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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	RNAStructure_TB
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< Automorphism >	AutomorphismVec
typedef Point3D< double >	DblPoint
typedef std::set< DblPoint >	DPointSet
typedef std::vector< DblPoint >	DPointVec
typedef biu::Matrix< double >	EnergyMatrix
typedef std::set< biu::LatticeFrame::index_type >	IndexSet
typedef std::vector< biu::LatticeFrame::index_type >	IndexVec
typedef Point3D< int >	IntPoint
typedef std::set< IntPoint >	IPointSet
typedef std::vector< IntPoint >	IPointVec
typedef MoveAlphabet::AlphElem	Move
typedef Alphabet	MoveAlphabet
typedef MoveAlphabet::Sequence	MoveSequence
typedef std::set< NeighborVector >	NeighSet
typedef std::vector< COption >	OptionMap
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)

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Typedef Documentation

typedef biu::SquareMatrix<int,3> biu::Automorphism

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 87 of file DistanceEnergyFunction.hh.

typedef std::set<biu::LatticeFrame::index_type> biu::IndexSet

Definition at line 87 of file LatticeFrame.hh.

typedef std::vector<biu::LatticeFrame::index_type> biu::IndexVec

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.

typedef MoveAlphabet::AlphElem biu::Move

an internal single move string representation

Definition at line 21 of file NeighborVector.hh.

typedef Alphabet biu::MoveAlphabet

an alphabet over Move strings

Definition at line 18 of file NeighborVector.hh.

typedef MoveAlphabet::Sequence biu::MoveSequence

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 82 of file OptionParser.hh.

typedef OptionMap::const_iterator biu::OptionMapIt

Constant iterator for an OptionMap.

Definition at line 84 of file OptionParser.hh.

typedef RandomNumberFactory biu::RNF

shortcut typedef

Definition at line 72 of file RandomNumberFactory.hh.

typedef Alphabet::Sequence biu::Sequence

A type for sequence representation

Definition at line 9 of file BioMolecule.hh.

typedef Alphabet::Sequence biu::Structure

A type for structure representation

Definition at line 12 of file BioMolecule.hh.

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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.