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biu Namespace Reference


Data Structures

class  AllowedBasePairs
class  Alphabet
class  BackboneStructure3D
class  BioMolecule
class  ContactEnergyFunction
class  COption
class  COptionParser
class  DistanceEnergyFunction
class  Graph_UD
class  IntervalEnergyFunction
class  LatticeDescriptor
class  LatticeDescriptorCUB
class  LatticeDescriptorFCC
class  LatticeDescriptorSQR
class  LatticeFrame
class  LatticeModel
class  LatticeMoveSet
class  LatticeNeighborhood
class  LatticeNeighborhoodCUB
class  LatticeProtein
class  LatticeProtein_I
class  LatticeProtein_Ipnt
class  Matrix
class  NeighborVector
class  OffLatticeProtein
class  PivotMoveSet
class  Point3D
class  PullMoveSet
class  QuasiRandomNumberGenerator
class  RandomNumberFactory
class  RandomNumberGenerator
class  RNAStructure
class  RNG_ISO
class  RNG_LCG
class  SquareMatrix
class  Timer
class  VirtualList

Namespaces

namespace  util

Typedefs

typedef biu::SquareMatrix<
int, 3 > 
Automorphism
typedef std::vector< AutomorphismAutomorphismVec
typedef Point3D< double > DblPoint
typedef std::set< DblPointDPointSet
typedef std::vector< DblPointDPointVec
typedef biu::Matrix< double > EnergyMatrix
typedef std::set< biu::LatticeFrame::index_typeIndexSet
typedef std::vector< biu::LatticeFrame::index_typeIndexVec
typedef Point3D< int > IntPoint
typedef std::set< IntPointIPointSet
typedef std::vector< IntPointIPointVec
typedef MoveAlphabet::AlphElem Move
typedef Alphabet MoveAlphabet
typedef MoveAlphabet::Sequence MoveSequence
typedef std::set< NeighborVectorNeighSet
typedef std::vector< COptionOptionMap
typedef OptionMap::const_iterator OptionMapIt
typedef RandomNumberFactory RNF
typedef Alphabet::Sequence Sequence
typedef Alphabet::Sequence Structure

Functions

template<class T>
bool isSubset (const std::set< Point3D< T > > &s, const std::set< Point3D< T > > &sub)
std::ostream & operator<< (std::ostream &os, IndexVec &x)
std::ostream & operator<< (std::ostream &os, IndexSet &x)


Typedef Documentation

a matrix to calculate lattice specific automorphisms like rotation

Definition at line 12 of file NeighborVector.hh.

typedef std::vector<Automorphism> biu::AutomorphismVec

a std::vector of Automorphism objects

Definition at line 15 of file NeighborVector.hh.

typedef Point3D<double> biu::DblPoint

A DblPoint represents a positions in 3-dimensional space.

Definition at line 28 of file Point.hh.

typedef std::set<DblPoint> biu::DPointSet

a std::set of DblPoint objects

Definition at line 29 of file Point.hh.

typedef std::vector<DblPoint> biu::DPointVec

a std::vector if DblPoint objects

Definition at line 30 of file Point.hh.

typedef biu::Matrix<double> biu::EnergyMatrix

The contact energy matrix for a ContactEnergyFunction object.

Definition at line 12 of file ContactEnergyFunction.hh.

Definition at line 87 of file LatticeFrame.hh.

Definition at line 88 of file LatticeFrame.hh.

typedef Point3D<int> biu::IntPoint

An IntPoint represents an integer position in 3-dimensional space.

Definition at line 15 of file Point.hh.

typedef std::set<IntPoint> biu::IPointSet

a std::set of IntPoint objects

Definition at line 23 of file Point.hh.

typedef std::vector<IntPoint> biu::IPointVec

a std::vector of IntPoint objects

Definition at line 24 of file Point.hh.

an internal single move string representation

Definition at line 21 of file NeighborVector.hh.

an alphabet over Move strings

Definition at line 18 of file NeighborVector.hh.

an internal move string sequence representation

Definition at line 24 of file NeighborVector.hh.

typedef std::set<NeighborVector> biu::NeighSet

a std::set of NeighborVector objects

Definition at line 74 of file NeighborVector.hh.

typedef std::vector<COption> biu::OptionMap

The list of the possible options for the parameter list.

Definition at line 81 of file OptionParser.hh.

typedef OptionMap::const_iterator biu::OptionMapIt

Constant iterator for an OptionMap.

Definition at line 83 of file OptionParser.hh.

shortcut typedef

Definition at line 72 of file RandomNumberFactory.hh.

A type for sequence representation

Definition at line 9 of file BioMolecule.hh.

A type for structure representation

Definition at line 12 of file BioMolecule.hh.


Function Documentation

template<class T>
bool biu::isSubset ( const std::set< Point3D< T > > &  s,
const std::set< Point3D< T > > &  sub 
)

Checks whether or not the P set sub is a subset of s.

std::ostream & biu::operator<< ( std::ostream &  os,
IndexVec &  x 
)

Definition at line 97 of file LatticeFrame.cc.

std::ostream & biu::operator<< ( std::ostream &  os,
IndexSet &  x 
)

Definition at line 89 of file LatticeFrame.cc.