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BALL Namespace Reference


Detailed Description

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

TODO: POPULATION_ANALYSIS


Classes

struct  ACEFastAtomType
class  AddHydrogenProcessor
class  Addition
class  AmberBend
class  AmberEvaluation
class  AmberFF
class  AmberNonBonded
class  AmberStretch
class  AmberTorsion
class  AnisotropyShiftProcessor
class  AromaticBondsPredicate
class  AromaticityProcessor
class  AromaticRingStacking
class  AssignBaseProcessor
 Only used for deriving interface. More...
class  AssignBondOrderProcessor
class  AssignChargeProcessor
class  AssignRadiusProcessor
class  AssignShiftProcessor
class  AssignTypeNameProcessor
class  AssignTypeProcessor
class  Atom
class  AtomBijection
class  AtomContainer
class  AtomContainerIteratorTraits
class  AtomicPolarizabilities
class  AtomInformationContent
class  AtomIteratorTraits
class  AtomNamePredicate
class  AtomTypePredicate
class  AtomTyper
class  AtomTypes
class  AtomVector
class  AutoDeletable
class  AxialPredicate
class  BackBonePredicate
class  BalabanIndexJ
class  BALLPlugin
class  BaseIterator
class  BidirectionalIterator
 Mutable bidirectional iterator. More...
class  BinaryFileAdaptor
class  BinaryFunctor
class  BinaryPredicate
class  BinaryProcessor
class  BindingPocketProcessor
class  Bit
class  BitVector
class  Bond
class  BondPolarizabilities
class  BoundingBoxProcessor
class  Bruker1DFile
class  Bruker2DFile
class  BuildBondsProcessor
class  BuriedPolar
class  CanonicalMD
class  Chain
class  ChainBuilder
 This class provides methods for analysis of the chains in a molecule. More...
class  ChainIteratorTraits
class  ChainPredicate
class  ChargePredicate
class  ChargeRuleProcessor
class  CharmmBend
class  CharmmEEF1
class  CharmmFF
class  CharmmImproperTorsion
class  CharmmNonBonded
class  CharmmStretch
class  CharmmTorsion
class  ChemScoreMetal
class  CHPI
class  ClaverieParameter
class  ClearChargeProcessor
class  ClearRadiusProcessor
class  ClearShiftProcessor
class  Client
class  Comparator
class  ComposedEnergyProcessor
class  Composite
class  CompositeIteratorTraits
class  Conformation4C1Predicate
class  ConformationSet
class  ConjugateGradientMinimizer
class  ConnectedToPredicate
class  ConnectivityBase
class  Constant
class  ConstantFunction
class  ConstBidirectionalIterator
class  ConstForwardIterator
class  ConstRandomAccessIterator
class  CosineTorsion
class  CreateSpectrumProcessor
class  CubicFunction
class  DCDFile
class  Density
class  Descriptor
class  Directory
class  Division
class  DNAMutator
class  DockingAlgorithm
class  DockResult
class  DoubleBondsPredicate
struct  DoubleTraits
class  DSN6File
class  EdgeItem
class  EFShiftProcessor
class  ElectrostaticPotentialCalculator
class  Element
class  ElementPredicate
class  Embeddable
class  EnergeticEvaluation
class  EnergyMinimizer
class  EnergyProcessor
class  Enumerator
class  EnumeratorIndex
class  Experiment
class  Expression
class  ExpressionParser
class  ExpressionPredicate
class  ExpressionTree
class  Factory
class  FalsePredicate
class  FDPB
class  FermiBaseFunction
class  File
class  FileSystem
struct  FloatTraits
class  ForceField
class  ForceFieldComponent
class  ForceFieldEvaluation
class  ForceFieldParameters
class  FormalCharge
class  ForwardIterator
class  Fragment
class  FragmentDB
class  FragmentDistanceCollector
class  FragmentIteratorTraits
class  FresnoTypes
class  GAFFCESParser
class  GAFFTypeProcessor
class  GAMESSDatFile
class  GAMESSLogFile
class  GeneralizedBornModel
class  GenericMolFile
class  GeometricCenterProcessor
class  GeometricFit
class  GlobalInitializer
class  Gradient
class  GraphEdge
class  GraphFace
class  GraphTriangle
class  GraphVertex
class  HaighMallionShiftProcessor
class  HashFunction
class  HashGrid3
class  HashGridBox3
class  HashMap
 HashMap class based on the STL map (containing serveral convenience functions). More...
class  HashSet
class  HBondProcessor
class  HBondShiftProcessor
class  HINFile
struct  HINFileBondStruct
class  HybridisationProcessor
class  HydrogenBond
class  HydrophobicVdWSurface
class  INIFile
class  InRingPredicate
class  JCAMPFile
class  JohnsonBoveyShiftProcessor
class  KCFFile
class  Kekuliser
class  KernelPredicate
 Kernel predicate class. More...
class  LennardJones
class  Limits
class  Limits< bool >
class  Limits< char >
class  Limits< double >
class  Limits< float >
class  Limits< int >
class  Limits< long >
class  Limits< short >
class  Limits< signed char >
class  Limits< unsigned char >
class  Limits< unsigned int >
class  Limits< unsigned long >
class  Limits< unsigned short >
class  LinearBaseFunction
class  LineBasedFile
class  LineSearch
class  Lipophilic
class  List
class  LogStream
class  LogStreamBuf
class  LogStreamNotifier
struct  LongDoubleTraits
class  Mainframe
class  MD5Hash
class  MeanAtomInformationContent
class  MicroCanonicalMD
class  MMFF94
struct  MMFF94AtomType
 Class to store the values of an atom type from MMFFPROP.PAR. More...
class  MMFF94AtomTypeEquivalences
class  MMFF94AtomTyper
class  MMFF94AtomTypes
class  MMFF94BendParameters
class  MMFF94ChargeProcessor
class  MMFF94ESParameters
class  MMFF94NonBonded
class  MMFF94OutOfPlaneBend
class  MMFF94ParametersBase
class  MMFF94PlaneParameters
class  MMFF94StretchBend
class  MMFF94StretchBendParameters
class  MMFF94StretchParameters
class  MMFF94Torsion
class  MMFF94TorsionParameters
class  MMFF94VDWParameters
class  MOL2File
class  MolecularDynamics
class  MolecularInformation
class  MolecularWeight
class  Molecule
class  MoleculeAssembler
 class, providing methods for the assembly of a structure diagram More...
class  MoleculeIteratorTraits
class  MoleculeObjectCreator
class  MoleculePredicate
class  MOLFile
class  MolFileFactory
class  MutableConstant
class  MutablePower
class  NamedProperty
struct  NBStruct
class  NegativePolarVdWSurface
class  NegativeVdWSurface
struct  NMRAtomData
struct  NMRAtomDataSet
class  NMRStarFile
class  NodeItem
class  NonpolarSolvation
class  NotificationManager_
class  NotificationSlot_
class  NotificationSource_
class  NotificationTarget
class  NotificationTarget1
class  NotificationTarget2
class  NotificationTarget_
class  NucleicAcid
class  NucleicAcidIteratorTraits
class  NucleicAcidPredicate
class  Nucleotide
class  NucleotideIteratorTraits
class  NucleotidePredicate
class  NumberOfAromaticAtoms
class  NumberOfAromaticBonds
class  NumberOfAtoms
class  NumberOfBonds
class  NumberOfBondsPredicate
class  NumberOfBoron
class  NumberOfBromine
class  NumberOfCarbon
class  NumberOfChlorine
class  NumberOfDoubleBonds
class  NumberOfFlourine
class  NumberOfHeavyAtoms
class  NumberOfHeavyBonds
class  NumberOfHydrogen
class  NumberOfHydrogenBondAcceptors
class  NumberOfHydrogenBondDonors
class  NumberOfHydrophobicAtoms
class  NumberOfIodine
class  NumberOfNitrogen
class  NumberOfOxygen
class  NumberOfPhosphorus
class  NumberOfRotatableBonds
class  NumberOfRotatableSingleBonds
class  NumberOfSingleBonds
class  NumberOfSulfur
class  NumberOfTripleBonds
class  NumericalIntegrator
class  NumericalSAS
class  Object
class  ObjectCreator
class  Options
class  Pair6_12InteractionEnergyProcessor
class  Pair6_12RDFIntegrator
class  PairExpInteractionEnergyProcessor
class  PairExpRDFIntegrator
class  Parameters
class  ParameterSection
class  ParsedFunction
class  PartialChargeBase
class  PartialChargeProcessor
class  Path
class  PCMCavFreeEnergyProcessor
class  PDBAtom
class  PDBAtomIteratorTraits
class  PDBFile
class  PDBInfo
class  PDBRecords
class  Peak
class  PeakList
class  PeriodicBoundary
class  PersistenceManager
class  PersistenceTest
class  PersistentObject
class  PiecewiseFunction
class  PiecewisePolynomial
class  PierottiCavFreeEnergyProcessor
class  PluginHandler
class  PluginManager
struct  PointerPairComparator
class  PolarSolvation
class  PolarVdWSurface
class  PositivePolarVdWSurface
class  PositiveVdWSurface
class  Potential1210
class  PreciseTime
class  PreferencesObject
class  PrincipalMomentOfInertia
class  PrincipalMomentOfInertiaX
class  PrincipalMomentOfInertiaY
class  PrincipalMomentOfInertiaZ
class  Processor
class  Product
class  PropertyManager
class  Protein
class  ProteinIteratorTraits
class  ProteinPredicate
class  PTE_
class  PyColorRGBAVector
class  PyCompositeList
class  PyDatasetVector
class  PyIndexList
class  PyInterpreter
class  QuadraticAngleBend
class  QuadraticBondStretch
class  QuadraticImproperTorsion
class  Quadruple
class  RadialDistributionFunction
class  RadiusRuleProcessor
class  RandomAccessIterator
class  RandomCoilShiftProcessor
class  RandomEvaluation
class  RandomNumberGenerator
class  RDFIntegrator
class  RDFParameter
class  RDFSection
class  Reciprocal
class  ReconstructFragmentProcessor
class  ReducedSurface
class  RegularExpression
class  ReissCavFreeEnergyProcessor
class  RelHydrophobicVdWSurface
class  RelNegativePartialCharge
class  RelNegativePolarVdWSurface
class  RelNegativeVdWSurface
class  RelNumberOfRotatableBonds
class  RelNumberOfRotatableSingleBonds
class  RelPolarVdWSurface
class  RelPositivePartialCharge
class  RelPositivePolarVdWSurface
class  RelPositiveVdWSurface
class  Residue
class  ResidueChecker
class  ResidueIDPredicate
class  ResidueIteratorTraits
class  ResiduePredicate
class  ResidueRotamerSet
class  ResidueTorsions
class  ResourceEntry
class  ResourceFile
class  RingAnalyser
 class, providing methods for the analysis of the structure of ringsystems More...
class  RingClusterer
 class, providing a method for agglomerative clustering of single rings to ringsystems More...
class  RingFinder
class  RingPerceptionProcessor
class  RMSDMinimizer
class  RombergIntegrator
class  Rotamer
class  RotamerLibrary
 Rotamer Library Class. More...
class  RotationalEntropyLoss
class  RSComputer
class  RSConstructor
 class, performing the prefabication of ringsystems (i.e. providing them with relative 2D-coordinates) More...
class  RSEdge
class  RSFace
class  RSVertex
class  RuleEvaluator
class  RuleProcessor
struct  SampleCondition
class  SASEdge
class  SASFace
class  SASTriangulator
class  SASVertex
class  ScoringBaseFunction
class  ScoringComponent
class  ScoringFunction
class  ScoringTypes
class  SCWRLRotamerFile
 Reads Dunbrack/SCWRL rotamer library files. More...
class  SDFile
class  SDGenerator
 The main class, provides methods for analysis of the input. More...
class  SecondaryStructure
class  SecondaryStructureIteratorTraits
class  SecondaryStructurePredicate
class  SecondaryStructureProcessor
class  Selectable
class  SelectedPredicate
class  Selector
class  SESComputer
class  SESEdge
class  SESFace
class  SESSingularityCleaner
class  SESTriangulator
class  SESVertex
class  ShiftedLVMMMinimizer
class  ShiftModel
class  ShiftModule
struct  ShiftReferenceElement
struct  ShiftReferenceSet
class  SimpleBase
class  SimpleExperiment1D
class  SingleBondsPredicate
class  SizeOfSSSR
class  SLICKEnergy
class  SLICKScore
class  SmartsMatcher
class  SmartsParser
class  SMARTSPredicate
class  SmilesParser
class  SnapShot
class  SnapShotManager
class  SolventAccessibleSurface
class  SolventAtomDescriptor
class  SolventDescriptor
class  SolventExcludedSurface
class  SolventParameter
class  SolventPredicate
class  Sp2HybridizedPredicate
class  Sp3HybridizedPredicate
class  Spectrum
class  SpHybridizedPredicate
class  SquareFunction
class  SteepestDescentMinimizer
class  StrangLBFGSMinimizer
class  String
class  StringHashMap
class  StructureMapper
class  Substring
class  Subtraction
class  SurfaceBase
class  SurfaceProcessor
struct  SwitchingCutOnOff
class  System
class  TAngle
class  TBox3
class  TCircle3
class  TContour
class  TContourLine
class  TContourSurface
class  TCPIOStream
class  TCPServer
class  TCPServerThread
class  TCPTransfer
class  Templates
class  TestPDBFile
class  TestProcessor
class  TestProcessor2
class  TextPersistenceManager
class  TFFT1D
class  TFFT2D
class  TFFT3D
class  Timer
class  TimeStamp
class  TLine3
class  TMatrix4x4
class  TMolecularGraph
class  TMutex
class  TMutex< QMutex >
class  TMutexLocker
class  TotalNegativePartialCharge
class  TotalPositivePartialCharge
class  TPlane3
class  TQuaternion
class  TrajectoryFile
class  TransformationManager
class  TransformationProcessor
class  TranslationProcessor
class  TReadLocker
class  TReadWriteLock
class  TReadWriteLock< QReadWriteLock >
class  TRegularData1D
class  TRegularData2D
class  TRegularData3D
class  Triangle
class  TriangleEdge
class  TrianglePoint
class  TriangulatedSAS
class  TriangulatedSES
class  TriangulatedSphere
class  TriangulatedSurface
class  Triple
class  TripleBondsPredicate
class  TRRFile
class  TruePredicate
class  TSimpleBox3
class  TSphere3
class  TSurface
class  TVector2
class  TVector3
class  TVector4
class  TWriteLocker
class  TypenameRuleProcessor
class  TypeRuleProcessor
class  UCK
class  UhligCavFreeEnergyProcessor
class  UnaryFunctor
class  UnaryPredicate
class  UnaryProcessor
class  VanDerWaals
class  VdWSurface
class  VdWVolume
class  VersionInfo
class  VertexAdjacency
class  VertexAdjacencyEquality
class  Visitor
class  XDRPersistenceManager
class  XYZFile
class  ZagrebIndex

Namespaces

namespace  Constants
namespace  Exception
namespace  MolmecSupport
namespace  PDB
namespace  RTTI
namespace  SysInfo

Storers

typedef TSimpleBox3< float > SimpleBox3
template<typename T>
std::ostream & operator<< (std::ostream &s, const TSimpleBox3< T > &box)
template<typename T>
std::istream & operator>> (std::istream &s, TSimpleBox3< T > &box)

Typedefs

typedef std::pair
< ACETypeTable, ACEParameter > 
ACEData
typedef std::vector
< std::vector< double > > 
ACEParameter
typedef StringHashMap< Atom::TypeACETypeTable
typedef TAngle< float > Angle
typedef TBox3< float > Box3
typedef TCircle3< float > Circle3
typedef std::vector< double > Coefficients
typedef int(* ComparatorType )(const void *, const void *)
typedef std::complex
< BALL_COMPLEX_PRECISION > 
Complex
typedef TContour< float > Contour
typedef TContourLine< float > ContourLine
typedef TContourSurface< float > ContourSurface
 Default type.
typedef TVector3< double > DVector3
typedef std::map< std::pair
< TrianglePoint
*, TrianglePoint * >
, TriangleEdge
*, PointerPairComparator > 
EdgeMap
typedef List< EnergyProcessor * > EnergyProcessorList
typedef float(* ESEnergyFunction )(float square_dist, float q1_q2)
typedef Index FacetArray [256][12]
typedef TFFT1D
< BALL_FFTW_DEFAULT_TRAITS > 
FFT1D
typedef TFFT2D
< BALL_FFTW_DEFAULT_TRAITS > 
FFT2D
typedef TFFT3D
< BALL_FFTW_DEFAULT_TRAITS > 
FFT3D
typedef
ConstBidirectionalIterator
< Composite, Fragment,
Composite::CompositeIterator,
FragmentIteratorTraits
FragmentConstIterator
typedef std::reverse_iterator
< FragmentConstIterator
FragmentConstReverseIterator
typedef BidirectionalIterator
< Composite, Fragment,
Composite::CompositeIterator,
FragmentIteratorTraits
FragmentIterator
typedef std::reverse_iterator
< FragmentIterator
FragmentReverseIterator
typedef std::pair< double, double > Interval
typedef TLine3< float > Line3
typedef TMatrix4x4< float > Matrix4x4
typedef TMolecularGraph< Index,
Index
MolecularGraph
typedef
ConstBidirectionalIterator
< Composite, Molecule,
Composite::CompositeIterator,
MoleculeIteratorTraits
MoleculeConstIterator
typedef std::reverse_iterator
< MoleculeConstIterator
MoleculeConstReverseIterator
typedef BidirectionalIterator
< Composite, Molecule,
Composite::CompositeIterator,
MoleculeIteratorTraits
MoleculeIterator
typedef std::reverse_iterator
< MoleculeIterator
MoleculeReverseIterator
typedef TMutex
< BALL_DEFAULT_MUTEX_TYPE > 
Mutex
typedef TMutexLocker
< BALL_DEFAULT_MUTEXLOCKER_TYPE,
BALL_DEFAULT_MUTEX_TYPE > 
MutexLocker
typedef
ConstBidirectionalIterator
< Composite, NucleicAcid,
Composite::CompositeIterator,
NucleicAcidIteratorTraits
NucleicAcidConstIterator
typedef std::reverse_iterator
< NucleicAcidConstIterator
NucleicAcidConstReverseIterator
typedef BidirectionalIterator
< Composite, NucleicAcid,
Composite::CompositeIterator,
NucleicAcidIteratorTraits
NucleicAcidIterator
typedef std::reverse_iterator
< NucleicAcidIterator
NucleicAcidReverseIterator
typedef
ConstBidirectionalIterator
< Composite, Nucleotide,
Composite::CompositeIterator,
NucleotideIteratorTraits
NucleotideConstIterator
typedef std::reverse_iterator
< NucleotideConstIterator
NucleotideConstReverseIterator
typedef BidirectionalIterator
< Composite, Nucleotide,
Composite::CompositeIterator,
NucleotideIteratorTraits
NucleotideIterator
typedef std::reverse_iterator
< NucleotideIterator
NucleotideReverseIterator
typedef vector< pair< Size,
Size > > 
PairVector
typedef TPlane3< float > Plane3
typedef
ConstBidirectionalIterator
< Composite, Protein,
Composite::CompositeIterator,
ProteinIteratorTraits
ProteinConstIterator
typedef std::reverse_iterator
< ProteinConstIterator
ProteinConstReverseIterator
typedef BidirectionalIterator
< Composite, Protein,
Composite::CompositeIterator,
ProteinIteratorTraits
ProteinIterator
typedef std::reverse_iterator
< ProteinIterator
ProteinReverseIterator
typedef TQuaternion< float > Quaternion
typedef TReadLocker
< BALL_DEFAULT_READLOCKER_TYPE,
BALL_DEFAULT_READWRITELOCK_TYPE > 
ReadLocker
typedef TReadWriteLock
< BALL_DEFAULT_READWRITELOCK_TYPE > 
ReadWriteLock
typedef TRegularData1D< float > RegularData1D
typedef TRegularData2D< float > RegularData2D
typedef TRegularData3D< float > RegularData3D
typedef List< RegularData3D * > RegularData3DList
typedef
ConstBidirectionalIterator
< Composite, Residue,
Composite::CompositeIterator,
ResidueIteratorTraits
ResidueConstIterator
typedef std::reverse_iterator
< ResidueConstIterator
ResidueConstReverseIterator
typedef BidirectionalIterator
< Composite, Residue,
Composite::CompositeIterator,
ResidueIteratorTraits
ResidueIterator
typedef std::reverse_iterator
< ResidueIterator
ResidueReverseIterator
typedef
ConstBidirectionalIterator
< Composite,
SecondaryStructure,
Composite::CompositeIterator,
SecondaryStructureIteratorTraits
SecondaryStructureConstIterator
typedef std::reverse_iterator
< SecondaryStructureConstIterator
SecondaryStructureConstReverseIterator
typedef BidirectionalIterator
< Composite,
SecondaryStructure,
Composite::CompositeIterator,
SecondaryStructureIteratorTraits
SecondaryStructureIterator
typedef std::reverse_iterator
< SecondaryStructureIterator
SecondaryStructureReverseIterator
typedef vector< vector< Size > > SizeVector
typedef TSphere3< float > Sphere3
typedef HashSet< StringStringHashSet
typedef TSurface< float > Surface
typedef float(* SwitchingFunction )(double square_distance, const SwitchingCutOnOff &cutoffs)
typedef float(* VdwEnergyFunction )(float square_dist, float A, float B)
typedef TVector2< float > Vector2
typedef TVector3< float > Vector3
typedef TVector4< float > Vector4
typedef TWriteLocker
< BALL_DEFAULT_WRITELOCKER_TYPE,
BALL_DEFAULT_READWRITELOCK_TYPE > 
WriteLocker
Typedefs for the various BondIterators
typedef Atom::BondConstIterator AtomBondConstIterator
typedef
Atom::BondConstReverseIterator 
AtomBondConstReverseIterator
typedef Atom::BondIterator AtomBondIterator
typedef Atom::BondReverseIterator AtomBondReverseIterator
Iterator type definitions for the various AtomIterators
typedef
ConstBidirectionalIterator
< Composite, Atom,
Composite::CompositeIterator,
AtomIteratorTraits
AtomConstIterator
typedef std::reverse_iterator
< AtomConstIterator
AtomConstReverseIterator
 A constant reverse bidirectional iterator for the Atom class.
typedef BidirectionalIterator
< Composite, Atom,
Composite::CompositeIterator,
AtomIteratorTraits
AtomIterator
typedef std::reverse_iterator
< AtomIterator
AtomReverseIterator
 A mutable reverse bidirectional iterator for the Atom class.
Iterator type definitions for the various AtomContainerIterators.
typedef
ConstBidirectionalIterator
< Composite, AtomContainer,
Composite::CompositeIterator,
AtomContainerIteratorTraits
AtomContainerConstIterator
typedef std::reverse_iterator
< AtomContainerConstIterator
AtomContainerConstReverseIterator
 A constant reverse bidirectional iterator for the AtomContainer class.
typedef BidirectionalIterator
< Composite, AtomContainer,
Composite::CompositeIterator,
AtomContainerIteratorTraits
AtomContainerIterator
typedef std::reverse_iterator
< AtomContainerIterator
AtomContainerReverseIterator
 A mutable reverse bidirectional iterator for the AtomContainer class.
typedef std::list
< AtomContainer * > 
AtomContainerList
typedef std::list< Atom * > AtomList
typedef std::list< Bond * > BondList
typedef std::list< Chain * > ChainList
typedef std::list< Fragment * > FragmentList
typedef std::list< Molecule * > MoleculeList
typedef std::list< NucleicAcid * > NucleicAcidList
typedef std::list< Nucleotide * > NucleotideList
typedef std::list< PDBAtom * > PDBAtomList
typedef std::list< Protein * > ProteinList
typedef std::list< Residue * > ResidueList
typedef std::list
< SecondaryStructure * > 
SecondaryStructureList
Type aliases defined by BALL.
These predefined types are used in BALL for portability and comprehensibility.

typedef unsigned char Byte
typedef BALL_INDEX_TYPE Distance
typedef double DoubleReal
typedef BALL_INDEX_TYPE ErrorCode
typedef BALL_SIZE_TYPE Handle
typedef BALL_SIZE_TYPE HashIndex
typedef BALL_INDEX_TYPE Index
typedef BALL_LONG64_TYPE LongIndex
typedef BALL_ULONG64_TYPE LongSize
typedef BALL_POINTERSIZEUINT_TYPE PointerSizeUInt
typedef BALL_SIZE_TYPE Position
typedef BALL_SIZE_TYPE Property
typedef float Real
typedef BALL_SIZE_TYPE Size
typedef time_t Time
Iterator type definitions for the various ChainIterators
typedef
ConstBidirectionalIterator
< Composite, Chain,
Composite::CompositeIterator,
ChainIteratorTraits
ChainConstIterator
 A constant bidirectional iterator for the Chain class.
typedef std::reverse_iterator
< ChainConstIterator
ChainConstReverseIterator
 A constant reverse bidirectional iterator for the Chain class.
typedef BidirectionalIterator
< Composite, Chain,
Composite::CompositeIterator,
ChainIteratorTraits
ChainIterator
 A mutable bidirectional iterator for the Chain class.
typedef std::reverse_iterator
< ChainIterator
ChainReverseIterator
 A mutable reverse bidirectional iterator for the Chain class.
Convenience typedefs
typedef Experiment< PeakList1DExperiment1D
typedef Experiment< PeakList3DExperiment3D
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< CompositeKernelPredicateType
Iterator type definitions for the various PDBAtomIterators
typedef
ConstBidirectionalIterator
< Composite, PDBAtom,
Composite::CompositeIterator,
PDBAtomIteratorTraits
PDBAtomConstIterator
 A constant bidirectional iterator for the PDBAtom class.
typedef std::reverse_iterator
< PDBAtomConstIterator
PDBAtomConstReverseIterator
 A constant reverse bidirectional iterator for the PDBAtom class.
typedef BidirectionalIterator
< Composite, PDBAtom,
Composite::CompositeIterator,
PDBAtomIteratorTraits
PDBAtomIterator
 A mutable bidirectional iterator for the PDBAtom class.
typedef std::reverse_iterator
< PDBAtomIterator
PDBAtomReverseIterator
 A mutable reverse bidirectional iterator for the PDBAtom class.
Convenience typedefs
typedef Peak< float > Peak1D
typedef Peak< Vector2Peak2D
typedef Peak< Vector3Peak3D
Standard typedefs
typedef PeakList< Peak< float > > PeakList1D
 1D peak list
typedef PeakList< Peak< Vector2 > > PeakList2D
 2D peak list
typedef PeakList< Peak< Vector3 > > PeakList3D
 3D peak list
typedef Spectrum
< RegularData1D, Peak1D
Spectrum1D
 One-dimensional spectrum.
typedef Spectrum
< RegularData1D, Peak2D
Spectrum2D
 Two-dimensional spectrum.
typedef Spectrum
< RegularData1D, Peak3D
Spectrum3D
 Three-dimensional spectrum.

Enumerations

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

Functions

const ACEData & ACEBuildTable (const String &type_filename, const String &parameter_filename)
BALL_INLINE void AMBERcalculateMinimumImage (Vector3 &difference, const Vector3 &period)
BALL_INLINE void AMBERcalculateNBForce (LennardJones::Data &LJ_data, Vector3 &period, const double cut_off_vdw_2, const double cut_on_vdw_2, const double inverse_distance_off_on_vdw_3, const double cut_off_electrostatic_2, const double cut_on_electrostatic_2, const double inverse_distance_off_on_electrostatic_3, const double e_scaling_factor, const double vdw_scaling_factor, bool is_hydrogen_bond, bool use_periodic_boundary, bool use_dist_depend, bool use_selection)
template<ESEnergyFunction ESEnergy, VdwEnergyFunction VdwEnergy, SwitchingFunction Switch>
BALL_INLINE void AmberNBEnergy (LennardJones::Data *ptr, LennardJones::Data *end_ptr, double &es_energy, double &vdw_energy, const SwitchingCutOnOff &switching_es, const SwitchingCutOnOff &switching_vdw)
template<ESEnergyFunction ESEnergyFct, VdwEnergyFunction VdwEnergyFct, SwitchingFunction SwitchFct>
BALL_INLINE void AmberNBEnergyPeriodic (LennardJones::Data *ptr, LennardJones::Data *end_ptr, double &es_energy, double &vdw_energy, SwitchingCutOnOff es_switching, SwitchingCutOnOff vdw_switching, const Vector3 &period)
template<VdwEnergyFunction VdwEnergy, SwitchingFunction Switch>
BALL_INLINE void AmberVDWEnergy (LennardJones::Data *ptr, LennardJones::Data *end_ptr, double &vdw_energy, const SwitchingCutOnOff &switching_vdw, float softening_limit)
double anorm_ (double *x)
void applyTrafoToList_ (const Matrix4x4 &trafo, const std::list< Atom * > &atoms)
bool atomPairSortPred (const std::pair< Position, const Atom * > &left, const std::pair< Position, const Atom * > &right)
int BALLString_vsnprintf (char *s, size_t n, const char *format, va_list ap)
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 double calculateOoiEnergy (AtomContainer &atoms)
BALL_EXPORT TRegularData3D
< char > * 
calculateSASGrid (const Vector3 &lower, const Vector3 &upper, float spacing, const System &system, float probe_radius)
BALL_EXPORT float calculateSESArea (const AtomContainer &fragment, float probe_radius=1.5)
BALL_EXPORT float calculateSESAtomAreas (const AtomContainer &fragment, HashMap< const Atom *, float > &atom_areas, float probe_radius=1.5)
BALL_EXPORT TRegularData3D
< char > * 
calculateSESGrid (const Vector3 &lower, const Vector3 &upper, float spacing, const System &system, float probe_radius)
BALL_EXPORT float calculateSESVolume (const AtomContainer &fragment, float probe_radius=1.5)
BALL_INLINE void CHARMMcalculateMinimumImage (Vector3 &difference, Vector3 &period, Vector3 &half_period)
BALL_INLINE void CHARMMcalculateVdWAndElectrostaticEnergy (vector< LennardJones::Data >::iterator it, Vector3 &period, Vector3 &half_period, const double &cut_off_electrostatic_2, const double &cut_on_electrostatic_2, const double &inverse_difference_off_on_electrostatic_3, const double &cut_off_vdw_2, const double &cut_on_vdw_2, const double &inverse_difference_off_on_vdw_3, const double &cut_off_solvation_2, const double &cut_on_solvation_2, const double &inverse_difference_off_on_solvation_3, bool use_solvation, vector< CharmmEEF1::Values > &solvation, bool use_periodic_boundary, bool use_dist_depend, double &electrostatic_energy, double &vdw_energy, double &solvation_energy)
BALL_INLINE void CHARMMcalculateVdWAndElectrostaticForce (vector< LennardJones::Data >::iterator it, const double &e_scaling_factor, const double &vdw_scaling_factor, Vector3 &period, Vector3 &half_period, const double &cut_off_electrostatic_2, const double &cut_on_electrostatic_2, const double &inverse_difference_off_on_electrostatic_3, const double &cut_off_vdw_2, const double &cut_on_vdw_2, const double &inverse_difference_off_on_vdw_3, const double &cut_off_solvation_2, const double &cut_on_solvation_2, const double &inverse_difference_off_on_solvation_3, bool use_solvation, vector< CharmmEEF1::Values > &solvation, bool use_selection, bool use_periodic_boundary, bool use_dist_depend)
void Circle2HIN (const TCircle3< double > &circle, const String &file)
int cirpln_ (double *circen, double *cirrad, double *cirvec, double *plncen, double *plnvec, bool *cinsp, bool *cintp, double *xpnt1, double *xpnt2)
template<class AtomContainerType>
void cloneBonds (const AtomContainerType &atom_container, AtomContainerType &cloned)
int comparePointerSizeIntPtr_ (const void *a, const void *b)
int compress_ ()
int connolly_ (int number_of_atoms, double *coordinates, double *radius, double *volume, double *area, double probe, double exclude, double *atom_areas)
int contact_ ()
BALL_TPL_ARG_INLINE float coulomb (float inverse_square_distance, float charge_product)
BALL_TPL_ARG_INLINE float cubicSwitch (double square_distance, const SwitchingCutOnOff &cutoffs)
double depth_ (int *ip, double *alt)
TVector3< double > diffV3 (const Vector3 &a, const Vector3 &b)
double dist2_ (double *x, double *y)
BALL_TPL_ARG_INLINE float distanceDependentCoulomb (float inverse_square_distance, float charge_product)
double dot_ (double *x, double *y)
const char * eatDelimiters_ (const char *start, const char *end, const char *delimiters)
int epuclc_ (double *spv, int *nedge, double *epu)
int gendot_ (int *ndots, double *dots, double *radius, double *xcenter, double *ycenter, double *zcenter)
template<class NucleotideContainerType>
const Nucleotideget3Prime (const NucleotideContainerType &nucleotide_container)
template<class NucleotideContainerType>
const Nucleotideget5Prime (const NucleotideContainerType &nucleotide_container)
template<typename T>
BALL_INLINE bool GetAngle (const TPlane3< T > &a, const TPlane3< T > &b, 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 > &plane, const TLine3< T > &line, 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 TVector3< T > &vector, 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 TVector3< T > &a, const TVector3< T > &b, TAngle< T > &intersection_angle)
BALL_EXPORT const FacetArray & getContourSurfaceFacetData (double threshold)
template<class ResidueContainerType>
const ResiduegetCTerminal (const ResidueContainerType &residue_container)
template<typename T>
getDeterminant (const T *m, Size dim)
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 getDeterminant2 (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>
BALL_INLINE T getDeterminant3 (const T *m)
template<typename T>
BALL_INLINE T getDeterminant_ (const T *m, Size dim)
template<typename T>
BALL_INLINE T GetDistance (const TPlane3< T > &a, const TPlane3< T > &b) throw (Exception::DivisionByZero)
template<typename T>
BALL_INLINE T GetDistance (const TPlane3< T > &plane, const TLine3< T > &line) throw (Exception::DivisionByZero)
template<typename T>
BALL_INLINE T GetDistance (const TLine3< T > &line, const TPlane3< T > &plane) throw (Exception::DivisionByZero)
template<typename T>
BALL_INLINE T GetDistance (const TPlane3< T > &plane, const TVector3< T > &point) throw (Exception::DivisionByZero)
template<typename T>
BALL_INLINE T GetDistance (const TVector3< T > &point, const TPlane3< T > &plane) throw (Exception::DivisionByZero)
template<typename T>
GetDistance (const TLine3< T > &a, const TLine3< T > &b) throw (Exception::DivisionByZero)
template<typename T>
BALL_INLINE T GetDistance (const TVector3< T > &point, const TLine3< T > &line) throw (Exception::DivisionByZero)
template<typename T>
BALL_INLINE T GetDistance (const TLine3< T > &line, const TVector3< T > &point) throw (Exception::DivisionByZero)
template<typename T>
BALL_INLINE T GetDistance (const TVector3< T > &a, const TVector3< T > &b)
TriangleEdgegetEdge_ (EdgeMap &edges, TrianglePoint *a, TrianglePoint *b)
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>
bool GetIntersection (const TSphere3< T > &a, const TSphere3< T > &b, 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 > &sphere, const TPlane3< T > &plane, TCircle3< T > &intersection_circle)
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 TLine3< T > &line, TVector3< T > &intersection_point1, TVector3< T > &intersection_point2)
template<typename T>
bool GetIntersection (const TPlane3< T > &plane1, const TPlane3< T > &plane2, TLine3< T > &line)
template<typename T>
BALL_INLINE bool GetIntersection (const TLine3< T > &line, const TPlane3< T > &plane, TVector3< T > &intersection_point)
template<typename T>
BALL_INLINE bool GetIntersection (const TPlane3< T > &plane, const TLine3< T > &line, TVector3< T > &intersection_point)
template<typename T>
bool GetIntersection (const TLine3< T > &a, const TLine3< T > &b, TVector3< T > &point)
istream & getline (istream &s, String &str, char delimiter)
Position getMMFF94Index (Position atom_type1, Position atom_type2)
template<class ResidueContainerType>
const ResiduegetNTerminal (const ResidueContainerType &residue_container)
template<typename T>
BALL_INLINE TAngle< T > getOrientedAngle (const TVector3< T > &a, const TVector3< T > &b, const TVector3< T > &normal) throw (Exception::DivisionByZero)
template<typename T>
TAngle< T > getOrientedAngle (const T &ax, const T &ay, const T &az, const T &bx, const T &by, const T &bz, const T &nx, const T &ny, const T &nz) throw (Exception::DivisionByZero)
template<typename T>
BALL_INLINE TVector3< T > GetPartition (const TVector3< T > &a, const TVector3< T > &b, const T &r, const T &s) throw (Exception::DivisionByZero)
template<typename T>
BALL_INLINE TVector3< T > GetPartition (const TVector3< T > &a, const TVector3< T > &b)
int getprb_ (int *ia, int *ja, int *ka, bool *prbok, bool *tb, double *bijk, double *hijk, double *uijk)
int gettor_ (int *ia, int *ja, bool *ttok, double *torcen, double *torad, double *torax)
template<typename T>
TAngle< T > getTorsionAngle (const T &ax, const T &ay, const T &az, const T &bx, const T &by, const T &bz, const T &cx, const T &cy, const T &cz, const T &dx, const T &dy, const T &dz) throw (Exception::DivisionByZero)
template<>
HashIndex Hash (const std::pair< Atom *, Atom * > &item) throw ()
BALL_EXPORT HashIndex Hash (const PDBFile::ResidueQuadruple &quadruple)
template<>
BALL_EXPORT HashIndex Hash (const std::pair< Position, Position > &p)
int inedge_ (int *ien, int *itt)
int ipedge_ (int *iep, int *ia)
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, const TVector3< T > &d)
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 isIntersecting (const TPlane3< T > &a, const TPlane3< T > &b)
template<typename T>
BALL_INLINE bool isIntersecting (const TPlane3< T > &plane, const TLine3< T > &line)
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 TVector3< T > &point)
template<typename T>
BALL_INLINE bool isIntersecting (const TVector3< T > &point, const TPlane3< T > &plane)
template<typename T>
BALL_INLINE bool isIntersecting (const TLine3< T > &a, const TLine3< T > &b)
template<typename T>
BALL_INLINE bool isIntersecting (const TLine3< T > &line, const TVector3< T > &point)
template<typename T>
BALL_INLINE bool isIntersecting (const TVector3< T > &point, const TLine3< T > &line)
template<typename T>
BALL_INLINE bool isOrthogonal (const TPlane3< T > &a, const TPlane3< T > &b)
template<typename T>
BALL_INLINE bool isOrthogonal (const TPlane3< T > &plane, const TVector3< T > &vector)
template<typename T>
BALL_INLINE bool isOrthogonal (const TVector3< T > &vector, const TPlane3< T > &plane)
template<typename T>
BALL_INLINE bool isOrthogonal (const TLine3< T > &a, const TLine3< T > &b)
template<typename T>
BALL_INLINE bool isOrthogonal (const TLine3< T > &line, const TVector3< T > &vector)
template<typename T>
BALL_INLINE bool isOrthogonal (const TVector3< T > &vector, const TLine3< T > &line)
template<typename T>
BALL_INLINE bool isOrthogonal (const TVector3< T > &a, const TVector3< T > &b)
template<typename T>
BALL_INLINE bool isParallel (const TPlane3< T > &a, const TPlane3< T > &b)
template<typename T>
BALL_INLINE bool isParallel (const TPlane3< T > &plane, const TLine3< T > &line)
template<typename T>
BALL_INLINE bool isParallel (const TLine3< T > &line, const TPlane3< T > &plane)
BALL_EXPORT LogStream Log (new LogStreamBuf, true, true)
int measfn_ (int *ifn, double *arean, double *voln, int *a1, int *a2, int *a3)
int measfp_ (int *ifp, double *areap, double *volp)
int measfs_ (int *ifs, double *areas, double *vols, double *areasp, double *volsp, int *a1, int *a2)
int measpm_ (int *ifn, double *prism)
int neighbor_ ()
float noSwitch (double, const SwitchingCutOnOff &)
template<typename T>
BALL_INLINE TVector4< T > operator* (const TVector4< T > &v, const T &scalar)
template<typename T>
BALL_INLINE TVector4< T > operator* (const T &scalar, const TVector4< T > &v)
template<typename T>
TVector3< T > operator* (const TMatrix4x4< T > &matrix, const TVector3< T > &vector)
template<typename T>
TMatrix4x4< T > operator* (const T &scalar, const TMatrix4x4< T > &m)
template<typename T>
BALL_INLINE TAngle< T > operator* (const T &val, const TAngle< T > &angle)
String operator+ (char c, const String &s)
String operator+ (const char *char_ptr, const String &s)
template<typename T>
BALL_INLINE TAngle< T > operator+ (const T &val, const TAngle< T > &angle)
template<typename Container, typename DataType, typename Position, typename Traits>
ConstRandomAccessIterator
< Container, DataType,
Position, Traits > 
operator+ (Distance distance, const ConstRandomAccessIterator< Container, DataType, Position, Traits > &iterator) throw (Exception::InvalidIterator)
template<typename DataT, typename PeakT, typename PositionT>
double operator- (const Spectrum< DataT, PeakT, PositionT > &s1, const Spectrum< DataT, PeakT, PositionT > &s2)
template<typename T>
BALL_INLINE TAngle< T > operator- (const T &val, const TAngle< T > &angle)
std::ostream & operator<< (std::ostream &s, const BALL::HBondProcessor::ResidueData &p)
ostream & operator<< (ostream &s, const Element &element)
ostream & operator<< (::std::ostream &s, const NMRAtomDataSet &set)
ostream & operator<< (::std::ostream &s, const ShiftReferenceSet &sr)
ostream & operator<< (::std::ostream &s, const ShiftReferenceElement &sre)
ostream & operator<< (::std::ostream &s, const SampleCondition &sc)
ostream & operator<< (ostream &s, const NMRAtomData &ad)
ostream & operator<< (ostream &s, const Substring &substring)
ostream & operator<< (ostream &s, const RegularExpression &regular_expression)
std::ostream & operator<< (std::ostream &s, const BitVector &bit_vector)
ostream & operator<< (ostream &os, const TimeStamp &stamp)
ostream & operator<< (ostream &os, const PreciseTime &time)
template<typename T>
std::ostream & operator<< (std::ostream &os, const BinaryFileAdaptor< T > &data)
 Output stream for BinaryFileAdaptors.
template<typename Node, typename Edge>
std::ostream & operator<< (std::ostream &os, const TMolecularGraph< Node, Edge > &G)
std::ostream & operator<< (std::ostream &out, const DockResult &dock_res)
template<typename PositionType>
std::ostream & operator<< (std::ostream &os, const Peak< PositionType > &peak)
BALL_EXPORT const RegularData1Doperator<< (RegularData1D &data, const PeakList1D &peak_list)
::std::ostream & operator<< (::std::ostream &os, const SnapShot &ss)
 Output stream operator for SnapShots.
template<typename T>
std::ostream & operator<< (std::ostream &s, const TQuaternion< T > &q)
template<typename ComplexTraits>
const RegularData3Doperator<< (RegularData3D &to, const TFFT3D< 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 RegularData2Doperator<< (RegularData2D &to, const TFFT2D< 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 RegularData1Doperator<< (RegularData1D &to, const TFFT1D< ComplexTraits > &from)
template<typename T>
std::ostream & operator<< (std::ostream &s, const TAngle< T > &angle)
BALL_EXPORT std::ostream & operator<< (std::ostream &s, const Element &element)
BALL_EXPORT std::ostream & operator<< (std::ostream &s, const Quadruple< String, PDB::Character, PDB::Integer, PDB::AChar > &)
BALL_EXPORT std::ostream & operator<< (std::ostream &os, const Exception::GeneralException &e)
istream & operator>> (istream &s, ResourceFile &resource_file)
istream & operator>> (istream &s, RegularExpression &regular_expression)
std::istream & operator>> (std::istream &s, BitVector &bit_vector) throw (Exception::OutOfMemory)
template<typename T>
std::istream & operator>> (std::istream &is, BinaryFileAdaptor< T > &data)
 Input stream for BinaryFileAdaptors.
std::istream & operator>> (std::istream &in, DockResult &dock_res)
::std::istream & operator>> (::std::istream &is, SnapShot &ss)
 Input stream operator for SnapShots.
template<typename T>
std::istream & operator>> (std::istream &s, TQuaternion< T > &q)
template<typename T>
std::istream & operator>> (std::istream &s, TAngle< T > &angle)
void PartitionOfCircle (const TCircle3< double > &circle, std::list< Vector3 > &partition)
int PDBFileRecordNameComparator_ (const void *a_ptr, const void *b_ptr)
int place_ ()
void Plane2HIN (const TPlane3< double > &plane, const String &file, Position size=20)
int projct_ (double *pnt, double *unvect, int *icy, int *ia, double *spv, int *nedge, bool *fail)
int PTEcompare_ (const void *a_ptr, const void *b_ptr)
bool ptincy_ (double *pnt, double *unvect, int *icy)
PyObject * pyMapBALLObjectToSip (Composite &object)
double rotang_ (double *epu, int *nedge, double *unvect)
PyObject * runSingleString_ (const String &str, int mode)
int saddles_ ()
BALL_EXPORT void sleepFor (Size mseconds)
template<typename T>
short SolveQuadraticEquation (const T &a, const T &b, const T &c, T &x1, T &x2)
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)
BALL_INLINE double SQR (double x)
BALL_EXPORT string streamClassName (const std::type_info &t)
template<typename T>
BALL_INLINE void swapBytes (T &t)
int torus_ ()
double triple_ (double *x, double *y, double *z__)
void update () throw (Exception::TooManyErrors)
int vam_ (double *volume, double *area, double *atom_areas)
int vcross_ (double *x, double *y, double *z__)
float vdwSixTwelve (float inverse_square_distance, float A, float B, float)
BALL_TPL_ARG_INLINE float vdwSixTwelve (float inverse_square_distance, float A, float B)
BALL_TPL_ARG_INLINE float vdwSixTwelveSoftLog (float inverse_square_distance, float A, float B, float limit)
BALL_TPL_ARG_INLINE float vdwSixTwelveSoftSimple (float inverse_square_distance, float A, float B, float limit)
BALL_TPL_ARG_INLINE float vdwTenTwelve (float inverse_square_distance, float A, float B, float)
BALL_TPL_ARG_INLINE float vdwTenTwelve (float inverse_square_distance, float A, float B)
BALL_TPL_ARG_INLINE float vdwTenTwelveSoftLog (float inverse_square_distance, float A, float B, float limit)
BALL_TPL_ARG_INLINE float vdwTenTwelveSoftSimple (float inverse_square_distance, float A, float B, float limit)
double vecang_ (double *v1, double *v2, double *axis, double *hand)
int vnorm_ (double *x, double *xn)
int XDRError_ (void *, void *, unsigned int)
int XDRReadStream_ (void *stream_ptr, void *buffer, unsigned int number)
int XDRWriteStream_ (void *stream_ptr, void *buffer, unsigned int number)
BALL_EXPORT AtomContainerList atomContainers (const AtomContainer &fragment, bool selected_only=false)
BALL_EXPORT AtomList atoms (const AtomList &atoms, const String &expression)
BALL_EXPORT AtomList atoms (const AtomContainer &fragment, const String &expression=String())
BALL_EXPORT BondList bonds (const Atom &atom)
BALL_EXPORT BondList bonds (const AtomContainer &fragment, bool selected_only=false)
BALL_EXPORT ChainList chains (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 NucleicAcidList nucleicAcids (const AtomContainer &fragment, bool selected_only=false)
BALL_EXPORT NucleotideList nucleotides (const AtomContainer &fragment, bool selected_only=false)
BALL_EXPORT PDBAtomList PDBAtoms (const AtomContainer &fragment, const String &expression=String())
BALL_EXPORT ProteinList proteins (const AtomContainer &fragment, bool selected_only=false)
BALL_EXPORT ResidueList residues (const AtomContainer &fragment, bool selected_only=false)
BALL_EXPORT SecondaryStructureList secondaryStructures (const AtomContainer &fragment, bool selected_only=false)
Angle Calculation
BALL_EXPORT Angle calculateBondAngle (const Atom &a1, const Atom &a2, const Atom &a3) throw (Exception::IllegalPosition)
BALL_EXPORT Angle calculateTorsionAngle (const Atom &a1, const Atom &a2, const Atom &a3, const Atom &a4) throw (Exception::IllegalPosition)
Fast Numerical Calculation of Solvent Accessible Surface Area.
These functions are loosely based on the algorithm by Eisenhaber, Lijnzaad, Argos, Sander, and Scharf ("The Double Cubic Lattice Method: Efficient Approaches to numerical Integration of Surface Area and Volume and to Dot Surface Contouring of Molecular Assemblies", J. Comput. Chem. (1995), 15 , 273-284) and Eisenhaber and Argos ("Improved Strategy in Analytic Surface Calculation for Molecular Systems: Handling of Singularities and Computational Efficiency" J. Comput. Chem. (1993), 14 , 1272-1280).

BALL_EXPORT BALL_DEPRECATED float calculateSASArea (const AtomContainer &fragment, float probe_radius=1.5, Size number_of_dots=400)
BALL_EXPORT BALL_DEPRECATED float calculateSASAtomAreas (const AtomContainer &fragment, HashMap< const Atom *, float > &atom_areas, float probe_radius=1.5, Size number_of_dots=400)
BALL_EXPORT BALL_DEPRECATED float calculateSASAtomPoints (const AtomContainer &fragment, std::vector< std::pair< Vector3, Surface > > &atom_surfaces, float probe_radius=1.5, Size number_of_dots=400)
BALL_EXPORT BALL_DEPRECATED float calculateSASPoints (const AtomContainer &fragment, Surface &surface_points, float probe_radius=1.5, Size number_of_dots=400)
BALL_EXPORT BALL_DEPRECATED float calculateSASVolume (const AtomContainer &fragment, float probe_radius=1.5, Size number_of_dots=400)
BALL_EXPORT HashIndex getNextPrime (HashIndex l)
Specialized Hash Functions.
BALL_EXPORT HashIndex Hash (void *const &ptr)
BALL_EXPORT HashIndex Hash (const String &s)
BALL_EXPORT HashIndex Hash (const string &s)
template<typename T>
HashIndex Hash (const T &key)
BALL_EXPORT HashIndex hashElfString (const char *str)
BALL_EXPORT HashIndex hashPJWString (const char *str)
BALL_EXPORT HashIndex hashPointer (void *const ptr)
BALL_EXPORT HashIndex hashString (const char *str)
Notification Management.
Using the notification management, objects may exchange data and notify each other of events by invoking methods of the other object (remotely similar to the signal/slot mechanism of QT).


template<class Source, class Target>
bool NotificationIsRegistered (const Source &source, const Target &target)
template<class NotificationSource>
bool NotificationIsRegistered (const NotificationSource &notification_source)
NotificationManager_ & NotificationManager ()
void NotificationManagerDisable ()
void NotificationManagerEnable ()
bool NotificationManagerIsDisabled ()
bool NotificationManagerIsEnabled ()
template<class Source, class Target>
void NotificationRegister (const Source &source, const Target &target)
template<class Source, class Target, class T1>
void NotificationRegister1 (const Source &source, const Target &target, const T1 &)
template<class NotificationSource, class NotificationTarget, class T1, class T2>
void NotificationRegister2 (const NotificationSource &notification_source, const NotificationTarget &notification_target, const T1 &, const T2 &)
template<class NotificationSource>
void NotificationSourceDisable (NotificationSource &notification_source)
template<class NotificationSource>
void NotificationSourceEnable (NotificationSource &notification_source)
template<class NotificationSource>
bool NotificationSourceIsDisabled (NotificationSource &notification_source)
template<class NotificationSource>
bool NotificationSourceIsEnabled (NotificationSource &notification_source)
template<class Source, class Target>
void NotificationUnregister (const Source &source, const Target &target)
template<class NotificationSource>
void NotificationUnregister (const NotificationSource &notification_source)
template<class NotificationSource, class NotificationTarget, class T1>
void NotificationUnregister1 (const NotificationSource &notification_source, const NotificationTarget &notification_target, const T1 &)
template<class NotificationSource, class NotificationTarget, class T1, class T2>
void NotificationUnregister2 (const NotificationSource &notification_source, const NotificationTarget &notification_target, const T1 &, const T2 &)
void NotificationUnregisterAll ()
template<class NotificationSource, class T1, class T2>
bool Notify (NotificationSource &notification_source, const T1 &data1, const T2 &data2)
template<class NotificationSource, class T1>
bool Notify (NotificationSource &notification_source, const T1 &data1)
template<class NotificationSource>
bool Notify (NotificationSource &notification_source)
Global binary operators for three-dimensional vectors.
template<typename T>
BALL_INLINE TVector3< T > operator* (const T &a, const TVector3< T > &b)
template<typename T>
std::ostream & operator<< (std::ostream &s, const TVector3< T > &vector)
template<typename T>
std::istream & operator>> (std::istream &s, TVector3< T > &vector)
Global binary operator functions for two dimensional vectors.
template<typename T>
BALL_INLINE TVector2< T > operator* (const T &scalar, const TVector2< T > &vector)
template<typename T>
std::ostream & operator<< (std::ostream &s, const TVector2< T > &vector)
template<typename T>
std::istream & operator>> (std::istream &s, TVector2< T > &vector)
Global binary operators for three-dimensional vectors.
template<typename T>
BALL_INLINE TVector4< T > operator+ (const TVector4< T > &a, const TVector4< T > &b)
template<typename T>
BALL_INLINE TVector4< T > operator- (const TVector4< T > &a, const TVector4< T > &b)
template<typename T>
std::ostream & operator<< (std::ostream &s, const TVector4< T > &vector)
template<typename T>
std::istream & operator>> (std::istream &s, TVector4< T > &vector)
Storers
BALL_EXPORT std::ostream & operator<< (std::ostream &s, const TriangulatedSurface &surface)
Storers
BALL_EXPORT std::ostream & operator<< (std::ostream &s, const TrianglePoint &point)
Storers
BALL_EXPORT std::ostream & operator<< (std::ostream &s, const TriangleEdge &edge)
Storers
BALL_EXPORT std::ostream & operator<< (std::ostream &s, const Triangle &triangle)
Storers
BALL_EXPORT std::ostream & operator<< (std::ostream &s, const SolventExcludedSurface &ses)
Storers
BALL_EXPORT std::ostream & operator<< (std::ostream &s, const SolventAccessibleSurface &sas)
Storers
BALL_EXPORT std::ostream & operator<< (std::ostream &s, const SESVertex &sesvertex)
Storers
BALL_EXPORT std::ostream & operator<< (std::ostream &s, const SESFace &sesface)
Storers
BALL_EXPORT std::ostream & operator<< (std::ostream &s, const SESEdge &sesedge)
Storers
BALL_EXPORT std::ostream & operator<< (std::ostream &s, const SASVertex &sasvertex)
Storers
BALL_EXPORT std::ostream & operator<< (std::ostream &s, const SASFace &sasface)
Storers
BALL_EXPORT std::ostream & operator<< (std::ostream &s, const SASEdge &sasedge)
Storers
BALL_EXPORT std::ostream & operator<< (std::ostream &s, const RSVertex &rsvertex)
Storers
BALL_EXPORT std::ostream & operator<< (std::ostream &s, const RSFace &rsface)
Storers
BALL_EXPORT std::ostream & operator<< (std::ostream &s, const RSEdge &rsedge)
Storers
BALL_EXPORT std::ostream & operator<< (std::ostream &s, const ReducedSurface &rs)
Storers
Stream operators for the class Sphere

template<typename T>
std::ostream & operator<< (std::ostream &s, const TSphere3< T > &sphere)
template<typename T>
std::istream & operator>> (std::istream &s, TSphere3< T > &sphere)
Storers
Stream operators for class TPlane3

template<typename T>
std::ostream & operator<< (std::ostream &s, const TPlane3< T > &plane)
template<typename T>
std::istream & operator>> (std::istream &s, TPlane3< T > &plane)
Storers
template<typename T>
std::ostream & operator<< (std::ostream &s, const TMatrix4x4< T > &m)
template<typename T>
std::istream & operator>> (std::istream &s, TMatrix4x4< T > &m)
Storers
Stream operators of Line3

template<typename T>
std::ostream & operator<< (std::ostream &s, const TLine3< T > &line)
template<typename T>
std::istream & operator>> (std::istream &s, TLine3< T > &line)
Storers
template<typename T>
std::ostream & operator<< (std::ostream &s, const TCircle3< T > &circle)
template<typename T>
std::istream & operator>> (std::istream &s, TCircle3< T > &circle)
Storers
template<typename T>
std::ostream & operator<< (std::ostream &s, const TBox3< T > &box)
template<typename T>
std::istream & operator>> (std::istream &s, TBox3< T > &box)
std::ostream & operator<< (std::ostream &s, const NMRAtomDataSet &set)
std::ostream & operator<< (std::ostream &s, const ShiftReferenceSet &sr)
std::ostream & operator<< (std::ostream &s, const ShiftReferenceElement &sre)
std::ostream & operator<< (std::ostream &s, const SampleCondition &sc)
std::ostream & operator<< (std::ostream &s, const NMRAtomData &ad)
Stream I/O


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


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


template<typename ValueType>
std::ostream & operator<< (std::ostream &os, const TRegularData1D< ValueType > &data)
 Output operator.
template<typename ValueType>
std::istream & operator>> (std::istream &is, TRegularData1D< ValueType > &grid)
 Input operator.
BALL_EXPORT std::ostream & operator<< (std::ostream &os, const TimeStamp &stamp)
BALL_EXPORT std::ostream & operator<< (std::ostream &os, const PreciseTime &time)

Variables

struct {
   int   n
   double   x [10000]
   double   y [10000]
   double   z__ [10000]
atoms_
Vector3 BALL_vtable_constructing_vector
const double BEND_K0 = 0.021922 * Constants::JOULE_PER_CAL
 0.043844 / 2
const double BEND_K0_FORCES = BEND_K0 * (180.0 / Constants::PI)
 for forces:
const double BEND_KX = 143.9325 * Constants::JOULE_PER_CAL
static double c_b157 = -1.0
static double c_b158 = 1.0
static double c_b94 = 0.0
BALL_EXPORT const char CCONN__INSIDE = 0
BALL_EXPORT const char CCONN__INSIDE_PROBE = (char) 64
BALL_EXPORT const char CCONN__OUTSIDE = 1
bool clone_bonds = true
PyObject * context_
static Position contour_surface_corner_rotation [24][8]
static Index contour_surface_edge_rotation [24][12]
bool contour_surface_facet_data_initialized = false
static FacetArray contour_surface_facet_data_negative
static FacetArray contour_surface_facet_data_positive
static Index contour_surface_init_facet_data [15][12]
static Index contour_surface_init_facet_index [15][8]
const float cut_off2 = 225.0
const double DEGREE_TO_RADIAN = (Constants::PI / (double)180.0)
static const Distance DISTANCE_MAX = INT_MAX
static const Distance DISTANCE_MIN = (INT_MIN + 1)
String error_message_
double ES_CONSTANT = 332.0716 * Constants::JOULE_PER_CAL
struct {
   double   a [30000]
   double   ar [10000]
   int   na
   double   pr
face01_
struct {
   bool   abur [10000]
   bool   afree [10000]
   bool   nosurf [10000]
   bool   skip [10000]
face02_
struct {
   int   anbr [40000]
   int   nbr [1000000]
   int   nbrt [1000000]
face03_
struct {
   int   enext [100000]
   int   ntt
   int   tta [1000000]
   bool   ttbur [500000]
   int   ttfe [500000]
   bool   ttfree [500000]
   int   ttle [500000]
face04_
struct {
   int   nt
   double   t [90000]
   int   ta [60000]
   double   tax [90000]
   int   tfe [30000]
   bool   tfree [30000]
   double   tr [45000]
face05_
struct {
   int   np
   double   p [60000]
   int   pa [60000]
face06_
struct {
   int   nv
   double   v [150000]
   int   va [50000]
   int   vp [50000]
face07_
struct {
   int   env [100000]
   int   fnen [60000]
   int   nen
   int   nfn
face08_
struct {
   double   c__ [150000]
   int   ca [50000]
   double   cr [50000]
   int   ct [50000]
   int   nc
face09_
struct {
   int   afe [10000]
   int   ale [10000]
   int   epc [50000]
   int   epnext [50000]
   int   epv [100000]
   int   nep
face10_
struct {
   int   fsen [60000]
   int   fsep [60000]
   int   nfs
face11_
struct {
   int   cyep [300000]
   int   cynep [10000]
   int   ncy
face12_
struct {
   int   fpa [10000]
   int   fpcy [100000]
   int   fpncy [10000]
   int   nfp
face13_
double FORCES_FACTOR = 1000 * 1E10 / Constants::AVOGADRO
GlobalInitializergi = GlobalInitializer::init()
static const Handle HANDLE_MAX = INT_MAX - 1
static const Handle HANDLE_MIN = 0
static const Index INDEX_MAX = INT_MAX
static const Index INDEX_MIN = 0
static const double INFINITY = Limits<double>::max()
static const Distance INVALID_DISTANCE = INT_MIN
static const Handle INVALID_HANDLE = INT_MAX
static const Index INVALID_INDEX = -1
static const Position INVALID_POSITION = INT_MAX
static const Size INVALID_SIZE = INT_MAX
float MIN_DISTANCE = 1e-6
Size MMFF94_number_atom_types = 100
 hold the maximum number of MMFF94 atom types + 1 (wildcard)
StringHashMap< double * > * ParsedFunctionConstants
StringHashMap< double(*)(double)> * ParsedFunctionFunctions
static const Position POSITION_MAX = INT_MAX - 1
static const Position POSITION_MIN = 0
BALL_EXPORT PTE_ PTE
const double RADIAN_TO_DEGREE = 180.0 / Constants::PI
static const char *const REGEXP_CONFORM_PARENT_DIRECTORY = "\\.\\."
const int RING_MAX_ATOMS = 6
static const Size SIZE_MAX = INT_MAX - 1
static const Size SIZE_MIN = 0
const double STRETCH_BEND_K0 = Constants::JOULE_PER_CAL * (double)143.9325 * DEGREE_TO_RADIAN
const double STRETCH_K0 = Constants::JOULE_PER_CAL * 143.9325 / 2.0
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


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