerceptionProcessor
- allowed_sf_ : BALL::VIEW::DockDialog
- ALPHA : BALL::PairExpInteractionEnergyProcessor::Default, BALL::PairExpInteractionEnergyProcessor::Option, BALL::RegularExpression
- alpha_ : BALL::DSN6File
- ALPHANUMERIC : BALL::RegularExpression
- AmberBend() : BALL::AmberBend
- AmberConfigurationDialog() : BALL::VIEW::AmberConfigurationDialog
- AmberFF() : BALL::AmberFF
- AmberNonBonded() : BALL::AmberNonBonded
- AmberStretch() : BALL::AmberStretch
- AmberTorsion() : BALL::AmberTorsion
- AMBIENT : BALL::VIEW::LightSource
- AminoAcidDescriptor() : BALL::Peptides::AminoAcidDescriptor
- analyseRings() : BALL::RingAnalyser
- AND : BALL::ExpressionTree
- angle : BALL::TQuaternion< T >
- animateClicked() : BALL::VIEW::SnapshotVisualisationDialog
- AnisotropyShiftProcessor() : BALL::AnisotropyShiftProcessor
- ANY_TYPE : BALL::Atom
- append() : BALL::System, BALL::SecondaryStructure, BALL::Residue, BALL::Nucleotide, BALL::Molecule, BALL::Chain, BALL::AtomContainer, BALL::TRRFile, BALL::TrajectoryFile, BALL::DCDFile
- appendChild() : BALL::ExpressionTree, BALL::Composite
- appendHotkey() : BALL::VIEW::HotkeyTable
- appendLine() : BALL::INIFile
- appendSection() : BALL::INIFile
- apply() : BALL::VIEW::StageSettings, BALL::VIEW::MaterialSettings, BALL::VIEW::LightSettings, BALL::VIEW::DisplayProperties, BALL::ElectrostaticPotentialCalculator, BALL::PTE_, BALL::INIFile, BALL::List< Value >, BALL::HashSet< Key >, BALL::HashMap< Key, T >, BALL::Composite
- applyAncestor() : BALL::Composite
- applyBonds() : BALL::Atom
- applyChild() : BALL::Composite
- applyDescendant() : BALL::Composite
- applyDescendantPostorder() : BALL::Composite
- applyDescendantPreorder() : BALL::Composite
- applyFirstSnapShot() : BALL::SnapShotManager
- applyInterBond() : BALL::AtomContainer
- applyIntraBond() : BALL::AtomContainer
- applyLastSnapShot() : BALL::SnapShotManager
- applyLevel() : BALL::Composite
- applyNextSnapShot() : BALL::SnapShotManager
- applyPostorder() : BALL::Composite
- applyPreferences() : BALL::VIEW::Scene, BALL::VIEW::PyWidget, BALL::VIEW::EditableScene, BALL::VIEW::Server, BALL::VIEW::ModularWidget, BALL::VIEW::MainControl, BALL::VIEW::Preferences, BALL::VIEW::DisplayProperties
- applyPreorder() : BALL::Composite
- applyProcessors_() : BALL::VIEW::DockDialog
- applySelector() : BALL::VIEW::MolecularControl
- applySnapShot() : BALL::SnapShotManager, BALL::SnapShot
- applyTo() : BALL::VIEW::MMFF94ConfigurationDialog, BALL::VIEW::CharmmConfigurationDialog, BALL::VIEW::AmberConfigurationDialog
- applyValues_() : BALL::VIEW::DockDialog
- argument : BALL::ExpressionParser::SyntaxTree
- arom : BALL::MMFF94AtomType
- AromaticityProcessor() : BALL::AromaticityProcessor
- aromatize() : BALL::AromaticityProcessor
- aromatizeSimple() : BALL::AromaticityProcessor
- aspec : BALL::MMFF94AtomType
- assembleChain() : BALL::MoleculeAssembler
- assembleMolecule() : BALL::MoleculeAssembler
- assembleRS() : BALL::MoleculeAssembler
- assembleSubstituents() : BALL::MoleculeAssembler
- assign() : BALL::Templates
- ASSIGN_CHARGES : BALL::MMFF94::Default, BALL::MMFF94::Option, BALL::CharmmFF::Default, BALL::CharmmFF::Option, BALL::AmberFF::Default, BALL::AmberFF::Option
- ASSIGN_TYPENAMES : BALL::MMFF94::Default, BALL::MMFF94::Option, BALL::CharmmFF::Default, BALL::CharmmFF::Option, BALL::AmberFF::Default, BALL::AmberFF::Option
- ASSIGN_TYPES : BALL::MMFF94::Default, BALL::MMFF94::Option, BALL::CharmmFF::Default, BALL::CharmmFF::Option, BALL::AmberFF::Default, BALL::AmberFF::Option
- assignBackboneAtoms() : BALL::AtomBijection
- assignByName() : BALL::AtomBijection
- assignCAlphaAtoms() : BALL::AtomBijection
- AssignChargeProcessor() : BALL::AssignChargeProcessor
- assignCharges() : BALL::Templates
- assignParameters() : BALL::QuadraticImproperTorsion, BALL::QuadraticBondStretch, BALL::QuadraticAngleBend, BALL::Potential1210, BALL::LennardJones, BALL::CosineTorsion, BALL::CharmmEEF1
- AssignRadiusProcessor() : BALL::AssignRadiusProcessor
- AssignShiftProcessor() : BALL::AssignShiftProcessor
- assignSpecificValues_() : BALL::AtomTyper
- assignTorsion() : BALL::ResidueTorsions
- assignTrivial() : BALL::AtomBijection
- assignTypeNames() : BALL::Templates
- atom : BALL::CharmmEEF1::Data
- Atom() : BALL::Atom
- atom_ : BALL::SmartsParser::SPAtom
- atom_array : BALL::FDPB
- atom_data_sets_ : BALL::NMRStarFile
- atom_format_ : BALL::MOLFile
- AtomBijection() : BALL::AtomBijection
- AtomBondModelBaseProcessor() : BALL::VIEW::AtomBondModelBaseProcessor
- AtomBox : BALL::VIEW::ColorProcessor
- AtomChargeColorProcessor() : BALL::VIEW::AtomChargeColorProcessor
- AtomContainer() : BALL::AtomContainer
- AtomDistanceColorProcessor() : BALL::VIEW::AtomDistanceColorProcessor
- AtomGrid : BALL::VIEW::ColorProcessor
- atomic_number_ : BALL::Element
- atomic_radius_ : BALL::Element
- atomic_weight_ : BALL::Element
- AtomicNumber : BALL::Element
- AtomicPolarizabilities() : BALL::AtomicPolarizabilities
- AtomInformationContent() : BALL::AtomInformationContent
- AtomOverview() : BALL::VIEW::AtomOverview
- AtomPair : BALL::AtomBijection
- atoms_ : BALL::GeneralizedBornModel
- AtomStatus : BALL::RSComputer
- AtomTypes() : BALL::AtomTypes
- AtomVector() : BALL::AtomVector
- attachBridged() : BALL::RSConstructor
- attachFused() : BALL::RSConstructor
- attachSpiro() : BALL::RSConstructor
- attachTemplate() : BALL::RSConstructor
- attributes_changed_time_ : BALL::Atom
- AVERAGE_SECTION_NAME : BALL::CreateSpectrumProcessor
- AVERAGING__NONE : BALL::PolarSolvation
- AVERAGING__RANDOM : BALL::PolarSolvation
- AVERAGING__RANDOM_FACTOR : BALL::PolarSolvation
- AVERAGING__STATIC : BALL::PolarSolvation
- AveragingMethod : BALL::PolarSolvation
- AVOGADRO : BALL::Constant
- b -
- b : BALL::TSimpleBox3< T >
- b_ : BALL::HBondShiftProcessor
- b_i_ : BALL::ConjugateGradientMinimizer
- backbone_dependent_ : BALL::RotamerLibrary
- backup_ : BALL::VIEW::GeometricFitDialog, BALL::VIEW::DockDialog
- backward() : BALL::CompositeIteratorTraits
- BalabanIndexJ() : BALL::BalabanIndexJ
- BALANCING_VALUE : BALL::ShiftedLVMMMinimizer
- BaseIterator() : BALL::BaseIterator< Container, DataType, Position, Traits >
- baseName() : BALL::FileSystem
- BATH_RELAXATION_TIME : BALL::MolecularDynamics::Option
- bath_relaxation_time_ : BALL::CanonicalMD
- bb_dep_sets_ : BALL::RotamerLibrary
- bb_indep_sets_ : BALL::RotamerLibrary
- before() : BALL::String
- begin() : BALL::VIEW::RepresentationManager, BALL::SmartsParser::SPNode, BALL::Gradient, BALL::AtomVector, BALL::ExpressionParser::SyntaxTree, BALL::PDBRecords, BALL::RandomAccessIterator< Container, DataType, Position, Traits >, BALL::ForwardIterator< Container, DataType, Position, Traits >, BALL::ConstForwardIterator< Container, DataType, Position, Traits >, BALL::BidirectionalIterator< Container, DataType, Position, Traits >, BALL::ConstBidirectionalIterator< Container, DataType, Position, Traits >
- beginBond() : BALL::Atom
- beginBox() : BALL::HashGridBox3< Item >
- BendMap : BALL::MMFF94BendParameters
- beta_ : BALL::DSN6File
- BidirectionalIterator() : BALL::BidirectionalIterator< Container, DataType, Position, Traits >
- BinaryFileAdaptor() : BALL::BinaryFileAdaptor< T >
- BinaryProcessor() : BALL::BinaryProcessor< T1, T2 >
- binaryRead() : BALL::TRegularData3D< ValueType >, BALL::TRegularData2D< ValueType >, BALL::TRegularData1D< ValueType >
- binaryWrite() : BALL::TRegularData3D< ValueType >, BALL::TRegularData2D< ValueType >, BALL::TRegularData1D< ValueType >
- bind() : BALL::Substring
- Bit() : BALL::Bit
- BitVector() : BALL::BitVector
- bitwiseAnd() : BALL::BitVector
- bitwiseOr() : BALL::BitVector
- bitwiseXor() : BALL::BitVector
- blockname : BALL::GAMESSDatFile::block
- blowUp() : BALL::TriangulatedSurface
- BOHR_RADIUS : BALL::Constant
- BOLTZMANN : BALL::Constant
- Bond() : BALL::Bond
- bond_ : BALL::SmartsParser::SPEdge
- BOND__PROPERTIES : BALL::VIEW::MolecularControl
- bond_format_ : BALL::MOLFile
- bond_lengths_ : BALL::BuildBondsProcessor
- bond_order_ : BALL::SmartsParser::SPBond
- bond_to_index_ : BALL::RingPerceptionProcessor
- BondConstIterator : BALL::Atom
- BondConstReverseIterator : BALL::Atom
- BondIterator : BALL::Atom
- BONDLENGTHS_FILENAME : BALL::BuildBondsProcessor::Default, BALL::BuildBondsProcessor::Option
- BondOrder : BALL::Bond
- BondPolarizabilities() : BALL::BondPolarizabilities
- bondProperties() : BALL::VIEW::MolecularControl
- BondReverseIterator : BALL::Atom
- BondType : BALL::Bond
- book_keeping_ : BALL::PDBFile
- BOOL : BALL::NamedProperty
- BORDER : BALL::FDPB::Default, BALL::FDPB::Option
- born_radii_ : BALL::GeneralizedBornModel
- bound_ : BALL::CompositeIteratorTraits
- BOUNDARY : BALL::FDPB::Default, BALL::FDPB::Option
- bounding_box_data_size : BALL::TRRFile::TRRHeader
- BOUNDING_BOX_LOWER : BALL::FDPB::Option
- BOUNDING_BOX_UPPER : BALL::FDPB::Option
- Box() : BALL::VIEW::Box
- BoxIterator : BALL::HashGridBox3< Item >
- BREAK : BALL::Processor
- browseChargesData() : BALL::VIEW::DockDialog
- browseChargesRules() : BALL::VIEW::DockDialog
- browseRadiiData() : BALL::VIEW::DockDialog
- browseRadiiRules() : BALL::VIEW::DockDialog
- Bruker1DFile() : BALL::Bruker1DFile
- Bruker2DFile() : BALL::Bruker2DFile
- bucket_ : BALL::HashMap< Key, T >
- bufferRepresentation() : BALL::VIEW::GLRenderer
- BUILD : BALL::VIEW::MainControl
- build_bonds : BALL::FragmentDB
- buildBondModels_() : BALL::VIEW::AtomBondModelBaseProcessor
- buildBonds() : BALL::VIEW::MolecularStructure, BALL::VIEW::MolecularControl
- buildBondsHashGrid3_() : BALL::BuildBondsProcessor
- BuildBondsProcessor() : BALL::BuildBondsProcessor
- buildChains() : BALL::ChainBuilder
- buildConnection_() : BALL::FragmentDB::BuildBondsProcessor
- buildContextMenu() : BALL::VIEW::GeometricControl, BALL::VIEW::VectorGridController, BALL::VIEW::DockResultController, BALL::VIEW::TrajectoryController, BALL::VIEW::RegularData3DController, BALL::VIEW::DatasetController
- buildFragmentBonds() : BALL::FragmentDB::BuildBondsProcessor
- buildInterFragmentBonds() : BALL::FragmentDB::BuildBondsProcessor
- buildPeptide() : BALL::VIEW::MolecularStructure
- buildRegularPolygon() : BALL::RSConstructor
- buildVectorOfNonBondedAtomPairs() : BALL::CharmmNonBonded, BALL::AmberNonBonded
- BuriedPolar() : BALL::BuriedPolar
- c -
- c : BALL::Constant
- c_str() : BALL::Substring
- CAL_PER_JOULE : BALL::Constant
- calcAdjMatrix() : BALL::ChainBuilder
- calculate() : BALL::VIEW::FDPBDialog
- calculateAbsoluteCoordinates() : BALL::VIEW::Stage
- calculateBendEmpericalForceConstant() : BALL::MMFF94StretchBend
- calculateBendEmpericalReferenceAngle() : BALL::MMFF94StretchBend
- calculateBornRadii_() : BALL::GeneralizedBornModel
- calculateCreationEnergy_() : BALL::GeneralizedBornModel
- calculateDefaultBijection() : BALL::StructureMapper
- calculateDistances() : BALL::VIEW::AtomDistanceColorProcessor
- calculateEnergy() : BALL::GeneralizedBornModel
- calculateFactors_() : BALL::CanonicalMD
- calculateForceFieldEnergy() : BALL::VIEW::MolecularStructure
- calculateFragmentBijection() : BALL::StructureMapper
- calculateHBonds() : BALL::VIEW::MolecularStructure
- calculateMinSpacing() : BALL::HashGrid3< Item >
- calculatePEOE() : BALL::PartialChargeProcessor
- calculatePotential() : BALL::GeneralizedBornModel
- calculateRamachandranPlot() : BALL::VIEW::MolecularStructure
- calculateReactionFieldEnergy() : BALL::FDPB
- calculateRelativeCoordinates() : BALL::VIEW::Stage
- calculateRMSD() : BALL::VIEW::MolecularStructure, BALL::StructureMapper, BALL::AtomBijection
- calculateScore() : BALL::RotationalEntropyLoss, BALL::PolarSolvation, BALL::NonpolarSolvation, BALL::Lipophilic, BALL::BuriedPolar
- calculateSecondaryStructure() : BALL::VIEW::MolecularStructure
- calculateSolvationEnergy() : BALL::GeneralizedBornModel
- calculateSSSR() : BALL::RingPerceptionProcessor
- calculateStretchR0() : BALL::MMFF94StretchBend
- calculateTransferEnergy_() : BALL::GeneralizedBornModel
- calculateTransformation() : BALL::StructureMapper
- CALCULATION__BOEHM : BALL::RotationalEntropyLoss
- CALCULATION__FROZEN_GLYCOSIDIC_BONDS : BALL::RotationalEntropyLoss
- CALCULATION__FULL_LJ_POTENTIAL : BALL::VanDerWaals
- CALCULATION__GLYCOSIDIC_BONDS : BALL::RotationalEntropyLoss
- CALCULATION__GLYCOSIDIC_CONTRIBUTION : BALL::RotationalEntropyLoss
- CALCULATION__ORIGINAL : BALL::RotationalEntropyLoss
- CALCULATION__SOFTENED_LJ_POTENTIAL_LOG : BALL::VanDerWaals
- CALCULATION__SOFTENED_LJ_POTENTIAL_SIMPLE : BALL::VanDerWaals
- CalculationMethod : BALL::VanDerWaals, BALL::RotationalEntropyLoss
- Camera() : BALL::VIEW::Camera
- CAMERA__CENTER : BALL::VIEW::MolecularControl
- cancelPressed() : BALL::VIEW::DockDialog
- canHandle() : BALL::VIEW::TestFramework, BALL::VIEW::PyWidget, BALL::VIEW::DatasetControl, BALL::VIEW::ModularWidget, BALL::VIEW::MolecularFileDialog
- CanonicalMD() : BALL::CanonicalMD
- canonizePath() : BALL::FileSystem
- capacity_ : BALL::HashMap< Key, T >
- CASE_INSENSITIVE : BALL::String
- CASE_SENSITIVE : BALL::String
- cell_scaling_ : BALL::DSN6File
- CENTER_CAMERA : BALL::VIEW::CompositeMessage
- centerCamera() : BALL::VIEW::MolecularStructure, BALL::VIEW::MolecularControl
- Chain() : BALL::Chain
- ChainBuilder() : BALL::ChainBuilder
- CHANGED_COMPOSITE : BALL::VIEW::CompositeMessage
- CHANGED_COMPOSITE_HIERARCHY : BALL::VIEW::CompositeMessage
- changeToUserHomeDir() : BALL::Directory
- CHARACTER_CLASS__ASCII_ALPHA : BALL::String
- CHARACTER_CLASS__ASCII_ALPHANUMERIC : BALL::String
- CHARACTER_CLASS__ASCII_FLOAT : BALL::String
- CHARACTER_CLASS__ASCII_LOWER : BALL::String
- CHARACTER_CLASS__ASCII_NUMERIC : BALL::String
- CHARACTER_CLASS__ASCII_UPPER : BALL::String
- CHARACTER_CLASS__QUOTES : BALL::String
- CHARACTER_CLASS__WHITESPACE : BALL::String
- CHARGE_DISTRIBUTION : BALL::FDPB::Default, BALL::FDPB::Option
- ChargeRuleProcessor() : BALL::ChargeRuleProcessor
- CharmmBend() : BALL::CharmmBend
- CharmmConfigurationDialog() : BALL::VIEW::CharmmConfigurationDialog
- CharmmEEF1() : BALL::CharmmEEF1
- CharmmFF() : BALL::CharmmFF
- CharmmImproperTorsion() : BALL::CharmmImproperTorsion
- CharmmNonBonded() : BALL::CharmmNonBonded
- CharmmStretch() : BALL::CharmmStretch
- CharmmTorsion() : BALL::CharmmTorsion
- CHECK_AFTER_ITERATIONS : BALL::FDPB::Default, BALL::FDPB::Option
- checkAtoms() : BALL::SDGenerator
- checkAtomType() : BALL::MMFF94
- checkFusedOrBridged() : BALL::RingAnalyser
- checkHeader() : BALL::XDRPersistenceManager, BALL::TextPersistenceManager, BALL::PersistenceManager
- checkMenu() : BALL::VIEW::TestFramework, BALL::VIEW::Scene, BALL::VIEW::PyWidget, BALL::VIEW::MolecularStructure, BALL::VIEW::MolecularControl, BALL::VIEW::GeometricControl, BALL::VIEW::FileObserver, BALL::VIEW::EditableScene, BALL::VIEW::DockingController, BALL::VIEW::DatasetControl, BALL::VIEW::ModularWidget, BALL::VIEW::PubChemDialog, BALL::VIEW::MolecularFileDialog, BALL::VIEW::LabelDialog, BALL::VIEW::DownloadPDBFile, BALL::VIEW::DisplayProperties, BALL::VIEW::DatasetController
- checkMenus() : BALL::VIEW::MainControl
- checkName() : BALL::XDRPersistenceManager, BALL::TextPersistenceManager, BALL::PersistenceManager
- checkObjectHeader() : BALL::PersistenceManager
- checkObjectPointerArrayHeader() : BALL::XDRPersistenceManager, BALL::TextPersistenceManager, BALL::PersistenceManager
- checkObjectPointerArrayTrailer() : BALL::XDRPersistenceManager, BALL::TextPersistenceManager, BALL::PersistenceManager
- checkObjectPointerHeader() : BALL::XDRPersistenceManager, BALL::TextPersistenceManager, BALL::PersistenceManager
- checkObjectReferenceHeader() : BALL::XDRPersistenceManager, BALL::TextPersistenceManager, BALL::PersistenceManager
- checkObjectTrailer() : BALL::PersistenceManager
- checkPrimitiveHeader() : BALL::XDRPersistenceManager, BALL::TextPersistenceManager, BALL::PersistenceManager
- checkPrimitiveTrailer() : BALL::XDRPersistenceManager, BALL::TextPersistenceManager, BALL::PersistenceManager
- checkResidue() : BALL::VIEW::MolecularStructure, BALL::VIEW::MolecularControl
- checkRTD() : BALL::RingAnalyser
- checkSpiro() : BALL::RingAnalyser
- checkStorableHeader() : BALL::XDRPersistenceManager, BALL::TextPersistenceManager, BALL::PersistenceManager
- checkStorableTrailer() : BALL::XDRPersistenceManager, BALL::TextPersistenceManager, BALL::PersistenceManager
- checkStreamHeader() : BALL::XDRPersistenceManager, BALL::TextPersistenceManager, BALL::PersistenceManager
- checkStreamTrailer() : BALL::XDRPersistenceManager, BALL::TextPersistenceManager, BALL::PersistenceManager
- checkTrailer() : BALL::XDRPersistenceManager, BALL::TextPersistenceManager, BALL::PersistenceManager
- ChemScoreMetal() : BALL::ChemScoreMetal
- chi1 : BALL::Rotamer
- chi2 : BALL::Rotamer
- chi3 : BALL::Rotamer
- chi4 : BALL::Rotamer
- children : BALL::ExpressionParser::SyntaxTree
- ChiralClass : BALL::SmartsParser
- CHOOSE_FF : BALL::VIEW::MainControl
- CHOOSE_MODEL : BALL::PDBFile::Default, BALL::PDBFile::Option
- chooseAmberFF() : BALL::VIEW::MolecularStructure
- chooseCharmmFF() : BALL::VIEW::MolecularStructure
- chooseFile() : BALL::VIEW::FileObserver
- chooseMMFF94() : BALL::VIEW::MolecularStructure
- ClaverieParameter() : BALL::ClaverieParameter
- clean() : BALL::ReducedSurface
- clear() : BALL::VIEW::Scene, BALL::VIEW::PyWidget, BALL::VIEW::GeometricControl, BALL::VIEW::VRMLRenderer, BALL::VIEW::MeshBuffer, BALL::VIEW::Renderer, BALL::VIEW::POVRenderer, BALL::VIEW::GLRenderer, BALL::VIEW::GLDisplayList, BALL::VIEW::TwoColoredTube, BALL::VIEW::TwoColoredLine, BALL::VIEW::Tube, BALL::VIEW::Sphere, BALL::VIEW::SimpleBox, BALL::VIEW::Point, BALL::VIEW::MultiLine, BALL::VIEW::Mesh, BALL::VIEW::Line, BALL::VIEW::Label, BALL::VIEW::Disc, BALL::VIEW::Box, BALL::VIEW::AddSurfaceModel, BALL::VIEW::ModelProcessor, BALL::VIEW::HBondModelProcessor, BALL::VIEW::ColorProcessor, BALL::VIEW::AddBallAndStickModel, BALL::VIEW::AddBackboneModel, BALL::VIEW::AtomBondModelBaseProcessor, BALL::VIEW::Stage, BALL::VIEW::Camera, BALL::VIEW::Server, BALL::VIEW::RepresentationManager, BALL::VIEW::Representation, BALL::VIEW::ModularWidget, BALL::VIEW::MainControl, BALL::VIEW::GeometricObject, BALL::VIEW::ConnectionObject, BALL::VIEW::CompositeManager, BALL::VIEW::Vertex2, BALL::VIEW::Vertex, BALL::VIEW::Dataset, BALL::VIEW::ColorUnitHue, BALL::VIEW::ColorUnit, BALL::VIEW::ColorRGBA, BALL::VIEW::ColorHSV, BALL::VIEW::MultiColorExtension, BALL::VIEW::ColorExtension2, BALL::Timer, BALL::TCPTransfer, BALL::File, BALL::Directory, BALL::TriangulatedSurface, BALL::SmartsParser, BALL::SmartsMatcher::RecStruct_, BALL::SmartsMatcher::RecStructCore_, BALL::RotamerLibrary, BALL::ReducedSurface, BALL::RDFSection, BALL::RDFParameter, BALL::RDFIntegrator, BALL::RadialDistributionFunction, BALL::UhligCavFreeEnergyProcessor, BALL::SolventParameter, BALL::SolventDescriptor, BALL::ReissCavFreeEnergyProcessor, BALL::PierottiCavFreeEnergyProcessor, BALL::PCMCavFreeEnergyProcessor, BALL::PairExpRDFIntegrator, BALL::PairExpInteractionEnergyProcessor, BALL::Pair6_12RDFIntegrator, BALL::Pair6_12InteractionEnergyProcessor, BALL::ClaverieParameter, BALL::SLICKScore, BALL::SLICKEnergy, BALL::RotationalEntropyLoss, BALL::PolarSolvation, BALL::NonpolarSolvation, BALL::ChemScoreMetal, BALL::Lipophilic, BALL::HydrogenBond, BALL::CHPI, BALL::BuriedPolar, BALL::Spectrum< DataT, PeakT, PositionT >, BALL::ShiftModule, BALL::ShiftModel, BALL::Templates, BALL::ResidueTorsions, BALL::QuadraticImproperTorsion, BALL::QuadraticBondStretch, BALL::QuadraticAngleBend, BALL::Potential1210, BALL::LennardJones, BALL::ForceFieldParameters, BALL::CosineTorsion, BALL::CharmmEEF1, BALL::AtomTypes, BALL::MMFF94ESParameters, BALL::MMFF94VDWParameters, BALL::MMFF94PlaneParameters, BALL::MMFF94TorsionParameters, BALL::MMFF94StretchBendParameters, BALL::MMFF94BendParameters, BALL::MMFF94StretchParameters, BALL::MMFF94AtomTypeEquivalences, BALL::MMFF94ParametersBase, BALL::MMFF94NonBonded, BALL::MMFF94, BALL::SnapShotManager, BALL::SnapShot, BALL::RuleEvaluator, BALL::PeriodicBoundary, BALL::ForceField, BALL::CharmmNonBonded, BALL::CharmmFF, BALL::AmberNonBonded, BALL::AmberFF, BALL::TVector4< T >, BALL::TVector3< T >, BALL::TVector2< T >, BALL::TSphere3< T >, BALL::TSimpleBox3< T >, BALL::RombergIntegrator< Function, DataType >, BALL::TQuaternion< T >, BALL::TPlane3< T >, BALL::PiecewisePolynomial, BALL::PiecewiseFunction, BALL::TMatrix4x4< T >, BALL::TLine3< T >, BALL::TFFT3D< ComplexTraits >, BALL::TFFT2D< ComplexTraits >, BALL::TFFT1D< ComplexTraits >, BALL::TCircle3< T >, BALL::TBox3< T >, BALL::TAngle< T >, BALL::ConnectedToPredicate, BALL::Selector, BALL::SecondaryStructure, BALL::Residue, BALL::PTE_, BALL::Element, BALL::Protein, BALL::PDBAtom, BALL::Nucleotide, BALL::NucleicAcid, BALL::ExpressionTree, BALL::ExpressionPredicate, BALL::ExpressionParser::SyntaxTree, BALL::Expression, BALL::Bond, BALL::AtomContainer, BALL::Atom, BALL::TRRFile, BALL::TrajectoryFile, BALL::ResourceFile, BALL::PDBInfo, BALL::PDBFile, BALL::ParameterSection, BALL::Parameters, BALL::NMRStarFile, BALL::LineBasedFile, BALL::INIFile, BALL::DSN6File, BALL::DCDFile, BALL::EnergyProcessor, BALL::ComposedEnergyProcessor, BALL::Triple< T1, T2, T3 >, BALL::Substring, BALL::String, BALL::RegularExpression, BALL::TRegularData3D< ValueType >, BALL::TRegularData2D< ValueType >, BALL::TRegularData1D< ValueType >, BALL::Quadruple< T1, T2, T3, T4 >, BALL::Options, BALL::HashSet< Key >, BALL::HashMap< Key, T >, BALL::HashGrid3< Item >, BALL::HashGridBox3< Item >, BALL::TContourSurface< T >, BALL::TContourLine< T >, BALL::TContour< T >, BALL::BitVector, BALL::Bit, BALL::TimeStamp, BALL::PreciseTime, BALL::Selectable, BALL::PropertyManager, BALL::NamedProperty, BALL::ObjectCreator, BALL::Object, BALL::MoleculeObjectCreator, BALL::MolecularInformation, BALL::Composite, BALL::Client, BALL::LogStream
- clearBuffer() : BALL::VIEW::MeshBuffer, BALL::SnapShotManager
- clearClipboard() : BALL::VIEW::MolecularControl
- clearComposites() : BALL::VIEW::AddSurfaceModel, BALL::VIEW::ModelProcessor, BALL::VIEW::AtomBondModelBaseProcessor
- clearData() : BALL::VIEW::MainControl
- clearGeometricObjects() : BALL::VIEW::Representation
- clearNormals() : BALL::TSurface< T >
- clearProperty() : BALL::PropertyManager
- clearSelection() : BALL::VIEW::MainControl
- clearSelector() : BALL::VIEW::MolecularControl
- ClearShiftProcessor() : BALL::ClearShiftProcessor
- clearTriangles() : BALL::TSurface< T >
- clearUsedAtoms_() : BALL::VIEW::AtomBondModelBaseProcessor
- clearVertices() : BALL::TSurface< T >
- Client() : BALL::Client
- ClippingDialog() : BALL::VIEW::ClippingDialog
- clone() : BALL::Composite
- cloneBond() : BALL::Atom
- close() : BALL::File, BALL::ResourceFile
- closeClicked() : BALL::VIEW::DockResultDialog
- clusterRings() : BALL::RingClusterer
- COLLAPSE_ALL : BALL::VIEW::MolecularControl
- collapseAll() : BALL::VIEW::MolecularControl
- ColorExtension2() : BALL::VIEW::ColorExtension2
- ColorHSV() : BALL::VIEW::ColorHSV
- coloringMuteableByDisplayProperties() : BALL::VIEW::ModelInformation
- ColoringSettingsDialog() : BALL::VIEW::ColoringSettingsDialog
- ColorMap() : BALL::VIEW::ColorMap
- colorPressed() : BALL::VIEW::StageSettings, BALL::VIEW::LightSettings
- ColorProcessor() : BALL::VIEW::ColorProcessor
- ColorRGBA() : BALL::VIEW::ColorRGBA
- ColorUnit() : BALL::VIEW::ColorUnit
- ColorUnitHue() : BALL::VIEW::ColorUnitHue
- Command : BALL::Client
- COMMAND__SEND_OBJECT : BALL::Client
- COMMAND__UNKOWN : BALL::Client
- compact() : BALL::Atom
- Comparator() : BALL::Comparator< T >
- compare() : BALL::Object
- Compare_() : BALL::VIEW::DockResultDialog::Compare_, BALL::DockResult::Compare_
- compareChains() : BALL::ChainBuilder
- CompareMode : BALL::String
- compareRingsystems() : BALL::MoleculeAssembler
- component_grouping_ : BALL::SmartsParser
- component_no_ : BALL::SmartsParser, BALL::SmartsParser::SPNode
- ComposedEnergyProcessor() : BALL::ComposedEnergyProcessor
- Composite() : BALL::Composite
- COMPOSITE__PROPERTIES : BALL::VIEW::MolecularControl
- composite_iterator_ : BALL::CompositeIteratorTraits
- CompositeIteratorTraits() : BALL::CompositeIteratorTraits
- CompositeManager() : BALL::VIEW::CompositeManager
- CompositeMessage() : BALL::VIEW::CompositeMessage
- CompositeMessageType : BALL::VIEW::CompositeMessage
- compositeProperties() : BALL::VIEW::MolecularControl
- compositesAreLocked() : BALL::VIEW::MainControl
- CompositeSet : BALL::VIEW::ColorProcessor
- compute() : BALL::TriangulatedSAS, BALL::SolventExcludedSurface, BALL::SolventAccessibleSurface, BALL::ReducedSurface
- compute_() : BALL::SecondaryStructureProcessor
- computeTopology() : BALL::TContourSurface< T >::Cube
- Conformation : BALL::ConformationSet
- conformation_set_ : BALL::VIEW::DockingFinishedMessage, BALL::DockResult
- ConjugateGradientMinimizer() : BALL::ConjugateGradientMinimizer
- connect() : BALL::Client
- ConnectionObject() : BALL::VIEW::ConnectionObject
- ConnectivityBase() : BALL::ConnectivityBase
- CONST : BALL::SLICKScore::Default, BALL::SLICKScore::Option, BALL::SLICKEnergy::Default, BALL::SLICKEnergy::Option
- CONSTANT : BALL::UhligCavFreeEnergyProcessor::Default, BALL::UhligCavFreeEnergyProcessor::Option
- constants_ : BALL::ParsedFunction< arg >
- ConstBidirectionalIterator() : BALL::ConstBidirectionalIterator< Container, DataType, Position, Traits >
- ConstBoxIterator : BALL::HashGridBox3< Item >
- ConstDataIterator : BALL::HashGridBox3< Item >
- ConstForwardIterator() : BALL::ConstForwardIterator< Container, DataType, Position, Traits >
- ConstIterator : BALL::PyIndexList, BALL::PyDatasetVector, BALL::PyCompositeList, BALL::PyColorRGBAVector, BALL::Spectrum< DataT, PeakT, PositionT >, BALL::PeakList< PT >, BALL::Gradient, BALL::AtomVector, BALL::ExpressionParser::SyntaxTree, BALL::StringHashMap< Value >, BALL::TRegularData3D< ValueType >, BALL::TRegularData2D< ValueType >, BALL::TRegularData1D< ValueType >, BALL::List< Value >, BALL::Enumerator< Container, SiteIterator, Variant >
- ConstReverseIterator : BALL::Gradient
- construct() : BALL::Peptides::PeptideBuilder
- constructRS() : BALL::RSConstructor
- containsSelection() : BALL::Composite
- CONTINUE : BALL::Processor
- convertObject() : BALL::ObjectCreator, BALL::MoleculeObjectCreator
- coordinateSystemEnabled() : BALL::VIEW::Stage
- CoordinateType : BALL::TRegularData3D< ValueType >, BALL::TRegularData2D< ValueType >, BALL::TRegularData1D< ValueType >
- copy() : BALL::VIEW::MolecularControl, BALL::File
- copyTo() : BALL::File
- corr_par_ : BALL::ShiftedLVMMMinimizer
- CORRECTION_PARAMETER : BALL::ShiftedLVMMMinimizer::Option
- CorrectionParameter : BALL::ShiftedLVMMMinimizer
- CosineTorsion() : BALL::CosineTorsion
- COULOMB : BALL::FDPB::Boundary
- coulombIntegralApproximation_() : BALL::GeneralizedBornModel
- count() : BALL::Composite
- countAtomContainers() : BALL::Residue, BALL::Nucleotide, BALL::AtomContainer
- countAtoms() : BALL::System, BALL::AtomContainer
- countBonds() : BALL::AtomContainer, BALL::Atom
- countChains() : BALL::System, BALL::Protein
- countChildren() : BALL::ResourceEntry
- countComponents() : BALL::ForceField
- countDescendants() : BALL::ResourceEntry, BALL::Composite
- countDirectories() : BALL::Directory
- countEdges() : BALL::SmartsParser::SPNode
- countFields() : BALL::String
- countFieldsQuoted() : BALL::String
- countFiles() : BALL::Directory
- countFragments() : BALL::System
- countInstances_() : BALL::Embeddable
- countInterBonds() : BALL::AtomContainer
- countIntraBonds() : BALL::AtomContainer
- countItems() : BALL::VIEW::MolecularControl, BALL::Directory
- countMolecules() : BALL::System
- countNamedProperties() : BALL::PropertyManager
- countNonEmptyBoxes() : BALL::HashGrid3< Item >
- countNucleicAcids() : BALL::System
- countNucleotides() : BALL::System, BALL::NucleicAcid
- countPDBAtoms() : BALL::SecondaryStructure, BALL::Residue, BALL::Protein, BALL::Chain
- countProperties() : BALL::SmartsParser::SPAtom, BALL::PropertyManager
- countProteins() : BALL::System
- countRealValences() : BALL::SmartsParser::SPAtom
- countRecord() : BALL::PDBFile
- countRecordFields() : BALL::PDBFile
- countRecords() : BALL::PDBFile
- countResidues() : BALL::System, BALL::SecondaryStructure, BALL::Protein, BALL::Chain
- counts_format_ : BALL::MOLFile
- countSecondaryStructures() : BALL::System, BALL::Protein, BALL::Chain
- countSubexpressions() : BALL::RegularExpression
- countValue() : BALL::BitVector
- countVariants() : BALL::Enumerator< Container, SiteIterator, Variant >
- covalent_radius_ : BALL::Element
- Cp_ref : BALL::CharmmEEF1::Values
- crd : BALL::MMFF94AtomType
- create() : BALL::Directory, BALL::Factory< T >
- CREATE_REPRESENTATION : BALL::VIEW::MolecularControl
- createAtom() : BALL::SmartsParser
- createBond() : BALL::Bond, BALL::Atom
- createCombination() : BALL::Enumerator< Container, SiteIterator, Variant >
- createContourLine() : BALL::TContourLine< T >
- createCoordinateSystem() : BALL::VIEW::Scene
- createCoordinateSystemAtOrigin() : BALL::VIEW::Scene
- createGeometricObjects() : BALL::VIEW::AddSurfaceModel, BALL::VIEW::ModelProcessor, BALL::VIEW::LabelModel, BALL::VIEW::AddBallAndStickModel, BALL::VIEW::AddBackboneModel, BALL::VIEW::AtomBondModelBaseProcessor
- createGridFromDistance() : BALL::VIEW::MolecularStructure
- createMap() : BALL::VIEW::ColorMap
- createMapJet() : BALL::VIEW::ColorMap
- createMenuEntries() : BALL::VIEW::VectorGridController, BALL::VIEW::DockResultController, BALL::VIEW::TrajectoryController, BALL::VIEW::RegularData3DController, BALL::VIEW::DatasetController
- CreateMethod : BALL::ShiftModel, BALL::PersistenceManager
- CreateMethodMap : BALL::ShiftModel
- createObject() : BALL::PersistenceManager
- createPlot() : BALL::VIEW::RegularData2DWidget, BALL::VIEW::RegularData1DWidget
- createRepresentation() : BALL::VIEW::MolecularControl, BALL::VIEW::RepresentationManager
- createRepresentationMode() : BALL::VIEW::DisplayProperties
- createResidue_() : BALL::Peptides::PeptideBuilder
- CreateSpectrumProcessor() : BALL::CreateSpectrumProcessor
- createTemporaryFilename() : BALL::File
- createVoid() : BALL::Factory< T >
- CreationMethod : BALL::Expression
- crystal_dimension_ : BALL::DSN6File
- CubicFunction() : BALL::CubicFunction< Function, DataType >
- curr_num_of_vect_pairs_ : BALL::StrangLBFGSMinimizer
- curr_number_of_cols_ : BALL::ShiftedLVMMMinimizer
- CURRENT_DIRECTORY : BALL::FileSystem
- current_energy_ : BALL::EnergyMinimizer
- current_grad_ : BALL::EnergyMinimizer
- current_parser_ : BALL::SmartsParser
- CURRENT_TIME : BALL::MolecularDynamics::Option
- currentStackPage() : BALL::VIEW::PreferencesEntry
- cut() : BALL::VIEW::MolecularControl, BALL::TriangulatedSurface
- cutlo_ : BALL::EnergyMinimizer
- d -
- d : BALL::TLine3< T >
- D_1_ : BALL::ConjugateGradientMinimizer
- D_4_ : BALL::ConjugateGradientMinimizer
- data : BALL::GAMESSDatFile::block
- data_ : BALL::TRegularData3D< ValueType >, BALL::TRegularData2D< ValueType >, BALL::TRegularData1D< ValueType >
- DataIterator : BALL::HashGridBox3< Item >
- Dataset() : BALL::VIEW::Dataset
- DatasetControl() : BALL::VIEW::DatasetControl
- DataType : BALL::Spectrum< DataT, PeakT, PositionT >
- dc_solute_ : BALL::GeneralizedBornModel
- DCDFile() : BALL::DCDFile
- deactivate() : BALL::VIEW::Server
- DEBYE : BALL::FDPB::Boundary
- decodeBase64() : BALL::String
- DEFAULT_FRAGMENT_DB : BALL::RotamerLibrary
- DEFAULT_LIBRARY : BALL::RotamerLibrary
- defaultsPressed() : BALL::VIEW::LightSettings
- DEG_PER_RAD : BALL::Constant
- DELETE_EXISTING_BONDS : BALL::BuildBondsProcessor::Default, BALL::BuildBondsProcessor::Option
- DELETE_OVERESTIMATED_BONDS : BALL::BuildBondsProcessor::Default, BALL::BuildBondsProcessor::Option
- deleteColumn_() : BALL::VIEW::DockResultDialog
- deleteCurrentItems() : BALL::VIEW::MolecularControl, BALL::VIEW::GeometricControl,