A class that implements DRMSD calculations. More...

#include <DRMSD.h>

Public Member Functions
	DRMSD ()
	Constructor. More...

void	clear ()
	clear the structure More...

void	setFromPDB (const PDB &, double lbound=0.0, double ubound=std::numeric_limits< double >::max())
	set reference, align and displace from input pdb structure More...

void	setReference (const std::vector< Vector > &reference, double lbound=0.0, double ubound=std::numeric_limits< double >::max())
	set reference coordinates More...

double	calculate (const std::vector< Vector > &positions, std::vector< Vector > &derivatives, Tensor &virial) const
	Compute drmsd ( no pbc ) More...

double	calculate (const std::vector< Vector > &positions, const Pbc &pbc, std::vector< Vector > &derivatives, Tensor &virial, bool do_pbc=true) const
	Compute drmsd ( with pbc ) More...

Private Attributes
std::map< std::pair< unsigned, unsigned >, double >	targets

unsigned	natoms

Detailed Description

A class that implements DRMSD calculations.

Definition at line 37 of file DRMSD.h.

Constructor & Destructor Documentation

PLMD::DRMSD::DRMSD ( )

inline

Constructor.

Definition at line 42 of file DRMSD.h.

Compute drmsd ( no pbc )

Definition at line 51 of file DRMSD.cpp.

Compute drmsd ( with pbc )

Definition at line 58 of file DRMSD.cpp.

void PLMD::DRMSD::clear ( )

clear the structure

Definition at line 34 of file DRMSD.cpp.

void PLMD::DRMSD::setFromPDB	(	const PDB &	pdb,
		double	lbound = `0.0`,
		double	ubound = `std::numeric_limits<double>::max( )`
	)

set reference, align and displace from input pdb structure

Definition at line 30 of file DRMSD.cpp.

void PLMD::DRMSD::setReference	(	const std::vector< Vector > &	reference,
		double	lbound = `0.0`,
		double	ubound = `std::numeric_limits<double>::max( )`
	)

set reference coordinates

Definition at line 38 of file DRMSD.cpp.

unsigned PLMD::DRMSD::natoms

private

Definition at line 39 of file DRMSD.h.

std::map< std::pair <unsigned,unsigned> , double> PLMD::DRMSD::targets

private

Definition at line 38 of file DRMSD.h.

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