PLMD::ERMSD Class Reference

A class that implements ERMSD calculations. More...

#include <ERMSD.h>

Public Member Functions
	ERMSD ()
	Constructor. More...
void	calcMat (const std::vector< Vector > &positions, const Pbc &pbc, std::vector< Vector4d > &mat, std::vector< TensorGeneric< 4, 3 > > &Gderivatives)
double	calculate (const std::vector< Vector > &positions, const Pbc &pbc, std::vector< Vector > &derivatives, Tensor &virial)
	Compute ermsd ( no pbc ) More...
void	clear ()
	clear the structure More...
bool	inPair (unsigned i, unsigned j)
void	setReference (const std::vector< Vector > &reference, const std::vector< unsigned > &pairs_vec, double mycutoff=0.24)
	set reference coordinates More...

Private Attributes
double	cutoff
std::size_t	natoms
std::size_t	nresidues
std::vector< std::pair< unsigned, unsigned > >	pairs
std::vector< Vector4d >	reference_mat

Detailed Description

A class that implements ERMSD calculations.

Constructor & Destructor Documentation

ERMSD()

PLMD::ERMSD::ERMSD ( )

inline

Constructor.

Member Function Documentation

calcMat()

void PLMD::ERMSD::calcMat	(	const std::vector< Vector > &	positions,
		const Pbc &	pbc,
		std::vector< Vector4d > &	mat,
		std::vector< TensorGeneric< 4, 3 > > &	Gderivatives
	)

calculate()

double PLMD::ERMSD::calculate	(	const std::vector< Vector > &	positions,
		const Pbc &	pbc,
		std::vector< Vector > &	derivatives,
		Tensor &	virial
	)

Compute ermsd ( no pbc )

Compute ermsd ( with pbc )

clear()

void PLMD::ERMSD::clear

(

)

clear the structure

inPair()

bool PLMD::ERMSD::inPair	(	unsigned	i,
		unsigned	j
	)

setReference()

void PLMD::ERMSD::setReference	(	const std::vector< Vector > &	reference,
		const std::vector< unsigned > &	pairs_vec,
		double	mycutoff = 0.24
	)

set reference coordinates

Member Data Documentation

cutoff

double PLMD::ERMSD::cutoff

private

natoms

std::size_t PLMD::ERMSD::natoms

private

nresidues

std::size_t PLMD::ERMSD::nresidues

private

pairs

std::vector<std::pair <unsigned,unsigned> > PLMD::ERMSD::pairs

private

reference_mat

std::vector<Vector4d> PLMD::ERMSD::reference_mat

private

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

• tools/ERMSD.h
• tools/ERMSD.cpp