BALL 1.5.0
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Namespaces | Classes | Typedefs | Functions | Variables
BALL Namespace Reference

Namespaces

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

Classes

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

Typedefs

typedef int(* ComparatorType) (const void *, const void *)
 
typedef TContour< floatContour
 
typedef TContourLine< floatContourLine
 
typedef Index FacetArray[256][12]
 
typedef TContourSurface< floatContourSurface
 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< MolecularGraphMolecularGraphTraits
 
typedef MolecularGraph::EditableGraph EditableMolecularGraph
 
typedef TRegularData1D< floatRegularData1D
 
typedef TRegularData2D< floatRegularData2D
 
typedef TRegularData3D< floatRegularData3D
 
typedef HashSet< StringStringHashSet
 
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, FragmentIteratorTraitsFragmentIterator
 
typedef ConstBidirectionalIterator< Composite, Fragment, Composite::CompositeIterator, FragmentIteratorTraitsFragmentConstIterator
 
typedef std::reverse_iterator< FragmentIteratorFragmentReverseIterator
 
typedef std::reverse_iterator< FragmentConstIteratorFragmentConstReverseIterator
 
typedef BidirectionalIterator< Composite, Molecule, Composite::CompositeIterator, MoleculeIteratorTraitsMoleculeIterator
 
typedef ConstBidirectionalIterator< Composite, Molecule, Composite::CompositeIterator, MoleculeIteratorTraitsMoleculeConstIterator
 
typedef std::reverse_iterator< MoleculeIteratorMoleculeReverseIterator
 
typedef std::reverse_iterator< MoleculeConstIteratorMoleculeConstReverseIterator
 
typedef BidirectionalIterator< Composite, NucleicAcid, Composite::CompositeIterator, NucleicAcidIteratorTraitsNucleicAcidIterator
 
typedef ConstBidirectionalIterator< Composite, NucleicAcid, Composite::CompositeIterator, NucleicAcidIteratorTraitsNucleicAcidConstIterator
 
typedef std::reverse_iterator< NucleicAcidIteratorNucleicAcidReverseIterator
 
typedef std::reverse_iterator< NucleicAcidConstIteratorNucleicAcidConstReverseIterator
 
typedef BidirectionalIterator< Composite, Nucleotide, Composite::CompositeIterator, NucleotideIteratorTraitsNucleotideIterator
 
typedef ConstBidirectionalIterator< Composite, Nucleotide, Composite::CompositeIterator, NucleotideIteratorTraitsNucleotideConstIterator
 
typedef std::reverse_iterator< NucleotideIteratorNucleotideReverseIterator
 
typedef std::reverse_iterator< NucleotideConstIteratorNucleotideConstReverseIterator
 
typedef BidirectionalIterator< Composite, Protein, Composite::CompositeIterator, ProteinIteratorTraitsProteinIterator
 
typedef ConstBidirectionalIterator< Composite, Protein, Composite::CompositeIterator, ProteinIteratorTraitsProteinConstIterator
 
typedef std::reverse_iterator< ProteinIteratorProteinReverseIterator
 
typedef std::reverse_iterator< ProteinConstIteratorProteinConstReverseIterator
 
typedef BidirectionalIterator< Composite, Residue, Composite::CompositeIterator, ResidueIteratorTraitsResidueIterator
 
typedef ConstBidirectionalIterator< Composite, Residue, Composite::CompositeIterator, ResidueIteratorTraitsResidueConstIterator
 
typedef std::reverse_iterator< ResidueIteratorResidueReverseIterator
 
typedef std::reverse_iterator< ResidueConstIteratorResidueConstReverseIterator
 
typedef BidirectionalIterator< Composite, SecondaryStructure, Composite::CompositeIterator, SecondaryStructureIteratorTraitsSecondaryStructureIterator
 
typedef ConstBidirectionalIterator< Composite, SecondaryStructure, Composite::CompositeIterator, SecondaryStructureIteratorTraitsSecondaryStructureConstIterator
 
typedef std::reverse_iterator< SecondaryStructureIteratorSecondaryStructureReverseIterator
 
typedef std::reverse_iterator< SecondaryStructureConstIteratorSecondaryStructureConstReverseIterator
 
typedef TAngle< floatAngle
 
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< doubleCoefficients
 
typedef std::pair< double, doubleInterval
 
typedef TQuaternion< floatQuaternion
 
typedef TSurface< floatSurface
 
typedef Spectrum< RegularData1D, Peak1DSpectrum1D
 One-dimensional spectrum.
 
typedef Spectrum< RegularData2D, Peak2DSpectrum2D
 Two-dimensional spectrum.
 
typedef Spectrum< RegularData3D, Peak3DSpectrum3D
 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, IndexSimpleMolecularGraph
 
typedef TMutex< BALL_DEFAULT_MUTEX_TYPEMutex
 
typedef TReadWriteLock< BALL_DEFAULT_READWRITELOCK_TYPEReadWriteLock
 
typedef TMutexLocker< BALL_DEFAULT_MUTEXLOCKER_TYPE, BALL_DEFAULT_MUTEX_TYPEMutexLocker
 
typedef TReadLocker< BALL_DEFAULT_READLOCKER_TYPE, BALL_DEFAULT_READWRITELOCK_TYPEReadLocker
 
typedef TWriteLocker< BALL_DEFAULT_WRITELOCKER_TYPE, BALL_DEFAULT_READWRITELOCK_TYPEWriteLocker
 
Properties
typedef std::vector< NamedProperty >::iterator NamedPropertyIterator
 
Iterator type definitions for the various AtomContainerIterators.
typedef BidirectionalIterator< Composite, AtomContainer, Composite::CompositeIterator, AtomContainerIteratorTraitsAtomContainerIterator
 
typedef ConstBidirectionalIterator< Composite, AtomContainer, Composite::CompositeIterator, AtomContainerIteratorTraitsAtomContainerConstIterator
 
typedef std::reverse_iterator< AtomContainerIteratorAtomContainerReverseIterator
 A mutable reverse bidirectional iterator for the AtomContainer class.
 
typedef std::reverse_iterator< AtomContainerConstIteratorAtomContainerConstReverseIterator
 A constant reverse bidirectional iterator for the AtomContainer class.
 
Iterator type definitions for the various AtomIterators
typedef BidirectionalIterator< Composite, Atom, Composite::CompositeIterator, AtomIteratorTraitsAtomIterator
 
typedef ConstBidirectionalIterator< Composite, Atom, Composite::CompositeIterator, AtomIteratorTraitsAtomConstIterator
 
typedef std::reverse_iterator< AtomIteratorAtomReverseIterator
 A mutable reverse bidirectional iterator for the Atom class.
 
typedef std::reverse_iterator< AtomConstIteratorAtomConstReverseIterator
 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, ChainIteratorTraitsChainIterator
 A mutable bidirectional iterator for the Chain class.
 
typedef ConstBidirectionalIterator< Composite, Chain, Composite::CompositeIterator, ChainIteratorTraitsChainConstIterator
 A constant bidirectional iterator for the Chain class.
 
typedef std::reverse_iterator< ChainIteratorChainReverseIterator
 A mutable reverse bidirectional iterator for the Chain class.
 
typedef std::reverse_iterator< ChainConstIteratorChainConstReverseIterator
 A constant reverse bidirectional iterator for the Chain class.
 
Iterator type definitions for the various PDBAtomIterators
typedef BidirectionalIterator< Composite, PDBAtom, Composite::CompositeIterator, PDBAtomIteratorTraitsPDBAtomIterator
 A mutable bidirectional iterator for the PDBAtom class.
 
typedef ConstBidirectionalIterator< Composite, PDBAtom, Composite::CompositeIterator, PDBAtomIteratorTraitsPDBAtomConstIterator
 A constant bidirectional iterator for the PDBAtom class.
 
typedef std::reverse_iterator< PDBAtomIteratorPDBAtomReverseIterator
 A mutable reverse bidirectional iterator for the PDBAtom class.
 
typedef std::reverse_iterator< PDBAtomConstIteratorPDBAtomConstReverseIterator
 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< CompositeKernelPredicateType
 
Convenience typedefs

<>

typedef Experiment< PeakList1DExperiment1D
 
typedef Experiment< PeakList3DExperiment3D
 
typedef Peak< floatPeak1D
 
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
 

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 FacetArraygetContourSurfaceFacetData (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 Nucleotideget5Prime (const NucleotideContainerType &nucleotide_container)
 
template<class NucleotideContainerType >
const Nucleotideget3Prime (const NucleotideContainerType &nucleotide_container)
 
BALL_EXPORT std::ostream & operator<< (std::ostream &s, const Element &element)
 
template<class ResidueContainerType >
const ResiduegetNTerminal (const ResidueContainerType &residue_container)
 
template<class ResidueContainerType >
const ResiduegetCTerminal (const ResidueContainerType &residue_container)
 
template<typename T >
BALL_INLINEgetDeterminant_ (const T *m, Size dim)
 
template<typename T >
getDeterminant (const T *m, Size dim)
 
template<typename T >
BALL_INLINEgetDeterminant2 (const T *m)
 
template<typename T >
BALL_INLINEgetDeterminant2 (const T &m00, const T &m01, const T &m10, const T &m11)
 
template<typename T >
BALL_INLINEgetDeterminant3 (const T *m)
 
template<typename T >
BALL_INLINEgetDeterminant3 (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_INLINEGetDistance (const TVector3< T > &a, const TVector3< T > &b)
 
template<typename T >
BALL_INLINEGetDistance (const TLine3< T > &line, const TVector3< T > &point)
 
template<typename T >
BALL_INLINEGetDistance (const TVector3< T > &point, const TLine3< T > &line)
 
template<typename T >
GetDistance (const TLine3< T > &a, const TLine3< T > &b)
 
template<typename T >
BALL_INLINEGetDistance (const TVector3< T > &point, const TPlane3< T > &plane)
 
template<typename T >
BALL_INLINEGetDistance (const TPlane3< T > &plane, const TVector3< T > &point)
 
template<typename T >
BALL_INLINEGetDistance (const TLine3< T > &line, const TPlane3< T > &plane)
 
template<typename T >
BALL_INLINEGetDistance (const TPlane3< T > &plane, const TLine3< T > &line)
 
template<typename T >
BALL_INLINEGetDistance (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 RegularData1Doperator<< (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 RegularData2Doperator<< (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 RegularData3Doperator<< (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 RegularData1Doperator<< (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< floatBox3
 
typedef TCircle3< floatCircle3
 
typedef TLine3< floatLine3
 
typedef TMatrix4x4< floatMatrix4x4
 
typedef TPlane3< floatPlane3
 
typedef TSimpleBox3< floatSimpleBox3
 
typedef TSphere3< floatSphere3
 
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< floatVector2
 
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< floatVector3
 
typedef TVector4< floatVector4
 
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

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

A constant iterator for atom bonds.

Definition at line 27 of file bondIterator.h.

◆ AtomBondConstReverseIterator

A constant reverse iterator for atom bonds.

Definition at line 35 of file bondIterator.h.

◆ AtomBondIterator

A mutable iterator for atom bonds.

Definition at line 23 of file bondIterator.h.

◆ AtomBondReverseIterator

A mutable reverse iterator for atom bonds.

Definition at line 31 of file bondIterator.h.

◆ 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

A constant bidirectional iterator for the AtomContainer class.

Definition at line 94 of file atomContainerIterator.h.

◆ AtomContainerConstReverseIterator

A constant reverse bidirectional iterator for the AtomContainer class.

Definition at line 100 of file atomContainerIterator.h.

◆ AtomContainerIterator

A mutable bidirectional iterator for the AtomContainer class.

Definition at line 88 of file atomContainerIterator.h.

◆ AtomContainerList

Definition at line 55 of file extractors.h.

◆ AtomContainerProcessor

Definition at line 8 of file pyUnaryProcessors.h.

◆ AtomContainerReverseIterator

A mutable reverse bidirectional iterator for the AtomContainer class.

Definition at line 97 of file atomContainerIterator.h.

◆ 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

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

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

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

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

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

Definition at line 12 of file pyUnaryProcessors.h.

◆ ConstAtomProcessor

Definition at line 16 of file pyUnaryProcessors.h.

◆ ConstCompositeProcessor

Definition at line 17 of file pyUnaryProcessors.h.

◆ ContourLine

Default type

Definition at line 153 of file contourLine.h.

◆ ContourSurface

Default type.

Definition at line 250 of file contourSurface.h.

◆ 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

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

Definition at line 78 of file molecularGraph.h.

◆ 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

1D NMR experiment

Definition at line 136 of file experiment.h.

◆ 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

Definition at line 81 of file fragmentIterator.h.

◆ FragmentConstReverseIterator

Definition at line 87 of file fragmentIterator.h.

◆ 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

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

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

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

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

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

◆ 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

Definition at line 77 of file molecularGraph.h.

◆ MoleculeConstIterator

Definition at line 70 of file moleculeIterator.h.

◆ MoleculeConstReverseIterator

Definition at line 76 of file moleculeIterator.h.

◆ 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

Definition at line 224 of file mutex.h.

◆ 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

Definition at line 76 of file nucleicAcidIterator.h.

◆ NucleicAcidConstReverseIterator

Definition at line 80 of file nucleicAcidIterator.h.

◆ 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

Definition at line 71 of file nucleotideIterator.h.

◆ NucleotideConstReverseIterator

Definition at line 75 of file nucleotideIterator.h.

◆ 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

A constant bidirectional iterator for the PDBAtom class.

Definition at line 92 of file PDBAtomIterator.h.

◆ PDBAtomConstReverseIterator

A constant reverse bidirectional iterator for the PDBAtom class.

Definition at line 98 of file PDBAtomIterator.h.

◆ 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

Definition at line 261 of file peak.h.

◆ Peak2D

Definition at line 262 of file peak.h.

◆ Peak3D

Definition at line 263 of file peak.h.

◆ PeakList1D

1D peak list

Definition at line 125 of file peakList.h.

◆ PeakList2D

2D peak list

Definition at line 128 of file peakList.h.

◆ 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

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

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

Definition at line 71 of file proteinIterator.h.

◆ ProteinConstReverseIterator

Definition at line 77 of file proteinIterator.h.

◆ 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

Definition at line 626 of file quaternion.h.

◆ ReadLocker

Definition at line 227 of file mutex.h.

◆ 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

Default type

Definition at line 358 of file regularData1D.h.

◆ RegularData2D

Default type

Definition at line 414 of file regularData2D.h.

◆ RegularData3D

Default type

Definition at line 515 of file regularData3D.h.

◆ RegularData3DList

Definition at line 15 of file pyListHelper.h.

◆ ResidueConstIterator

Definition at line 67 of file residueIterator.h.

◆ ResidueConstReverseIterator

Definition at line 73 of file residueIterator.h.

◆ 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

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

Definition at line 75 of file secondaryStructureIterator.h.

◆ SecondaryStructureConstReverseIterator

Definition at line 81 of file secondaryStructureIterator.h.

◆ SecondaryStructureIterator

Definition at line 70 of file secondaryStructureIterator.h.

◆ SecondaryStructureList

Definition at line 67 of file extractors.h.

◆ SecondaryStructureReverseIterator

Definition at line 78 of file secondaryStructureIterator.h.

◆ SimpleMolecularGraph

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

Definition at line 202 of file simpleMolecularGraph.h.

◆ 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

Two-dimensional spectrum.

Definition at line 322 of file spectrum.h.

◆ 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

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

Default four-dimensional vector type

Definition at line 815 of file vector4.h.

◆ WriteLocker

Definition at line 228 of file mutex.h.

Enumeration Type Documentation

◆ 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
atomsthe AtomContainer containing the atoms
expressionthe expression that selects the atoms

◆ ball_macro_abs()

template<class X >
int BALL_DEPRECATED BALL_INLINE BALL::ball_macro_abs ( 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 ( 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 ( 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 
)

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 
)

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 
)

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 ( 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 
)

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 ( 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)

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)

Definition at line 68 of file macros.h.

◆ ball_macro_max()

template<class T >
T BALL_DEPRECATED BALL_INLINE BALL::ball_macro_max ( a,
b 
)

Definition at line 26 of file macros.h.

◆ ball_macro_max3()

template<class T >
T BALL_DEPRECATED BALL_INLINE BALL::ball_macro_max3 ( a,
b,
c 
)

Definition at line 32 of file macros.h.

◆ ball_macro_min()

template<class T >
T BALL_DEPRECATED BALL_INLINE BALL::ball_macro_min ( a,
b 
)

Definition at line 38 of file macros.h.

◆ ball_macro_min3()

template<class T >
T BALL_DEPRECATED BALL_INLINE BALL::ball_macro_min3 ( a,
b,
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 ( 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)

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)

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)

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,
y,
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)

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)

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,
y,
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,
y,
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,
y,
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,
y,
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,
y,
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)

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)

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)

Definition at line 152 of file macros.h.

◆ ball_macro_sgn()

template<class X >
int BALL_DEPRECATED BALL_INLINE BALL::ball_macro_sgn ( 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 ( 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_anglesa hash map containing the chi2 angles of the residues (returned)
fragmentthe 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_anglesa hash map containing the chi2 angles the residues (returned)
fragmentthe 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_anglesa hash map containing the chi angles of the residues (returned)
fragmentthe 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_anglesa hash map containing the chi angles of the residues (returned)
fragmentthe 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
athe first line
bthe second line
intersection_anglethe 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
linethe line
planethe plane
intersection_anglethe 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
athe first plane
bthe second plane
intersection_anglethe 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
planethe plane
linethe line
intersection_anglethe 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
planethe plane
vectorthe Vector3
intersection_anglethe 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
athe first vector
bthe second vector
intersection_anglethe 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
vectorthe vector3
planethe plane
intersection_anglethe 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
mpointer to matrix
dimdimension 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
m00first value of the matrix
m01second value of the matrix
m10third value of the matrix
m11fourth 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
mpointer 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,m22the 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
mpointer 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
mpointer to matrix
dimdimension 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
athe first line
bthe second line
Returns
T the distance
Exceptions
Exception::DivisionByZeroif 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
linethe line
planethe plane
Returns
T the distance
Exceptions
Exception::DivisionByZeroif 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
linethe line
pointthe point
Returns
T the distance
Exceptions
Exception::DivisionByZeroif 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
athe first plane
bthe second plane
Returns
T the distance
Exceptions
Exception::DivisionByZeroif 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
planethe plane
linethe line
Returns
T the distance
Exceptions
Exception::DivisionByZeroif 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
planethe plane
pointthe point
Returns
T the distance
Exceptions
Exception::DivisionByZeroif 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
athe first point
bthe 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
pointthe point
linethe line
Returns
T the distance
Exceptions
Exception::DivisionByZeroif 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
pointthe point
planethe plane
Returns
T the distance
Exceptions
Exception::DivisionByZeroif 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
athe first line
bthe second line
pointthe 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
linethe line
planethe plane
intersection_pointthe 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
linethe line
spherethe sphere
intersection_point1the first intersection point
intersection_point2the 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
planethe plane
linethe line
intersection_pointthe 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
planethe plane
spherethe sphere
intersection_circlethe 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
plane1the first plane
plane2the second plane
linethe 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
athe first sphere
bthe second sphere
intersection_circlethe 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
s1the first sphere
s2the second sphere
s3the third sphere
p1the first intersection point
p2the 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
spherethe sphere
linethe line
intersection_point1the first intersection point
intersection_point2the 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
spherethe sphere
planethe plane
intersection_circlethe 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::DivisionByZeroif 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::DivisionByZeroif 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
athe first vector
bthe 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
athe first vector
bthe second vector
rthe ratio factor of the first vector
sthe ratio factor of the second vector
Returns
TVector3 the partition
Exceptions
Exception::DivisionByZeroif 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
ax1. vector x component
ay1. vector y component
az1. vector z component
bx2. vector x component
by2. vector y component
bz2. vector z component
cx3. vector x component
cy3. vector y component
cz3. vector z component
dx4. vector x component
dy4. vector y component
dz4. vector z component
Returns
TAngle the torsion angle
Exceptions
Exception::DivisionByZeroif 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 STL strings. In fact, it is only an inline wrapper around hashString .

Definition at line 56 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 BALL strings. In fact, it is only an inline wrapper around hashString .

Definition at line 65 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
keythe 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
athe first vector3
bthe 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
athe first vector3
bthe second vector3
cthe 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
athe first vector3
bthe second vector3
cthe third vector3
dthe 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
athe first line
bthe 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
linethe line
planethe 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
linethe line
pointthe 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
athe first plane
bthe 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
planethe plane
linethe 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
planethe plane
pointthe 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
pointthe point
linethe 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
pointthe point
planethe 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
athe first line
bthe 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
linethe line
vectorthe 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
athe first plane
bthe 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
planethe plane
vectorthe 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
athe first vector3
bthe 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
vectorthe vector
linethe 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
vectorthe vector3
planethe 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
linethe line
planethe 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
athe first plane
bthe 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
planethe plane
linethe 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
fragmentthe AtomContainer containing the atoms
expressionthe 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 $x^2 + b x + c = 0$.

Parameters
a
b
c
x1the first solution
x2the 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

$
  \begin{array}{ccccccccc}
   a_{1,1} x_1 & + & a_{1,2} x_2 & + & \ldots & + & a_{1,n} x_n & = & a_{1,(n+1)} \\
   a_{2,1} x_1 & + & a_{2,2} x_2 & + & \ldots & + & a_{2,n} x_n & = & a_{2,(n+1)} \\
     \vdots    &   &   \vdots    &   & \ddots &   &   \vdots    &   &   \vdots \\
   a_{n,1} x_1 & + & a_{n,2} x_2 & + & \ldots & + & a_{n,n} x_n & = & a_{n,(n+1)} \\
  \end{array}
$
in matrix form, identify the solution $x = (x_1, x_2,\ldots x_N)$.
m should point to a C-style array containing the $n\times(n+1)$ matrix A.
The elements of A are row-ordered, i.e., they are ordered like this:
$
  a_{1,1}, a_{1,2}, \cdot, a_{1,(n+1)}, a_{2,1}, \ldots a_{n,(n+1)}
$
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
mpointer to the factors in the equations
xpointer in which the results are stored
dimthe 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 $a_1 x_1 + b_1 x_2 = c_1$ and $a_2 x_1 + b_2 x_2 = c_2$.

Parameters
a1,b1,c1,a2,b2,c2constants of the system
x1the first solution
x2the 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