Representation of a conformer. More...

#include <frame.h>

Public Member Functions
	Frame (Molecule *molecule)

	Frame (const Frame &frame)

Frame &	operator= (const Frame &frame)

const std::vector< Bond > &	Bonds () const

std::vector< Bond > &	Bonds ()

const std::vector< Coordinate > &	XYZ () const

std::vector< Coordinate > &	XYZ ()

D2Array< double >	InertiaTensor () const

D2Array< double >	GyrationTensor () const

void	SetDihedral (size_t i, size_t j, size_t k, size_t l, float dihedral)

void	RotateBond (size_t i, size_t j, float angle, bool clockwise)

Energy &	KineticEnergy ()

const Energy &	KineticEnergy () const

const Energy &	PotentialEnergy () const

Energy &	PotentialEnergy ()

Energy	TotalEnergy () const

float	Distance (int i, int j) const

float	Angle (int i, int j, int l) const

float	Dihedral (int i, int j, int k, int l) const

Coordinate	MassCenter () const

Coordinate	Centroid () const

std::vector< std::vector< size_t > >	Rings (size_t size=0) const

Coordinate	Vector (int i, int j) const

const Molecule *	ParentMolecule () const

Molecule *	ParentMolecule ()

const std::vector< D2Array< double > > &	ChemicalShieldingTensors () const

std::vector< D2Array< double > > &	ChemicalShieldingTensors ()

const std::vector< D2Array< double > > &	EFGTensors () const

std::vector< D2Array< double > > &	EFGTensors ()

void	SetTitle (const std::string &string)

const std::string &	Title () const

const std::string &	FileName () const

void	SetFileName (const std::string &filename)

void	Reparent (Molecule *mol)

Detailed Description

Representation of a conformer.

Member Function Documentation

§ Angle()

float magnes::Frame::Angle	(	int	i,
		int	j,
		int	l
	)		const

Returns: angle between atoms i j and l

§ Bonds() [1/2]

const std::vector<Bond>& magnes::Frame::Bonds ( ) const

Returns: a const vector of bonds

§ Bonds() [2/2]

std::vector<Bond>& magnes::Frame::Bonds ( )

Returns: a const vector of bonds

§ Centroid()

Coordinate magnes::Frame::Centroid ( ) const

Returns: position of the centroid

§ ChemicalShieldingTensors() [1/2]

const std::vector< D2Array<double> >& magnes::Frame::ChemicalShieldingTensors ( ) const

return a const vector with the chemical shift tensors

§ ChemicalShieldingTensors() [2/2]

std::vector< D2Array<double> >& magnes::Frame::ChemicalShieldingTensors ( )

return a vector with the chemical shift tensors

§ Dihedral()

float magnes::Frame::Dihedral	(	int	i,
		int	j,
		int	k,
		int	l
	)		const

Returns: dihedral angle between atoms i,j,k,l

§ Distance()

float magnes::Frame::Distance	(	int	i,
		int	j
	)		const

Returns: the distance in Angstroms between atoms i and j

§ EFGTensors() [1/2]

const std::vector< D2Array<double> >& magnes::Frame::EFGTensors ( ) const

return a const vector with the chemical shift tensors

§ EFGTensors() [2/2]

std::vector< D2Array<double> >& magnes::Frame::EFGTensors ( )

return a vector with the chemical shift tensors

§ FileName()

const std::string& magnes::Frame::FileName ( ) const

return the filename corresponding to the frame

§ GyrationTensor()

D2Array<double> magnes::Frame::GyrationTensor ( ) const

Returns: the Gyration tensor

§ InertiaTensor()

D2Array<double> magnes::Frame::InertiaTensor ( ) const

Returns: the inertia tensor

§ KineticEnergy() [1/2]

Energy& magnes::Frame::KineticEnergy ( )

Returns: the kinetic energy of this frame

§ KineticEnergy() [2/2]

const Energy& magnes::Frame::KineticEnergy ( ) const

Returns: the kinetic energy of this frame

§ MassCenter()

Coordinate magnes::Frame::MassCenter ( ) const

Returns: position of the Center of mass

§ ParentMolecule() [1/2]

const Molecule* magnes::Frame::ParentMolecule ( ) const

inline

Returns: a const pointer to the parent molecule of this conformer

§ ParentMolecule() [2/2]

Molecule* magnes::Frame::ParentMolecule ( )

inline

Returns: a const pointer to the parent molecule of this conformer

References magnes::operator<<().

§ PotentialEnergy() [1/2]

const Energy& magnes::Frame::PotentialEnergy ( ) const

Returns: the potential energy of this frame

§ PotentialEnergy() [2/2]

Energy& magnes::Frame::PotentialEnergy ( )

Returns: the potential energy of this frame

§ Reparent()

void magnes::Frame::Reparent ( Molecule * mol )

Reparent the frame

§ Rings()

std::vector< std::vector<size_t> > magnes::Frame::Rings ( size_t size = 0 ) const

Returns: rings of size

Parameters

size	or all rings if 0

§ RotateBond()

void magnes::Frame::RotateBond	(	size_t	i,
		size_t	j,
		float	angle,
		bool	clockwise
	)

rotate bond between atoms i and j

§ SetDihedral()

void magnes::Frame::SetDihedral	(	size_t	i,
		size_t	j,
		size_t	k,
		size_t	l,
		float	dihedral
	)

set the dihedral angle in radians

§ SetFileName()

void magnes::Frame::SetFileName ( const std::string & filename )

set the filename for the frame

§ SetTitle()

void magnes::Frame::SetTitle ( const std::string & string )

put a tile

§ Title()

const std::string& magnes::Frame::Title ( ) const

return the title of the frame

§ TotalEnergy()

Energy magnes::Frame::TotalEnergy ( ) const

Returns: total energy as the sum of potential and kinetic energy

§ Vector()

Coordinate magnes::Frame::Vector	(	int	i,
		int	j
	)		const

Returns: 3D vector betwwen atoms i and j

§ XYZ() [1/2]

const std::vector<Coordinate>& magnes::Frame::XYZ ( ) const

Returns: coordinates for this frame

§ XYZ() [2/2]

std::vector<Coordinate>& magnes::Frame::XYZ ( )

Returns: coordinates for this frame

The documentation for this class was generated from the following file:

/Users/armando/worksrc/magnes-code/trunk/magnes/core/frame.h

Public Member Functions