BALL Namespace Reference

-*- Mode: C++; tab-width: 2; -*- More...

Namespaces
	__private
	Constants
	Exception
	GRAPH
	Maths
	MolmecSupport
	PDB
	Peptides
	QSAR
	RTTI
	SimpleDownloaderHelper
	SysInfo
	VIEW

Classes
class	AddHydrogenProcessor
class	Addition
class	AdvancedElectrostatic
class	AmberBend
class	AmberEvaluation
class	AmberFF
class	AmberNonBonded
class	AmberStretch
class	AmberTorsion
class	AmiraMeshFile
class	AnisotropyShiftProcessor
class	AntechamberFile
class	AromaticBondsPredicate
class	AromaticityProcessor
	This processor provides methods for detection and assignment of aromaticity. More...
class	AromaticRingStacking
class	AssignBaseProcessor
	Only used for deriving interface. More...
class	AssignBondOrderProcessor
	Assignment of bond orders from topology information. More...
class	AssignChargeProcessor
class	AssignRadiusProcessor
class	AssignTypeNameProcessor
class	AssignTypeProcessor
class	AStarBondOrderStrategy
class	Atom
class	AtomBijection
class	AtomContainer
class	AtomContainerIteratorTraits
class	AtomicPolarizabilities
class	AtomInformationContent
class	AtomIteratorTraits
class	AtomNamePredicate
class	AtomTypePredicate
class	AtomTyper
class	AtomTypes
class	AtomVector
class	AutoDeletable
class	AxialPredicate
class	BackBonePredicate
class	BalabanIndexJ
class	BALLPlugin
class	BaseIterator
class	BendComponent
class	BidirectionalIterator
	Mutable bidirectional iterator. More...
class	BinaryFileAdaptor
class	BinaryFingerprintMethods
	This class provides efficient similarity calculation functionality for 2D binary fingerprints. More...
class	BinaryFunctor
class	BinaryPredicate
class	BinaryProcessor
class	BindingPocketProcessor
class	Bit
class	BitVector
class	Bond
class	BondOrderAssignment
	A solution to the bond order assignment problem. More...
class	BondOrderAssignmentStrategy
	Base class for bond order assignment algorithms. More...
class	BondPolarizabilities
class	BoundingBoxProcessor
class	BranchAndBoundBondOrderStrategy
class	Bruker1DFile
class	Bruker2DFile
class	BuildBondsProcessor
class	BurialDepth
class	BuriedPolar
class	CanonicalMD
class	CCP4File
class	Chain
class	ChainIteratorTraits
class	ChainPredicate
class	ChargePredicate
class	ChargeRuleProcessor
class	CharmmBend
class	CharmmEEF1
class	CharmmFF
class	CharmmImproperTorsion
class	CharmmNonBonded
class	CharmmStretch
class	CharmmTorsion
class	CHPI
class	CHPISlick
class	CIFFile
class	ClaverieParameter
class	ClearChargeProcessor
class	ClearRadiusProcessor
class	ClearShiftProcessor
class	Client
class	CommandlineParser
class	Comparator
class	ComposedEnergyProcessor
class	Composite
class	CompositeIteratorTraits
class	Conformation
class	Conformation4C1Predicate
class	ConformationSet
class	ConjugateGradientMinimizer
class	ConnectedComponentsProcessor
class	ConnectedToPredicate
class	ConnectivityBase
class	Constant
class	ConstantFunction
class	ConstBidirectionalIterator
class	ConstBinaryProcessor
class	ConstForwardIterator
class	Constraint
class	ConstRandomAccessIterator
class	ConstUnaryProcessor
class	CosineTorsion
class	CreateSpectrumProcessor
class	CrystalGenerator
class	CrystalInfo
class	CubicFunction
class	CubicSpline1D
class	CubicSpline2D
class	DCDFile
class	Density
class	Descriptor
class	DifferentiableScoringFunction
class	DiffGridBasedScoring
class	Directory
class	DisulfidBondProcessor
class	Division
class	DNAMutator
class	DockingAlgorithm
class	DockProblem
class	DockResult
class	DockResultFile
class	DoubleBondsPredicate
class	DoubleGene
class	DoubleParameter
struct	DoubleTraits
class	DSN6File
class	EdgeItem
class	EFShiftProcessor
class	Electrostatic
class	ElectrostaticPotentialCalculator
class	Element
class	ElementPredicate
class	Embeddable
class	EmpiricalHSShiftProcessor
class	EnergeticEvaluation
class	EnergyMinimizer
class	EnergyProcessor
class	Enumerator
class	EnumeratorIndex
class	EvolutionaryDocking
class	Experiment
class	Expression
class	ExpressionParser
class	ExpressionPredicate
class	ExpressionTree
class	Factory
class	FalsePredicate
class	FDPB
class	FermiBaseFunction
class	File
class	FileSystem
class	FlexDefinition
class	FlexibleMolecule
struct	FloatTraits
class	ForceField
class	ForceFieldComponent
class	ForceFieldEvaluation
class	ForceFieldParameters
class	FormalCharge
class	ForwardIterator
class	FPTBondOrderStrategy
class	Fragment
class	FragmentationalSolvation
class	FragmentDB
class	FragmentDistanceCollector
class	FragmentIteratorTraits
class	FresnoTypes
class	GAFFCESParser
class	GAFFTypeProcessor
class	GAMESSDatFile
class	GAMESSLogFile
class	GeneralizedBornModel
class	GenericGene
class	GenericMolFile
class	GenericParameter
class	GeneticAlgorithm
class	GeneticIndividual
class	GeometricCenterProcessor
class	GeometricFit
class	GlobalInitializer
class	Gradient
class	GraphEdge
class	GraphFace
class	GraphTriangle
class	GraphVertex
class	GridAnalysis
class	GridBasedScoring
class	GridedMM
class	GridedPLP
class	HaighMallionShiftProcessor
class	HashGrid3
class	HashGridBox3
class	HashMap
	HashMap class based on the STL map (containing serveral convenience functions) More...
class	HashSet
class	HBondProcessor
	Computation of hydrogen bonds from topology information. More...
class	HBondShiftProcessor
class	HINFile
class	HMOFile
class	HybridisationProcessor
class	HydrogenBond
class	HydrogenBondSlick
class	HydrophobicVdWSurface
class	ILPBondOrderStrategy
class	IMGDock
class	INIFile
class	InRingPredicate
class	JCAMPFile
class	JohnsonBoveyShiftProcessor
class	KCFFile
class	Kekuliser
class	KernelPredicate
	Kernel predicate class. More...
class	KernelPredicate< Atom >
class	KernelPredicate< Chain >
class	KernelPredicate< Fragment >
class	KernelPredicate< Molecule >
class	KernelPredicate< Protein >
class	KernelPredicate< Residue >
class	KGreedyBondOrderStrategy
class	LennardJones
class	Limits
class	Limits< bool >
class	Limits< char >
class	Limits< double >
class	Limits< float >
class	Limits< int >
class	Limits< long >
class	Limits< short >
class	Limits< signed char >
class	Limits< unsigned char >
class	Limits< unsigned int >
class	Limits< unsigned long >
class	Limits< unsigned short >
class	LinearBaseFunction
class	LineBasedFile
class	LineSearch
class	Lipophilic
class	List
class	LogP
class	LogStream
class	LogStreamBuf
class	LogStreamNotifier
struct	LongDoubleTraits
class	Mainframe
class	MeanAtomInformationContent
class	MicroCanonicalMD
class	MMFF94
struct	MMFF94AtomType
	Class to store the values of an atom type from MMFFPROP.PAR. More...
class	MMFF94AtomTypeEquivalences
class	MMFF94AtomTyper
class	MMFF94AtomTypes
class	MMFF94BendParameters
class	MMFF94ChargeProcessor
class	MMFF94ESParameters
class	MMFF94NonBonded
class	MMFF94OutOfPlaneBend
class	MMFF94ParametersBase
class	MMFF94PlaneParameters
class	MMFF94StretchBend
class	MMFF94StretchBendParameters
class	MMFF94StretchParameters
class	MMFF94Torsion
class	MMFF94TorsionParameters
class	MMFF94VDWParameters
class	MMScoring
class	MOL2File
class	MolDB
class	MolecularDynamics
class	MolecularGraph
class	MolecularInformation
class	MolecularInteractions
class	MolecularSimilarity
class	MolecularWeight
class	Molecule
class	MoleculeIteratorTraits
class	MoleculeObjectCreator
class	MoleculePredicate
class	MOLFile
class	MolFileFactory
class	MOPACInputFile
class	MOPACOutputFile
class	MPISupport
class	MutableConstant
class	MutablePower
class	Mutator
class	NamedProperty
class	NegativePolarVdWSurface
class	NegativeVdWSurface
class	NMRStarFile
	This class provides methods for reading and assigning chemical shifts. More...
class	NodeItem
class	NonpolarSolvation
class	NucleicAcid
class	NucleicAcidIteratorTraits
class	NucleicAcidPredicate
class	Nucleotide
class	NucleotideIteratorTraits
class	NucleotideMapping
class	NucleotidePredicate
class	NumberOfAromaticAtoms
class	NumberOfAromaticBonds
class	NumberOfAtoms
class	NumberOfBonds
class	NumberOfBondsPredicate
class	NumberOfBoron
class	NumberOfBromine
class	NumberOfCarbon
class	NumberOfChlorine
class	NumberOfDoubleBonds
class	NumberOfFlourine
class	NumberOfHeavyAtoms
class	NumberOfHeavyBonds
class	NumberOfHydrogen
class	NumberOfHydrogenBondAcceptors
class	NumberOfHydrogenBondDonors
class	NumberOfHydrophobicAtoms
class	NumberOfIodine
class	NumberOfNitrogen
class	NumberOfOxygen
class	NumberOfPhosphorus
class	NumberOfRotatableBonds
class	NumberOfRotatableSingleBonds
class	NumberOfSingleBonds
class	NumberOfSulfur
class	NumberOfTripleBonds
class	NumericalIntegrator
class	NumericalSAS
class	Object
class	ObjectCreator
class	Options
class	Pair6_12InteractionEnergyProcessor
class	Pair6_12RDFIntegrator
class	PairExpInteractionEnergyProcessor
class	PairExpRDFIntegrator
struct	ParameterDescription
class	Parameters
class	ParameterSection
class	ParamFile
class	ParsedFunction
class	PartialBondOrderAssignment
	A full or partial solution to the AStar-based bond order assignment problem. More...
class	PartialChargeBase
class	PartialChargeProcessor
class	Path
class	PB
class	PBScoring
class	PCMCavFreeEnergyProcessor
class	PDBAtom
class	PDBAtomIteratorTraits
class	PDBFile
class	PDBInfo
class	PDBRecords
class	Peak
class	PeakList
class	PeptideCapProcessor
	This processor adds ACE-N and NME-C caps to proteins. More...
class	PeriodicBoundary
class	PersistenceManager
class	PersistentObject
class	PharmacophoreConstraint
class	PiecewiseFunction
class	PiecewisePolynomial
class	PierottiCavFreeEnergyProcessor
class	PLP
class	PLPScoring
class	PluginHandler
class	PluginManager
class	Polarity
class	PolarSolvation
class	PolarVdWSurface
class	PoseClustering
	Computation of clusters of docking poses. More...
class	PositivePolarVdWSurface
class	PositiveVdWSurface
class	Potential1210
class	PreciseTime
class	PreferencesObject
class	PrincipalMomentOfInertia
class	PrincipalMomentOfInertiaX
class	PrincipalMomentOfInertiaY
class	PrincipalMomentOfInertiaZ
class	Processor
class	Product
class	PropertyManager
class	Protein
class	ProteinIteratorTraits
class	ProteinPredicate
class	PTE_
class	PubChemDownloader
	Downloads PubChem entries. More...
class	PyColorRGBAVector
class	PyCompositeList
class	PyDatasetVector
class	PyIndexList
class	PyInterpreter
class	QuadraticAngleBend
class	QuadraticBondStretch
class	QuadraticImproperTorsion
class	Quadruple
class	QuaternionGene
class	QuaternionParameter
class	RadialDistributionFunction
class	RadiusRuleProcessor
class	RandomAccessIterator
class	RandomCoilShiftProcessor
class	RandomEvaluation
class	RandomNumberGenerator
class	RDFIntegrator
class	RDFParameter
class	RDFSection
class	Receptor
class	Reciprocal
class	ReconstructFragmentProcessor
class	ReducedSurface
class	ReferenceArea
class	RegularExpression
class	ReissCavFreeEnergyProcessor
class	RelHydrophobicVdWSurface
class	RelNegativePartialCharge
class	RelNegativePolarVdWSurface
class	RelNegativeVdWSurface
class	RelNumberOfRotatableBonds
class	RelNumberOfRotatableSingleBonds
class	RelPolarVdWSurface
class	RelPositivePartialCharge
class	RelPositivePolarVdWSurface
class	RelPositiveVdWSurface
class	Rescorer
class	Rescoring
class	Rescoring1D
class	Rescoring3D
class	Rescoring4D
class	Residue
class	ResidueChecker
class	ResidueIDPredicate
class	ResidueIteratorTraits
class	ResiduePredicate
class	ResidueRotamerSet
class	ResidueTorsions
class	ResourceEntry
class	ResourceFile
class	Result
class	RGroupAssembler
class	RingAnalyser
	Methods for the analysis of the structure of ringsystems. More...
class	RingFinder
class	RingPerceptionProcessor
class	RMSDMinimizer
class	RombergIntegrator
class	Rotamer
class	RotamerLibrary
	Rotamer Library Class. More...
class	RotateBond
class	RotateBonds
class	RotationalEntropy
class	RSComputer
class	RSEdge
class	RSFace
class	RSVertex
class	RuleEvaluator
class	RuleProcessor
class	SASEdge
class	SASFace
class	SASTriangulator
class	SASVertex
class	ScoreGridSet
class	ScoringBaseFunction
class	ScoringComponent
class	ScoringFunction
class	ScoringOptimizer
class	SCWRLRotamerFile
	Reads Dunbrack/SCWRL rotamer library files. More...
class	SDFile
class	SDGenerator
class	SecondaryStructure
class	SecondaryStructureIteratorTraits
class	SecondaryStructurePredicate
class	SecondaryStructureProcessor
	Secondary structure extraction from 3D structure. More...
class	Selectable
class	SelectedPredicate
class	Selector
class	SESComputer
class	SESEdge
class	SESFace
class	SESSingularityCleaner
class	SESTriangulator
class	SESVertex
class	ShiftedLVMMMinimizer
class	ShiftModel
class	ShiftModel1D
class	ShiftModel2D
class	ShiftModule
class	SideChainOptimizer
class	SideChainPlacementProcessor
class	SimpleBase
class	SimpleDownloader
class	SimpleExperiment1D
class	SingleBondsPredicate
class	SizeOfSSSR
class	SLICKEnergy
class	SLICKScore
class	SmartsMatcher
class	SmartsParser
class	SMARTSPredicate
class	SmilesParser
class	SnapShot
class	SnapShotManager
class	Solvation
class	SolventAccessibleSurface
class	SolventAtomDescriptor
class	SolventDescriptor
class	SolventExcludedSurface
class	SolventParameter
class	SolventPredicate
struct	SortedPosition2
struct	SortedPosition3
class	Sp2HybridizedPredicate
class	Sp3HybridizedPredicate
class	SpaceGroupParameters
class	Spectrum
class	SpHybridizedPredicate
class	SquareFunction
class	StaticLigandFragment
class	SteepestDescentMinimizer
class	StrangLBFGSMinimizer
class	StretchComponent
class	String
class	StringHashMap
class	StructureMapper
class	StructurePreparer
class	Substring
class	Subtraction
class	SurfaceBase
class	SurfaceProcessor
class	System
class	TAngle
class	TBox3
class	TCircle3
class	TContour
class	TContourLine
class	TContourSurface
class	TCPIOStream
class	TCPServer
class	TCPServerThread
class	Templates
class	TextPersistenceManager
class	TFFT1D
class	TFFT2D
class	TFFT3D
class	Timer
class	TimeStamp
class	TLine3
class	TMatrix4x4
	Default Type. More...
class	TMutex
class	TMutex< QMutex >
class	TMutexLocker
class	TotalNegativePartialCharge
class	TotalPositivePartialCharge
class	TPlane3
class	TQuaternion
class	TrajectoryFile
class	TrajectoryFileFactory
class	TransformationManager
class	TransformationProcessor
class	TranslationProcessor
class	TReadLocker
class	TReadWriteLock
class	TReadWriteLock< QReadWriteLock >
class	TreeWidth
class	TreeWidthImplementation
class	TRegularData1D
class	TRegularData2D
class	TRegularData3D
class	Triangle
class	TriangleEdge
class	TrianglePoint
class	TriangulatedSAS
class	TriangulatedSES
class	TriangulatedSphere
class	TriangulatedSurface
class	Triple
class	TripleBondsPredicate
class	TRRFile
class	TruePredicate
class	TSimpleBox3
class	TSimpleMolecularGraph
class	TSphere3
class	TSurface
class	TVector2
class	TVector3
class	TVector4
class	TWriteLocker
class	TypenameRuleProcessor
class	TypeRuleProcessor
class	UCK
class	UhligCavFreeEnergyProcessor
class	UnaryFunctor
class	UnaryPredicate
class	UnaryProcessor
class	VanDerWaals
class	VanDerWaalsSlick
class	VdWSurface
class	VdWVolume
class	VertexAdjacency
class	VertexAdjacencyEquality
class	Visitor
class	XDRPersistenceManager
class	XYZFile
class	ZagrebIndex

Typedefs
typedef int(*	ComparatorType )(const void *, const void *)
typedef TContour< float >	Contour
typedef TContourLine< float >	ContourLine
typedef Index	FacetArray [256][12]
typedef TContourSurface< float >	ContourSurface
	Default type. More...
typedef boost::adjacency_list < boost::vecS, boost::vecS, boost::undirectedS, boost::property < boost::vertex_atom_ptr_t, const Atom * > , boost::property < boost::edge_bond_ptr_t, const Bond * > >	MolecularGraphBase
typedef GRAPH::GraphTraits < MolecularGraph >	MolecularGraphTraits
typedef MolecularGraph::EditableGraph	EditableMolecularGraph
typedef TRegularData1D< float >	RegularData1D
typedef TRegularData2D< float >	RegularData2D
typedef TRegularData3D< float >	RegularData3D
typedef HashSet< String >	StringHashSet
typedef FlexibleMolecule	Ligand
typedef std::list < EnergyProcessor * >	EnergyProcessorList
typedef BidirectionalIterator < Composite, Fragment, Composite::CompositeIterator, FragmentIteratorTraits >	FragmentIterator
typedef ConstBidirectionalIterator < Composite, Fragment, Composite::CompositeIterator, FragmentIteratorTraits >	FragmentConstIterator
typedef std::reverse_iterator < FragmentIterator >	FragmentReverseIterator
typedef std::reverse_iterator < FragmentConstIterator >	FragmentConstReverseIterator
typedef BidirectionalIterator < Composite, Molecule, Composite::CompositeIterator, MoleculeIteratorTraits >	MoleculeIterator
typedef ConstBidirectionalIterator < Composite, Molecule, Composite::CompositeIterator, MoleculeIteratorTraits >	MoleculeConstIterator
typedef std::reverse_iterator < MoleculeIterator >	MoleculeReverseIterator
typedef std::reverse_iterator < MoleculeConstIterator >	MoleculeConstReverseIterator
typedef BidirectionalIterator < Composite, NucleicAcid, Composite::CompositeIterator, NucleicAcidIteratorTraits >	NucleicAcidIterator
typedef ConstBidirectionalIterator < Composite, NucleicAcid, Composite::CompositeIterator, NucleicAcidIteratorTraits >	NucleicAcidConstIterator
typedef std::reverse_iterator < NucleicAcidIterator >	NucleicAcidReverseIterator
typedef std::reverse_iterator < NucleicAcidConstIterator >	NucleicAcidConstReverseIterator
typedef BidirectionalIterator < Composite, Nucleotide, Composite::CompositeIterator, NucleotideIteratorTraits >	NucleotideIterator
typedef ConstBidirectionalIterator < Composite, Nucleotide, Composite::CompositeIterator, NucleotideIteratorTraits >	NucleotideConstIterator
typedef std::reverse_iterator < NucleotideIterator >	NucleotideReverseIterator
typedef std::reverse_iterator < NucleotideConstIterator >	NucleotideConstReverseIterator
typedef BidirectionalIterator < Composite, Protein, Composite::CompositeIterator, ProteinIteratorTraits >	ProteinIterator
typedef ConstBidirectionalIterator < Composite, Protein, Composite::CompositeIterator, ProteinIteratorTraits >	ProteinConstIterator
typedef std::reverse_iterator < ProteinIterator >	ProteinReverseIterator
typedef std::reverse_iterator < ProteinConstIterator >	ProteinConstReverseIterator
typedef BidirectionalIterator < Composite, Residue, Composite::CompositeIterator, ResidueIteratorTraits >	ResidueIterator
typedef ConstBidirectionalIterator < Composite, Residue, Composite::CompositeIterator, ResidueIteratorTraits >	ResidueConstIterator
typedef std::reverse_iterator < ResidueIterator >	ResidueReverseIterator
typedef std::reverse_iterator < ResidueConstIterator >	ResidueConstReverseIterator
typedef BidirectionalIterator < Composite, SecondaryStructure, Composite::CompositeIterator, SecondaryStructureIteratorTraits >	SecondaryStructureIterator
typedef ConstBidirectionalIterator < Composite, SecondaryStructure, Composite::CompositeIterator, SecondaryStructureIteratorTraits >	SecondaryStructureConstIterator
typedef std::reverse_iterator < SecondaryStructureIterator >	SecondaryStructureReverseIterator
typedef std::reverse_iterator < SecondaryStructureConstIterator >	SecondaryStructureConstReverseIterator
typedef TAngle< float >	Angle
typedef TBox3< float >	Box3
typedef TCircle3< float >	Circle3
typedef std::complex < BALL_COMPLEX_PRECISION >	Complex
typedef TFFT1D < BALL_FFTW_DEFAULT_TRAITS >	FFT1D
typedef TFFT2D < BALL_FFTW_DEFAULT_TRAITS >	FFT2D
typedef TFFT3D < BALL_FFTW_DEFAULT_TRAITS >	FFT3D
typedef TLine3< float >	Line3
typedef TMatrix4x4< float >	Matrix4x4
typedef std::vector< double >	Coefficients
typedef std::pair< double, double >	Interval
typedef TPlane3< float >	Plane3
typedef TQuaternion< float >	Quaternion
typedef TSphere3< float >	Sphere3
typedef TSurface< float >	Surface
typedef TVector2< float >	Vector2
typedef TVector3< float >	Vector3
typedef TVector4< float >	Vector4
typedef std::list < RegularData3D * >	RegularData3DList
typedef std::vector < Eigen::MatrixXd, Eigen::aligned_allocator < Eigen::MatrixXd > >	MatrixVector
typedef vector< vector< vector < double > > >	ScoreGrid
typedef std::list< std::pair < Atom *, Atom * > >	AtomPairList
typedef std::vector< std::pair < Atom *, Atom * > >	AtomPairVector
typedef TSimpleMolecularGraph < Index, Index >	SimpleMolecularGraph
typedef TMutex < BALL_DEFAULT_MUTEX_TYPE >	Mutex
typedef TReadWriteLock < BALL_DEFAULT_READWRITELOCK_TYPE >	ReadWriteLock
typedef TMutexLocker < BALL_DEFAULT_MUTEXLOCKER_TYPE, BALL_DEFAULT_MUTEX_TYPE >	MutexLocker
typedef TReadLocker < BALL_DEFAULT_READLOCKER_TYPE, BALL_DEFAULT_READWRITELOCK_TYPE >	ReadLocker
typedef TWriteLocker < BALL_DEFAULT_WRITELOCKER_TYPE, BALL_DEFAULT_READWRITELOCK_TYPE >	WriteLocker
Type aliases defined by BALL.
These predefined types are used in BALL for portability and comprehensibility.
typedef BALL_INDEX_TYPE	Distance
typedef BALL_SIZE_TYPE	Handle
typedef BALL_INDEX_TYPE	Index
typedef BALL_SIZE_TYPE	Size
typedef time_t	Time
typedef BALL_SIZE_TYPE	HashIndex
typedef BALL_SIZE_TYPE	Position
typedef float	Real
typedef double	DoubleReal
typedef BALL_SIZE_TYPE	Property
typedef BALL_INDEX_TYPE	ErrorCode
typedef unsigned char	Byte
typedef BALL_ULONG64_TYPE	LongSize
typedef BALL_LONG64_TYPE	LongIndex
typedef BALL_POINTERSIZEUINT_TYPE	PointerSizeUInt
Properties
typedef std::vector < NamedProperty >::iterator	NamedPropertyIterator
Iterator type definitions for the various AtomContainerIterators.
typedef BidirectionalIterator < Composite, AtomContainer, Composite::CompositeIterator, AtomContainerIteratorTraits >	AtomContainerIterator
typedef ConstBidirectionalIterator < Composite, AtomContainer, Composite::CompositeIterator, AtomContainerIteratorTraits >	AtomContainerConstIterator
typedef std::reverse_iterator < AtomContainerIterator >	AtomContainerReverseIterator
	A mutable reverse bidirectional iterator for the AtomContainer class. More...
typedef std::reverse_iterator < AtomContainerConstIterator >	AtomContainerConstReverseIterator
	A constant reverse bidirectional iterator for the AtomContainer class. More...
Iterator type definitions for the various AtomIterators
typedef BidirectionalIterator < Composite, Atom, Composite::CompositeIterator, AtomIteratorTraits >	AtomIterator
typedef ConstBidirectionalIterator < Composite, Atom, Composite::CompositeIterator, AtomIteratorTraits >	AtomConstIterator
typedef std::reverse_iterator < AtomIterator >	AtomReverseIterator
	A mutable reverse bidirectional iterator for the Atom class. More...
typedef std::reverse_iterator < AtomConstIterator >	AtomConstReverseIterator
	A constant reverse bidirectional iterator for the Atom class. More...
Typedefs for the various BondIterators
typedef Atom::BondIterator	AtomBondIterator
typedef Atom::BondConstIterator	AtomBondConstIterator
typedef Atom::BondReverseIterator	AtomBondReverseIterator
typedef Atom::BondConstReverseIterator	AtomBondConstReverseIterator
Iterator type definitions for the various ChainIterators
typedef BidirectionalIterator < Composite, Chain, Composite::CompositeIterator, ChainIteratorTraits >	ChainIterator
	A mutable bidirectional iterator for the Chain class. More...
typedef ConstBidirectionalIterator < Composite, Chain, Composite::CompositeIterator, ChainIteratorTraits >	ChainConstIterator
	A constant bidirectional iterator for the Chain class. More...
typedef std::reverse_iterator < ChainIterator >	ChainReverseIterator
	A mutable reverse bidirectional iterator for the Chain class. More...
typedef std::reverse_iterator < ChainConstIterator >	ChainConstReverseIterator
	A constant reverse bidirectional iterator for the Chain class. More...
typedef std::list< Atom * >	AtomList
typedef std::list< Bond * >	BondList
typedef std::list < AtomContainer * >	AtomContainerList
typedef std::list< PDBAtom * >	PDBAtomList
typedef std::list< Residue * >	ResidueList
typedef std::list< Fragment * >	FragmentList
typedef std::list< Molecule * >	MoleculeList
typedef std::list< Protein * >	ProteinList
typedef std::list < SecondaryStructure * >	SecondaryStructureList
typedef std::list< Chain * >	ChainList
typedef std::list< Nucleotide * >	NucleotideList
typedef std::list< NucleicAcid * >	NucleicAcidList
Iterator type definitions for the various PDBAtomIterators
typedef BidirectionalIterator < Composite, PDBAtom, Composite::CompositeIterator, PDBAtomIteratorTraits >	PDBAtomIterator
	A mutable bidirectional iterator for the PDBAtom class. More...
typedef ConstBidirectionalIterator < Composite, PDBAtom, Composite::CompositeIterator, PDBAtomIteratorTraits >	PDBAtomConstIterator
	A constant bidirectional iterator for the PDBAtom class. More...
typedef std::reverse_iterator < PDBAtomIterator >	PDBAtomReverseIterator
	A mutable reverse bidirectional iterator for the PDBAtom class. More...
typedef std::reverse_iterator < PDBAtomConstIterator >	PDBAtomConstReverseIterator
	A constant reverse bidirectional iterator for the PDBAtom class. More...
KernelPredicates Kernel predicates
This chapter describes a set of unary predicates acting on Composite instances, that can be used to identify the class type of a composite at runtime. This predicates are functionally similar to the RTTI:isKindOf function. They decide whether a given composite is an instance of a certain class (or of a class derived thereof). For instance, the application of a MoleculePredicate to a composite will yield true, if the given composite was an instance of Molecule (or Protein , as Protein is derived from Molecule). Otherwise false is returned. Each KernelPredicate possesses three methods: -operator (const Composite&) -operator (const Composite&) const The two operators are functionally identical (two methods are needed, because the class is derived from TUnaryPredicate and we want to make sure both methods are overwritten). operator() returns true, if the given composite is a kind of the class corresponding to the respective predicate, false otherwise. See also UnaryPredicate RTTI
typedef UnaryPredicate< Composite >	KernelPredicateType
Convenience typedefs
typedef Experiment< PeakList1D >	Experiment1D
typedef Experiment< PeakList3D >	Experiment3D
typedef Peak< float >	Peak1D
typedef Peak< Vector2 >	Peak2D
typedef Peak< Vector3 >	Peak3D
Standard typedefs
typedef PeakList< Peak< float > >	PeakList1D
	1D peak list More...
typedef PeakList< Peak< Vector2 > >	PeakList2D
	2D peak list More...
typedef PeakList< Peak< Vector3 > >	PeakList3D
	3D peak list More...
typedef Spectrum < RegularData1D, Peak1D >	Spectrum1D
	One-dimensional spectrum. More...
typedef Spectrum < RegularData2D, Peak2D >	Spectrum2D
	Two-dimensional spectrum. More...
typedef Spectrum < RegularData3D, Peak3D >	Spectrum3D
	Three-dimensional spectrum. More...

Enumerations
enum	ASCII {   ASCII__BACKSPACE = '\b', ASCII__BELL = '\a', ASCII__CARRIAGE_RETURN = '\r', ASCII__HORIZONTAL_TAB = '\t',   ASCII__NEWLINE = '\n', ASCII__RETURN = ASCII__NEWLINE, ASCII__SPACE = ' ', ASCII__TAB = ASCII__HORIZONTAL_TAB,   ASCII__VERTICAL_TAB = '\v', ASCII__COLON = ':', ASCII__COMMA = ',', ASCII__EXCLAMATION_MARK = '!',   ASCII__POINT = '.', ASCII__QUESTION_MARK = '?', ASCII__SEMICOLON = ';' }

Functions
BALL_EXPORT std::ostream &	operator<< (std::ostream &os, const Exception::GeneralException &e)
BALL_EXPORT string	streamClassName (const std::type_info &t)
template<typename Container , typename DataType , typename Position , typename Traits >
ConstRandomAccessIterator < Container, DataType, Position, Traits >	operator+ (Distance distance, const ConstRandomAccessIterator< Container, DataType, Position, Traits > &iterator)
template<>
BALL_EXPORT HashIndex	Hash (const std::pair< Position, Position > &p)
BALL_EXPORT const FacetArray &	getContourSurfaceFacetData (double threshold)
BALL_EXPORT bool	operator== (const String &s1, const String &s2)
BALL_EXPORT bool	operator!= (const String &s1, const String &s2)
BALL_EXPORT bool	operator< (const String &s1, const String &s2)
BALL_EXPORT bool	operator<= (const String &s1, const String &s2)
BALL_EXPORT bool	operator> (const String &s1, const String &s2)
BALL_EXPORT bool	operator>= (const String &s1, const String &s2)
BALL_EXPORT String	operator+ (const String &s1, const string &s2)
	Concatenates two strings. More...
BALL_EXPORT String	operator+ (const string &s1, const String &s2)
	Concatenates two strings. More...
BALL_EXPORT String	operator+ (const String &s1, const String &s2)
	Concatenates two strings. More...
BALL_EXPORT String	operator+ (const String &s1, const char *char_ptr)
	Concatenates a string and a C type string. More...
BALL_EXPORT String	operator+ (const char *char_ptr, const String &s)
	Concatenates a C type string and a string. More...
BALL_EXPORT String	operator+ (const String &s, char c)
	Concatenates a string and a character. More...
BALL_EXPORT String	operator+ (char c, const String &s)
	Concatenates a character and a string. More...
std::ostream &	operator<< (std::ostream &out, const DockResult &dock_res) throw ()
std::istream &	operator>> (std::istream &in, DockResult &dock_res) throw ()
BALL_EXPORT double	calculateACE (const AtomContainer &atom_container, const string &type_filename="energy/ACE_types.dat", const string &parameter_filename="energy/ACE_parameters.dat")
BALL_EXPORT double	calculateCoulomb (const AtomContainer &atoms)
BALL_EXPORT double	calculateDistanceCoulomb (const AtomContainer &fragment)
BALL_EXPORT HashIndex	Hash (const PDBFile::ResidueQuadruple &quadruple)
BALL_EXPORT std::ostream &	operator<< (std::ostream &s, const Quadruple< String, PDB::Character, PDB::Integer, PDB::AChar > &)
template<class AtomContainerType >
void	cloneBonds (const AtomContainerType &atom_container, AtomContainerType &cloned)
template<class NucleotideContainerType >
const Nucleotide *	get5Prime (const NucleotideContainerType &nucleotide_container)
template<class NucleotideContainerType >
const Nucleotide *	get3Prime (const NucleotideContainerType &nucleotide_container)
BALL_EXPORT std::ostream &	operator<< (std::ostream &s, const Element &element)
template<class ResidueContainerType >
const Residue *	getNTerminal (const ResidueContainerType &residue_container)
template<class ResidueContainerType >
const Residue *	getCTerminal (const ResidueContainerType &residue_container)
template<typename T >
BALL_INLINE T	getDeterminant_ (const T *m, Size dim)
template<typename T >
T	getDeterminant (const T *m, Size dim)
template<typename T >
BALL_INLINE T	getDeterminant2 (const T *m)
template<typename T >
BALL_INLINE T	getDeterminant2 (const T &m00, const T &m01, const T &m10, const T &m11)
template<typename T >
BALL_INLINE T	getDeterminant3 (const T *m)
template<typename T >
BALL_INLINE T	getDeterminant3 (const T &m00, const T &m01, const T &m02, const T &m10, const T &m11, const T &m12, const T &m20, const T &m21, const T &m22)
template<typename T >
bool	SolveSystem (const T *m, T *x, const Size dim)
template<typename T >
BALL_INLINE bool	SolveSystem2 (const T &a1, const T &b1, const T &c1, const T &a2, const T &b2, const T &c2, T &x1, T &x2)
template<typename T >
short	SolveQuadraticEquation (const T &a, const T &b, const T &c, T &x1, T &x2)
template<typename T >
BALL_INLINE TVector3< T >	GetPartition (const TVector3< T > &a, const TVector3< T > &b)
template<typename T >
BALL_INLINE TVector3< T >	GetPartition (const TVector3< T > &a, const TVector3< T > &b, const T &r, const T &s)
template<typename T >
BALL_INLINE T	GetDistance (const TVector3< T > &a, const TVector3< T > &b)
template<typename T >
BALL_INLINE T	GetDistance (const TLine3< T > &line, const TVector3< T > &point)
template<typename T >
BALL_INLINE T	GetDistance (const TVector3< T > &point, const TLine3< T > &line)
template<typename T >
T	GetDistance (const TLine3< T > &a, const TLine3< T > &b)
template<typename T >
BALL_INLINE T	GetDistance (const TVector3< T > &point, const TPlane3< T > &plane)
template<typename T >
BALL_INLINE T	GetDistance (const TPlane3< T > &plane, const TVector3< T > &point)
template<typename T >
BALL_INLINE T	GetDistance (const TLine3< T > &line, const TPlane3< T > &plane)
template<typename T >
BALL_INLINE T	GetDistance (const TPlane3< T > &plane, const TLine3< T > &line)
template<typename T >
BALL_INLINE T	GetDistance (const TPlane3< T > &a, const TPlane3< T > &b)
template<typename T >
BALL_INLINE bool	GetAngle (const TVector3< T > &a, const TVector3< T > &b, TAngle< T > &intersection_angle)
template<typename T >
BALL_INLINE bool	GetAngle (const TLine3< T > &a, const TLine3< T > &b, TAngle< T > &intersection_angle)
template<typename T >
BALL_INLINE bool	GetAngle (const TPlane3< T > &plane, const TVector3< T > &vector, TAngle< T > &intersection_angle)
template<typename T >
BALL_INLINE bool	GetAngle (const TVector3< T > &vector, const TPlane3< T > &plane, TAngle< T > &intersection_angle)
template<typename T >
BALL_INLINE bool	GetAngle (const TPlane3< T > &plane, const TLine3< T > &line, TAngle< T > &intersection_angle)
template<typename T >
BALL_INLINE bool	GetAngle (const TLine3< T > &line, const TPlane3< T > &plane, TAngle< T > &intersection_angle)
template<typename T >
BALL_INLINE bool	GetAngle (const TPlane3< T > &a, const TPlane3< T > &b, TAngle< T > &intersection_angle)
template<typename T >
bool	GetIntersection (const TLine3< T > &a, const TLine3< T > &b, TVector3< T > &point)
template<typename T >
BALL_INLINE bool	GetIntersection (const TPlane3< T > &plane, const TLine3< T > &line, TVector3< T > &intersection_point)
template<typename T >
BALL_INLINE bool	GetIntersection (const TLine3< T > &line, const TPlane3< T > &plane, TVector3< T > &intersection_point)
template<typename T >
bool	GetIntersection (const TPlane3< T > &plane1, const TPlane3< T > &plane2, TLine3< T > &line)
template<typename T >
bool	GetIntersection (const TSphere3< T > &sphere, const TLine3< T > &line, TVector3< T > &intersection_point1, TVector3< T > &intersection_point2)
template<typename T >
BALL_INLINE bool	GetIntersection (const TLine3< T > &line, const TSphere3< T > &sphere, TVector3< T > &intersection_point1, TVector3< T > &intersection_point2)
template<typename T >
bool	GetIntersection (const TSphere3< T > &sphere, const TPlane3< T > &plane, TCircle3< T > &intersection_circle)
template<typename T >
BALL_INLINE bool	GetIntersection (const TPlane3< T > &plane, const TSphere3< T > &sphere, TCircle3< T > &intersection_circle)
template<typename T >
bool	GetIntersection (const TSphere3< T > &a, const TSphere3< T > &b, TCircle3< T > &intersection_circle)
template<class T >
bool	GetIntersection (const TSphere3< T > &s1, const TSphere3< T > &s2, const TSphere3< T > &s3, TVector3< T > &p1, TVector3< T > &p2, bool test=true)
template<typename T >
BALL_INLINE bool	isCollinear (const TVector3< T > &a, const TVector3< T > &b)
template<typename T >
BALL_INLINE bool	isComplanar (const TVector3< T > &a, const TVector3< T > &b, const TVector3< T > &c)
template<typename T >
BALL_INLINE bool	isComplanar (const TVector3< T > &a, const TVector3< T > &b, const TVector3< T > &c, const TVector3< T > &d)
template<typename T >
BALL_INLINE bool	isOrthogonal (const TVector3< T > &a, const TVector3< T > &b)
template<typename T >
BALL_INLINE bool	isOrthogonal (const TVector3< T > &vector, const TLine3< T > &line)
template<typename T >
BALL_INLINE bool	isOrthogonal (const TLine3< T > &line, const TVector3< T > &vector)
template<typename T >
BALL_INLINE bool	isOrthogonal (const TLine3< T > &a, const TLine3< T > &b)
template<typename T >
BALL_INLINE bool	isOrthogonal (const TVector3< T > &vector, const TPlane3< T > &plane)
template<typename T >
BALL_INLINE bool	isOrthogonal (const TPlane3< T > &plane, const TVector3< T > &vector)
template<typename T >
BALL_INLINE bool	isOrthogonal (const TPlane3< T > &a, const TPlane3< T > &b)
template<typename T >
BALL_INLINE bool	isIntersecting (const TVector3< T > &point, const TLine3< T > &line)
template<typename T >
BALL_INLINE bool	isIntersecting (const TLine3< T > &line, const TVector3< T > &point)
template<typename T >
BALL_INLINE bool	isIntersecting (const TLine3< T > &a, const TLine3< T > &b)
template<typename T >
BALL_INLINE bool	isIntersecting (const TVector3< T > &point, const TPlane3< T > &plane)
template<typename T >
BALL_INLINE bool	isIntersecting (const TPlane3< T > &plane, const TVector3< T > &point)
template<typename T >
BALL_INLINE bool	isIntersecting (const TLine3< T > &line, const TPlane3< T > &plane)
template<typename T >
BALL_INLINE bool	isIntersecting (const TPlane3< T > &plane, const TLine3< T > &line)
template<typename T >
BALL_INLINE bool	isIntersecting (const TPlane3< T > &a, const TPlane3< T > &b)
template<typename T >
BALL_INLINE bool	isParallel (const TLine3< T > &line, const TPlane3< T > &plane)
template<typename T >
BALL_INLINE bool	isParallel (const TPlane3< T > &plane, const TLine3< T > &line)
template<typename T >
BALL_INLINE bool	isParallel (const TPlane3< T > &a, const TPlane3< T > &b)
template<typename T >
TAngle< T >	getOrientedAngle (const T &ax, const T &ay, const T &az, const T &bx, const T &by, const T &bz, const T &nx, const T &ny, const T &nz)
template<typename T >
BALL_INLINE TAngle< T >	getOrientedAngle (const TVector3< T > &a, const TVector3< T > &b, const TVector3< T > &normal)
template<typename T >
TAngle< T >	getTorsionAngle (const T &ax, const T &ay, const T &az, const T &bx, const T &by, const T &bz, const T &cx, const T &cy, const T &cz, const T &dx, const T &dy, const T &dz)
template<typename T >
BALL_INLINE TAngle< T >	operator* (const T &val, const TAngle< T > &angle)
template<typename T >
BALL_INLINE TAngle< T >	operator+ (const T &val, const TAngle< T > &angle)
template<typename T >
BALL_INLINE TAngle< T >	operator- (const T &val, const TAngle< T > &angle)
template<typename T >
std::istream &	operator>> (std::istream &s, TAngle< T > &angle)
template<typename T >
std::ostream &	operator<< (std::ostream &s, const TAngle< T > &angle)
template<typename ComplexTraits >
const RegularData1D &	operator<< (RegularData1D &to, const TFFT1D< ComplexTraits > &from)
template<typename ComplexTraits >
const TRegularData2D< typename TFFT2D< ComplexTraits > ::Complex > &	operator<< (TRegularData2D< typename TFFT2D< ComplexTraits >::Complex > &to, const TFFT2D< ComplexTraits > &from)
template<typename ComplexTraits >
const RegularData2D &	operator<< (RegularData2D &to, const TFFT2D< ComplexTraits > &from)
template<typename ComplexTraits >
const TRegularData3D< typename TFFT3D< ComplexTraits > ::Complex > &	operator<< (TRegularData3D< typename TFFT3D< ComplexTraits >::Complex > &to, const TFFT3D< ComplexTraits > &from)
template<typename ComplexTraits >
const RegularData3D &	operator<< (RegularData3D &to, const TFFT3D< ComplexTraits > &from)
template<typename T >
TMatrix4x4< T >	operator* (const T &scalar, const TMatrix4x4< T > &m)
template<typename T >
TVector3< T >	operator* (const TMatrix4x4< T > &matrix, const TVector3< T > &vector)
template<typename T >
std::istream &	operator>> (std::istream &s, TQuaternion< T > &q)
template<typename T >
std::ostream &	operator<< (std::ostream &s, const TQuaternion< T > &q)
template<typename T >
BALL_INLINE TVector4< T >	operator* (const T &scalar, const TVector4< T > &v)
template<typename T >
BALL_INLINE TVector4< T >	operator* (const TVector4< T > &v, const T &scalar)
::std::ostream &	operator<< (::std::ostream &os, const SnapShot &ss)
	Output stream operator for SnapShots. More...
::std::istream &	operator>> (::std::istream &is, SnapShot &ss)
	Input stream operator for SnapShots. More...
Position	getMMFF94Index (Position atom_type1, Position atom_type2)
BALL_EXPORT const RegularData1D &	operator<< (RegularData1D &data, const PeakList1D &peak_list)
template<typename PositionType >
std::ostream &	operator<< (std::ostream &os, const Peak< PositionType > &peak)
std::ostream &	operator<< (std::ostream &os, const BALL::ShiftModel2D &shiftmodel)
template<typename DataT , typename PeakT , typename PositionT >
double	operator- (const Spectrum< DataT, PeakT, PositionT > &s1, const Spectrum< DataT, PeakT, PositionT > &s2)
template<typename DataT , typename PeakT , typename PositionT >
std::ostream &	operator<< (std::ostream &os, const Spectrum< DataT, PeakT, PositionT > &spectrum)
template<typename DataT , typename PeakT , typename PositionT >
std::istream &	operator>> (std::istream &is, Spectrum< DataT, PeakT, PositionT > &spectrum)
PyObject *	pyMapBALLObjectToSip (Composite &object)
BALL_EXPORT void	calculateResidueChiAngles (const Protein &protein, HashMap< const Residue *, float > &residue_angles)
BALL_EXPORT void	calculateResidueChiAngles (const Chain &fragment, HashMap< const Residue *, float > &residue_angles)
BALL_EXPORT float	calculateResidueChiAngles (const Residue &residue)
BALL_EXPORT void	calculateResidueChi2Angles (const Protein &protein, HashMap< const Residue *, float > &residue_angles)
BALL_EXPORT void	calculateResidueChi2Angles (const Chain &fragment, HashMap< const Residue *, float > &residue_angles)
BALL_EXPORT float	calculateResidueChi2Angles (const Residue &residue)
static double	getMean (const list< double > &v)
static double	getCovariance (const list< double > &v1, const list< double > &v2, double mean1, double mean2)
static double	getStddev (const list< double > &m, double mean)
static double	getSumOfSquares (const list< double > &m, double mean)
BALL_EXPORT TRegularData3D < char > *	calculateSESGrid (const Vector3 &lower, const Vector3 &upper, float spacing, const System &system, float probe_radius)
BALL_EXPORT TRegularData3D < char > *	calculateSASGrid (const Vector3 &lower, const Vector3 &upper, float spacing, const System &system, float probe_radius)
BALL_EXPORT double	calculateOoiEnergy (AtomContainer &atoms)
BALL_EXPORT float	calculateSESAtomAreas (const AtomContainer &fragment, HashMap< const Atom *, float > &atom_areas, float probe_radius=1.5)
BALL_EXPORT float	calculateSESArea (const AtomContainer &fragment, float probe_radius=1.5)
BALL_EXPORT float	calculateSESVolume (const AtomContainer &fragment, float probe_radius=1.5)
template<typename Node , typename Edge >
std::ostream &	operator<< (std::ostream &os, const TSimpleMolecularGraph< Node, Edge > &G)
template<typename T >
void	swapBytes (T &t)
template<>
BALL_EXPORT void	swapBytes (unsigned short &)
template<>
BALL_EXPORT void	swapBytes (short &)
template<>
BALL_EXPORT void	swapBytes (unsigned int &)
template<>
BALL_EXPORT void	swapBytes (int &)
template<>
BALL_EXPORT void	swapBytes (unsigned long &)
template<>
BALL_EXPORT void	swapBytes (long &)
template<>
BALL_EXPORT void	swapBytes (float &)
template<>
BALL_EXPORT void	swapBytes (double &)
template<typename T >
std::ostream &	operator<< (std::ostream &os, const BinaryFileAdaptor< T > &data)
	Output stream for BinaryFileAdaptors. More...
template<typename T >
std::istream &	operator>> (std::istream &is, BinaryFileAdaptor< T > &data)
	Input stream for BinaryFileAdaptors. More...
BALL_EXPORT void	sleepFor (Size mseconds)
Specialized Hash Functions.
BALL_EXPORT HashIndex	hashPointer (void *const ptr)
BALL_EXPORT HashIndex	hashString (const char *str)
BALL_EXPORT HashIndex	hashPJWString (const char *str)
BALL_EXPORT HashIndex	hashElfString (const char *str)
template<typename T >
HashIndex	Hash (const T &key)
BALL_EXPORT HashIndex	Hash (const string &s)
BALL_EXPORT HashIndex	Hash (const String &s)
BALL_EXPORT HashIndex	Hash (void *const &ptr)
BALL_EXPORT HashIndex	getNextPrime (HashIndex l)
BALL_EXPORT std::ostream &	operator<< (std::ostream &os, const PreciseTime &time)
BALL_EXPORT std::ostream &	operator<< (std::ostream &os, const TimeStamp &stamp)
Stream I/O
template<typename ValueType >
std::ostream &	operator<< (std::ostream &os, const TRegularData1D< ValueType > &data)
	Output operator. More...
template<typename ValueType >
std::istream &	operator>> (std::istream &is, TRegularData1D< ValueType > &grid)
	Input operator. More...
template<typename ValueType >
std::ostream &	operator<< (std::ostream &os, const TRegularData2D< ValueType > &data)
	Output operator. More...
template<typename ValueType >
std::istream &	operator>> (std::istream &is, TRegularData2D< ValueType > &grid)
	Input operator. More...
template<typename ValueType >
std::ostream &	operator<< (std::ostream &os, const TRegularData3D< ValueType > &grid)
	Output operator. More...
template<typename ValueType >
std::istream &	operator>> (std::istream &is, TRegularData3D< ValueType > &grid)
	Input operator. More...
BALL_EXPORT AtomList	atoms (const AtomContainer &fragment, const String &expression=String())
BALL_EXPORT AtomList	atoms (const AtomList &atoms, const String &expression)
BALL_EXPORT PDBAtomList	PDBAtoms (const AtomContainer &fragment, const String &expression=String())
BALL_EXPORT BondList	bonds (const AtomContainer &fragment, bool selected_only=false)
BALL_EXPORT BondList	bonds (const Atom &atom)
BALL_EXPORT AtomContainerList	atomContainers (const AtomContainer &fragment, bool selected_only=false)
BALL_EXPORT ResidueList	residues (const AtomContainer &fragment, bool selected_only=false)
BALL_EXPORT FragmentList	fragments (const AtomContainer &fragment, bool selected_only=false)
BALL_EXPORT MoleculeList	molecules (const AtomContainer &fragment, bool selected_only=false)
BALL_EXPORT ProteinList	proteins (const AtomContainer &fragment, bool selected_only=false)
BALL_EXPORT SecondaryStructureList	secondaryStructures (const AtomContainer &fragment, bool selected_only=false)
BALL_EXPORT ChainList	chains (const AtomContainer &fragment, bool selected_only=false)
BALL_EXPORT NucleicAcidList	nucleicAcids (const AtomContainer &fragment, bool selected_only=false)
BALL_EXPORT NucleotideList	nucleotides (const AtomContainer &fragment, bool selected_only=false)
Global binary operator functions for two dimensional vectors.
template<typename T >
BALL_INLINE TVector2< T >	operator* (const T &scalar, const TVector2< T > &vector)
template<typename T >
std::istream &	operator>> (std::istream &s, TVector2< T > &vector)
template<typename T >
std::ostream &	operator<< (std::ostream &s, const TVector2< T > &vector)
Global binary operators for three-dimensional vectors.
template<typename T >
BALL_INLINE TVector3< T >	operator* (const T &a, const TVector3< T > &b)
template<typename T >
std::istream &	operator>> (std::istream &s, TVector3< T > &vector)
template<typename T >
std::ostream &	operator<< (std::ostream &s, const TVector3< T > &vector)
template<typename T >
BALL_INLINE TVector4< T >	operator+ (const TVector4< T > &a, const TVector4< T > &b)
template<typename T >
BALL_INLINE TVector4< T >	operator- (const TVector4< T > &a, const TVector4< T > &b)
template<typename T >
std::istream &	operator>> (std::istream &s, TVector4< T > &vector)
template<typename T >
std::ostream &	operator<< (std::ostream &s, const TVector4< T > &vector)
Angle Calculation
BALL_EXPORT Angle	calculateTorsionAngle (const Atom &a1, const Atom &a2, const Atom &a3, const Atom &a4) throw (Exception::IllegalPosition)
BALL_EXPORT bool	setTorsionAngle (const Atom &a1, const Atom &a2, Atom &a3, const Atom &a4, Angle angle)
BALL_EXPORT Angle	calculateBondAngle (const Atom &a1, const Atom &a2, const Atom &a3) throw (Exception::IllegalPosition)

Variables
static const Distance	INVALID_DISTANCE = std::numeric_limits<Distance>::max()
static const Distance	DISTANCE_MIN = (std::numeric_limits<Distance>::min() + 1)
static const Distance	DISTANCE_MAX = std::numeric_limits<Distance>::max()
static const Handle	INVALID_HANDLE = std::numeric_limits<Handle>::max()
static const Handle	HANDLE_MIN = 0
static const Handle	HANDLE_MAX = std::numeric_limits<Handle>::max() - 1
static const Index	INVALID_INDEX = -1
static const Index	INDEX_MIN = 0
static const Index	INDEX_MAX = std::numeric_limits<Index>::max()
static const Position	INVALID_POSITION = std::numeric_limits<Position>::max()
static const Position	POSITION_MIN = 0
static const Position	POSITION_MAX = std::numeric_limits<Position>::max() - 1
static const Size	INVALID_SIZE = std::numeric_limits<Size>::max()
static const Size	SIZE_MIN = 0
static const Size	SIZE_MAX = std::numeric_limits<Size>::max() - 1
bool	clone_bonds
BALL_EXPORT PTE_	PTE
StringHashMap< double * > *	ParsedFunctionConstants
StringHashMap< double(*)(double)> *	ParsedFunctionFunctions
Size	MMFF94_number_atom_types
	hold the maximum number of MMFF94 atom types + 1 (wildcard) More...
BALL_EXPORT const char	CCONN__INSIDE
BALL_EXPORT const char	CCONN__OUTSIDE
BALL_EXPORT const char	CCONN__INSIDE_PROBE
Log streams
Logging, filtering, and storing messages. Many programs emit warning messages, error messages, or simply informations and remarks to their users. The LogStream class provides a convenient and straight-forward interface to classify these messages according to their importance (via the loglevel), filter and store them in files or write them to streams. As the LogStream class is derived from ostream, it behaves as any ostream object. Additionally you may associate streams with each LogStream object that catch only messages of certain loglevels. So the user might decide to redirect all error messages to cerr, all warning messages to cout and all informations to a file. Along with each message its time of creation and its loglevel is stored. So the user might also decide to store all errors he got in the last two hours or alike. The LogStream class heavily relies on the LogStreamBuf class, which does the actual buffering and storing, but is only of interest if you want to implement a derived class, as the actual user interface is implemented in the LogStream class.
BALL_EXPORT LogStream	Log

Storers
typedef TSimpleBox3< float >	SimpleBox3
template<typename T >
std::istream &	operator>> (std::istream &s, TBox3< T > &box)
template<typename T >
std::ostream &	operator<< (std::ostream &s, const TBox3< T > &box)
template<typename T >
std::istream &	operator>> (std::istream &s, TCircle3< T > &circle)
template<typename T >
std::ostream &	operator<< (std::ostream &s, const TCircle3< T > &circle)
template<typename T >
std::ostream &	operator<< (std::ostream &s, const TLine3< T > &line)
template<typename T >
std::istream &	operator>> (std::istream &s, TLine3< T > &line)
template<typename T >
std::istream &	operator>> (std::istream &s, TMatrix4x4< T > &m)
template<typename T >
std::ostream &	operator<< (std::ostream &s, const TMatrix4x4< T > &m)
template<typename T >
std::istream &	operator>> (std::istream &s, TPlane3< T > &plane)
template<typename T >
std::ostream &	operator<< (std::ostream &s, const TPlane3< T > &plane)
template<typename T >
std::istream &	operator>> (std::istream &s, TSimpleBox3< T > &box)
template<typename T >
std::ostream &	operator<< (std::ostream &s, const TSimpleBox3< T > &box)
template<typename T >
std::istream &	operator>> (std::istream &s, TSphere3< T > &sphere)
template<typename T >
std::ostream &	operator<< (std::ostream &s, const TSphere3< T > &sphere)
BALL_EXPORT std::ostream &	operator<< (std::ostream &s, const ReducedSurface &rs)
BALL_EXPORT std::ostream &	operator<< (std::ostream &s, const RSEdge &rsedge)
BALL_EXPORT std::ostream &	operator<< (std::ostream &s, const RSFace &rsface)
BALL_EXPORT std::ostream &	operator<< (std::ostream &s, const RSVertex &rsvertex)
BALL_EXPORT std::ostream &	operator<< (std::ostream &s, const SASEdge &sasedge)
BALL_EXPORT std::ostream &	operator<< (std::ostream &s, const SASFace &sasface)
BALL_EXPORT std::ostream &	operator<< (std::ostream &s, const SASVertex &sasvertex)
BALL_EXPORT std::ostream &	operator<< (std::ostream &s, const SESEdge &sesedge)
BALL_EXPORT std::ostream &	operator<< (std::ostream &s, const SESFace &sesface)
BALL_EXPORT std::ostream &	operator<< (std::ostream &s, const SESVertex &sesvertex)
BALL_EXPORT std::ostream &	operator<< (std::ostream &s, const SolventAccessibleSurface &sas)
BALL_EXPORT std::ostream &	operator<< (std::ostream &s, const SolventExcludedSurface &ses)
BALL_EXPORT std::ostream &	operator<< (std::ostream &s, const Triangle &triangle)
BALL_EXPORT std::ostream &	operator<< (std::ostream &s, const TriangleEdge &edge)
BALL_EXPORT std::ostream &	operator<< (std::ostream &s, const TrianglePoint &point)
BALL_EXPORT std::ostream &	operator<< (std::ostream &s, const TriangulatedSurface &surface)

Detailed Description

-*- Mode: C++; tab-width: 2; -*-

Typedef Documentation

typedef TAngle<float> BALL::Angle

The Default Angle Type. If double precision is not needed, TAngle<float> should be used. It is predefined as Angle for convenience.

Definition at line 705 of file angle.h.

typedef Atom::BondConstIterator BALL::AtomBondConstIterator

A constant iterator for atom bonds.

Definition at line 27 of file bondIterator.h.

typedef Atom::BondConstReverseIterator BALL::AtomBondConstReverseIterator

A constant reverse iterator for atom bonds.

Definition at line 35 of file bondIterator.h.

typedef Atom::BondIterator BALL::AtomBondIterator

A mutable iterator for atom bonds.

Definition at line 23 of file bondIterator.h.

typedef Atom::BondReverseIterator BALL::AtomBondReverseIterator

A mutable reverse iterator for atom bonds.

Definition at line 31 of file bondIterator.h.

typedef ConstBidirectionalIterator<Composite, Atom, Composite::CompositeIterator, AtomIteratorTraits> BALL::AtomConstIterator

A constant bidirectional iterator for the Atom class.

Definition at line 90 of file atomIterator.h.

typedef std::reverse_iterator<AtomConstIterator> BALL::AtomConstReverseIterator

A constant reverse bidirectional iterator for the Atom class.

Definition at line 96 of file atomIterator.h.

typedef ConstBidirectionalIterator<Composite, AtomContainer, Composite::CompositeIterator, AtomContainerIteratorTraits> BALL::AtomContainerConstIterator

A constant bidirectional iterator for the AtomContainer class.

Definition at line 94 of file atomContainerIterator.h.

typedef std::reverse_iterator<AtomContainerConstIterator> BALL::AtomContainerConstReverseIterator

A constant reverse bidirectional iterator for the AtomContainer class.

Definition at line 100 of file atomContainerIterator.h.

typedef BidirectionalIterator<Composite, AtomContainer, Composite::CompositeIterator, AtomContainerIteratorTraits> BALL::AtomContainerIterator

A mutable bidirectional iterator for the AtomContainer class.

Definition at line 88 of file atomContainerIterator.h.

typedef std::reverse_iterator<AtomContainerIterator> BALL::AtomContainerReverseIterator

A mutable reverse bidirectional iterator for the AtomContainer class.

Definition at line 97 of file atomContainerIterator.h.

typedef BidirectionalIterator<Composite, Atom, Composite::CompositeIterator, AtomIteratorTraits> BALL::AtomIterator

A mutable bidirectional iterator for the Atom class.

Definition at line 84 of file atomIterator.h.

typedef std::list<std::pair<Atom*, Atom*> > BALL::AtomPairList

Definition at line 23 of file scoringFunction.h.

typedef std::vector<std::pair<Atom*, Atom*> > BALL::AtomPairVector

Definition at line 24 of file scoringFunction.h.

typedef std::reverse_iterator<AtomIterator> BALL::AtomReverseIterator

A mutable reverse bidirectional iterator for the Atom class.

Definition at line 93 of file atomIterator.h.

typedef unsigned char BALL::Byte

Byte type. Use this type to represent byte data (8 bit length). A Byte is always unsigned.

Size: 8 bit

persistent

Definition at line 185 of file COMMON/global.h.

typedef ConstBidirectionalIterator<Composite, Chain, Composite::CompositeIterator, ChainIteratorTraits> BALL::ChainConstIterator

A constant bidirectional iterator for the Chain class.

Definition at line 89 of file chainIterator.h.

typedef std::reverse_iterator<ChainConstIterator> BALL::ChainConstReverseIterator

A constant reverse bidirectional iterator for the Chain class.

Definition at line 95 of file chainIterator.h.

typedef BidirectionalIterator<Composite, Chain, Composite::CompositeIterator, ChainIteratorTraits> BALL::ChainIterator

A mutable bidirectional iterator for the Chain class.

Definition at line 85 of file chainIterator.h.

typedef std::reverse_iterator<ChainIterator> BALL::ChainReverseIterator

A mutable reverse bidirectional iterator for the Chain class.

Definition at line 92 of file chainIterator.h.

typedef int(* BALL::ComparatorType)(const void *, const void *)

Definition at line 72 of file COMMON/global.h.

typedef std::complex<BALL_COMPLEX_PRECISION> BALL::Complex

Definition at line 21 of file complex.h.

typedef TContourLine<float> BALL::ContourLine

Default type

Definition at line 153 of file contourLine.h.

typedef TContourSurface<float> BALL::ContourSurface

Default type.

Definition at line 251 of file contourSurface.h.

typedef BALL_INDEX_TYPE BALL::Distance

Distance type. Use this type to represent distances in indices. Signed.

Size: 32 bit

persistent

Definition at line 88 of file COMMON/global.h.

typedef double BALL::DoubleReal

Double-precision real type. Use this type to represent double precision floating point numbers.

Size: 64 bit

persistent

Definition at line 158 of file COMMON/global.h.

typedef MolecularGraph::EditableGraph BALL::EditableMolecularGraph

Definition at line 78 of file molecularGraph.h.

typedef BALL_INDEX_TYPE BALL::ErrorCode

Error code property type. Use this type to represent (signed) error codes.

Size: 32 bit

persistent

See also

PropertyManager

Definition at line 175 of file COMMON/global.h.

typedef Experiment<PeakList1D> BALL::Experiment1D

1D NMR experiment

Definition at line 136 of file experiment.h.

typedef Experiment<PeakList3D> BALL::Experiment3D

2D NMR experiment3D NMR experiment

Definition at line 145 of file experiment.h.

typedef Index BALL::FacetArray[256][12]

Definition at line 33 of file contourSurface.h.

typedef TFFT1D<BALL_FFTW_DEFAULT_TRAITS> BALL::FFT1D

Default type

Definition at line 266 of file FFT1D.h.

typedef TFFT2D<BALL_FFTW_DEFAULT_TRAITS> BALL::FFT2D

Default type

Definition at line 318 of file FFT2D.h.

typedef TFFT3D<BALL_FFTW_DEFAULT_TRAITS> BALL::FFT3D

Default type

Definition at line 347 of file FFT3D.h.

typedef ConstBidirectionalIterator<Composite, Fragment, Composite::CompositeIterator, FragmentIteratorTraits> BALL::FragmentConstIterator

Definition at line 81 of file fragmentIterator.h.

typedef std::reverse_iterator<FragmentConstIterator> BALL::FragmentConstReverseIterator

Definition at line 87 of file fragmentIterator.h.

typedef BidirectionalIterator<Composite, Fragment, Composite::CompositeIterator, FragmentIteratorTraits> BALL::FragmentIterator

Definition at line 76 of file fragmentIterator.h.

typedef std::reverse_iterator<FragmentIterator> BALL::FragmentReverseIterator

Definition at line 84 of file fragmentIterator.h.

typedef BALL_SIZE_TYPE BALL::Handle

Handle type. Use this type to represent handles. Handles are used for the non-ambiguous identification of objects (e.g. object derived from Object ). Handles are unsigned.

Size: 32 bit

persistent

Definition at line 98 of file COMMON/global.h.

typedef BALL_SIZE_TYPE BALL::HashIndex

HashIndex type. Use this type to access the result of a hash functions. HashIndex is unsigned.

Size: 32 bit

persistent

Definition at line 133 of file COMMON/global.h.

typedef BALL_INDEX_TYPE BALL::Index

Index type. Use this type to represent indices (e.g. in strings or other sequences). Theses indices may be signed, contrary to the Size type.

Size: 32 bit

persistent

Definition at line 107 of file COMMON/global.h.

typedef std::pair<double,double> BALL::Interval

An interval is defined by its limits

Definition at line 23 of file piecewiseFunction.h.

typedef UnaryPredicate<Composite> BALL::KernelPredicateType

Definition at line 59 of file KERNEL/predicate.h.

typedef FlexibleMolecule BALL::Ligand

Definition at line 121 of file flexibleMolecule.h.

typedef BALL_LONG64_TYPE BALL::LongIndex

Long signed int type. This type holds unsigned 64 bit numbers and is used to store pointers in a portable fashion (for both 32-bit and 64-bit systems).

Size: 64 bit

persistent

Definition at line 203 of file COMMON/global.h.

typedef BALL_ULONG64_TYPE BALL::LongSize

Long unsigned int type. This type holds unsigned 64 bit integer numbers and is used to store pointers in a portable fashion (for both 32-bit and 64-bit systems).

Size: 64 bit

persistent

Definition at line 194 of file COMMON/global.h.

typedef std::vector<Eigen::MatrixXd, Eigen::aligned_allocator<Eigen::MatrixXd> > BALL::MatrixVector

Definition at line 10 of file QSAR/common.h.

typedef boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS, boost::property<boost::vertex_atom_ptr_t, const Atom*>, boost::property<boost::edge_bond_ptr_t, const Bond*> > BALL::MolecularGraphBase

Definition at line 24 of file molecularGraph.h.

typedef GRAPH::GraphTraits<MolecularGraph> BALL::MolecularGraphTraits

Definition at line 77 of file molecularGraph.h.

typedef ConstBidirectionalIterator<Composite, Molecule, Composite::CompositeIterator, MoleculeIteratorTraits> BALL::MoleculeConstIterator

Definition at line 70 of file moleculeIterator.h.

typedef std::reverse_iterator<MoleculeConstIterator> BALL::MoleculeConstReverseIterator

Definition at line 76 of file moleculeIterator.h.

typedef BidirectionalIterator<Composite, Molecule, Composite::CompositeIterator, MoleculeIteratorTraits> BALL::MoleculeIterator

Definition at line 65 of file moleculeIterator.h.

typedef std::reverse_iterator<MoleculeIterator> BALL::MoleculeReverseIterator

Definition at line 73 of file moleculeIterator.h.

typedef TMutex<BALL_DEFAULT_MUTEX_TYPE> BALL::Mutex

Definition at line 240 of file mutex.h.

typedef TMutexLocker<BALL_DEFAULT_MUTEXLOCKER_TYPE, BALL_DEFAULT_MUTEX_TYPE> BALL::MutexLocker

Definition at line 242 of file mutex.h.

typedef std::vector<NamedProperty>::iterator BALL::NamedPropertyIterator

Definition at line 317 of file property.h.

typedef ConstBidirectionalIterator<Composite, NucleicAcid, Composite::CompositeIterator, NucleicAcidIteratorTraits> BALL::NucleicAcidConstIterator

Definition at line 76 of file nucleicAcidIterator.h.

typedef std::reverse_iterator<NucleicAcidConstIterator> BALL::NucleicAcidConstReverseIterator

Definition at line 80 of file nucleicAcidIterator.h.

typedef BidirectionalIterator<Composite, NucleicAcid, Composite::CompositeIterator, NucleicAcidIteratorTraits> BALL::NucleicAcidIterator

Definition at line 72 of file nucleicAcidIterator.h.

typedef std::reverse_iterator<NucleicAcidIterator> BALL::NucleicAcidReverseIterator

Definition at line 78 of file nucleicAcidIterator.h.

typedef ConstBidirectionalIterator<Composite, Nucleotide, Composite::CompositeIterator, NucleotideIteratorTraits> BALL::NucleotideConstIterator

Definition at line 71 of file nucleotideIterator.h.

typedef std::reverse_iterator<NucleotideConstIterator> BALL::NucleotideConstReverseIterator

Definition at line 75 of file nucleotideIterator.h.

typedef BidirectionalIterator<Composite, Nucleotide, Composite::CompositeIterator, NucleotideIteratorTraits> BALL::NucleotideIterator

Definition at line 67 of file nucleotideIterator.h.

typedef std::reverse_iterator<NucleotideIterator> BALL::NucleotideReverseIterator

Definition at line 73 of file nucleotideIterator.h.

typedef ConstBidirectionalIterator<Composite, PDBAtom, Composite::CompositeIterator, PDBAtomIteratorTraits> BALL::PDBAtomConstIterator

A constant bidirectional iterator for the PDBAtom class.

Definition at line 92 of file PDBAtomIterator.h.

typedef std::reverse_iterator<PDBAtomConstIterator> BALL::PDBAtomConstReverseIterator

A constant reverse bidirectional iterator for the PDBAtom class.

Definition at line 98 of file PDBAtomIterator.h.

typedef BidirectionalIterator<Composite, PDBAtom, Composite::CompositeIterator, PDBAtomIteratorTraits> BALL::PDBAtomIterator

A mutable bidirectional iterator for the PDBAtom class.

Definition at line 88 of file PDBAtomIterator.h.

typedef std::reverse_iterator<PDBAtomIterator> BALL::PDBAtomReverseIterator

A mutable reverse bidirectional iterator for the PDBAtom class.

Definition at line 95 of file PDBAtomIterator.h.

typedef Peak<float> BALL::Peak1D

Definition at line 261 of file peak.h.

typedef Peak<Vector2> BALL::Peak2D

Definition at line 262 of file peak.h.

typedef Peak<Vector3> BALL::Peak3D

Definition at line 263 of file peak.h.

typedef PeakList<Peak<float> > BALL::PeakList1D

1D peak list

Definition at line 125 of file peakList.h.

typedef PeakList<Peak<Vector2> > BALL::PeakList2D

2D peak list

Definition at line 128 of file peakList.h.

typedef PeakList<Peak<Vector3> > BALL::PeakList3D

3D peak list

Definition at line 131 of file peakList.h.

typedef BALL_POINTERSIZEUINT_TYPE BALL::PointerSizeUInt

Unsigned int with the same size as a pointer. Used for internal conversion issues mostly. Size: 32/64 bit (platform dependent)

Definition at line 209 of file COMMON/global.h.

typedef BALL_SIZE_TYPE BALL::Position

Position type. Use this type to represent positions (e.g. in a container) that cannot be negative (contrary to Index ).

Size: 32 bit

persistent

Definition at line 142 of file COMMON/global.h.

typedef BALL_SIZE_TYPE BALL::Property

Unnamed property type. Use this type to represent (unnamed) properties.

Size: 32 bit

persistent

See also

PropertyManager

Definition at line 167 of file COMMON/global.h.

typedef ConstBidirectionalIterator<Composite, Protein, Composite::CompositeIterator, ProteinIteratorTraits> BALL::ProteinConstIterator

Definition at line 71 of file proteinIterator.h.

typedef std::reverse_iterator<ProteinConstIterator> BALL::ProteinConstReverseIterator

Definition at line 77 of file proteinIterator.h.

typedef BidirectionalIterator<Composite, Protein, Composite::CompositeIterator,ProteinIteratorTraits> BALL::ProteinIterator

Definition at line 66 of file proteinIterator.h.

typedef std::reverse_iterator<ProteinIterator> BALL::ProteinReverseIterator

Definition at line 74 of file proteinIterator.h.

typedef TQuaternion<float> BALL::Quaternion

Definition at line 673 of file quaternion.h.

typedef TReadLocker<BALL_DEFAULT_READLOCKER_TYPE, BALL_DEFAULT_READWRITELOCK_TYPE> BALL::ReadLocker

Definition at line 243 of file mutex.h.

typedef TReadWriteLock<BALL_DEFAULT_READWRITELOCK_TYPE> BALL::ReadWriteLock

Definition at line 241 of file mutex.h.

typedef float BALL::Real

Real type. Use this type to represent standard floating point numbers.

Size: 32 bit

persistent

Definition at line 150 of file COMMON/global.h.

typedef TRegularData1D<float> BALL::RegularData1D

Default type

Definition at line 357 of file regularData1D.h.

typedef TRegularData2D<float> BALL::RegularData2D

Default type

Definition at line 414 of file regularData2D.h.

typedef TRegularData3D<float> BALL::RegularData3D

Default type

Definition at line 515 of file regularData3D.h.

typedef std::list<RegularData3D*> BALL::RegularData3DList

Definition at line 15 of file pyListHelper.h.

typedef ConstBidirectionalIterator<Composite, Residue, Composite::CompositeIterator, ResidueIteratorTraits> BALL::ResidueConstIterator

Definition at line 67 of file residueIterator.h.

typedef std::reverse_iterator<ResidueConstIterator> BALL::ResidueConstReverseIterator

Definition at line 73 of file residueIterator.h.

typedef BidirectionalIterator<Composite, Residue, Composite::CompositeIterator, ResidueIteratorTraits> BALL::ResidueIterator

Definition at line 62 of file residueIterator.h.

typedef std::reverse_iterator<ResidueIterator> BALL::ResidueReverseIterator

Definition at line 70 of file residueIterator.h.

typedef vector<vector<vector<double> > > BALL::ScoreGrid

Definition at line 17 of file scoreGridSet.h.

typedef ConstBidirectionalIterator<Composite, SecondaryStructure, Composite::CompositeIterator, SecondaryStructureIteratorTraits> BALL::SecondaryStructureConstIterator

Definition at line 75 of file secondaryStructureIterator.h.

typedef std::reverse_iterator<SecondaryStructureConstIterator> BALL::SecondaryStructureConstReverseIterator

Definition at line 81 of file secondaryStructureIterator.h.

typedef BidirectionalIterator<Composite, SecondaryStructure, Composite::CompositeIterator, SecondaryStructureIteratorTraits> BALL::SecondaryStructureIterator

Definition at line 70 of file secondaryStructureIterator.h.

typedef std::reverse_iterator<SecondaryStructureIterator> BALL::SecondaryStructureReverseIterator

Definition at line 78 of file secondaryStructureIterator.h.

typedef TSimpleMolecularGraph<Index, Index> BALL::SimpleMolecularGraph

Default molecular graph type. Each edge and node has a label of type Index .

Definition at line 202 of file simpleMolecularGraph.h.

typedef BALL_SIZE_TYPE BALL::Size

Size type. Use this type to represent sizes of containers, sequences or alike. Variables of type Size are unsigned.

Size: 32 bit

persistent

Definition at line 116 of file COMMON/global.h.

typedef time_t BALL::Time

Time type. Use this type to represent a point in time (as a replaecement for time_t).

Size: platform dependent

not persistent

Definition at line 125 of file COMMON/global.h.

typedef TVector3<float> BALL::Vector3

Default three-dimensional vector class. This is the class used in BALL kernel to represent points, coordinates.

Definition at line 1084 of file vector3.h.

typedef TWriteLocker<BALL_DEFAULT_WRITELOCKER_TYPE, BALL_DEFAULT_READWRITELOCK_TYPE> BALL::WriteLocker

Definition at line 244 of file mutex.h.

Enumeration Type Documentation

enum BALL::ASCII

Enumerator
ASCII__BACKSPACE
ASCII__BELL
ASCII__CARRIAGE_RETURN
ASCII__HORIZONTAL_TAB
ASCII__NEWLINE
ASCII__RETURN
ASCII__SPACE
ASCII__TAB
ASCII__VERTICAL_TAB
ASCII__COLON
ASCII__COMMA
ASCII__EXCLAMATION_MARK
ASCII__POINT
ASCII__QUESTION_MARK
ASCII__SEMICOLON

Definition at line 213 of file COMMON/global.h.

Function Documentation

BALL_EXPORT Angle BALL::calculateBondAngle	(	const Atom &	a1,
		const Atom &	a2,
		const Atom &	a3
	)
throw	(	Exception::IllegalPosition
	)

Calculate the bond angle between three atoms

BALL_EXPORT void BALL::calculateResidueChi2Angles	(	const Protein &	protein,
		HashMap< const Residue *, float > &	residue_angles
	)

Calculate the Chi2 Angles for each residue. This method computes the chi2 angle of each residue and stores it in the given hash map. All angles are in radian. Note, that the hash map is NOT cleaned up, but the results are appended to it.

Parameters

residue_angles	a hash map containing the chi2 angles the residues (returned)
fragment	the kernel object containing the residues

BALL_EXPORT void BALL::calculateResidueChi2Angles	(	const Chain &	fragment,
		HashMap< const Residue *, float > &	residue_angles
	)

Calculate the Chi2 Angles for each residue. This method computes the chi2 angle of each residue and stores it in the given hash map. All angles are in radian. Note, that the hash map is NOT cleaned up, but the results are appended to it.

Parameters

residue_angles	a hash map containing the chi2 angles of the residues (returned)
fragment	the kernel object containing the residues

BALL_EXPORT float BALL::calculateResidueChi2Angles

(

const Residue &

residue

)

Calculate the Chi2 Angles for a given residue in radian. If the given residue has no chi angle, zero is returned.

BALL_EXPORT void BALL::calculateResidueChiAngles	(	const Protein &	protein,
		HashMap< const Residue *, float > &	residue_angles
	)

Calculate the Chi Angles for each residue. This method computes the chi angle of each residue and stores it in the given hash map. All angles are in radian. Note, that the hash map is NOT cleaned up, but the results are appended to it.

Parameters

residue_angles	a hash map containing the chi angles of the residues (returned)
fragment	the kernel object containing the residues

BALL_EXPORT void BALL::calculateResidueChiAngles	(	const Chain &	fragment,
		HashMap< const Residue *, float > &	residue_angles
	)

Calculate the Chi Angles for each residue. This method computes the chi angle of each residue and stores it in the given hash map. All angles are in radian. Note, that the hash map is NOT cleaned up, but the results are appended to it.

Parameters

residue_angles	a hash map containing the chi angles of the residues (returned)
fragment	the kernel object containing the residues

BALL_EXPORT float BALL::calculateResidueChiAngles

(

const Residue &

residue

)

Calculate the Chi Angles for a given residue in radian. If the given residue has no chi angle, zero is returned.

BALL_EXPORT Angle BALL::calculateTorsionAngle	(	const Atom &	a1,
		const Atom &	a2,
		const Atom &	a3,
		const Atom &	a4
	)
throw	(	Exception::IllegalPosition
	)

Calculate the torsion angle between four atoms

template<class NucleotideContainerType >

const Nucleotide* BALL::get3Prime

(

const NucleotideContainerType &

nucleotide_container

)

Definition at line 325 of file nucleotide.h.

template<class NucleotideContainerType >

const Nucleotide* BALL::get5Prime

(

const NucleotideContainerType &

nucleotide_container

)

Definition at line 313 of file nucleotide.h.

BALL_EXPORT const FacetArray& BALL::getContourSurfaceFacetData

(

double

threshold

)

static double BALL::getCovariance ( const list< double > &  v1, const list< double > &  v2, double  mean1, double  mean2  )

static

template<class ResidueContainerType >

const Residue* BALL::getCTerminal

(

const ResidueContainerType &

residue_container

)

Definition at line 459 of file residue.h.

static double BALL::getMean ( const list< double > &  v )

static

Position BALL::getMMFF94Index	(	Position	atom_type1,
		Position	atom_type2
	)

BALL_EXPORT HashIndex BALL::getNextPrime

(

HashIndex

l

)

Calculate the next prime number. This method returns the first prime number that is greater or equal to the number given as the argument. Only odd prime numbers are returned, the lowest number returned is 3.

template<class ResidueContainerType >

const Residue* BALL::getNTerminal

(

const ResidueContainerType &

residue_container

)

Definition at line 444 of file residue.h.

static double BALL::getStddev ( const list< double > &  m, double  mean  )

static

static double BALL::getSumOfSquares ( const list< double > &  m, double  mean  )

static

template<>

BALL_EXPORT HashIndex BALL::Hash

(

const std::pair< Position, Position > &

p

)

template<typename T >

HashIndex BALL::Hash ( const T &  key )

inline

General default hash function. This method converts a given key to a HashIndex by calling (HashIndex)key. If the key type T is not convertible to HashIndex by default, a converter should be defined (operator HashIndex).

Parameters

key	the key to be hashed

Returns

HashIndex the hash index

Definition at line 47 of file hash.h.

BALL_EXPORT HashIndex BALL::Hash ( const string &  s )

inline

String hash function. This method is optimized for the hashing of STL strings. In fact, it is only an inline wrapper around hashString .

Definition at line 56 of file hash.h.

BALL_EXPORT HashIndex BALL::Hash ( const String &  s )

inline

String hash function. This method is optimized for the hashing of BALL strings. In fact, it is only an inline wrapper around hashString .

Definition at line 65 of file hash.h.

BALL_EXPORT HashIndex BALL::Hash ( void *const &  ptr )

inline

Pointer hash function. Use this function to hash pointers to objects.

Definition at line 73 of file hash.h.

BALL_EXPORT HashIndex BALL::hashElfString

(

const char *

str

)

BALL_EXPORT HashIndex BALL::hashPJWString

(

const char *

str

)

BALL_EXPORT HashIndex BALL::hashPointer

(

void *const

ptr

)

BALL_EXPORT HashIndex BALL::hashString

(

const char *

str

)

template<typename T >

TMatrix4x4< T > BALL::operator*	(	const T &	scalar,
		const TMatrix4x4< T > &	m
	)

Definition at line 1295 of file matrix44.h.

template<typename T >

TVector3< T > BALL::operator*	(	const TMatrix4x4< T > &	matrix,
		const TVector3< T > &	vector
	)

Definition at line 1328 of file matrix44.h.

template<typename Container , typename DataType , typename Position , typename Traits >

ConstRandomAccessIterator<Container, DataType, Position, Traits> BALL::operator+	(	Distance	distance,
		const ConstRandomAccessIterator< Container, DataType, Position, Traits > &	iterator
	)

Return an incremented iterator. It points to the element with the given distance from the element of the given iterator.

Exceptions

Exception::InvalidIterator

Definition at line 192 of file randomAccessIterator.h.

template<typename DataT , typename PeakT , typename PositionT >

double BALL::operator-	(	const Spectrum< DataT, PeakT, PositionT > &	s1,
		const Spectrum< DataT, PeakT, PositionT > &	s2
	)

Difference operator. Calculate the sum of the unsigned differences of the two spectra

Definition at line 213 of file spectrum.h.

template<typename T >

std::ostream& BALL::operator<<	(	std::ostream &	os,
		const BinaryFileAdaptor< T > &	data
	)

Output stream for BinaryFileAdaptors.

Definition at line 147 of file binaryFileAdaptor.h.

::std::ostream& BALL::operator<<	(	::std::ostream &	os,
		const SnapShot &	ss
	)

Output stream operator for SnapShots.

std::ostream& BALL::operator<<	(	std::ostream &	os,
		const BALL::ShiftModel2D &	shiftmodel
	)

template<typename PositionType >

std::ostream& BALL::operator<<	(	std::ostream &	os,
		const Peak< PositionType > &	peak
	)

Output operator

Definition at line 249 of file peak.h.

BALL_EXPORT std::ostream& BALL::operator<<	(	std::ostream &	os,
		const PreciseTime &	time
	)

Global stream operators for PreciseTime and TimeStampPrint the contents of a PreciseTime object to a stream.

BALL_EXPORT std::ostream& BALL::operator<<	(	std::ostream &	os,
		const TimeStamp &	stamp
	)

Print the contents of a TimeStamp object to a stream.

template<typename Node , typename Edge >

std::ostream& BALL::operator<<	(	std::ostream &	os,
		const TSimpleMolecularGraph< Node, Edge > &	G
	)

Definition at line 290 of file simpleMolecularGraph.h.

std::ostream& BALL::operator<<	(	std::ostream &	out,
		const DockResult &	dock_res
	)
throw	(
	)

Operator to write dock result into an ostream. Calls writeDockResult(std::ostream& file).

template<typename ComplexTraits >

const TRegularData2D< typename TFFT2D< ComplexTraits >::Complex > & BALL::operator<<	(	TRegularData2D< typename TFFT2D< ComplexTraits >::Complex > &	to,
		const TFFT2D< ComplexTraits > &	from
	)

Global assignment operator from TFFT2D to TRegularData2D<Complex>

Definition at line 769 of file FFT2D.h.

template<typename DataT , typename PeakT , typename PositionT >

std::ostream& BALL::operator<<	(	std::ostream &	os,
		const Spectrum< DataT, PeakT, PositionT > &	spectrum
	)

template<typename ComplexTraits >

const RegularData2D & BALL::operator<<	(	RegularData2D &	to,
		const TFFT2D< ComplexTraits > &	from
	)

Global assignment operator from FFT3D to TRegularData3D<float>. This operator assigns the real part of the complex TFFT2D-data to the TRegularData2D<float> to.

Definition at line 865 of file FFT2D.h.

template<typename ComplexTraits >

const TRegularData3D< typename TFFT3D< ComplexTraits >::Complex > & BALL::operator<<	(	TRegularData3D< typename TFFT3D< ComplexTraits >::Complex > &	to,
		const TFFT3D< ComplexTraits > &	from
	)

Global assignment operator from TFFT3D to TRegularData3D<Complex>

Definition at line 928 of file FFT3D.h.

template<typename ComplexTraits >

const RegularData3D & BALL::operator<<	(	RegularData3D &	to,
		const TFFT3D< ComplexTraits > &	from
	)

Global assignment operator from TFFT3D to TRegularData3D<float>. This operator assigns the real part of the complex TFFT3D-data to the TRegularData3D<float> to.

Definition at line 1038 of file FFT3D.h.

template<typename T >

std::ostream& BALL::operator<<	(	std::ostream &	s,
		const TQuaternion< T > &	q
	)

Definition at line 640 of file quaternion.h.

template<typename ComplexTraits >

const RegularData1D& BALL::operator<<	(	RegularData1D &	to,
		const TFFT1D< ComplexTraits > &	from
	)

Definition at line 673 of file FFT1D.h.

template<typename T >

std::ostream& BALL::operator<<	(	std::ostream &	s,
		const TAngle< T > &	angle
	)

Output Operator. Writes the value of the angle to an output stream. The stream operator operator << has to be defined for the template parameter T.

Definition at line 754 of file angle.h.

template<typename ValueType >

std::ostream& BALL::operator<<	(	std::ostream &	os,
		const TRegularData1D< ValueType > &	data
	)

Output operator.

Definition at line 787 of file regularData1D.h.

template<typename ValueType >

std::ostream& BALL::operator<<	(	std::ostream &	os,
		const TRegularData2D< ValueType > &	data
	)

Output operator.

Definition at line 960 of file regularData2D.h.

template<typename ValueType >

std::ostream& BALL::operator<<	(	std::ostream &	os,
		const TRegularData3D< ValueType > &	grid
	)

Output operator.

Definition at line 1405 of file regularData3D.h.

template<typename T >

std::istream& BALL::operator>>	(	std::istream &	is,
		BinaryFileAdaptor< T > &	data
	)

Input stream for BinaryFileAdaptors.

Definition at line 165 of file binaryFileAdaptor.h.

::std::istream& BALL::operator>>	(	::std::istream &	is,
		SnapShot &	ss
	)

Input stream operator for SnapShots.

std::istream& BALL::operator>>	(	std::istream &	in,
		DockResult &	dock_res
	)
throw	(
	)

Operator to read dock result into an istream. Calls readDockResult(std::istream& file) .

template<typename DataT , typename PeakT , typename PositionT >

std::istream& BALL::operator>>	(	std::istream &	is,
		Spectrum< DataT, PeakT, PositionT > &	spectrum
	)

template<typename T >

std::istream& BALL::operator>>	(	std::istream &	s,
		TQuaternion< T > &	q
	)

Definition at line 631 of file quaternion.h.

template<typename T >

std::istream& BALL::operator>>	(	std::istream &	s,
		TAngle< T > &	angle
	)

Input Operator. Reads the value (in radians) of an angle from an instream using T::operator >>

Definition at line 741 of file angle.h.

template<typename ValueType >

std::istream& BALL::operator>>	(	std::istream &	is,
		TRegularData1D< ValueType > &	grid
	)

Input operator.

Definition at line 801 of file regularData1D.h.

template<typename ValueType >

std::istream& BALL::operator>>	(	std::istream &	is,
		TRegularData2D< ValueType > &	grid
	)

Input operator.

Definition at line 978 of file regularData2D.h.

template<typename ValueType >

std::istream& BALL::operator>>	(	std::istream &	is,
		TRegularData3D< ValueType > &	grid
	)

Input operator.

Definition at line 1425 of file regularData3D.h.

BALL_EXPORT bool BALL::setTorsionAngle	(	const Atom &	a1,
		const Atom &	a2,
		Atom &	a3,
		const Atom &	a4,
		Angle	angle
	)

Set the torsion angle defined by a1, a2, a3, a4. The atoms should be connected by bonds The position of a1 and a2 is kept fix, while the connected component containing a4 is rotated accordingly.

Returns

false if the bond is not rotatable or if the molecule graph is not divided into two connected components upon removal of the bond (a2,a3)

BALL_EXPORT void BALL::sleepFor

(

Size

mseconds

)

template<typename T >

void BALL::swapBytes

(

T &

t

)

Coping with endianness. This function swaps the bytes of a variable of type T if this type is of size 2n.

Definition at line 17 of file binaryFileAdaptor.h.

template<>

BALL_EXPORT void BALL::swapBytes

(

unsigned short &

)

template<>

BALL_EXPORT void BALL::swapBytes

(

short &

)

template<>

BALL_EXPORT void BALL::swapBytes

(

unsigned int &

)

template<>

BALL_EXPORT void BALL::swapBytes

(

int &

)

template<>

BALL_EXPORT void BALL::swapBytes

(

unsigned long &

)

template<>

BALL_EXPORT void BALL::swapBytes

(

long &

)

template<>

BALL_EXPORT void BALL::swapBytes

(

float &

)

template<>

BALL_EXPORT void BALL::swapBytes

(

double &

)

Variable Documentation

BALL_EXPORT const char BALL::CCONN__INSIDE

BALL_EXPORT const char BALL::CCONN__INSIDE_PROBE

BALL_EXPORT const char BALL::CCONN__OUTSIDE

const Distance BALL::DISTANCE_MAX = std::numeric_limits<Distance>::max()

static

Definition at line 235 of file COMMON/global.h.

const Distance BALL::DISTANCE_MIN = (std::numeric_limits<Distance>::min() + 1)

static

Definition at line 234 of file COMMON/global.h.

const Handle BALL::HANDLE_MAX = std::numeric_limits<Handle>::max() - 1

static

Definition at line 239 of file COMMON/global.h.

const Handle BALL::HANDLE_MIN = 0

static

Definition at line 238 of file COMMON/global.h.

const Index BALL::INDEX_MAX = std::numeric_limits<Index>::max()

static

Definition at line 243 of file COMMON/global.h.

const Index BALL::INDEX_MIN = 0

static

Definition at line 242 of file COMMON/global.h.

const Distance BALL::INVALID_DISTANCE = std::numeric_limits<Distance>::max()

static

Definition at line 233 of file COMMON/global.h.

const Handle BALL::INVALID_HANDLE = std::numeric_limits<Handle>::max()

static

Definition at line 237 of file COMMON/global.h.

const Index BALL::INVALID_INDEX = -1

static

Definition at line 241 of file COMMON/global.h.

const Position BALL::INVALID_POSITION = std::numeric_limits<Position>::max()

static

Definition at line 245 of file COMMON/global.h.

const Size BALL::INVALID_SIZE = std::numeric_limits<Size>::max()

static

Definition at line 250 of file COMMON/global.h.

BALL_EXPORT LogStream BALL::Log

Global static instance of a logstream. This instance of LogStream is by default bound to cout cerr by calling the default constructor.

Size BALL::MMFF94_number_atom_types

hold the maximum number of MMFF94 atom types + 1 (wildcard)

const Position BALL::POSITION_MAX = std::numeric_limits<Position>::max() - 1

static

Definition at line 247 of file COMMON/global.h.

const Position BALL::POSITION_MIN = 0

static

Definition at line 246 of file COMMON/global.h.

const Size BALL::SIZE_MAX = std::numeric_limits<Size>::max() - 1

static

Definition at line 252 of file COMMON/global.h.

const Size BALL::SIZE_MIN = 0

static

Definition at line 251 of file COMMON/global.h.