BALL Namespace Reference

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

Classes
class	GlobalInitializer
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	Object
class	ObjectCreator
class	PersistenceManager
class	PersistentObject
class	UnaryPredicate
class	BinaryPredicate
class	PreferencesObject
class	Processor
class	UnaryProcessor
class	ConstUnaryProcessor
class	BinaryProcessor
class	ConstBinaryProcessor
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	MolecularGraph
class	TreeWidthImplementation
class	TreeWidth
class	HashGrid3
	Three-dimensional Hash Grid Class. More...
class	HashGridBox3
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	Conformation
class	ConformationSet
class	Constraint
class	ReferenceArea
class	PharmacophoreConstraint
class	DockingAlgorithm
class	DockResult
class	FlexDefinition
class	FlexibleMolecule
class	GridAnalysis
class	PoseClustering
	Computation of clusters of docking poses. More...
class	Receptor
class	Result
class	SideChainOptimizer
class	StaticLigandFragment
class	StructurePreparer
class	DockProblem
class	EvolutionaryDocking
class	GenericGene
class	DoubleGene
class	QuaternionGene
class	GeneticAlgorithm
class	GeneticIndividual
class	GenericParameter
class	DoubleParameter
class	QuaternionParameter
class	RotateBond
class	RotateBonds
class	GeometricFit
class	IMGDock
class	ComposedEnergyProcessor
class	EnergyProcessor
class	AmiraMeshFile
class	AntechamberFile
class	Bruker1DFile
class	Bruker2DFile
class	CCP4File
class	CIFFile
class	CommandlineParser
class	DCDFile
class	DockResultFile
class	DSN6File
class	GAMESSDatFile
class	GAMESSLogFile
class	GenericMolFile
class	HINFile
class	HMOFile
class	INIFile
class	JCAMPFile
class	KCFFile
class	LineBasedFile
class	MOL2File
class	MOLFile
class	MolFileFactory
class	MOPACInputFile
class	MOPACOutputFile
class	NMRStarFile
	This class provides methods for reading and assigning chemical shifts. More...
class	Parameters
class	ParameterSection
class	ParamFile
class	PDBFile
class	PDBInfo
class	PDBRecords
class	PubChemDownloader
	Downloads PubChem entries. More...
class	ResourceEntry
class	ResourceFile
class	SCWRLRotamerFile
	Reads Dunbrack/SCWRL rotamer library files. More...
class	SDFile
class	TrajectoryFile
class	TrajectoryFileFactory
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	MolecularInteractions
class	Molecule
class	MoleculeIteratorTraits
class	NucleicAcid
class	NucleicAcidIteratorTraits
class	Nucleotide
class	NucleotideIteratorTraits
class	PDBAtom
class	PDBAtomIteratorTraits
class	KernelPredicate
	Kernel predicate class. More...
class	KernelPredicate< Atom >
class	KernelPredicate< Molecule >
class	KernelPredicate< Protein >
class	KernelPredicate< Fragment >
class	KernelPredicate< Residue >
class	KernelPredicate< Chain >
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	CubicSpline1D
class	CubicSpline2D
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
	Default Type. More...
class	NumericalIntegrator
class	ParsedFunction
class	PiecewiseFunction
class	PiecewisePolynomial
class	TPlane3
class	TQuaternion
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	BendComponent
class	ChargeRuleProcessor
class	ForceField
class	ForceFieldComponent
class	Gradient
class	PeriodicBoundary
class	RadiusRuleProcessor
class	RuleEvaluator
class	RuleProcessor
class	SnapShot
class	SnapShotManager
class	StretchComponent
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	ClearShiftProcessor
class	CreateSpectrumProcessor
class	EFShiftProcessor
class	EmpiricalHSShiftProcessor
class	Experiment
class	SimpleExperiment1D
class	HaighMallionShiftProcessor
class	HBondShiftProcessor
class	JohnsonBoveyShiftProcessor
class	Peak
class	PeakList
class	RandomCoilShiftProcessor
class	ShiftModel
class	ShiftModel1D
class	ShiftModel2D
class	ShiftModule
class	Spectrum
class	BALLPlugin
class	PluginHandler
class	PluginManager
class	PyColorRGBAVector
class	PyCompositeList
class	Constant
class	PyDatasetVector
class	PyIndexList
class	PyCAPIKernel
class	PyInterpreter
class	PyKernel
class	PyServer
class	AromaticityProcessor
	This processor provides methods for detection and assignment of aromaticity. More...
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	DiffGridBasedScoring
class	DifferentiableScoringFunction
class	FermiBaseFunction
class	GridBasedScoring
class	LinearBaseFunction
class	Rescorer
class	ScoreGridSet
class	ScoringComponent
class	ScoringFunction
class	ScoringOptimizer
class	AdvancedElectrostatic
class	AromaticRingStacking
class	BurialDepth
class	BuriedPolar
class	CHPI
class	CHPISlick
class	Electrostatic
class	FragmentationalSolvation
class	FresnoTypes
class	HydrogenBond
class	HydrogenBondSlick
class	Lipophilic
class	NonpolarSolvation
class	PB
class	PLP
class	Polarity
class	PolarSolvation
class	RotationalEntropy
class	Solvation
class	VanDerWaals
class	VanDerWaalsSlick
class	AmberEvaluation
class	EnergeticEvaluation
class	ForceFieldEvaluation
class	GridedMM
class	GridedPLP
class	MMScoring
class	PBScoring
class	PLPScoring
class	RandomEvaluation
class	Rescoring
class	Rescoring1D
class	Rescoring3D
class	Rescoring4D
class	SLICKEnergy
class	SLICKScore
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
	Assignment of bond orders from topology information. More...
class	AtomBijection
class	AtomTyper
class	BinaryFingerprintMethods
	This class provides efficient similarity calculation functionality for 2D binary fingerprints. More...
class	BindingPocketProcessor
class	AStarBondOrderStrategy
class	BondOrderAssignment
	A solution to the bond order assignment problem. More...
class	BondOrderAssignmentStrategy
	Base class for bond order assignment algorithms. More...
class	BranchAndBoundBondOrderStrategy
class	FPTBondOrderStrategy
class	ILPBondOrderStrategy
class	KGreedyBondOrderStrategy
class	PartialBondOrderAssignment
	A full or partial solution to the AStar-based bond order assignment problem. More...
class	BuildBondsProcessor
class	ConnectedComponentsProcessor
	Computation of the connected components of the molecular graph. More...
class	ClearChargeProcessor
class	ClearRadiusProcessor
class	AssignRadiusProcessor
class	AssignChargeProcessor
class	DisulfidBondProcessor
class	DNAMutator
class	FragmentDB
class	BoundingBoxProcessor
class	GeometricCenterProcessor
class	FragmentDistanceCollector
class	TranslationProcessor
class	TransformationProcessor
class	GraphVertex
class	GraphFace
class	GraphTriangle
class	GraphEdge
class	HBondProcessor
	Computation of hydrogen bonds from topology information. More...
class	HybridisationProcessor
class	Kekuliser
class	LogP
class	MolecularSimilarity
class	Mutator
class	NucleotideMapping
class	NumericalSAS
class	PeptideCapProcessor
	This processor adds ACE-N and NME-C caps to proteins. More...
class	RadialDistributionFunction
class	RDFIntegrator
class	RDFParameter
class	RDFSection
class	ReconstructFragmentProcessor
struct	SortedPosition2
struct	SortedPosition3
class	ReducedSurface
class	RSComputer
class	ResidueChecker
class	Rotamer
class	ResidueRotamerSet
class	RGroupAssembler
class	RingAnalyser
	Methods for the analysis of the structure of ringsystems. More...
class	RMSDMinimizer
class	RotamerLibrary
	Rotamer Library Class. More...
class	RSEdge
class	RSFace
class	RSVertex
class	SASEdge
class	SASFace
class	SASVertex
class	SDGenerator
class	SecondaryStructureProcessor
	Secondary structure extraction from 3D structure. More...
class	SESEdge
class	SESFace
class	SESVertex
class	SideChainPlacementProcessor
class	EdgeItem
class	TSimpleMolecularGraph
class	NodeItem
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	BinaryFileAdaptor
class	Directory
class	TransformationManager
class	File
class	FileSystem
class	MPISupport
class	TMutex
class	TMutex< QMutex >
class	TMutexLocker
class	TReadWriteLock
class	TReadWriteLock< QReadWriteLock >
class	TReadLocker
class	TWriteLocker
class	TMutex< boost::mutex >
class	TCPIOStream
class	TCPServer
class	TCPServerThread
class	Path
class	SimpleDownloader
class	Timer
class	CrystalGenerator
class	CrystalInfo
class	SpaceGroupParameters
class	binary_function
class	vector
	STL class. More...

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 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 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
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 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 std::vector< double >	Coefficients
typedef std::pair< double, double >	Interval
typedef TQuaternion< float >	Quaternion
typedef TSurface< float >	Surface
typedef Spectrum< RegularData1D, Peak1D >	Spectrum1D
	One-dimensional spectrum.
typedef Spectrum< RegularData2D, Peak2D >	Spectrum2D
	Two-dimensional spectrum.
typedef Spectrum< RegularData3D, Peak3D >	Spectrum3D
	Three-dimensional spectrum.
typedef std::list< RegularData3D * >	RegularData3DList
using	AtomContainerProcessor = UnaryProcessor<AtomContainer>
using	AtomProcessor = UnaryProcessor<Atom>
using	BondProcessor = UnaryProcessor<Bond>
using	ChainProcessor = UnaryProcessor<Chain>
using	CompositeProcessor = UnaryProcessor<Composite>
using	FragmentProcessor = UnaryProcessor<Fragment>
using	ResidueProcessor = UnaryProcessor<Residue>
using	ConstAtomProcessor = ConstUnaryProcessor<Atom>
using	ConstCompositeProcessor = ConstUnaryProcessor<Composite>
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
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.
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.
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
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

Functions
BALL_EXPORT std::ostream &	operator<< (std::ostream &os, const Exception::GeneralException &e)
template<class T>
void BALL_DEPRECATED BALL_INLINE	ball_macro_sleepfor (T ms)
template<class T>
T BALL_DEPRECATED BALL_INLINE	ball_macro_max (T a, T b)
template<class T>
T BALL_DEPRECATED BALL_INLINE	ball_macro_max3 (T a, T b, T c)
template<class T>
T BALL_DEPRECATED BALL_INLINE	ball_macro_min (T a, T b)
template<class T>
T BALL_DEPRECATED BALL_INLINE	ball_macro_min3 (T a, T b, T c)
template<class X>
int BALL_DEPRECATED BALL_INLINE	ball_macro_abs (X x)
template<class X>
int BALL_DEPRECATED BALL_INLINE	ball_macro_sgn (X x)
template<class X>
bool BALL_DEPRECATED BALL_INLINE	ball_macro_odd (X x)
template<class X>
bool BALL_DEPRECATED BALL_INLINE	ball_macro_int_odd (X x)
template<class X>
bool BALL_DEPRECATED BALL_INLINE	ball_macro_int_even (X x)
template<class X>
X BALL_DEPRECATED BALL_INLINE	ball_macro_real_round (X x)
template<class X, class Y, class E>
bool BALL_DEPRECATED BALL_INLINE	ball_macro_real_equal (X x, Y y, E e)
template<class X, class Y, class E>
bool BALL_DEPRECATED BALL_INLINE	ball_macro_real_not_equal (X x, Y y, E e)
template<class X, class Y, class E>
bool BALL_DEPRECATED BALL_INLINE	ball_macro_real_less (X x, Y y, E e)
template<class X, class Y, class E>
bool BALL_DEPRECATED BALL_INLINE	ball_macro_real_less_or_equal (X x, Y y, E e)
template<class X, class Y, class E>
bool BALL_DEPRECATED BALL_INLINE	ball_macro_real_greater (X x, Y y, E e)
template<class X, class Y, class E>
bool BALL_DEPRECATED BALL_INLINE	ball_macro_real_greater_or_equal (X x, Y y, E e)
template<class X>
X BALL_DEPRECATED BALL_INLINE	ball_macro_real_abs (X x)
template<class X>
bool BALL_DEPRECATED BALL_INLINE	ball_macro_real_odd (X x)
template<class X>
bool BALL_DEPRECATED BALL_INLINE	ball_macro_real_even (X x)
template<class X>
long BALL_DEPRECATED BALL_INLINE	ball_macro_real_floor (X x)
template<class X>
long BALL_DEPRECATED BALL_INLINE	ball_macro_real_ceiling (X x)
template<class X>
int BALL_DEPRECATED BALL_INLINE	ball_macro_real_round_int (X x)
template<class T>
T BALL_DEPRECATED BALL_INLINE	ball_macro_char_bits ()
template<class T>
T BALL_DEPRECATED BALL_INLINE	ball_macro_char_mask ()
template<class T>
T BALL_DEPRECATED BALL_INLINE	ball_macro_char_shift ()
template<class T>
T BALL_DEPRECATED BALL_INLINE	ball_macro_all_bits_set ()
template<class T>
T BALL_DEPRECATED BALL_INLINE	ball_macro_all_bits_cleared ()
template<class T>
T BALL_DEPRECATED BALL_INLINE	ball_macro_number_of_bytes (T x)
template<class T, std::size_t N>
std::size_t BALL_DEPRECATED BALL_INLINE	ball_macro_sizeof_array (T(&)[N])
template<class T>
T BALL_DEPRECATED BALL_INLINE	ball_macro_bitarray_size (T x)
template<class BitArray, class X>
void BALL_DEPRECATED BALL_INLINE	ball_macro_bitarray_clear_bit (BitArray *a, X x)
template<class BitArray, class X>
void BALL_DEPRECATED BALL_INLINE	ball_macro_bitarray_set_bit (BitArray *a, X x)
template<class BitArray, class X>
void BALL_DEPRECATED BALL_INLINE	ball_macro_bitarray_toggle_bit (BitArray *a, X x)
template<class BitArray, class X>
bool BALL_DEPRECATED BALL_INLINE	ball_macro_bitarray_is_bit_set (BitArray *a, X x)
template<class Bit>
unsigned BALL_DEPRECATED BALL_INLINE	ball_macro_bit (Bit bit)
template<class Bitset, class Bit>
void BALL_DEPRECATED BALL_INLINE	ball_macro_bit_set (Bitset &bitset, Bit bit)
template<class Bitset>
void BALL_DEPRECATED BALL_INLINE	ball_macro_bit_set_all (Bitset &bitset)
template<class Bitset, class Bit>
void BALL_DEPRECATED BALL_INLINE	ball_macro_bit_set_all_to (Bitset &bitset, Bit bit)
template<class Bitset, class Bit>
void BALL_DEPRECATED BALL_INLINE	ball_macro_bit_set_all_from (Bitset &bitset, Bit bit)
template<class Bitset, class Bit>
void BALL_DEPRECATED BALL_INLINE	ball_macro_bit_clear (Bitset &bitset, Bit bit)
template<class Bitset>
void BALL_DEPRECATED BALL_INLINE	ball_macro_bit_clear_all (Bitset &bitset)
template<class Bitset, class Bit>
void BALL_DEPRECATED BALL_INLINE	ball_macro_bit_clear_all_to (Bitset &bitset, Bit bit)
template<class Bitset, class Bit>
void BALL_DEPRECATED BALL_INLINE	ball_macro_bit_clear_all_from (Bitset &bitset, Bit bit)
template<class Bitset, class Bit>
bool BALL_DEPRECATED BALL_INLINE	ball_macro_bit_is_set (Bitset &bitset, Bit bit)
template<class Bitset, class Bit>
bool BALL_DEPRECATED BALL_INLINE	ball_macro_bit_is_cleared (Bitset &bitset, Bit bit)
template<class T>
T BALL_DEPRECATED BALL_INLINE	ball_macro_angle_radians_to_degree (T rad_angle)
template<class T>
T BALL_DEPRECATED BALL_INLINE	ball_macro_angle_degree_to_radian (T deg_angle)
template<class T>
T BALL_DEPRECATED BALL_INLINE	ball_macro_generic_echo (T value)
BALL_EXPORT string	streamClassName (const std::type_info &t)
BALL_EXPORT std::ostream &	operator<< (std::ostream &os, const PreciseTime &time)
BALL_EXPORT std::ostream &	operator<< (std::ostream &os, const TimeStamp &stamp)
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.
BALL_EXPORT String	operator+ (const string &s1, const String &s2)
	Concatenates two strings.
BALL_EXPORT String	operator+ (const String &s1, const String &s2)
	Concatenates two strings.
BALL_EXPORT String	operator+ (const String &s1, const char *char_ptr)
	Concatenates a string and a C type string.
BALL_EXPORT String	operator+ (const char *char_ptr, const String &s)
	Concatenates a C type string and a string.
BALL_EXPORT String	operator+ (const String &s, char c)
	Concatenates a string and a character.
BALL_EXPORT String	operator+ (char c, const String &s)
	Concatenates a character and a string.
BALL_EXPORT String	operator+ (String &&s1, const string &s2)
	Concatenates two strings.
BALL_EXPORT String	operator+ (String &&s1, const String &s2)
	Concatenates two strings.
BALL_EXPORT String	operator+ (String &&s1, String &&s2)
	Concatenates two strings.
BALL_EXPORT String	operator+ (const String &s1, string &&s2)
	Concatenates two strings.
BALL_EXPORT String	operator+ (string &&s1, const String &s2)
	Concatenates two strings.
BALL_EXPORT String	operator+ (const string &s1, String &&s2)
	Concatenates two strings.
BALL_EXPORT String	operator+ (const String &s1, String &&s2)
	Concatenates two strings.
BALL_EXPORT String	operator+ (String &&s1, const char *char_ptr)
	Concatenates a string and a C type string.
BALL_EXPORT String	operator+ (const char *char_ptr, String &&s)
	Concatenates a C type string and a string.
BALL_EXPORT String	operator+ (String &&s, char c)
	Concatenates a string and a character.
BALL_EXPORT String	operator+ (char c, String &&s)
	Concatenates a character and a string.
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 > &)
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)
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>
std::istream &	operator>> (std::istream &s, TQuaternion< T > &q)
template<typename T>
std::ostream &	operator<< (std::ostream &s, const TQuaternion< T > &q)
::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)
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)
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.
template<typename T>
std::istream &	operator>> (std::istream &is, BinaryFileAdaptor< T > &data)
	Input stream for BinaryFileAdaptors.
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)
Generic Constant Random Access Iterator
template<typename Container, typename DataType, typename Position, typename Traits>
ConstRandomAccessIterator< Container, DataType, Position, Traits >	operator+ (Distance distance, const ConstRandomAccessIterator< Container, DataType, Position, Traits > &iterator)
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.
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.
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.
Angle Calculation
BALL_EXPORT Angle	calculateTorsionAngle (const Atom &a1, const Atom &a2, const Atom &a3, const Atom &a4)
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)

Variables
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)
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

Type aliases defined by BALL.
These predefined types are used in BALL for portability and comprehensibility.
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 = ';' }
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
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

Storers
typedef TBox3< float >	Box3
typedef TCircle3< float >	Circle3
typedef TLine3< float >	Line3
typedef TMatrix4x4< float >	Matrix4x4
typedef TPlane3< float >	Plane3
typedef TSimpleBox3< float >	SimpleBox3
typedef TSphere3< float >	Sphere3
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>
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, 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)

Global binary operator functions for two dimensional vectors.
typedef TVector2< float >	Vector2
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.
typedef TVector3< float >	Vector3
typedef TVector4< float >	Vector4
template class BALL_EXPORT	TVector3< float >
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)
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)

Typedef Documentation

Angle

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 697 of file angle.h.

AtomBondConstIterator

typedef Atom::BondConstIterator BALL::AtomBondConstIterator

A constant iterator for atom bonds.

Definition at line 27 of file bondIterator.h.

AtomBondConstReverseIterator

typedef Atom::BondConstReverseIterator BALL::AtomBondConstReverseIterator

A constant reverse iterator for atom bonds.

Definition at line 35 of file bondIterator.h.

AtomBondIterator

typedef Atom::BondIterator BALL::AtomBondIterator

A mutable iterator for atom bonds.

Definition at line 23 of file bondIterator.h.

AtomBondReverseIterator

typedef Atom::BondReverseIterator BALL::AtomBondReverseIterator

A mutable reverse iterator for atom bonds.

Definition at line 31 of file bondIterator.h.

AtomConstIterator

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.

AtomConstReverseIterator

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

A constant reverse bidirectional iterator for the Atom class.

Definition at line 96 of file atomIterator.h.

AtomContainerConstIterator

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.

AtomContainerConstReverseIterator

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

A constant reverse bidirectional iterator for the AtomContainer class.

Definition at line 100 of file atomContainerIterator.h.

AtomContainerIterator

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.

AtomContainerList

typedef std::list<AtomContainer*> BALL::AtomContainerList

Definition at line 55 of file extractors.h.

AtomContainerProcessor

using BALL::AtomContainerProcessor = UnaryProcessor<AtomContainer>

Definition at line 8 of file pyUnaryProcessors.h.

AtomContainerReverseIterator

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

A mutable reverse bidirectional iterator for the AtomContainer class.

Definition at line 97 of file atomContainerIterator.h.

AtomIterator

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.

AtomPairList

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

Definition at line 23 of file scoringFunction.h.

AtomPairVector

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

Definition at line 24 of file scoringFunction.h.

AtomProcessor

using BALL::AtomProcessor = UnaryProcessor<Atom>

Definition at line 9 of file pyUnaryProcessors.h.

AtomReverseIterator

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

A mutable reverse bidirectional iterator for the Atom class.

Definition at line 93 of file atomIterator.h.

BondList

typedef std::list<Bond*> BALL::BondList

Definition at line 53 of file extractors.h.

BondProcessor

using BALL::BondProcessor = UnaryProcessor<Bond>

Definition at line 10 of file pyUnaryProcessors.h.

Byte

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 183 of file COMMON/global.h.

ChainConstIterator

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.

ChainConstReverseIterator

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

A constant reverse bidirectional iterator for the Chain class.

Definition at line 95 of file chainIterator.h.

ChainIterator

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.

ChainList

typedef std::list<Chain*> BALL::ChainList

Definition at line 69 of file extractors.h.

ChainProcessor

using BALL::ChainProcessor = UnaryProcessor<Chain>

Definition at line 11 of file pyUnaryProcessors.h.

ChainReverseIterator

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

A mutable reverse bidirectional iterator for the Chain class.

Definition at line 92 of file chainIterator.h.

ComparatorType

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

Definition at line 70 of file COMMON/global.h.

Complex

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

Definition at line 21 of file complex.h.

CompositeProcessor

using BALL::CompositeProcessor = UnaryProcessor<Composite>

Definition at line 12 of file pyUnaryProcessors.h.

ConstAtomProcessor

using BALL::ConstAtomProcessor = ConstUnaryProcessor<Atom>

Definition at line 16 of file pyUnaryProcessors.h.

ConstCompositeProcessor

using BALL::ConstCompositeProcessor = ConstUnaryProcessor<Composite>

Definition at line 17 of file pyUnaryProcessors.h.

ContourLine

typedef TContourLine<float> BALL::ContourLine

Default type

Definition at line 153 of file contourLine.h.

ContourSurface

typedef TContourSurface<float> BALL::ContourSurface

Default type.

Definition at line 250 of file contourSurface.h.

Distance

typedef BALL_INDEX_TYPE BALL::Distance

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

Size: 32 bit

persistent

Definition at line 86 of file COMMON/global.h.

DoubleReal

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 156 of file COMMON/global.h.

EditableMolecularGraph

typedef MolecularGraph::EditableGraph BALL::EditableMolecularGraph

Definition at line 78 of file molecularGraph.h.

ErrorCode

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 173 of file COMMON/global.h.

Experiment1D

typedef Experiment<PeakList1D> BALL::Experiment1D

1D NMR experiment

Definition at line 136 of file experiment.h.

Experiment3D

typedef Experiment<PeakList3D> BALL::Experiment3D

2D NMR experiment 3D NMR experiment

Definition at line 145 of file experiment.h.

FacetArray

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

Definition at line 32 of file contourSurface.h.

FFT1D

typedef TFFT1D<BALL_FFTW_DEFAULT_TRAITS> BALL::FFT1D

Default type

Definition at line 267 of file FFT1D.h.

FFT2D

typedef TFFT2D<BALL_FFTW_DEFAULT_TRAITS> BALL::FFT2D

Default type

Definition at line 318 of file FFT2D.h.

FFT3D

typedef TFFT3D<BALL_FFTW_DEFAULT_TRAITS> BALL::FFT3D

Default type

Definition at line 347 of file FFT3D.h.

FragmentConstIterator

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

Definition at line 81 of file fragmentIterator.h.

FragmentConstReverseIterator

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

Definition at line 87 of file fragmentIterator.h.

FragmentIterator

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

Definition at line 76 of file fragmentIterator.h.

FragmentList

typedef std::list<Fragment*> BALL::FragmentList

Definition at line 61 of file extractors.h.

FragmentProcessor

using BALL::FragmentProcessor = UnaryProcessor<Fragment>

Definition at line 13 of file pyUnaryProcessors.h.

FragmentReverseIterator

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

Definition at line 84 of file fragmentIterator.h.

Handle

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 96 of file COMMON/global.h.

HashIndex

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 131 of file COMMON/global.h.

Index

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 105 of file COMMON/global.h.

Interval

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

An interval is defined by its limits

Definition at line 23 of file piecewiseFunction.h.

KernelPredicateType

typedef UnaryPredicate<Composite> BALL::KernelPredicateType

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

Ligand

typedef FlexibleMolecule BALL::Ligand

Definition at line 121 of file flexibleMolecule.h.

LongIndex

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 201 of file COMMON/global.h.

LongSize

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 192 of file COMMON/global.h.

MatrixVector

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

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

MolecularGraphBase

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 30 of file molecularGraph.h.

MolecularGraphTraits

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

Definition at line 77 of file molecularGraph.h.

MoleculeConstIterator

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

Definition at line 70 of file moleculeIterator.h.

MoleculeConstReverseIterator

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

Definition at line 76 of file moleculeIterator.h.

MoleculeIterator

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

Definition at line 65 of file moleculeIterator.h.

MoleculeList

typedef std::list<Molecule*> BALL::MoleculeList

Definition at line 63 of file extractors.h.

MoleculeReverseIterator

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

Definition at line 73 of file moleculeIterator.h.

Mutex

typedef TMutex<BALL_DEFAULT_MUTEX_TYPE> BALL::Mutex

Definition at line 224 of file mutex.h.

MutexLocker

typedef TMutexLocker<BALL_DEFAULT_MUTEXLOCKER_TYPE, BALL_DEFAULT_MUTEX_TYPE> BALL::MutexLocker

Definition at line 226 of file mutex.h.

NamedPropertyIterator

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

Definition at line 317 of file property.h.

NucleicAcidConstIterator

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

Definition at line 76 of file nucleicAcidIterator.h.

NucleicAcidConstReverseIterator

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

Definition at line 80 of file nucleicAcidIterator.h.

NucleicAcidIterator

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

Definition at line 72 of file nucleicAcidIterator.h.

NucleicAcidList

typedef std::list<NucleicAcid*> BALL::NucleicAcidList

Definition at line 73 of file extractors.h.

NucleicAcidReverseIterator

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

Definition at line 78 of file nucleicAcidIterator.h.

NucleotideConstIterator

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

Definition at line 71 of file nucleotideIterator.h.

NucleotideConstReverseIterator

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

Definition at line 75 of file nucleotideIterator.h.

NucleotideIterator

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

Definition at line 67 of file nucleotideIterator.h.

NucleotideList

typedef std::list<Nucleotide*> BALL::NucleotideList

Definition at line 71 of file extractors.h.

NucleotideReverseIterator

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

Definition at line 73 of file nucleotideIterator.h.

PDBAtomConstIterator

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.

PDBAtomConstReverseIterator

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

A constant reverse bidirectional iterator for the PDBAtom class.

Definition at line 98 of file PDBAtomIterator.h.

PDBAtomIterator

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.

PDBAtomList

typedef std::list<PDBAtom*> BALL::PDBAtomList

Definition at line 57 of file extractors.h.

PDBAtomReverseIterator

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

A mutable reverse bidirectional iterator for the PDBAtom class.

Definition at line 95 of file PDBAtomIterator.h.

Peak1D

typedef Peak<float> BALL::Peak1D

Definition at line 261 of file peak.h.

Peak2D

typedef Peak<Vector2> BALL::Peak2D

Definition at line 262 of file peak.h.

Peak3D

typedef Peak<Vector3> BALL::Peak3D

Definition at line 263 of file peak.h.

PeakList1D

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

1D peak list

Definition at line 125 of file peakList.h.

PeakList2D

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

2D peak list

Definition at line 128 of file peakList.h.

PeakList3D

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

3D peak list

Definition at line 131 of file peakList.h.

PointerSizeUInt

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 207 of file COMMON/global.h.

Position

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 140 of file COMMON/global.h.

Property

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 165 of file COMMON/global.h.

ProteinConstIterator

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

Definition at line 71 of file proteinIterator.h.

ProteinConstReverseIterator

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

Definition at line 77 of file proteinIterator.h.

ProteinIterator

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

Definition at line 66 of file proteinIterator.h.

ProteinList

typedef std::list<Protein*> BALL::ProteinList

Definition at line 65 of file extractors.h.

ProteinReverseIterator

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

Definition at line 74 of file proteinIterator.h.

Quaternion

typedef TQuaternion<float> BALL::Quaternion

Definition at line 626 of file quaternion.h.

ReadLocker

typedef TReadLocker<BALL_DEFAULT_READLOCKER_TYPE, BALL_DEFAULT_READWRITELOCK_TYPE> BALL::ReadLocker

Definition at line 227 of file mutex.h.

ReadWriteLock

typedef TReadWriteLock<BALL_DEFAULT_READWRITELOCK_TYPE> BALL::ReadWriteLock

Definition at line 225 of file mutex.h.

Real

typedef float BALL::Real

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

Size: 32 bit

persistent

Definition at line 148 of file COMMON/global.h.

RegularData1D

typedef TRegularData1D<float> BALL::RegularData1D

Default type

Definition at line 358 of file regularData1D.h.

RegularData2D

typedef TRegularData2D<float> BALL::RegularData2D

Default type

Definition at line 414 of file regularData2D.h.

RegularData3D

typedef TRegularData3D<float> BALL::RegularData3D

Default type

Definition at line 515 of file regularData3D.h.

RegularData3DList

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

Definition at line 15 of file pyListHelper.h.

ResidueConstIterator

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

Definition at line 67 of file residueIterator.h.

ResidueConstReverseIterator

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

Definition at line 73 of file residueIterator.h.

ResidueIterator

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

Definition at line 62 of file residueIterator.h.

ResidueList

typedef std::list<Residue*> BALL::ResidueList

Definition at line 59 of file extractors.h.

ResidueProcessor

using BALL::ResidueProcessor = UnaryProcessor<Residue>

Definition at line 14 of file pyUnaryProcessors.h.

ResidueReverseIterator

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

Definition at line 70 of file residueIterator.h.

ScoreGrid

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

Definition at line 17 of file scoreGridSet.h.

SecondaryStructureConstIterator

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

Definition at line 75 of file secondaryStructureIterator.h.

SecondaryStructureConstReverseIterator

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

Definition at line 81 of file secondaryStructureIterator.h.

SecondaryStructureIterator

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

Definition at line 70 of file secondaryStructureIterator.h.

SecondaryStructureList

typedef std::list<SecondaryStructure*> BALL::SecondaryStructureList

Definition at line 67 of file extractors.h.

SecondaryStructureReverseIterator

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

Definition at line 78 of file secondaryStructureIterator.h.

SimpleMolecularGraph

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.

Size

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 114 of file COMMON/global.h.

Spectrum2D

typedef Spectrum<RegularData2D, Peak2D> BALL::Spectrum2D

Two-dimensional spectrum.

Definition at line 322 of file spectrum.h.

Spectrum3D

typedef Spectrum<RegularData3D, Peak3D> BALL::Spectrum3D

Three-dimensional spectrum.

Definition at line 325 of file spectrum.h.

Time

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 123 of file COMMON/global.h.

Vector3

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.

Vector4

typedef TVector4<float> BALL::Vector4

Default four-dimensional vector type

Definition at line 815 of file vector4.h.

WriteLocker

typedef TWriteLocker<BALL_DEFAULT_WRITELOCKER_TYPE, BALL_DEFAULT_READWRITELOCK_TYPE> BALL::WriteLocker

Definition at line 228 of file mutex.h.

Enumeration Type Documentation

ASCII

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 211 of file COMMON/global.h.

Function Documentation

atomContainers()

BALL_EXPORT AtomContainerList BALL::atomContainers	(	const AtomContainer &	fragment,
		bool	selected_only = false )

Extract all base fragments from a kernel data structure.

atoms()

BALL_EXPORT AtomList BALL::atoms	(	const AtomList &	atoms,
		const String &	expression )

Extract atoms matching an expression. This method extracts all atoms from an atom list
that match the Expression expression.

Parameters

atoms	the AtomContainer containing the atoms
expression	the expression that selects the atoms

ball_macro_abs()

template<class X>

int BALL_DEPRECATED BALL_INLINE BALL::ball_macro_abs

(

X

x

)

Definition at line 50 of file macros.h.

ball_macro_all_bits_cleared()

template<class T>

T BALL_DEPRECATED BALL_INLINE BALL::ball_macro_all_bits_cleared

(

)

Definition at line 183 of file macros.h.

ball_macro_all_bits_set()

template<class T>

T BALL_DEPRECATED BALL_INLINE BALL::ball_macro_all_bits_set

(

)

Definition at line 177 of file macros.h.

ball_macro_angle_degree_to_radian()

template<class T>

T BALL_DEPRECATED BALL_INLINE BALL::ball_macro_angle_degree_to_radian

(

T

deg_angle

)

Definition at line 315 of file macros.h.

ball_macro_angle_radians_to_degree()

template<class T>

T BALL_DEPRECATED BALL_INLINE BALL::ball_macro_angle_radians_to_degree

(

T

rad_angle

)

Definition at line 309 of file macros.h.

ball_macro_bit()

template<class Bit>

unsigned BALL_DEPRECATED BALL_INLINE BALL::ball_macro_bit

(

Bit

bit

)

Definition at line 243 of file macros.h.

ball_macro_bit_clear()

template<class Bitset, class Bit>

void BALL_DEPRECATED BALL_INLINE BALL::ball_macro_bit_clear	(	Bitset &	bitset,
		Bit	bit )

Definition at line 273 of file macros.h.

ball_macro_bit_clear_all()

template<class Bitset>

void BALL_DEPRECATED BALL_INLINE BALL::ball_macro_bit_clear_all

(

Bitset &

bitset

)

Definition at line 279 of file macros.h.

ball_macro_bit_clear_all_from()

template<class Bitset, class Bit>

void BALL_DEPRECATED BALL_INLINE BALL::ball_macro_bit_clear_all_from	(	Bitset &	bitset,
		Bit	bit )

Definition at line 291 of file macros.h.

ball_macro_bit_clear_all_to()

template<class Bitset, class Bit>

void BALL_DEPRECATED BALL_INLINE BALL::ball_macro_bit_clear_all_to	(	Bitset &	bitset,
		Bit	bit )

Definition at line 285 of file macros.h.

ball_macro_bit_is_cleared()

template<class Bitset, class Bit>

bool BALL_DEPRECATED BALL_INLINE BALL::ball_macro_bit_is_cleared	(	Bitset &	bitset,
		Bit	bit )

Definition at line 303 of file macros.h.

ball_macro_bit_is_set()

template<class Bitset, class Bit>

bool BALL_DEPRECATED BALL_INLINE BALL::ball_macro_bit_is_set	(	Bitset &	bitset,
		Bit	bit )

Definition at line 297 of file macros.h.

ball_macro_bit_set()

template<class Bitset, class Bit>

void BALL_DEPRECATED BALL_INLINE BALL::ball_macro_bit_set	(	Bitset &	bitset,
		Bit	bit )

Definition at line 249 of file macros.h.

ball_macro_bit_set_all()

template<class Bitset>

void BALL_DEPRECATED BALL_INLINE BALL::ball_macro_bit_set_all

(

Bitset &

bitset

)

Definition at line 255 of file macros.h.

ball_macro_bit_set_all_from()

template<class Bitset, class Bit>

void BALL_DEPRECATED BALL_INLINE BALL::ball_macro_bit_set_all_from	(	Bitset &	bitset,
		Bit	bit )

Definition at line 267 of file macros.h.

ball_macro_bit_set_all_to()

template<class Bitset, class Bit>

void BALL_DEPRECATED BALL_INLINE BALL::ball_macro_bit_set_all_to	(	Bitset &	bitset,
		Bit	bit )

Definition at line 261 of file macros.h.

ball_macro_bitarray_clear_bit()

template<class BitArray, class X>

void BALL_DEPRECATED BALL_INLINE BALL::ball_macro_bitarray_clear_bit	(	BitArray *	a,
		X	x )

Definition at line 211 of file macros.h.

ball_macro_bitarray_is_bit_set()

template<class BitArray, class X>

bool BALL_DEPRECATED BALL_INLINE BALL::ball_macro_bitarray_is_bit_set	(	BitArray *	a,
		X	x )

Definition at line 235 of file macros.h.

ball_macro_bitarray_set_bit()

template<class BitArray, class X>

void BALL_DEPRECATED BALL_INLINE BALL::ball_macro_bitarray_set_bit	(	BitArray *	a,
		X	x )

Definition at line 219 of file macros.h.

ball_macro_bitarray_size()

template<class T>

T BALL_DEPRECATED BALL_INLINE BALL::ball_macro_bitarray_size

(

T

x

)

Definition at line 203 of file macros.h.

ball_macro_bitarray_toggle_bit()

template<class BitArray, class X>

void BALL_DEPRECATED BALL_INLINE BALL::ball_macro_bitarray_toggle_bit	(	BitArray *	a,
		X	x )

Definition at line 227 of file macros.h.

ball_macro_char_bits()

template<class T>

T BALL_DEPRECATED BALL_INLINE BALL::ball_macro_char_bits

(

)

Definition at line 158 of file macros.h.

ball_macro_char_mask()

template<class T>

T BALL_DEPRECATED BALL_INLINE BALL::ball_macro_char_mask

(

)

Definition at line 164 of file macros.h.

ball_macro_char_shift()

template<class T>

T BALL_DEPRECATED BALL_INLINE BALL::ball_macro_char_shift

(

)

Definition at line 170 of file macros.h.

ball_macro_generic_echo()

template<class T>

T BALL_DEPRECATED BALL_INLINE BALL::ball_macro_generic_echo

(

T

value

)

Definition at line 321 of file macros.h.

ball_macro_int_even()

template<class X>

bool BALL_DEPRECATED BALL_INLINE BALL::ball_macro_int_even

(

X

x

)

Definition at line 74 of file macros.h.

ball_macro_int_odd()

template<class X>

bool BALL_DEPRECATED BALL_INLINE BALL::ball_macro_int_odd

(

X

x

)

Definition at line 68 of file macros.h.

ball_macro_max()

template<class T>

T BALL_DEPRECATED BALL_INLINE BALL::ball_macro_max	(	T	a,
		T	b )

Definition at line 26 of file macros.h.

ball_macro_max3()

template<class T>

T BALL_DEPRECATED BALL_INLINE BALL::ball_macro_max3	(	T	a,
		T	b,
		T	c )

Definition at line 32 of file macros.h.

ball_macro_min()

template<class T>

T BALL_DEPRECATED BALL_INLINE BALL::ball_macro_min	(	T	a,
		T	b )

Definition at line 38 of file macros.h.

ball_macro_min3()

template<class T>

T BALL_DEPRECATED BALL_INLINE BALL::ball_macro_min3	(	T	a,
		T	b,
		T	c )

Definition at line 44 of file macros.h.

ball_macro_number_of_bytes()

template<class T>

T BALL_DEPRECATED BALL_INLINE BALL::ball_macro_number_of_bytes

(

T

x

)

Definition at line 189 of file macros.h.

ball_macro_odd()

template<class X>

bool BALL_DEPRECATED BALL_INLINE BALL::ball_macro_odd

(

X

x

)

Definition at line 62 of file macros.h.

ball_macro_real_abs()

template<class X>

X BALL_DEPRECATED BALL_INLINE BALL::ball_macro_real_abs

(

X

x

)

Definition at line 122 of file macros.h.

ball_macro_real_ceiling()

template<class X>

long BALL_DEPRECATED BALL_INLINE BALL::ball_macro_real_ceiling

(

X

x

)

Definition at line 146 of file macros.h.

ball_macro_real_equal()

template<class X, class Y, class E>

bool BALL_DEPRECATED BALL_INLINE BALL::ball_macro_real_equal	(	X	x,
		Y	y,
		E	e )

Definition at line 86 of file macros.h.

ball_macro_real_even()

template<class X>

bool BALL_DEPRECATED BALL_INLINE BALL::ball_macro_real_even

(

X

x

)

Definition at line 134 of file macros.h.

ball_macro_real_floor()

template<class X>

long BALL_DEPRECATED BALL_INLINE BALL::ball_macro_real_floor

(

X

x

)

Definition at line 140 of file macros.h.

ball_macro_real_greater()

template<class X, class Y, class E>

bool BALL_DEPRECATED BALL_INLINE BALL::ball_macro_real_greater	(	X	x,
		Y	y,
		E	e )

Definition at line 110 of file macros.h.

ball_macro_real_greater_or_equal()

template<class X, class Y, class E>

bool BALL_DEPRECATED BALL_INLINE BALL::ball_macro_real_greater_or_equal	(	X	x,
		Y	y,
		E	e )

Definition at line 116 of file macros.h.

ball_macro_real_less()

template<class X, class Y, class E>

bool BALL_DEPRECATED BALL_INLINE BALL::ball_macro_real_less	(	X	x,
		Y	y,
		E	e )

Definition at line 98 of file macros.h.

ball_macro_real_less_or_equal()

template<class X, class Y, class E>

bool BALL_DEPRECATED BALL_INLINE BALL::ball_macro_real_less_or_equal	(	X	x,
		Y	y,
		E	e )

Definition at line 104 of file macros.h.

ball_macro_real_not_equal()

template<class X, class Y, class E>

bool BALL_DEPRECATED BALL_INLINE BALL::ball_macro_real_not_equal	(	X	x,
		Y	y,
		E	e )

Definition at line 92 of file macros.h.

ball_macro_real_odd()

template<class X>

bool BALL_DEPRECATED BALL_INLINE BALL::ball_macro_real_odd

(

X

x

)

Definition at line 128 of file macros.h.

ball_macro_real_round()

template<class X>

X BALL_DEPRECATED BALL_INLINE BALL::ball_macro_real_round

(

X

x

)

Definition at line 80 of file macros.h.

ball_macro_real_round_int()

template<class X>

int BALL_DEPRECATED BALL_INLINE BALL::ball_macro_real_round_int

(

X

x

)

Definition at line 152 of file macros.h.

ball_macro_sgn()

template<class X>

int BALL_DEPRECATED BALL_INLINE BALL::ball_macro_sgn

(

X

x

)

Definition at line 56 of file macros.h.

ball_macro_sizeof_array()

template<class T, std::size_t N>

std::size_t BALL_DEPRECATED BALL_INLINE BALL::ball_macro_sizeof_array

(

T(&)

[N]

)

Definition at line 197 of file macros.h.

ball_macro_sleepfor()

template<class T>

void BALL_DEPRECATED BALL_INLINE BALL::ball_macro_sleepfor

(

T

ms

)

Definition at line 20 of file macros.h.

bonds() [1/2]

BALL_EXPORT BondList BALL::bonds

(

const Atom &

atom

)

Extract all bonds from an atom. This function returns all bonds of an atom.

bonds() [2/2]

BALL_EXPORT BondList BALL::bonds	(	const AtomContainer &	fragment,
		bool	selected_only = false )

Extract all bonds from a kernel data structure. This function extracts all bonds from the atoms contained in the base fragment. If selected_only is set to true, only bonds are extracted where both atoms are selected.

calculateBondAngle()

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

Calculate the bond angle between three atoms

Exceptions

BALL::Exception::IllegalPosition

calculateResidueChi2Angles() [1/3]

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

calculateResidueChi2Angles() [2/3]

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

calculateResidueChi2Angles() [3/3]

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.

calculateResidueChiAngles() [1/3]

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

calculateResidueChiAngles() [2/3]

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

calculateResidueChiAngles() [3/3]

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.

calculateTorsionAngle()

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

Calculate the torsion angle between four atoms

Exceptions

BALL::Exception::IllegalPosition

chains()

BALL_EXPORT ChainList BALL::chains	(	const AtomContainer &	fragment,
		bool	selected_only = false )

Extract all chains from a kernel data structure.

fragments()

BALL_EXPORT FragmentList BALL::fragments	(	const AtomContainer &	fragment,
		bool	selected_only = false )

Extract all fragments from a kernel data structure.

get3Prime()

template<class NucleotideContainerType>

const Nucleotide * BALL::get3Prime

(

const NucleotideContainerType &

nucleotide_container

)

Definition at line 338 of file nucleotide.h.

get5Prime()

template<class NucleotideContainerType>

const Nucleotide * BALL::get5Prime

(

const NucleotideContainerType &

nucleotide_container

)

Definition at line 326 of file nucleotide.h.

GetAngle() [1/7]

template<typename T>

BALL_INLINE bool BALL::GetAngle	(	const TLine3< T > &	a,
		const TLine3< T > &	b,
		TAngle< T > &	intersection_angle )

Get the angle between two lines.

Parameters

a	the first line
b	the second line
intersection_angle	the resulting angle

Returns

bool, true if an angle can be calculated, otherwise false

Definition at line 570 of file analyticalGeometry.h.

GetAngle() [2/7]

template<typename T>

BALL_INLINE bool BALL::GetAngle	(	const TLine3< T > &	line,
		const TPlane3< T > &	plane,
		TAngle< T > &	intersection_angle )

Get the angle between a line and a plane.

Parameters

line	the line
plane	the plane
intersection_angle	the resulting angle

Returns

bool, true if an angle can be calculated, otherwise false

Definition at line 647 of file analyticalGeometry.h.

GetAngle() [3/7]

template<typename T>

BALL_INLINE bool BALL::GetAngle	(	const TPlane3< T > &	a,
		const TPlane3< T > &	b,
		TAngle< T > &	intersection_angle )

Get the angle between two planes.

Parameters

a	the first plane
b	the second plane
intersection_angle	the resulting angle

Returns

bool, true if an angle can be calculated, otherwise false

Definition at line 661 of file analyticalGeometry.h.

GetAngle() [4/7]

template<typename T>

BALL_INLINE bool BALL::GetAngle	(	const TPlane3< T > &	plane,
		const TLine3< T > &	line,
		TAngle< T > &	intersection_angle )

Get the angle between a plane and a line.

Parameters

plane	the plane
line	the line
intersection_angle	the resulting angle

Returns

bool, true if an angle can be calculated, otherwise false

Definition at line 626 of file analyticalGeometry.h.

GetAngle() [5/7]

template<typename T>

BALL_INLINE bool BALL::GetAngle	(	const TPlane3< T > &	plane,
		const TVector3< T > &	vector,
		TAngle< T > &	intersection_angle )

Get the angle between a plane and a Vector3.

Parameters

plane	the plane
vector	the Vector3
intersection_angle	the resulting angle

Returns

bool, true if an angle can be calculated, otherwise false

Definition at line 590 of file analyticalGeometry.h.

GetAngle() [6/7]

template<typename T>

BALL_INLINE bool BALL::GetAngle	(	const TVector3< T > &	a,
		const TVector3< T > &	b,
		TAngle< T > &	intersection_angle )

Get the angle between two Vector3.

Parameters

a	the first vector
b	the second vector
intersection_angle	the resulting angle

Returns

bool, always true

Definition at line 551 of file analyticalGeometry.h.

GetAngle() [7/7]

template<typename T>

BALL_INLINE bool BALL::GetAngle	(	const TVector3< T > &	vector,
		const TPlane3< T > &	plane,
		TAngle< T > &	intersection_angle )

Get the angle between a vector3 and a plane.

Parameters

vector	the vector3
plane	the plane
intersection_angle	the resulting angle

Returns

bool, true if an angle can be calculated, otherwise false

Definition at line 613 of file analyticalGeometry.h.

getContourSurfaceFacetData()

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

extern

getCTerminal()

template<class ResidueContainerType>

const Residue * BALL::getCTerminal

(

const ResidueContainerType &

residue_container

)

Definition at line 472 of file residue.h.

getDeterminant()

template<typename T>

T BALL::getDeterminant	(	const T *	m,
		Size	dim )

Get the determinant of any matrix.

Parameters

m	pointer to matrix
dim	dimension of the matrix

Definition at line 93 of file analyticalGeometry.h.

getDeterminant2() [1/2]

template<typename T>

BALL_INLINE T BALL::getDeterminant2	(	const T &	m00,
		const T &	m01,
		const T &	m10,
		const T &	m11 )

Get the determinant of an 2x2 matrix.

Parameters

m00	first value of the matrix
m01	second value of the matrix
m10	third value of the matrix
m11	fourth value of the matrix

Definition at line 133 of file analyticalGeometry.h.

getDeterminant2() [2/2]

template<typename T>

BALL_INLINE T BALL::getDeterminant2

(

const T *

m

)

Get the determinant of an 2x2 matrix.

Parameters

m	pointer to matrix

Definition at line 119 of file analyticalGeometry.h.

getDeterminant3() [1/2]

template<typename T>

BALL_INLINE T BALL::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 )

Get the determinant of an 3x3 matrix.

Parameters

m00,m01,m02,m10,m11,m12,m20,m21,m22

the elements of the matrix

Definition at line 159 of file analyticalGeometry.h.

getDeterminant3() [2/2]

template<typename T>

BALL_INLINE T BALL::getDeterminant3

(

const T *

m

)

Get the determinant of an 3x3 matrix.

Parameters

m	pointer to matrix

Definition at line 143 of file analyticalGeometry.h.

getDeterminant_()

template<typename T>

BALL_INLINE T BALL::getDeterminant_	(	const T *	m,
		Size	dim )

Subroutine to get the determinant of any matrix. Direct usage of this function should be avoided. Instead use T getDeterminant(const T* m, Size dim)

Parameters

m	pointer to matrix
dim	dimension of the matrix

Definition at line 57 of file analyticalGeometry.h.

GetDistance() [1/9]

template<typename T>

T BALL::GetDistance	(	const TLine3< T > &	a,
		const TLine3< T > &	b )

Get the distance between two lines.

Parameters

a	the first line
b	the second line

Returns

T the distance

Exceptions

Exception::DivisionByZero

if the lines are parallel and a has length 0

Definition at line 433 of file analyticalGeometry.h.

GetDistance() [2/9]

template<typename T>

BALL_INLINE T BALL::GetDistance	(	const TLine3< T > &	line,
		const TPlane3< T > &	plane )

Get the distance between a line and a plane.

Parameters

line	the line
plane	the plane

Returns

T the distance

Exceptions

Exception::DivisionByZero

if the normal vector of plane has zero length

Definition at line 502 of file analyticalGeometry.h.

GetDistance() [3/9]

template<typename T>

BALL_INLINE T BALL::GetDistance	(	const TLine3< T > &	line,
		const TVector3< T > &	point )

Get the distance between a line and a point.

Parameters

line	the line
point	the point

Returns

T the distance

Exceptions

Exception::DivisionByZero

if the line has length 0

Definition at line 404 of file analyticalGeometry.h.

GetDistance() [4/9]

template<typename T>

BALL_INLINE T BALL::GetDistance	(	const TPlane3< T > &	a,
		const TPlane3< T > &	b )

Get the distance between two planes.

Parameters

a	the first plane
b	the second plane

Returns

T the distance

Exceptions

Exception::DivisionByZero

if the normal vector of a has zero length

Definition at line 533 of file analyticalGeometry.h.

GetDistance() [5/9]

template<typename T>

BALL_INLINE T BALL::GetDistance	(	const TPlane3< T > &	plane,
		const TLine3< T > &	line )

Get the distance between a plane and a line.

Parameters

plane	the plane
line	the line

Returns

T the distance

Exceptions

Exception::DivisionByZero

if the normal vector of plane has zero length

Definition at line 520 of file analyticalGeometry.h.

GetDistance() [6/9]

template<typename T>

BALL_INLINE T BALL::GetDistance	(	const TPlane3< T > &	plane,
		const TVector3< T > &	point )

Get the distance between a plane and a point.

Parameters

plane	the plane
point	the point

Returns

T the distance

Exceptions

Exception::DivisionByZero

if the normal vector of plane has zero length

Definition at line 489 of file analyticalGeometry.h.

GetDistance() [7/9]

template<typename T>

BALL_INLINE T BALL::GetDistance	(	const TVector3< T > &	a,
		const TVector3< T > &	b )

Get the distance between two points.

Parameters

a	the first point
b	the second point

Returns

T the distance

Definition at line 387 of file analyticalGeometry.h.

GetDistance() [8/9]

template<typename T>

BALL_INLINE T BALL::GetDistance	(	const TVector3< T > &	point,
		const TLine3< T > &	line )

Get the distance between a point and a line.

Parameters

point	the point
line	the line

Returns

T the distance

Exceptions

Exception::DivisionByZero

if the line has length 0

Definition at line 421 of file analyticalGeometry.h.

GetDistance() [9/9]

template<typename T>

BALL_INLINE T BALL::GetDistance	(	const TVector3< T > &	point,
		const TPlane3< T > &	plane )

Get the distance between a point and a plane.

Parameters

point	the point
plane	the plane

Returns

T the distance

Exceptions

Exception::DivisionByZero

if the normal vector of plane has zero length

Definition at line 470 of file analyticalGeometry.h.

GetIntersection() [1/10]

template<typename T>

bool BALL::GetIntersection	(	const TLine3< T > &	a,
		const TLine3< T > &	b,
		TVector3< T > &	point )

Get the intersection point between two lines.

Parameters

a	the first line
b	the second line
point	the resulting intersection

Returns

bool, true if an intersection can be calculated, otherwise false

Definition at line 681 of file analyticalGeometry.h.

GetIntersection() [2/10]

template<typename T>

BALL_INLINE bool BALL::GetIntersection	(	const TLine3< T > &	line,
		const TPlane3< T > &	plane,
		TVector3< T > &	intersection_point )

Get the intersection point between a line and a plane.

Parameters

line	the line
plane	the plane
intersection_point	the resulting intersection

Returns

bool, true if an intersection can be calculated, otherwise false

Definition at line 720 of file analyticalGeometry.h.

GetIntersection() [3/10]

template<typename T>

BALL_INLINE bool BALL::GetIntersection	(	const TLine3< T > &	line,
		const TSphere3< T > &	sphere,
		TVector3< T > &	intersection_point1,
		TVector3< T > &	intersection_point2 )

Get the intersection point between a line and a sphere.

Parameters

line	the line
sphere	the sphere
intersection_point1	the first intersection point
intersection_point2	the second intersection point

Returns

bool, true if an intersection can be calculated, otherwise false

Definition at line 824 of file analyticalGeometry.h.

GetIntersection() [4/10]

template<typename T>

BALL_INLINE bool BALL::GetIntersection	(	const TPlane3< T > &	plane,
		const TLine3< T > &	line,
		TVector3< T > &	intersection_point )

Get the intersection point between a plane and a line.

Parameters

plane	the plane
line	the line
intersection_point	the resulting intersection

Returns

bool, true if an intersection can be calculated, otherwise false

Definition at line 701 of file analyticalGeometry.h.

GetIntersection() [5/10]

template<typename T>

BALL_INLINE bool BALL::GetIntersection	(	const TPlane3< T > &	plane,
		const TSphere3< T > &	sphere,
		TCircle3< T > &	intersection_circle )

Get the intersection circle between a plane and a sphere.

Parameters

plane	the plane
sphere	the sphere
intersection_circle	the intersection circle

Returns

bool, true if an intersection can be calculated, otherwise false

Definition at line 870 of file analyticalGeometry.h.

GetIntersection() [6/10]

template<typename T>

bool BALL::GetIntersection	(	const TPlane3< T > &	plane1,
		const TPlane3< T > &	plane2,
		TLine3< T > &	line )

Get the intersection line between two planes.

Parameters

plane1	the first plane
plane2	the second plane
line	the resulting intersection

Returns

bool, true if an intersection can be calculated, otherwise false

Definition at line 732 of file analyticalGeometry.h.

GetIntersection() [7/10]

template<typename T>

bool BALL::GetIntersection	(	const TSphere3< T > &	a,
		const TSphere3< T > &	b,
		TCircle3< T > &	intersection_circle )

Get the intersection circle between two spheres. This methods returns false, if the two spheres are identical, since then no intersection circle exists.

Parameters

a	the first sphere
b	the second sphere
intersection_circle	the intersection circle

Returns

bool, true if an intersection can be calculated, otherwise false

Definition at line 884 of file analyticalGeometry.h.

GetIntersection() [8/10]

template<class T>

bool BALL::GetIntersection	(	const TSphere3< T > &	s1,
		const TSphere3< T > &	s2,
		const TSphere3< T > &	s3,
		TVector3< T > &	p1,
		TVector3< T > &	p2,
		bool	test = true )

Get the intersection points between three spheres.

Parameters

s1	the first sphere
s2	the second sphere
s3	the third sphere
p1	the first intersection point
p2	the second intersection point
test

Returns

bool, true if an intersection can be calculated, otherwise false

Definition at line 929 of file analyticalGeometry.h.

GetIntersection() [9/10]

template<typename T>

bool BALL::GetIntersection	(	const TSphere3< T > &	sphere,
		const TLine3< T > &	line,
		TVector3< T > &	intersection_point1,
		TVector3< T > &	intersection_point2 )

Get the intersection point between a sphere and a line.

Parameters

sphere	the sphere
line	the line
intersection_point1	the first intersection point
intersection_point2	the second intersection point

Returns

bool, true if an intersection can be calculated, otherwise false

Definition at line 799 of file analyticalGeometry.h.

GetIntersection() [10/10]

template<typename T>

bool BALL::GetIntersection	(	const TSphere3< T > &	sphere,
		const TPlane3< T > &	plane,
		TCircle3< T > &	intersection_circle )

Get the intersection circle between a sphere and a plane.

Parameters

sphere	the sphere
plane	the plane
intersection_circle	the intersection circle

Returns

bool, true if an intersection can be calculated, otherwise false

Definition at line 836 of file analyticalGeometry.h.

getMMFF94Index()

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

getNextPrime()

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.

getNTerminal()

template<class ResidueContainerType>

const Residue * BALL::getNTerminal

(

const ResidueContainerType &

residue_container

)

Definition at line 457 of file residue.h.

getOrientedAngle() [1/2]

template<typename T>

TAngle< T > BALL::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 )

Return the oriented angle of two vectors with a normal vector.

Exceptions

Exception::DivisionByZero

if at least one vector is zero

Definition at line 1259 of file analyticalGeometry.h.

getOrientedAngle() [2/2]

template<typename T>

BALL_INLINE TAngle< T > BALL::getOrientedAngle	(	const TVector3< T > &	a,
		const TVector3< T > &	b,
		const TVector3< T > &	normal )

Return the oriented angle of two vectors with a normal vector.

Exceptions

Exception::DivisionByZero

if at least one vector is zero

Definition at line 1301 of file analyticalGeometry.h.

GetPartition() [1/2]

template<typename T>

BALL_INLINE TVector3< T > BALL::GetPartition	(	const TVector3< T > &	a,
		const TVector3< T > &	b )

Get the partition of two vectors.

Parameters

a	the first vector
b	the second vector

Returns

TVector3 the partition

Definition at line 351 of file analyticalGeometry.h.

GetPartition() [2/2]

template<typename T>

BALL_INLINE TVector3< T > BALL::GetPartition	(	const TVector3< T > &	a,
		const TVector3< T > &	b,
		const T &	r,
		const T &	s )

Get the partition of two vectors, calculated with two ratio factors.

Parameters

a	the first vector
b	the second vector
r	the ratio factor of the first vector
s	the ratio factor of the second vector

Returns

TVector3 the partition

Exceptions

Exception::DivisionByZero

if r+s == 0

Definition at line 367 of file analyticalGeometry.h.

getTorsionAngle()

template<typename T>

TAngle< T > BALL::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 )

Return the torsion angle of four points to each other.

Parameters

ax	1. vector x component
ay	1. vector y component
az	1. vector z component
bx	2. vector x component
by	2. vector y component
bz	2. vector z component
cx	3. vector x component
cy	3. vector y component
cz	3. vector z component
dx	4. vector x component
dy	4. vector y component
dz	4. vector z component

Returns

TAngle the torsion angle

Exceptions

Exception::DivisionByZero

if one of the outer vectors is collinear with the middle one

Definition at line 1323 of file analyticalGeometry.h.

Hash() [1/5]

template<>

BALL_EXPORT HashIndex BALL::Hash

(

const std::pair< Position, Position > &

p

)

Hash() [2/5]

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.

Hash() [3/5]

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.

Hash() [4/5]

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.

Hash() [5/5]

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.

hashElfString()

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

extern

hashPJWString()

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

extern

hashPointer()

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

extern

hashString()

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

extern

isCollinear()

template<typename T>

BALL_INLINE bool BALL::isCollinear	(	const TVector3< T > &	a,
		const TVector3< T > &	b )

Test whether two vector3 are collinear

Parameters

a	the first vector3
b	the second vector3

Returns

bool, true or false

Definition at line 1007 of file analyticalGeometry.h.

isComplanar() [1/2]

template<typename T>

BALL_INLINE bool BALL::isComplanar	(	const TVector3< T > &	a,
		const TVector3< T > &	b,
		const TVector3< T > &	c )

Test whether three vector3 are complanar

Parameters

a	the first vector3
b	the second vector3
c	the third vector3

Returns

bool, true or false

Definition at line 1020 of file analyticalGeometry.h.

isComplanar() [2/2]

template<typename T>

BALL_INLINE bool BALL::isComplanar	(	const TVector3< T > &	a,
		const TVector3< T > &	b,
		const TVector3< T > &	c,
		const TVector3< T > &	d )

Test whether four vector3 are complanar

Parameters

a	the first vector3
b	the second vector3
c	the third vector3
d	the fourth vector3

Returns

bool, true or false

Definition at line 1034 of file analyticalGeometry.h.

isIntersecting() [1/8]

template<typename T>

BALL_INLINE bool BALL::isIntersecting	(	const TLine3< T > &	a,
		const TLine3< T > &	b )

Test whether two lines are intersecting.

Parameters

a	the first line
b	the second line

Returns

bool, true or false

Definition at line 1154 of file analyticalGeometry.h.

isIntersecting() [2/8]

template<typename T>

BALL_INLINE bool BALL::isIntersecting	(	const TLine3< T > &	line,
		const TPlane3< T > &	plane )

Test whether a line is intersecting a plane.

Parameters

line	the line
plane	the plane

Returns

bool, true or false

Definition at line 1190 of file analyticalGeometry.h.

isIntersecting() [3/8]

template<typename T>

BALL_INLINE bool BALL::isIntersecting	(	const TLine3< T > &	line,
		const TVector3< T > &	point )

Test whether a line is intersecting a point.

Parameters

line	the line
point	the point

Returns

bool, true or false

Definition at line 1142 of file analyticalGeometry.h.

isIntersecting() [4/8]

template<typename T>

BALL_INLINE bool BALL::isIntersecting	(	const TPlane3< T > &	a,
		const TPlane3< T > &	b )

Test whether two planes are intersecting.

Parameters

a	the first plane
b	the second plane

Returns

bool, true or false

Definition at line 1214 of file analyticalGeometry.h.

isIntersecting() [5/8]

template<typename T>

BALL_INLINE bool BALL::isIntersecting	(	const TPlane3< T > &	plane,
		const TLine3< T > &	line )

Test whether a plane is intersecting a line.

Parameters

plane	the plane
line	the line

Returns

bool, true or false

Definition at line 1202 of file analyticalGeometry.h.

isIntersecting() [6/8]

template<typename T>

BALL_INLINE bool BALL::isIntersecting	(	const TPlane3< T > &	plane,
		const TVector3< T > &	point )

Test whether a point lies in a plane.

Parameters

plane	the plane
point	the point

Returns

bool, true or false

Definition at line 1178 of file analyticalGeometry.h.

isIntersecting() [7/8]

template<typename T>

BALL_INLINE bool BALL::isIntersecting	(	const TVector3< T > &	point,
		const TLine3< T > &	line )

Test whether a line is intersecting a point.

Parameters

point	the point
line	the line

Returns

bool, true or false

Definition at line 1130 of file analyticalGeometry.h.

isIntersecting() [8/8]

template<typename T>

BALL_INLINE bool BALL::isIntersecting	(	const TVector3< T > &	point,
		const TPlane3< T > &	plane )

Test whether a point lies in a plane.

Parameters

point	the point
plane	the plane

Returns

bool, true or false

Definition at line 1166 of file analyticalGeometry.h.

isOrthogonal() [1/7]

template<typename T>

BALL_INLINE bool BALL::isOrthogonal	(	const TLine3< T > &	a,
		const TLine3< T > &	b )

Test whether two lines are orthogonal.

Parameters

a	the first line
b	the second line

Returns

bool, true or false

Definition at line 1082 of file analyticalGeometry.h.

isOrthogonal() [2/7]

template<typename T>

BALL_INLINE bool BALL::isOrthogonal	(	const TLine3< T > &	line,
		const TVector3< T > &	vector )

Test whether a line and a vector3 are orthogonal

Parameters

line	the line
vector	the vector

Returns

bool, true or false

Definition at line 1070 of file analyticalGeometry.h.

isOrthogonal() [3/7]

template<typename T>

BALL_INLINE bool BALL::isOrthogonal	(	const TPlane3< T > &	a,
		const TPlane3< T > &	b )

Test whether two planes are orthogonal.

Parameters

a	the first plane
b	the second plane

Returns

bool, true or false

Definition at line 1118 of file analyticalGeometry.h.

isOrthogonal() [4/7]

template<typename T>

BALL_INLINE bool BALL::isOrthogonal	(	const TPlane3< T > &	plane,
		const TVector3< T > &	vector )

Test whether a plane and a vector3 are orthogonal.

Parameters

plane	the plane
vector	the vector3

Returns

bool, true or false

Definition at line 1106 of file analyticalGeometry.h.

isOrthogonal() [5/7]

template<typename T>

BALL_INLINE bool BALL::isOrthogonal	(	const TVector3< T > &	a,
		const TVector3< T > &	b )

Test whether two vector3 are orthogonal

Parameters

a	the first vector3
b	the second vector3

Returns

bool, true or false

Definition at line 1046 of file analyticalGeometry.h.

isOrthogonal() [6/7]

template<typename T>

BALL_INLINE bool BALL::isOrthogonal	(	const TVector3< T > &	vector,
		const TLine3< T > &	line )

Test whether a vector3 and a line are orthogonal

Parameters

vector	the vector
line	the line

Returns

bool, true or false

Definition at line 1058 of file analyticalGeometry.h.

isOrthogonal() [7/7]

template<typename T>

BALL_INLINE bool BALL::isOrthogonal	(	const TVector3< T > &	vector,
		const TPlane3< T > &	plane )

Test whether a vector3 and a plane are orthogonal.

Parameters

vector	the vector3
plane	the plane

Returns

bool, true or false

Definition at line 1094 of file analyticalGeometry.h.

isParallel() [1/3]

template<typename T>

BALL_INLINE bool BALL::isParallel	(	const TLine3< T > &	line,
		const TPlane3< T > &	plane )

Test whether a line and a plane are parallel.

Parameters

line	the line
plane	the plane

Returns

bool, true or false

Definition at line 1226 of file analyticalGeometry.h.

isParallel() [2/3]

template<typename T>

BALL_INLINE bool BALL::isParallel	(	const TPlane3< T > &	a,
		const TPlane3< T > &	b )

Test whether two planes are parallel.

Parameters

a	the first plane
b	the second plane

Returns

bool, true or false

Definition at line 1250 of file analyticalGeometry.h.

isParallel() [3/3]

template<typename T>

BALL_INLINE bool BALL::isParallel	(	const TPlane3< T > &	plane,
		const TLine3< T > &	line )

Test whether a plane and a line are parallel.

Parameters

plane	the plane
line	the line

Returns

bool, true or false

Definition at line 1238 of file analyticalGeometry.h.

molecules()

BALL_EXPORT MoleculeList BALL::molecules	(	const AtomContainer &	fragment,
		bool	selected_only = false )

Extract all molecules from a kernel data structure.

nucleicAcids()

BALL_EXPORT NucleicAcidList BALL::nucleicAcids	(	const AtomContainer &	fragment,
		bool	selected_only = false )

Extract all nucleic acids from a kernel data structure.

nucleotides()

BALL_EXPORT NucleotideList BALL::nucleotides	(	const AtomContainer &	fragment,
		bool	selected_only = false )

Extract all nucleotides from a kernel data structure.

operator!=()

BALL_EXPORT bool BALL::operator!=	(	const String &	s1,
		const String &	s2 )

Inequality operator.

operator*() [1/4]

template<typename T>

BALL_INLINE TVector3< T > BALL::operator*	(	const T &	a,
		const TVector3< T > &	b )

Multiply a vector with a scalar. The symmetric case is a member of the vector class.

Definition at line 1121 of file vector3.h.

operator*() [2/4]

template<typename T>

BALL_INLINE TVector4< T > BALL::operator*	(	const T &	scalar,
		const TVector4< T > &	v )

Multiplication operator for a scalar and a vector

Returns

TVector4 the new vector

Definition at line 841 of file vector4.h.

operator*() [3/4]

template<typename T>

BALL_INLINE TAngle< T > BALL::operator*	(	const T &	val,
		const TAngle< T > &	angle )

Multiplication operator. Multiplies a number with an angle.

Definition at line 704 of file angle.h.

operator*() [4/4]

template<typename T>

BALL_INLINE TVector4< T > BALL::operator*	(	const TVector4< T > &	v,
		const T &	scalar )

Multiplication operator for a vector and a scalar

Returns

TVector4 the new vector

Definition at line 851 of file vector4.h.

operator+() [1/21]

BALL_EXPORT String BALL::operator+	(	char	c,
		const String &	s )

Concatenates a character and a string.

operator+() [2/21]

BALL_EXPORT String BALL::operator+	(	char	c,
		String &&	s )

Concatenates a character and a string.

operator+() [3/21]

BALL_EXPORT String BALL::operator+	(	const char *	char_ptr,
		const String &	s )

Concatenates a C type string and a string.

operator+() [4/21]

BALL_EXPORT String BALL::operator+	(	const char *	char_ptr,
		String &&	s )

Concatenates a C type string and a string.

operator+() [5/21]

BALL_EXPORT String BALL::operator+	(	const String &	s,
		char	c )

Concatenates a string and a character.

operator+() [6/21]

BALL_EXPORT String BALL::operator+	(	const String &	s1,
		const char *	char_ptr )

Concatenates a string and a C type string.

operator+() [7/21]

BALL_EXPORT String BALL::operator+	(	const String &	s1,
		const String &	s2 )

Concatenates two strings.

operator+() [8/21]

BALL_EXPORT String BALL::operator+	(	const String &	s1,
		const string &	s2 )

Concatenates two strings.

operator+() [9/21]

BALL_EXPORT String BALL::operator+	(	const string &	s1,
		const String &	s2 )

Concatenates two strings.

operator+() [10/21]

BALL_EXPORT String BALL::operator+	(	const String &	s1,
		String &&	s2 )

Concatenates two strings.

operator+() [11/21]

BALL_EXPORT String BALL::operator+	(	const String &	s1,
		string &&	s2 )

Concatenates two strings.

operator+() [12/21]

BALL_EXPORT String BALL::operator+	(	const string &	s1,
		String &&	s2 )

Concatenates two strings.

operator+() [13/21]

template<typename T>

BALL_INLINE TAngle< T > BALL::operator+	(	const T &	val,
		const TAngle< T > &	angle )

Plus operator. Adds a number with an angle (in rad!)

Definition at line 714 of file angle.h.

operator+() [14/21]

template<typename T>

BALL_INLINE TVector4< T > BALL::operator+	(	const TVector4< T > &	a,
		const TVector4< T > &	b )

Addition operator for two vectors

Definition at line 821 of file vector4.h.

operator+() [15/21]

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 191 of file randomAccessIterator.h.

operator+() [16/21]

BALL_EXPORT String BALL::operator+	(	String &&	s,
		char	c )

Concatenates a string and a character.

operator+() [17/21]

BALL_EXPORT String BALL::operator+	(	String &&	s1,
		const char *	char_ptr )

Concatenates a string and a C type string.

operator+() [18/21]

BALL_EXPORT String BALL::operator+	(	String &&	s1,
		const String &	s2 )

Concatenates two strings.

operator+() [19/21]

BALL_EXPORT String BALL::operator+	(	String &&	s1,
		const string &	s2 )

Concatenates two strings.

operator+() [20/21]

BALL_EXPORT String BALL::operator+	(	string &&	s1,
		const String &	s2 )

Concatenates two strings.

operator+() [21/21]

BALL_EXPORT String BALL::operator+	(	String &&	s1,
		String &&	s2 )

Concatenates two strings.

operator-() [1/3]

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.

operator-() [2/3]

template<typename T>

BALL_INLINE TAngle< T > BALL::operator-	(	const T &	val,
		const TAngle< T > &	angle )

Minus operator. Subtracts the value of an angle (in rad!) from a number.

Definition at line 724 of file angle.h.

operator-() [3/3]

template<typename T>

BALL_INLINE TVector4< T > BALL::operator-	(	const TVector4< T > &	a,
		const TVector4< T > &	b )

Subtraction operator for two vectors

Returns

TVector4 the new vector

Definition at line 831 of file vector4.h.

operator<()

BALL_EXPORT bool BALL::operator<	(	const String &	s1,
		const String &	s2 )

Less than comparison

operator<<() [1/22]

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

Output stream operator for SnapShots.

operator<<() [2/22]

template<typename ComplexTraits>

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

Definition at line 674 of file FFT1D.h.

operator<<() [3/22]

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.

operator<<() [4/22]

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.

operator<<() [5/22]

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

operator<<() [6/22]

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.

operator<<() [7/22]

template<typename PositionType>

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

Output operator

Definition at line 249 of file peak.h.

operator<<() [8/22]

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.

operator<<() [9/22]

template<typename DataT, typename PeakT, typename PositionT>

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

operator<<() [10/22]

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

Print the contents of a TimeStamp object to a stream.

operator<<() [11/22]

template<typename ValueType>

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

Output operator.

Definition at line 788 of file regularData1D.h.

operator<<() [12/22]

template<typename ValueType>

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

Output operator.

Definition at line 960 of file regularData2D.h.

operator<<() [13/22]

template<typename ValueType>

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

Output operator.

Definition at line 1405 of file regularData3D.h.

operator<<() [14/22]

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.

operator<<() [15/22]

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).

operator<<() [16/22]

BALL_EXPORT std::ostream & BALL::operator<<	(	std::ostream &	s,
		const Element &	element )

Element output operator. Prints the contents of an instance of Element to an ostream.

operator<<() [17/22]

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 746 of file angle.h.

operator<<() [18/22]

template<typename T>

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

Definition at line 596 of file quaternion.h.

operator<<() [19/22]

template<typename T>

std::ostream & BALL::operator<<	(	std::ostream &	s,
		const TVector3< T > &	vector )

Output operator. Writes the values of three vector components of type T to an ostream. The components are writen in the order of x, y, z.

Definition at line 1136 of file vector3.h.

operator<<() [20/22]

template<typename T>

std::ostream & BALL::operator<<	(	std::ostream &	s,
		const TVector4< T > &	v )

Output Operator. Write the four components of the vector to an output stream. The values are enclosed by brackets.

Example:

(0.1 2.0 0 1)

Definition at line 875 of file vector4.h.

operator<<() [21/22]

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 768 of file FFT2D.h.

operator<<() [22/22]

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 927 of file FFT3D.h.

operator<=()

BALL_EXPORT bool BALL::operator<=	(	const String &	s1,
		const String &	s2 )

Less than or equal comparison

operator==()

BALL_EXPORT bool BALL::operator==	(	const String &	s1,
		const String &	s2 )

Equality operator.

operator>()

BALL_EXPORT bool BALL::operator>	(	const String &	s1,
		const String &	s2 )

Greater than comparison

operator>=()

BALL_EXPORT bool BALL::operator>=	(	const String &	s1,
		const String &	s2 )

Greater than or equal comparison

operator>>() [1/11]

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

Input stream operator for SnapShots.

operator>>() [2/11]

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

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

operator>>() [3/11]

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.

operator>>() [4/11]

template<typename DataT, typename PeakT, typename PositionT>

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

operator>>() [5/11]

template<typename ValueType>

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

Input operator.

Definition at line 802 of file regularData1D.h.

operator>>() [6/11]

template<typename ValueType>

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

Input operator.

Definition at line 978 of file regularData2D.h.

operator>>() [7/11]

template<typename ValueType>

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

Input operator.

Definition at line 1425 of file regularData3D.h.

operator>>() [8/11]

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 733 of file angle.h.

operator>>() [9/11]

template<typename T>

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

Definition at line 588 of file quaternion.h.

operator>>() [10/11]

template<typename T>

std::istream & BALL::operator>>	(	std::istream &	s,
		TVector3< T > &	vector )

Input operator. Reads the values of three vector components of type T from an istream. The components are read in the order of x, y, z.

Definition at line 1127 of file vector3.h.

operator>>() [11/11]

template<typename T>

std::istream & BALL::operator>>	(	std::istream &	s,
		TVector4< T > &	v )

Input operator Reads four values of type T from an input stream and assigns them to the components x, y, z and h of the vector.

Definition at line 861 of file vector4.h.

PDBAtoms()

BALL_EXPORT PDBAtomList BALL::PDBAtoms	(	const AtomContainer &	fragment,
		const String &	expression = String() )

Extract PDB atoms matching an expression. This method extracts all PDB atoms of a kernel data structure into a list that match the Expression expression. If no expression is given, all PDB atoms will be returned.

Parameters

fragment	the AtomContainer containing the atoms
expression	the expression that selects the atoms (default: no expression)

proteins()

BALL_EXPORT ProteinList BALL::proteins	(	const AtomContainer &	fragment,
		bool	selected_only = false )

Extract all proteins from a kernel data structure.

residues()

BALL_EXPORT ResidueList BALL::residues	(	const AtomContainer &	fragment,
		bool	selected_only = false )

Extract all residues from a kernel data structure.

secondaryStructures()

BALL_EXPORT SecondaryStructureList BALL::secondaryStructures	(	const AtomContainer &	fragment,
		bool	selected_only = false )

Extract all secondary structures from a kernel data structure.

setTorsionAngle()

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)

SolveQuadraticEquation()

template<typename T>

short BALL::SolveQuadraticEquation	(	const T &	a,
		const T &	b,
		const T &	c,
		T &	x1,
		T &	x2 )

Solve a quadratic equation of the form a .

Parameters

a
b
c
x1	the first solution
x2	the second solution

Returns

short the number of solutions (0 - 2)

Definition at line 310 of file analyticalGeometry.h.

SolveSystem()

template<typename T>

bool BALL::SolveSystem	(	const T *	m,
		T *	x,
		const Size	dim )

Solve a system of linear equations. Given a system of linear equations

in matrix form, identify the solution .

m should point to a C-style array containing the matrix A.

The elements of A are row-ordered, i.e., they are ordered like this:

x points to a C-style array that will contain the solution vector x upon successful termination of the function.

If there is no solution or the system is under-determined, return false.

Parameters

m	pointer to the factors in the equations
x	pointer in which the results are stored
dim	the dimension of the equation system (number of variables)

Returns

bool true if a solution is found

Definition at line 191 of file analyticalGeometry.h.

SolveSystem2()

template<typename T>

BALL_INLINE bool BALL::SolveSystem2	(	const T &	a1,
		const T &	b1,
		const T &	c1,
		const T &	a2,
		const T &	b2,
		const T &	c2,
		T &	x1,
		T &	x2 )

Solve a system of two equations of the form and .

Parameters

a1,b1,c1,a2,b2,c2	constants of the system
x1	the first solution
x2	the second solution

Returns

bool true if a solution is found

Definition at line 285 of file analyticalGeometry.h.

swapBytes() [1/9]

template<>

BALL_EXPORT void BALL::swapBytes

(

double &

)

swapBytes() [2/9]

template<>

BALL_EXPORT void BALL::swapBytes

(

float &

)

swapBytes() [3/9]

template<>

BALL_EXPORT void BALL::swapBytes

(

int &

)

swapBytes() [4/9]

template<>

BALL_EXPORT void BALL::swapBytes

(

long &

)

swapBytes() [5/9]

template<>

BALL_EXPORT void BALL::swapBytes

(

short &

)

swapBytes() [6/9]

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.

swapBytes() [7/9]

template<>

BALL_EXPORT void BALL::swapBytes

(

unsigned int &

)

swapBytes() [8/9]

template<>

BALL_EXPORT void BALL::swapBytes

(

unsigned long &

)

swapBytes() [9/9]

template<>

BALL_EXPORT void BALL::swapBytes

(

unsigned short &

)

Variable Documentation

CCONN__INSIDE

BALL_EXPORT const char BALL::CCONN__INSIDE

extern

CCONN__INSIDE_PROBE

BALL_EXPORT const char BALL::CCONN__INSIDE_PROBE

extern

CCONN__OUTSIDE

BALL_EXPORT const char BALL::CCONN__OUTSIDE

extern

Distance_MAX

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

static

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

Distance_MIN

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

static

Definition at line 232 of file COMMON/global.h.

Handle_MAX

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

static

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

Handle_MIN

const Handle BALL::Handle_MIN = 0

static

Definition at line 236 of file COMMON/global.h.

Index_MAX

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

static

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

Index_MIN

const Index BALL::Index_MIN = 0

static

Definition at line 240 of file COMMON/global.h.

INVALID_Distance

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

static

Definition at line 231 of file COMMON/global.h.

INVALID_Handle

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

static

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

INVALID_Index

const Index BALL::INVALID_Index = -1

static

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

INVALID_Position

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

static

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

INVALID_Size

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

static

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

Log

BALL_EXPORT LogStream BALL::Log

extern

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

MMFF94_number_atom_types

Size BALL::MMFF94_number_atom_types

extern

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

Position_MAX

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

static

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

Position_MIN

const Position BALL::Position_MIN = 0

static

Definition at line 244 of file COMMON/global.h.

Size_MAX

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

static

Definition at line 249 of file COMMON/global.h.

Size_MIN

const Size BALL::Size_MIN = 0

static

Definition at line 248 of file COMMON/global.h.

TVector3< float >

template class BALL_EXPORT BALL::TVector3< float >

extern