PLMD::RMSD Class Reference

A class that implements RMSD calculations This is a class that implements the various infrastructure to calculate the RMSD or MSD respect a given frame. More...

#include <RMSD.h>

Public Member Functions
	RMSD ()
	Constructor. More...
void	clear ()
	clear the structure More...
void	set (const PDB &, std::string mytype)
	set reference, align and displace from input pdb structure More...
void	setType (std::string mytype)
	set the type of alignment we are doing More...
void	setReference (const std::vector< Vector > &reference)
	set reference coordinates More...
void	setAlign (const std::vector< double > &align)
	set weights More...
void	setDisplace (const std::vector< double > &displace)
	set align More...
std::string	getMethod ()
double	simpleAlignment (const std::vector< double > &align, const std::vector< double > &displace, const std::vector< Vector > &positions, const std::vector< Vector > &reference, std::vector< Vector > &derivatives, bool squared=false) const
template<bool safe, bool alEqDis>
double	optimalAlignment (const std::vector< double > &align, const std::vector< double > &displace, const std::vector< Vector > &positions, const std::vector< Vector > &reference, std::vector< Vector > &derivatives, bool squared=false) const
double	calculate (const std::vector< Vector > &positions, std::vector< Vector > &derivatives, bool squared=false) const
	Compute rmsd. More...

Private Types
enum	AlignmentMethod { SIMPLE, OPTIMAL, OPTIMAL_FAST }

Private Attributes
AlignmentMethod	alignmentMethod
std::vector< Vector >	reference
std::vector< double >	align
std::vector< double >	displace

Detailed Description

A class that implements RMSD calculations This is a class that implements the various infrastructure to calculate the RMSD or MSD respect a given frame.

It can be done through an optimal alignment scheme as Kearsley or, more simply, by resetting the center of mass. This is the class that decides this. A very simple use is

#include "tools/PDB.h"
#include "tools/RMSD.h"
#include "tools/Vector.h"
using namespace PLMD;
RMSD rmsd;
PDB pdb;
// get the pdb (see PDB documentation)
pdb.read("file.pdb",true,1.0);
string type;
type.assign("OPTIMAL");
// set the reference and the type 
rmsd.set(pdb,type);
// this calculates the rmsd and the derivatives
vector<Vector> derivs;
double val; 
val=rmsd.calculate(getPositions(),derivs,true);

Member Enumeration Documentation

enum PLMD::RMSD::AlignmentMethod

private

Enumerator
SIMPLE
OPTIMAL
OPTIMAL_FAST

Constructor & Destructor Documentation

PLMD::RMSD::RMSD

(

)

Constructor.

Member Function Documentation

double PLMD::RMSD::calculate	(	const std::vector< Vector > &	positions,
		std::vector< Vector > &	derivatives,
		bool	squared = false
	)		const

Compute rmsd.

void PLMD::RMSD::clear

(

)

clear the structure

string PLMD::RMSD::getMethod

(

)

template<bool safe, bool alEqDis>

double PLMD::RMSD::optimalAlignment	(	const std::vector< double > &	align,
		const std::vector< double > &	displace,
		const std::vector< Vector > &	positions,
		const std::vector< Vector > &	reference,
		std::vector< Vector > &	derivatives,
		bool	squared = false
	)		const

void PLMD::RMSD::set	(	const PDB &	pdb,
		std::string	mytype
	)

set reference, align and displace from input pdb structure

void PLMD::RMSD::setAlign

(

const std::vector< double > &

align

)

set weights

void PLMD::RMSD::setDisplace

(

const std::vector< double > &

displace

)

set align

void PLMD::RMSD::setReference

(

const std::vector< Vector > &

reference

)

set reference coordinates

void PLMD::RMSD::setType

(

std::string

mytype

)

set the type of alignment we are doing

double PLMD::RMSD::simpleAlignment	(	const std::vector< double > &	align,
		const std::vector< double > &	displace,
		const std::vector< Vector > &	positions,
		const std::vector< Vector > &	reference,
		std::vector< Vector > &	derivatives,
		bool	squared = false
	)		const

Member Data Documentation

std::vector<double> PLMD::RMSD::align

private

AlignmentMethod PLMD::RMSD::alignmentMethod

private

std::vector<double> PLMD::RMSD::displace

private

std::vector<Vector> PLMD::RMSD::reference

private

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

• tools/RMSD.h
• tools/RMSD.cpp