BALL Namespace Reference


Namespaces
namespace	Constants
namespace	Exception
namespace	Maths
namespace	MolmecSupport
namespace	PDB
namespace	Peptides
namespace	RTTI
namespace	SysInfo
namespace	VIEW
Classes
class	HashFunction
class	GlobalInitializer
class	Limits
class	Limits< float >
class	Limits< double >
class	Limits< bool >
class	Limits< char >
class	Limits< signed char >
class	Limits< unsigned char >
class	Limits< short >
class	Limits< unsigned short >
class	Limits< int >
class	Limits< unsigned int >
class	Limits< long >
class	Limits< unsigned long >
class	LogStreamBuf
class	LogStreamNotifier
class	LogStream
class	VersionInfo
class	AutoDeletable
class	UnaryFunctor
class	BinaryFunctor
class	BaseIterator
class	ConstBidirectionalIterator
class	BidirectionalIterator
	Mutable bidirectional iterator. More...
class	Client
class	Comparator
class	Composite
class	Embeddable
class	EnumeratorIndex
class	Enumerator
class	Factory
class	ConstForwardIterator
class	ForwardIterator
class	MolecularInformation
class	MoleculeObjectCreator
class	NotificationTarget_
class	NotificationSource_
class	NotificationSlot_
class	NotificationManager_
class	NotificationTarget
class	NotificationTarget1
class	NotificationTarget2
class	Object
class	ObjectCreator
class	PersistenceManager
class	PersistentObject
class	UnaryPredicate
class	BinaryPredicate
class	PreferencesObject
class	Processor
class	UnaryProcessor
class	BinaryProcessor
class	NamedProperty
class	PropertyManager
class	ConstRandomAccessIterator
class	RandomAccessIterator
class	Selectable
class	TextPersistenceManager
class	PreciseTime
class	TimeStamp
class	Visitor
class	XDRPersistenceManager
class	Bit
class	BitVector
class	TContour
class	TContourLine
class	TContourSurface
class	HashGridBox3
class	HashGrid3
class	HashMap
	HashMap class based on the STL map (containing serveral convenience functions). More...
class	HashSet
class	List
class	Options
class	Quadruple
class	TRegularData1D
class	TRegularData2D
class	TRegularData3D
class	RegularExpression
class	String
class	Substring
class	StringHashMap
class	Triple
class	ComposedEnergyProcessor
class	EnergyProcessor
class	Bruker1DFile
class	Bruker2DFile
class	DCDFile
class	DSN6File
class	GAMESSDatFile
class	GAMESSLogFile
class	GenericMolFile
class	HINFile
class	INIFile
class	JCAMPFile
class	KCFFile
class	LineBasedFile
class	MOL2File
class	MOLFile
class	MolFileFactory
struct	NMRAtomData
struct	SampleCondition
struct	ShiftReferenceElement
struct	ShiftReferenceSet
struct	NMRAtomDataSet
class	NMRStarFile
class	Parameters
class	ParameterSection
class	PDBFile
class	PDBInfo
class	PDBRecords
class	ResourceEntry
class	ResourceFile
class	SCWRLRotamerFile
	Reads Dunbrack/SCWRL rotamer library files. More...
class	SDFile
class	TrajectoryFile
class	TRRFile
class	XYZFile
class	Atom
class	AtomContainer
class	AtomContainerIteratorTraits
class	AtomIteratorTraits
class	Bond
class	Chain
class	ChainIteratorTraits
class	Expression
class	ExpressionParser
class	ExpressionPredicate
class	ExpressionTree
class	Fragment
class	FragmentIteratorTraits
class	CompositeIteratorTraits
class	Molecule
class	MoleculeIteratorTraits
class	NucleicAcid
class	NucleicAcidIteratorTraits
class	Nucleotide
class	NucleotideIteratorTraits
class	PDBAtom
class	PDBAtomIteratorTraits
class	KernelPredicate
	Kernel predicate class. More...
class	Protein
class	ProteinIteratorTraits
class	Element
class	PTE_
class	Residue
class	ResidueIteratorTraits
class	SecondaryStructure
class	SecondaryStructureIteratorTraits
class	Selector
class	TruePredicate
class	FalsePredicate
class	SelectedPredicate
class	AtomNamePredicate
class	AtomTypePredicate
class	ElementPredicate
class	ResiduePredicate
class	ResidueIDPredicate
class	ProteinPredicate
class	ChainPredicate
class	SecondaryStructurePredicate
class	SolventPredicate
class	MoleculePredicate
class	BackBonePredicate
class	NucleicAcidPredicate
class	NucleotidePredicate
class	InRingPredicate
class	NumberOfBondsPredicate
class	SingleBondsPredicate
class	DoubleBondsPredicate
class	TripleBondsPredicate
class	AromaticBondsPredicate
class	ConnectedToPredicate
class	SpHybridizedPredicate
class	Sp2HybridizedPredicate
class	Sp3HybridizedPredicate
class	ChargePredicate
class	AxialPredicate
class	Conformation4C1Predicate
class	RingFinder
class	SMARTSPredicate
class	System
class	TAngle
class	TBox3
class	TCircle3
class	TFFT1D
class	TFFT2D
class	TFFT3D
struct	DoubleTraits
struct	FloatTraits
struct	LongDoubleTraits
class	ConstantFunction
class	MutableConstant
class	Addition
class	Subtraction
class	Product
class	Division
class	Reciprocal
class	SquareFunction
class	CubicFunction
class	MutablePower
class	TLine3
class	TMatrix4x4
class	NumericalIntegrator
class	ParsedFunction
class	PiecewiseFunction
class	PiecewisePolynomial
class	TPlane3
class	TQuaternion
class	RandomNumberGenerator
class	RombergIntegrator
class	TSimpleBox3
class	TSphere3
class	TSurface
class	TVector2
class	TVector3
class	TVector4
class	AmberFF
class	AmberBend
class	AmberNonBonded
class	AmberStretch
class	AmberTorsion
class	GAFFCESParser
class	GAFFTypeProcessor
class	CharmmFF
class	CharmmBend
class	CharmmImproperTorsion
class	CharmmNonBonded
class	CharmmStretch
class	CharmmTorsion
class	AssignBaseProcessor
	Only used for deriving interface. More...
class	AssignTypeProcessor
class	AssignTypeNameProcessor
class	AtomVector
class	ChargeRuleProcessor
class	ForceField
class	ForceFieldComponent
class	Gradient
class	PeriodicBoundary
class	RadiusRuleProcessor
class	RuleEvaluator
class	RuleProcessor
class	SnapShot
class	SnapShotManager
class	TypenameRuleProcessor
class	TypeRuleProcessor
class	CanonicalMD
class	MicroCanonicalMD
class	MolecularDynamics
class	ConjugateGradientMinimizer
class	EnergyMinimizer
class	LineSearch
class	ShiftedLVMMMinimizer
class	SteepestDescentMinimizer
class	StrangLBFGSMinimizer
class	MMFF94
class	MMFF94NonBonded
class	MMFF94OutOfPlaneBend
class	MMFF94ParametersBase
class	MMFF94AtomTypeEquivalences
struct	MMFF94AtomType
	Class to store the values of an atom type from MMFFPROP.PAR. More...
class	MMFF94AtomTypes
class	MMFF94StretchParameters
class	MMFF94BendParameters
class	MMFF94StretchBendParameters
class	MMFF94TorsionParameters
class	MMFF94PlaneParameters
class	MMFF94VDWParameters
class	MMFF94ESParameters
class	MMFF94AtomTyper
class	MMFF94ChargeProcessor
class	MMFF94StretchBend
class	MMFF94Torsion
class	AtomTypes
class	CharmmEEF1
class	CosineTorsion
class	ForceFieldParameters
class	LennardJones
class	Potential1210
class	QuadraticAngleBend
class	QuadraticBondStretch
class	QuadraticImproperTorsion
class	ResidueTorsions
class	Templates
class	AnisotropyShiftProcessor
class	AssignShiftProcessor
class	ClearShiftProcessor
class	CreateSpectrumProcessor
class	EFShiftProcessor
class	Experiment
class	SimpleExperiment1D
class	HaighMallionShiftProcessor
class	HBondShiftProcessor
class	JohnsonBoveyShiftProcessor
class	Peak
class	PeakList
class	RandomCoilShiftProcessor
class	ShiftModel
class	ShiftModule
class	Spectrum
class	BALLPlugin
class	PluginHandler
class	PluginManager
class	PyColorRGBAVector
class	PyCompositeList
class	Constant
class	PyDatasetVector
class	PyIndexList
class	PyInterpreter
class	AromaticityProcessor
class	ConnectivityBase
class	ZagrebIndex
class	BalabanIndexJ
class	Descriptor
class	PartialChargeBase
class	TotalPositivePartialCharge
class	TotalNegativePartialCharge
class	RelPositivePartialCharge
class	RelNegativePartialCharge
class	PartialChargeProcessor
class	RingPerceptionProcessor
class	SimpleBase
class	MolecularWeight
class	NumberOfBonds
class	NumberOfSingleBonds
class	NumberOfDoubleBonds
class	NumberOfTripleBonds
class	NumberOfAromaticBonds
class	NumberOfAtoms
class	NumberOfBoron
class	NumberOfCarbon
class	NumberOfNitrogen
class	NumberOfOxygen
class	NumberOfFlourine
class	NumberOfPhosphorus
class	NumberOfSulfur
class	NumberOfChlorine
class	NumberOfBromine
class	NumberOfIodine
class	NumberOfHydrogen
class	FormalCharge
class	NumberOfHeavyAtoms
class	MeanAtomInformationContent
class	AtomInformationContent
class	NumberOfRotatableSingleBonds
class	RelNumberOfRotatableSingleBonds
class	NumberOfAromaticAtoms
class	NumberOfHeavyBonds
class	NumberOfRotatableBonds
class	RelNumberOfRotatableBonds
class	VertexAdjacency
class	VertexAdjacencyEquality
class	NumberOfHydrogenBondAcceptors
class	NumberOfHydrogenBondDonors
class	NumberOfHydrophobicAtoms
class	BondPolarizabilities
class	AtomicPolarizabilities
class	SizeOfSSSR
class	PrincipalMomentOfInertia
class	PrincipalMomentOfInertiaX
class	PrincipalMomentOfInertiaY
class	PrincipalMomentOfInertiaZ
class	SurfaceBase
class	PositiveVdWSurface
class	NegativeVdWSurface
class	PositivePolarVdWSurface
class	NegativePolarVdWSurface
class	HydrophobicVdWSurface
class	PolarVdWSurface
class	RelPositiveVdWSurface
class	RelNegativeVdWSurface
class	RelPositivePolarVdWSurface
class	RelNegativePolarVdWSurface
class	RelHydrophobicVdWSurface
class	RelPolarVdWSurface
class	VdWVolume
class	Density
class	VdWSurface
class	ScoringBaseFunction
class	FermiBaseFunction
class	LinearBaseFunction
class	ScoringComponent
class	ScoringFunction
class	ScoringTypes
class	AromaticRingStacking
class	BuriedPolar
class	CHPI
class	HydrogenBond
class	Lipophilic
class	ChemScoreMetal
class	NonpolarSolvation
class	PolarSolvation
class	RotationalEntropyLoss
class	VanDerWaals
class	SLICKEnergy
class	SLICKScore
class	FresnoTypes
class	ClaverieParameter
class	ElectrostaticPotentialCalculator
class	GeneralizedBornModel
class	Pair6_12InteractionEnergyProcessor
class	Pair6_12RDFIntegrator
class	PairExpInteractionEnergyProcessor
class	PairExpRDFIntegrator
class	PCMCavFreeEnergyProcessor
class	PierottiCavFreeEnergyProcessor
class	FDPB
class	ReissCavFreeEnergyProcessor
class	SolventAtomDescriptor
class	SolventDescriptor
class	SolventParameter
class	UhligCavFreeEnergyProcessor
class	AddHydrogenProcessor
class	AssignBondOrderProcessor
class	AtomBijection
class	AtomTyper
class	BindingPocketProcessor
class	BuildBondsProcessor
class	ChainBuilder
	This class provides methods for analysis of the chains in a molecule. More...
class	ClearChargeProcessor
class	ClearRadiusProcessor
class	AssignRadiusProcessor
class	AssignChargeProcessor
class	DNAMutator
class	AmberEvaluation
class	ConformationSet
class	DockingAlgorithm
class	DockResult
class	EnergeticEvaluation
class	ForceFieldEvaluation
class	GeometricFit
class	RandomEvaluation
class	FragmentDB
class	BoundingBoxProcessor
class	GeometricCenterProcessor
class	FragmentDistanceCollector
class	TranslationProcessor
class	TransformationProcessor
class	GraphEdge
class	GraphFace
class	GraphTriangle
class	GraphVertex
class	HBondProcessor
class	HybridisationProcessor
class	Kekuliser
class	NodeItem
class	EdgeItem
class	TMolecularGraph
class	MoleculeAssembler
	class, providing methods for the assembly of a structure diagram More...
class	NumericalSAS
class	RadialDistributionFunction
class	RDFIntegrator
class	RDFParameter
class	RDFSection
class	ReconstructFragmentProcessor
class	ReducedSurface
class	RSComputer
class	ResidueChecker
class	Rotamer
class	ResidueRotamerSet
class	RingAnalyser
	class, providing methods for the analysis of the structure of ringsystems More...
class	RingClusterer
	class, providing a method for agglomerative clustering of single rings to ringsystems More...
class	RMSDMinimizer
class	RotamerLibrary
	Rotamer Library Class. More...
class	RSConstructor
	class, performing the prefabication of ringsystems (i.e. providing them with relative 2D-coordinates) More...
class	RSEdge
class	RSFace
class	RSVertex
class	SASEdge
class	SASFace
class	SASVertex
class	SDGenerator
	The main class, provides methods for analysis of the input. More...
class	SecondaryStructureProcessor
class	SESEdge
class	SESFace
class	SESVertex
class	SmartsMatcher
class	SmartsParser
class	SmilesParser
class	SolventAccessibleSurface
class	SolventExcludedSurface
class	SESComputer
class	SESSingularityCleaner
class	StructureMapper
class	SurfaceProcessor
class	Triangle
class	TriangleEdge
class	TrianglePoint
class	TriangulatedSAS
class	SASTriangulator
class	TriangulatedSES
class	SESTriangulator
class	TriangulatedSurface
class	TriangulatedSphere
class	UCK
class	Directory
class	TransformationManager
class	File
class	BinaryFileAdaptor
class	FileSystem
class	TMutex
class	TMutex< QMutex >
class	TMutexLocker
class	TReadWriteLock
class	TReadWriteLock< QReadWriteLock >
class	TReadLocker
class	TWriteLocker
class	TCPIOStream
class	TCPServer
class	TCPServerThread
class	Path
class	TCPTransfer
class	Timer
class	Mainframe
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.
typedef TRegularData1D< float >	RegularData1D
typedef TRegularData2D< float >	RegularData2D
typedef TRegularData3D< float >	RegularData3D
typedef HashSet< String >	StringHashSet
typedef 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 List< RegularData3D * >	RegularData3DList
typedef TMolecularGraph< Index, Index >	MolecularGraph
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 BALL_LONG64_TYPE	LongIndex
typedef BALL_ULONG64_TYPE	LongSize
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_POINTERSIZEUINT_TYPE	PointerSizeUInt
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.
typedef std::reverse_iterator < AtomContainerConstIterator >	AtomContainerConstReverseIterator
	A constant reverse bidirectional iterator for the AtomContainer class.
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.
typedef std::reverse_iterator < AtomConstIterator >	AtomConstReverseIterator
	A constant reverse bidirectional iterator for the Atom class.
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.
typedef ConstBidirectionalIterator < Composite, Chain, Composite::CompositeIterator, ChainIteratorTraits >	ChainConstIterator
	A constant bidirectional iterator for the Chain class.
typedef std::reverse_iterator < ChainIterator >	ChainReverseIterator
	A mutable reverse bidirectional iterator for the Chain class.
typedef std::reverse_iterator < ChainConstIterator >	ChainConstReverseIterator
	A constant reverse bidirectional iterator for the Chain class.

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.
typedef ConstBidirectionalIterator < Composite, PDBAtom, Composite::CompositeIterator, PDBAtomIteratorTraits >	PDBAtomConstIterator
	A constant bidirectional iterator for the PDBAtom class.
typedef std::reverse_iterator < PDBAtomIterator >	PDBAtomReverseIterator
	A mutable reverse bidirectional iterator for the PDBAtom class.
typedef std::reverse_iterator < PDBAtomConstIterator >	PDBAtomConstReverseIterator
	A constant reverse bidirectional iterator for the PDBAtom class.
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
Convenience typedefs
typedef Peak< float >	Peak1D
typedef Peak< Vector2 >	Peak2D
typedef Peak< Vector3 >	Peak3D
Standard typedefs
typedef PeakList< Peak< float > >	PeakList1D
	1D peak list
typedef PeakList< Peak< Vector2 > >	PeakList2D
	2D peak list
typedef PeakList< Peak< Vector3 > >	PeakList3D
	3D peak list

typedef Spectrum < RegularData1D, Peak1D >	Spectrum1D
	One-dimensional spectrum.
typedef Spectrum < RegularData1D, Peak2D >	Spectrum2D
	Two-dimensional spectrum.
typedef Spectrum < RegularData1D, Peak3D >	Spectrum3D
	Three-dimensional spectrum.
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) throw (Exception::InvalidIterator)
template<>
BALL_EXPORT HashIndex	Hash (const std::pair< Position, Position > &p)
BALL_EXPORT const FacetArray &	getContourSurfaceFacetData (double threshold)
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) throw (Exception::DivisionByZero)
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) throw (Exception::DivisionByZero)
template<typename T >
BALL_INLINE T	GetDistance (const TVector3< T > &point, const TLine3< T > &line) throw (Exception::DivisionByZero)
template<typename T >
T	GetDistance (const TLine3< T > &a, const TLine3< T > &b) throw (Exception::DivisionByZero)
template<typename T >
BALL_INLINE T	GetDistance (const TVector3< T > &point, const TPlane3< T > &plane) throw (Exception::DivisionByZero)
template<typename T >
BALL_INLINE T	GetDistance (const TPlane3< T > &plane, const TVector3< T > &point) throw (Exception::DivisionByZero)
template<typename T >
BALL_INLINE T	GetDistance (const TLine3< T > &line, const TPlane3< T > &plane) throw (Exception::DivisionByZero)
template<typename T >
BALL_INLINE T	GetDistance (const TPlane3< T > &plane, const TLine3< T > &line) throw (Exception::DivisionByZero)
template<typename T >
BALL_INLINE T	GetDistance (const TPlane3< T > &a, const TPlane3< T > &b) throw (Exception::DivisionByZero)
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) throw (Exception::DivisionByZero)
template<typename T >
BALL_INLINE TAngle< T >	getOrientedAngle (const TVector3< T > &a, const TVector3< T > &b, const TVector3< T > &normal) throw (Exception::DivisionByZero)
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) throw (Exception::DivisionByZero)
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.
::std::istream &	operator>> (::std::istream &is, SnapShot &ss)
	Input stream operator for SnapShots.
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)
template<typename DataT , typename PeakT , typename PositionT >
double	operator- (const Spectrum< DataT, PeakT, PositionT > &s1, const Spectrum< DataT, PeakT, PositionT > &s2)
PyObject *	pyMapBALLObjectToSip (Composite &object)
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)
std::ostream &	operator<< (std::ostream &out, const DockResult &dock_res)
std::istream &	operator>> (std::istream &in, DockResult &dock_res)
template<typename Node , typename Edge >
std::ostream &	operator<< (std::ostream &os, const TMolecularGraph< Node, Edge > &G)
template<typename T >
std::ostream &	operator<< (std::ostream &os, const BinaryFileAdaptor< T > &data)
	Output stream for BinaryFileAdaptors.
template<typename T >
std::istream &	operator>> (std::istream &is, BinaryFileAdaptor< T > &data)
	Input stream for BinaryFileAdaptors.
template<typename T >
BALL_INLINE void	swapBytes (T &t)
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)
Notification Management.
Using the notification management, objects may exchange data and notify each other of events by invoking methods of the other object (remotely similar to the signal/slot mechanism of QT).
NotificationManager_ &	NotificationManager ()
void	NotificationManagerEnable ()
void	NotificationManagerDisable ()
bool	NotificationManagerIsEnabled ()
bool	NotificationManagerIsDisabled ()
template<class NotificationSource >
void	NotificationSourceEnable (NotificationSource &notification_source)
template<class NotificationSource >
void	NotificationSourceDisable (NotificationSource &notification_source)
template<class NotificationSource >
bool	NotificationSourceIsEnabled (NotificationSource &notification_source)
template<class NotificationSource >
bool	NotificationSourceIsDisabled (NotificationSource &notification_source)
template<class Source , class Target >
void	NotificationRegister (const Source &source, const Target &target)
template<class Source , class Target , class T1 >
void	NotificationRegister1 (const Source &source, const Target &target, const T1 &)
template<class NotificationSource , class NotificationTarget , class T1 , class T2 >
void	NotificationRegister2 (const NotificationSource &notification_source, const NotificationTarget &notification_target, const T1 &, const T2 &)
void	NotificationUnregisterAll ()
template<class NotificationSource >
void	NotificationUnregister (const NotificationSource &notification_source)
template<class Source , class Target >
void	NotificationUnregister (const Source &source, const Target &target)
template<class NotificationSource , class NotificationTarget , class T1 >
void	NotificationUnregister1 (const NotificationSource &notification_source, const NotificationTarget &notification_target, const T1 &)
template<class NotificationSource , class NotificationTarget , class T1 , class T2 >
void	NotificationUnregister2 (const NotificationSource &notification_source, const NotificationTarget &notification_target, const T1 &, const T2 &)
template<class NotificationSource >
bool	NotificationIsRegistered (const NotificationSource &notification_source)
template<class Source , class Target >
bool	NotificationIsRegistered (const Source &source, const Target &target)
template<class NotificationSource >
bool	Notify (NotificationSource &notification_source)
template<class NotificationSource , class T1 >
bool	Notify (NotificationSource &notification_source, const T1 &data1)
template<class NotificationSource , class T1 , class T2 >
bool	Notify (NotificationSource &notification_source, const T1 &data1, const T2 &data2)

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.
template<typename ValueType >
std::istream &	operator>> (std::istream &is, TRegularData1D< ValueType > &grid)
	Input operator.
Stream I/O

template<typename ValueType >
std::ostream &	operator<< (std::ostream &os, const TRegularData2D< ValueType > &data)
	Output operator.
template<typename ValueType >
std::istream &	operator>> (std::istream &is, TRegularData2D< ValueType > &grid)
	Input operator.
Stream I/O

template<typename ValueType >
std::ostream &	operator<< (std::ostream &os, const TRegularData3D< ValueType > &grid)
	Output operator.
template<typename ValueType >
std::istream &	operator>> (std::istream &is, TRegularData3D< ValueType > &grid)
	Input operator.

std::ostream &	operator<< (std::ostream &s, const NMRAtomData &ad)
std::ostream &	operator<< (std::ostream &s, const SampleCondition &sc)
std::ostream &	operator<< (std::ostream &s, const ShiftReferenceElement &sre)
std::ostream &	operator<< (std::ostream &s, const ShiftReferenceSet &sr)
std::ostream &	operator<< (std::ostream &s, const NMRAtomDataSet &set)

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)
Storers
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)
Storers
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)
Storers
Stream operators of Line3
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)
Storers
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)
Storers
Stream operators for class TPlane3
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)
Storers
Stream operators for the class Sphere
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)
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)
Global binary operators for three-dimensional vectors.
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 Angle	calculateBondAngle (const Atom &a1, const Atom &a2, const Atom &a3) throw (Exception::IllegalPosition)
Fast Numerical Calculation of Solvent Accessible Surface Area.
These functions are loosely based on the algorithm by Eisenhaber, Lijnzaad, Argos, Sander, and Scharf ("The Double Cubic Lattice Method: Efficient Approaches to numerical Integration of Surface Area and Volume and to Dot Surface Contouring of Molecular Assemblies", J. Comput. Chem. (1995), 15 , 273-284) and Eisenhaber and Argos ("Improved Strategy in Analytic Surface Calculation for Molecular Systems: Handling of Singularities and Computational Efficiency" J. Comput. Chem. (1993), 14 , 1272-1280).
BALL_EXPORT BALL_DEPRECATED float	calculateSASArea (const AtomContainer &fragment, float probe_radius=1.5, Size number_of_dots=400)
BALL_EXPORT BALL_DEPRECATED float	calculateSASVolume (const AtomContainer &fragment, float probe_radius=1.5, Size number_of_dots=400)
BALL_EXPORT BALL_DEPRECATED float	calculateSASAtomAreas (const AtomContainer &fragment, HashMap< const Atom *, float > &atom_areas, float probe_radius=1.5, Size number_of_dots=400)
BALL_EXPORT BALL_DEPRECATED float	calculateSASPoints (const AtomContainer &fragment, Surface &surface_points, float probe_radius=1.5, Size number_of_dots=400)
BALL_EXPORT BALL_DEPRECATED float	calculateSASAtomPoints (const AtomContainer &fragment, std::vector< std::pair< Vector3, Surface > > &atom_surfaces, float probe_radius=1.5, Size number_of_dots=400)
Storers
BALL_EXPORT std::ostream &	operator<< (std::ostream &s, const ReducedSurface &rs)
Storers
BALL_EXPORT std::ostream &	operator<< (std::ostream &s, const RSEdge &rsedge)
Storers
BALL_EXPORT std::ostream &	operator<< (std::ostream &s, const RSFace &rsface)
Storers
BALL_EXPORT std::ostream &	operator<< (std::ostream &s, const RSVertex &rsvertex)
Storers
BALL_EXPORT std::ostream &	operator<< (std::ostream &s, const SASEdge &sasedge)
Storers
BALL_EXPORT std::ostream &	operator<< (std::ostream &s, const SASFace &sasface)
Storers
BALL_EXPORT std::ostream &	operator<< (std::ostream &s, const SASVertex &sasvertex)
Storers
BALL_EXPORT std::ostream &	operator<< (std::ostream &s, const SESEdge &sesedge)
Storers
BALL_EXPORT std::ostream &	operator<< (std::ostream &s, const SESFace &sesface)
Storers
BALL_EXPORT std::ostream &	operator<< (std::ostream &s, const SESVertex &sesvertex)
Storers
BALL_EXPORT std::ostream &	operator<< (std::ostream &s, const SolventAccessibleSurface &sas)
Storers
BALL_EXPORT std::ostream &	operator<< (std::ostream &s, const SolventExcludedSurface &ses)
Storers
BALL_EXPORT std::ostream &	operator<< (std::ostream &s, const Triangle &triangle)
Storers
BALL_EXPORT std::ostream &	operator<< (std::ostream &s, const TriangleEdge &edge)
Storers
BALL_EXPORT std::ostream &	operator<< (std::ostream &s, const TrianglePoint &point)
Storers
BALL_EXPORT std::ostream &	operator<< (std::ostream &s, const TriangulatedSurface &surface)
Variables
static const Distance	INVALID_DISTANCE = INT_MIN
static const Distance	DISTANCE_MIN = (INT_MIN + 1)
static const Distance	DISTANCE_MAX = INT_MAX
static const Handle	INVALID_HANDLE = INT_MAX
static const Handle	HANDLE_MIN = 0
static const Handle	HANDLE_MAX = INT_MAX - 1
static const Index	INVALID_INDEX = -1
static const Index	INDEX_MIN = 0
static const Index	INDEX_MAX = INT_MAX
static const Position	INVALID_POSITION = INT_MAX
static const Position	POSITION_MIN = 0
static const Position	POSITION_MAX = INT_MAX - 1
static const Size	INVALID_SIZE = INT_MAX
static const Size	SIZE_MIN = 0
static const Size	SIZE_MAX = INT_MAX - 1
bool	clone_bonds
BALL_EXPORT PTE_	PTE
StringHashMap< double * > *	ParsedFunctionConstants
StringHashMap< double()(double)>	ParsedFunctionFunctions
static const double	INFINITY = Limits<double>::max()
Size	MMFF94_number_atom_types
	hold the maximum number of MMFF94 atom types + 1 (wildcard)
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, TSimpleBox3< T > &box)
template<typename T >
std::ostream &	operator<< (std::ostream &s, const TSimpleBox3< T > &box)

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.

typedef Atom::BondConstIterator BALL::AtomBondConstIterator

A constant iterator for atom bonds.

typedef Atom::BondConstReverseIterator BALL::AtomBondConstReverseIterator

A constant reverse iterator for atom bonds.

typedef Atom::BondIterator BALL::AtomBondIterator

A mutable iterator for atom bonds.

typedef Atom::BondReverseIterator BALL::AtomBondReverseIterator

A mutable reverse iterator for atom bonds.

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

A constant bidirectional iterator for the Atom class.

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

A constant reverse bidirectional iterator for the Atom class.

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

A constant bidirectional iterator for the AtomContainer class.

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

A constant reverse bidirectional iterator for the AtomContainer class.

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

A mutable bidirectional iterator for the AtomContainer class.

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

A mutable reverse bidirectional iterator for the AtomContainer class.

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

A mutable bidirectional iterator for the Atom class.

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

A mutable reverse bidirectional iterator for the Atom class.

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

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

A constant bidirectional iterator for the Chain class.

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

A constant reverse bidirectional iterator for the Chain class.

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

A mutable bidirectional iterator for the Chain class.

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

A mutable reverse bidirectional iterator for the Chain class.

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

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

typedef TContourLine<float> BALL::ContourLine

Default type

typedef TContourSurface<float> BALL::ContourSurface

Default type.

typedef BALL_INDEX_TYPE BALL::Distance

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

: Size: 32 bit

: persistent

typedef double BALL::DoubleReal

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

: Size: 64 bit

: persistent

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

typedef Experiment<PeakList1D> BALL::Experiment1D

1D NMR experiment

typedef Experiment<PeakList3D> BALL::Experiment3D

2D NMR experiment 3D NMR experiment

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

typedef TFFT1D<BALL_FFTW_DEFAULT_TRAITS> BALL::FFT1D

Default type

typedef TFFT2D<BALL_FFTW_DEFAULT_TRAITS> BALL::FFT2D

Default type

typedef TFFT3D<BALL_FFTW_DEFAULT_TRAITS> BALL::FFT3D

Default type

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

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

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

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

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

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

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

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

An interval is defined by its limits

typedef UnaryPredicate<Composite> BALL::KernelPredicateType

typedef BALL_LONG64_TYPE BALL::LongIndex

Long index type. Use this type to represent very long (64 bit) indices. Theses indices may be signed, contrary to the LongSize type.

: Size: 64 bit

: persistent

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

typedef BALL_ULONG64_TYPE BALL::LongSize

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

: Size: 64 bit

: persistent

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

typedef TMolecularGraph<Index, Index> BALL::MolecularGraph

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

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

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

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

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

typedef TMutex<BALL_DEFAULT_MUTEX_TYPE> BALL::Mutex

typedef TMutexLocker<BALL_DEFAULT_MUTEXLOCKER_TYPE, BALL_DEFAULT_MUTEX_TYPE> BALL::MutexLocker

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

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

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

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

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

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

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

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

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

A constant bidirectional iterator for the PDBAtom class.

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

A constant reverse bidirectional iterator for the PDBAtom class.

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

A mutable bidirectional iterator for the PDBAtom class.

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

A mutable reverse bidirectional iterator for the PDBAtom class.

typedef Peak<float> BALL::Peak1D

typedef Peak<Vector2> BALL::Peak2D

typedef Peak<Vector3> BALL::Peak3D

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

1D peak list

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

2D peak list

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

3D peak list

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)

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

typedef BALL_SIZE_TYPE BALL::Property

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

: Size: 32 bit

: persistent

See also:: PropertyManager

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

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

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

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

typedef TQuaternion<float> BALL::Quaternion

typedef TReadLocker<BALL_DEFAULT_READLOCKER_TYPE, BALL_DEFAULT_READWRITELOCK_TYPE> BALL::ReadLocker

typedef TReadWriteLock<BALL_DEFAULT_READWRITELOCK_TYPE> BALL::ReadWriteLock

typedef float BALL::Real

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

: Size: 32 bit

: persistent

typedef TRegularData1D<float> BALL::RegularData1D

Default type

typedef TRegularData2D<float> BALL::RegularData2D

Default type

typedef TRegularData3D<float> BALL::RegularData3D

Default type

typedef List<RegularData3D*> BALL::RegularData3DList

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

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

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

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

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

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

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

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

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

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

typedef TVector3<float> BALL::Vector3

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

typedef TWriteLocker<BALL_DEFAULT_WRITELOCKER_TYPE, BALL_DEFAULT_READWRITELOCK_TYPE> BALL::WriteLocker

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

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 BALL_DEPRECATED float BALL::calculateSASArea	(	const AtomContainer &	fragment,
		float	probe_radius = `1.5`,
		Size	number_of_dots = `400`
	)

Calculate the solvent accessible surface area numerically. This method returns the total Solvent Accessible Surface (SAS) of a BALL kernel object. Atoms with a radius of 0 are ignored.

Parameters:

	fragment	the kernel object containing the atoms
	probe_radius	the probe radius used for the SAS
	number_of_dots	the number of dots used per atom

Returns:: the total SAS area in $ A^2$

Deprecated:: Use NumericalSAS::getTotalArea() instead

BALL_EXPORT BALL_DEPRECATED float BALL::calculateSASAtomAreas	(	const AtomContainer &	fragment,
		HashMap< const Atom *, float > &	atom_areas,
		float	probe_radius = `1.5`,
		Size	number_of_dots = `400`
	)

Calculate the Solvent Accessible Surface area for each atom. This method returns the surface fraction of each atom at the Solvent Accessible Surface (SAS). Atoms with a radius of 0 are ignored. All areas are in $ A^2$.

Parameters:

	atom_areas	a hash map containing the areas of the atoms (returned)
	fragment	the kernel object containing the atoms
	probe_radius	the probe radius used for the SAS
	number_of_dots	the number of dots used per atom

Returns:: the total SAS area in $ A^2$

Deprecated:: Use NumericalSAS::getAtomAreas() instead

BALL_EXPORT BALL_DEPRECATED float BALL::calculateSASAtomPoints	(	const AtomContainer &	fragment,
		std::vector< std::pair< Vector3, Surface > > &	atom_surfaces,
		float	probe_radius = `1.5`,
		Size	number_of_dots = `400`
	)

Calculate a point set on the Solvent Accessible Surface for each atom. This method returns the point sets on the SAS used to calculate the surface area for each atom.

See also:: calculateSASAtomAreas

Parameters:

	fragment	the kernel object containing the atoms
	atom_surfaces	a hashmap of atoms and Surface objects containing the point sets for each atom (returned)
	probe_radius	the probe radius used for the SAS
	number_of_dots	the number of dots used per atom

Returns:: the total SAS area in $ A^2$

Deprecated:: Use NumericalSAS::getSurfaceMap() instead

BALL_EXPORT BALL_DEPRECATED float BALL::calculateSASPoints	(	const AtomContainer &	fragment,
		Surface &	surface_points,
		float	probe_radius = `1.5`,
		Size	number_of_dots = `400`
	)

Calculate a point set on the Solvent Accessible Surface. This method returns the points on the Solvent Accessible Surface (SAS) used to calculate the surface area. The Surface object holds just the vertices, it does not contain any triangles. The normals for each point normals to the SAS in that point, their length equals the fraction of the surface area represented by this point in $ A^2$:

$|\vec{n_i}| = \frac{\mathrm{SAS\quad\ of \quad atom} \quad i}{\mathrm{number\quad of\quad points\quad on\quad the\quad SAS\quad of\quad atom} \quad i}$

Atoms with a radius of 0 are ignored.

Parameters:

	surface_points	a surface object containing the point coordinates and their normals (returned)
	fragment	the kernel object containing the atoms
	probe_radius	the probe radius used for the SAS
	number_of_dots	the number of dots used per atom

Returns:: the total SAS area in $ A^2$

Deprecated:: Use NumericalSAS::getSurface() instead

BALL_EXPORT BALL_DEPRECATED float BALL::calculateSASVolume	(	const AtomContainer &	fragment,
		float	probe_radius = `1.5`,
		Size	number_of_dots = `400`
	)

Calculate the solvent accessible volume numerically. This method returns the total volume enclosd by the Solvent Accessible Surface (SAS) of a BALL kernel object. Atoms with a radius of 0 are ignored.

Parameters:

	fragment	the kernel object containing the atoms
	probe_radius	the probe radius used for the SAS
	number_of_dots	the number of dots used per atom

Returns:: the volume in $ A^3$

Deprecated:: Use NumericalSAS::getTotalVolume() instead

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 ) [inline]

template<class NucleotideContainerType >

const Nucleotide* BALL::get5Prime ( const NucleotideContainerType & nucleotide_container ) [inline]

References BALL::ConstBidirectionalIterator< Container, DataType, Position, Traits >::isEnd().

BALL_EXPORT const FacetArray& BALL::getContourSurfaceFacetData ( double threshold )

Referenced by BALL::TContourSurface< T >::operator<<().

template<class ResidueContainerType >

const Residue* BALL::getCTerminal ( const ResidueContainerType & residue_container ) [inline]

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.

Referenced by BALL::HashSet< Key >::rehash().

template<class ResidueContainerType >

const Residue* BALL::getNTerminal ( const ResidueContainerType & residue_container ) [inline]

template<>

BALL_EXPORT HashIndex BALL::Hash ( const std::pair< Position, Position > & p ) [inline]

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

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

References hashPointer().

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 .

References hashString().

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 .

References hashString().

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

Referenced by BALL::HashSet< Key >::hash(), and BALL::HashFunction< T >::operator()().

BALL_EXPORT HashIndex BALL::hashElfString ( const char * str )

BALL_EXPORT HashIndex BALL::hashPJWString ( const char * str )

BALL_EXPORT HashIndex BALL::hashPointer ( void *const ptr )

Referenced by Hash().

BALL_EXPORT HashIndex BALL::hashString ( const char * str )

Referenced by Hash().

template<class Source , class Target >

bool BALL::NotificationIsRegistered	(	const Source &	source,
		const Target &	target
	)			`[inline]`

References BALL::NotificationManager_::isInserted(), and NotificationManager().

template<class NotificationSource >

bool BALL::NotificationIsRegistered ( const NotificationSource & notification_source ) [inline]

References BALL::NotificationManager_::isInserted(), and NotificationManager().

NotificationManager_& BALL::NotificationManager ( )

Referenced by NotificationIsRegistered(), NotificationRegister(), NotificationRegister1(), NotificationRegister2(), NotificationSourceDisable(), NotificationSourceEnable(), NotificationSourceIsDisabled(), NotificationSourceIsEnabled(), NotificationUnregister(), NotificationUnregister1(), NotificationUnregister2(), and Notify().

void BALL::NotificationManagerDisable ( )

void BALL::NotificationManagerEnable ( )

bool BALL::NotificationManagerIsDisabled ( )

bool BALL::NotificationManagerIsEnabled ( )

template<class Source , class Target >

void BALL::NotificationRegister	(	const Source &	source,
		const Target &	target
	)			`[inline]`

References BALL::NotificationManager_::insert(), and NotificationManager().

template<class Source , class Target , class T1 >

void BALL::NotificationRegister1	(	const Source &	source,
		const Target &	target,
		const T1 &
	)			`[inline]`

References BALL::NotificationManager_::insert(), and NotificationManager().

template<class NotificationSource , class NotificationTarget , class T1 , class T2 >

void BALL::NotificationRegister2	(	const NotificationSource &	notification_source,
		const NotificationTarget &	notification_target,
		const T1 &	,
		const T2 &
	)			`[inline]`

References BALL::NotificationManager_::insert(), and NotificationManager().

template<class NotificationSource >

void BALL::NotificationSourceDisable ( NotificationSource & notification_source ) [inline]

References BALL::NotificationSource_::disable(), BALL::NotificationManager_::findSource(), and NotificationManager().

template<class NotificationSource >

void BALL::NotificationSourceEnable ( NotificationSource & notification_source ) [inline]

References BALL::NotificationSource_::enable(), BALL::NotificationManager_::findSource(), and NotificationManager().

template<class NotificationSource >

bool BALL::NotificationSourceIsDisabled ( NotificationSource & notification_source ) [inline]

References NotificationManager().

template<class NotificationSource >

bool BALL::NotificationSourceIsEnabled ( NotificationSource & notification_source ) [inline]

References NotificationManager().

template<class Source , class Target >

void BALL::NotificationUnregister	(	const Source &	source,
		const Target &	target
	)			`[inline]`

References NotificationManager(), and BALL::NotificationManager_::remove().

template<class NotificationSource >

void BALL::NotificationUnregister ( const NotificationSource & notification_source ) [inline]

References NotificationManager(), and BALL::NotificationManager_::remove().

template<class NotificationSource , class NotificationTarget , class T1 >

void BALL::NotificationUnregister1	(	const NotificationSource &	notification_source,
		const NotificationTarget &	notification_target,
		const T1 &
	)			`[inline]`

References NotificationManager(), and BALL::NotificationManager_::remove().

template<class NotificationSource , class NotificationTarget , class T1 , class T2 >

void BALL::NotificationUnregister2	(	const NotificationSource &	notification_source,
		const NotificationTarget &	notification_target,
		const T1 &	,
		const T2 &
	)			`[inline]`

References NotificationManager(), and BALL::NotificationManager_::remove().

void BALL::NotificationUnregisterAll ( )

template<class NotificationSource , class T1 , class T2 >

bool BALL::Notify	(	NotificationSource &	notification_source,
		const T1 &	data1,
		const T2 &	data2
	)			`[inline]`

References BALL::NotificationTarget2< NotificationSource, T1, T2 >::countNotificationTypes_(), BALL::NotificationTarget2< NotificationSource, T1, T2 >::getNotificationType_(), BALL::NotificationTarget2< NotificationSource, T1, T2 >::getVirtualNotificationType_(), and NotificationManager().

template<class NotificationSource , class T1 >

bool BALL::Notify	(	NotificationSource &	notification_source,
		const T1 &	data1
	)			`[inline]`

References BALL::NotificationTarget1< NotificationSource, T1 >::countNotificationTypes_(), BALL::NotificationTarget1< NotificationSource, T1 >::getNotificationType_(), and NotificationManager().

template<class NotificationSource >

bool BALL::Notify ( NotificationSource & notification_source ) [inline]

References BALL::NotificationTarget< NotificationSource >::countNotificationTypes_(), BALL::NotificationTarget< NotificationSource >::getNotificationType_(), BALL::NotificationTarget< NotificationSource >::getVirtualNotificationType_(), NotificationManager(), and BALL::NotificationTarget< NotificationSource >::onNotify().

template<typename T >

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

References BALL::TMatrix4x4< T >::m11, BALL::TMatrix4x4< T >::m12, BALL::TMatrix4x4< T >::m13, BALL::TMatrix4x4< T >::m14, BALL::TMatrix4x4< T >::m21, BALL::TMatrix4x4< T >::m22, BALL::TMatrix4x4< T >::m23, BALL::TMatrix4x4< T >::m24, BALL::TMatrix4x4< T >::m31, BALL::TMatrix4x4< T >::m32, BALL::TMatrix4x4< T >::m33, BALL::TMatrix4x4< T >::m34, BALL::TVector3< T >::x, BALL::TVector3< T >::y, and BALL::TVector3< T >::z.

template<typename T >

TMatrix4x4< T > BALL::operator*	(	const T &	scalar,
		const TMatrix4x4< T > &	m
	)			`[inline]`

References BALL::TMatrix4x4< T >::m11, BALL::TMatrix4x4< T >::m12, BALL::TMatrix4x4< T >::m13, BALL::TMatrix4x4< T >::m14, BALL::TMatrix4x4< T >::m21, BALL::TMatrix4x4< T >::m22, BALL::TMatrix4x4< T >::m23, BALL::TMatrix4x4< T >::m24, BALL::TMatrix4x4< T >::m31, BALL::TMatrix4x4< T >::m32, BALL::TMatrix4x4< T >::m33, BALL::TMatrix4x4< T >::m34, BALL::TMatrix4x4< T >::m41, BALL::TMatrix4x4< T >::m42, BALL::TMatrix4x4< T >::m43, and BALL::TMatrix4x4< T >::m44.

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
	)			throw (Exception::InvalidIterator) `[inline]`

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

template<typename DataT , typename PeakT , typename PositionT >

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

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

References BALL::Spectrum< DataT, PeakT, PositionT >::difference().

template<typename T >

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

Output stream for BinaryFileAdaptors.

References swapBytes().

BALL_EXPORT std::ostream& BALL::operator<<	(	std::ostream &	s,
		const TriangulatedSurface &	surface
	)

Output- Operator

BALL_EXPORT std::ostream& BALL::operator<<	(	std::ostream &	s,
		const TrianglePoint &	point
	)

Output- Operator

BALL_EXPORT std::ostream& BALL::operator<<	(	std::ostream &	s,
		const TriangleEdge &	edge
	)

Output- Operator

BALL_EXPORT std::ostream& BALL::operator<<	(	std::ostream &	s,
		const Triangle &	triangle
	)

Output- Operator

BALL_EXPORT std::ostream& BALL::operator<<	(	std::ostream &	s,
		const SolventExcludedSurface &	ses
	)

Output- Operator

BALL_EXPORT std::ostream& BALL::operator<<	(	std::ostream &	s,
		const SolventAccessibleSurface &	sas
	)

Output- Operator

BALL_EXPORT std::ostream& BALL::operator<<	(	std::ostream &	s,
		const SESVertex &	sesvertex
	)

Output- Operator

BALL_EXPORT std::ostream& BALL::operator<<	(	std::ostream &	s,
		const SESFace &	sesface
	)

Output- Operator

BALL_EXPORT std::ostream& BALL::operator<<	(	std::ostream &	s,
		const SESEdge &	sesedge
	)

Output- Operator

BALL_EXPORT std::ostream& BALL::operator<<	(	std::ostream &	s,
		const SASVertex &	sasvertex
	)

Output- Operator

BALL_EXPORT std::ostream& BALL::operator<<	(	std::ostream &	s,
		const SASFace &	sasface
	)

Output- Operator

BALL_EXPORT std::ostream& BALL::operator<<	(	std::ostream &	s,
		const SASEdge &	sasedge
	)

Output- Operator

BALL_EXPORT std::ostream& BALL::operator<<	(	std::ostream &	s,
		const RSVertex &	rsvertex
	)

Output- Operator prints out a rsvertex

BALL_EXPORT std::ostream& BALL::operator<<	(	std::ostream &	s,
		const RSFace &	rsface
	)

Output- Operator

BALL_EXPORT std::ostream& BALL::operator<<	(	std::ostream &	s,
		const RSEdge &	rsedge
	)

Output- Operator

BALL_EXPORT std::ostream& BALL::operator<<	(	std::ostream &	s,
		const ReducedSurface &	rs
	)

Output- Operator. Prints out a ReducedSurface

template<typename Node , typename Edge >

std::ostream& BALL::operator<<	(	std::ostream &	os,
		const TMolecularGraph< Node, Edge > &	G
	)			`[inline]`

References BALL::TMolecularGraph< Node, Edge >::beginEdge(), BALL::TMolecularGraph< Node, Edge >::endEdge(), and BALL::TMolecularGraph< Node, Edge >::endNode().

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

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

template<typename PositionType >

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

Output operator

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

Output stream operator for SnapShots.

template<typename T >

std::ostream& BALL::operator<<	(	std::ostream &	s,
		const TSphere3< T > &	sphere
	)			`[inline]`

Output Operator. Write the contents of p and radius to an output stream. The values are enclose in brackets.

: Example:

: ((0 1 1.5) 0.4)

template<typename T >

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

template<typename ComplexTraits >

const RegularData3D& BALL::operator<<	(	RegularData3D &	to,
		const TFFT3D< ComplexTraits > &	from
	)			`[inline]`

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

template<typename ComplexTraits >

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

Global assignment operator from TFFT3D to TRegularData3D<Complex>

References BALL::TVector3< T >::set().

template<typename ComplexTraits >

const RegularData2D& BALL::operator<<	(	RegularData2D &	to,
		const TFFT2D< ComplexTraits > &	from
	)			`[inline]`

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

template<typename ComplexTraits >

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

Global assignment operator from TFFT2D to TRegularData2D<Complex>

References BALL::TVector2< T >::set().

template<typename ComplexTraits >

const RegularData1D& BALL::operator<<	(	RegularData1D &	to,
		const TFFT1D< ComplexTraits > &	from
	)			`[inline]`

References BALL::TRegularData1D< ValueType >::setDimension(), and BALL::TRegularData1D< ValueType >::setOrigin().

template<typename T >

std::ostream& BALL::operator<<	(	std::ostream &	s,
		const TBox3< T > &	box
	)			`[inline]`

Output Operator. Writes the two coordinates of the box to an output stream. The vectors are enclosed by brackets.

: Example:

: ((0 1 2) (7.5 3.4 10))

See also:: TVector3::operator<<

template<typename T >

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

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.

std::ostream& BALL::operator<<	(	std::ostream &	s,
		const NMRAtomDataSet &	set
	)

std::ostream& BALL::operator<<	(	std::ostream &	s,
		const ShiftReferenceSet &	sr
	)

std::ostream& BALL::operator<<	(	std::ostream &	s,
		const ShiftReferenceElement &	sre
	)

std::ostream& BALL::operator<<	(	std::ostream &	s,
		const SampleCondition &	sc
	)

std::ostream& BALL::operator<<	(	std::ostream &	s,
		const NMRAtomData &	ad
	)

template<typename ValueType >

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

Output operator.

template<typename ValueType >

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

Output operator.

template<typename ValueType >

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

Output operator.

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

Print the contents of a TimeStamp object to a stream.

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

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

template<typename T >

std::istream& BALL::operator>>	(	std::istream &	is,
		BinaryFileAdaptor< T > &	data
	)			`[inline]`

Input stream for BinaryFileAdaptors.

References BALL::BinaryFileAdaptor< T >::getData(), BALL::BinaryFileAdaptor< T >::getSwapEndian(), BALL::BinaryFileAdaptor< T >::setData(), and swapBytes().

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

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

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

Input stream operator for SnapShots.

template<typename T >

std::istream& BALL::operator>>	(	std::istream &	s,
		TSphere3< T > &	sphere
	)			`[inline]`

Input operator. Reads in an instance of TVector3 and a T value : p, radius.

References BALL::Constants::c, BALL::TSphere3< T >::p, and BALL::TSphere3< T >::radius.

template<typename T >

std::istream& BALL::operator>>	(	std::istream &	s,
		TQuaternion< T > &	q
	)			`[inline]`

References BALL::Constants::c, BALL::TQuaternion< T >::i(), BALL::TQuaternion< T >::j(), BALL::TQuaternion< T >::k(), and BALL::TQuaternion< T >::w().

template<typename T >

std::istream& BALL::operator>>	(	std::istream &	s,
		TBox3< T > &	box
	)			`[inline]`

Input operator. Reads in two objects of type TVector3 a and b

References BALL::TBox3< T >::setDepth(), BALL::TBox3< T >::setHeightVector(), BALL::TBox3< T >::setPoint(), and BALL::TBox3< T >::setRightVector().

template<typename T >

std::istream& BALL::operator>>	(	std::istream &	s,
		TAngle< T > &	angle
	)			`[inline]`

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

References BALL::Constants::c, and BALL::TAngle< T >::value.

template<typename ValueType >

std::istream& BALL::operator>>	(	std::istream &	is,
		TRegularData3D< ValueType > &	grid
	)			`[inline]`

Input operator.

References BALL::TRegularData3D< ValueType >::begin(), BALL::TRegularData3D< ValueType >::resize(), BALL::TRegularData3D< ValueType >::setDimension(), BALL::TRegularData3D< ValueType >::setOrigin(), BALL::TRegularData3D< ValueType >::IndexType::x, BALL::TVector3< T >::x, BALL::TRegularData3D< ValueType >::IndexType::y, BALL::TVector3< T >::y, BALL::TRegularData3D< ValueType >::IndexType::z, and BALL::TVector3< T >::z.

template<typename ValueType >

std::istream& BALL::operator>>	(	std::istream &	is,
		TRegularData2D< ValueType > &	grid
	)			`[inline]`

Input operator.

References BALL::TRegularData2D< ValueType >::begin(), BALL::TRegularData2D< ValueType >::resize(), BALL::TRegularData2D< ValueType >::setDimension(), BALL::TRegularData2D< ValueType >::setOrigin(), BALL::TRegularData2D< ValueType >::IndexType::x, BALL::TVector2< T >::x, BALL::TRegularData2D< ValueType >::IndexType::y, and BALL::TVector2< T >::y.

template<typename ValueType >

std::istream& BALL::operator>>	(	std::istream &	is,
		TRegularData1D< ValueType > &	grid
	)			`[inline]`

Input operator.

References BALL::TRegularData1D< ValueType >::begin(), BALL::TRegularData1D< ValueType >::resize(), BALL::TRegularData1D< ValueType >::setDimension(), and BALL::TRegularData1D< ValueType >::setOrigin().

BALL_EXPORT void BALL::sleepFor ( Size mseconds )

template<typename T >

BALL_INLINE void BALL::swapBytes ( T & t ) [inline]

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

References BALL::LogStream::error(), and Log.

Referenced by operator<<(), and operator>>().

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 = INT_MAX [static]

const Distance BALL::DISTANCE_MIN = (INT_MIN + 1) [static]

const Handle BALL::HANDLE_MAX = INT_MAX - 1 [static]

const Handle BALL::HANDLE_MIN = 0 [static]

const Index BALL::INDEX_MAX = INT_MAX [static]

const Index BALL::INDEX_MIN = 0 [static]

const double BALL::INFINITY = Limits<double>::max() [static]

const Distance BALL::INVALID_DISTANCE = INT_MIN [static]

const Handle BALL::INVALID_HANDLE = INT_MAX [static]

const Index BALL::INVALID_INDEX = -1 [static]

Referenced by BALL::ResourceEntry::IteratorTraits_::forward(), BALL::HashGrid3< Item >::getIndex_(), BALL::HashGrid3< Item >::getIndices(), and BALL::ResourceEntry::IteratorTraits_::pop().

const Position BALL::INVALID_POSITION = INT_MAX [static]

Referenced by BALL::HashGrid3< Item >::getIndices(), and BALL::HashSet< Key >::IteratorTraits::invalidate().

const Size BALL::INVALID_SIZE = INT_MAX [static]

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 = INT_MAX - 1 [static]

const Position BALL::POSITION_MIN = 0 [static]

const Size BALL::SIZE_MAX = INT_MAX - 1 [static]

const Size BALL::SIZE_MIN = 0 [static]

BALL Namespace Reference

Namespaces

Classes

Typedefs

Enumerations

Functions

Variables

Storers

Typedef Documentation

Enumeration Type Documentation

Function Documentation

Variable Documentation