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 (Log &log)
	Constructor. More...
	RMSD (const RMSD &)
	a copy constructor More...
RMSD &	operator= (const RMSD &)
	assignment More...
	~RMSD ()
	the destructor needs to delete the myalignment object eventually 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, Log *&log, std::vector< Vector > &derivatives, bool squared=false)
template<bool safe>
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)
double	calculate (const std::vector< Vector > &positions, std::vector< Vector > &derivatives, bool squared=false)
	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
OptimalAlignment *	myoptimalalignment
Log *	log

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);

Definition at line 62 of file RMSD.h.

Constructor & Destructor Documentation

PLMD::RMSD::RMSD

(

Log &

log

)

Constructor.

Definition at line 35 of file RMSD.cpp.

PLMD::RMSD::RMSD

(

const RMSD &

oldrmsd

)

a copy constructor

Definition at line 54 of file RMSD.cpp.

PLMD::RMSD::~RMSD

(

)

the destructor needs to delete the myalignment object eventually

Definition at line 98 of file RMSD.cpp.

Member Function Documentation

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

Compute rmsd.

Definition at line 131 of file RMSD.cpp.

void PLMD::RMSD::clear

(

)

clear the structure

Definition at line 93 of file RMSD.cpp.

string PLMD::RMSD::getMethod

(

)

Definition at line 102 of file RMSD.cpp.

RMSD & PLMD::RMSD::operator=

(

const RMSD &

v

)

assignment

Definition at line 40 of file RMSD.cpp.

template<bool safe>

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
	)

Definition at line 225 of file RMSD.cpp.

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

set reference, align and displace from input pdb structure

Definition at line 65 of file RMSD.cpp.

void PLMD::RMSD::setAlign

(

const std::vector< double > &

align

)

set weights

Definition at line 121 of file RMSD.cpp.

void PLMD::RMSD::setDisplace

(

const std::vector< double > &

displace

)

set align

Definition at line 126 of file RMSD.cpp.

void PLMD::RMSD::setReference

(

const std::vector< Vector > &

reference

)

set reference coordinates

Definition at line 112 of file RMSD.cpp.

void PLMD::RMSD::setType

(

std::string

mytype

)

set the type of alignment we are doing

Definition at line 73 of file RMSD.cpp.

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

Definition at line 172 of file RMSD.cpp.

Member Data Documentation

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

private

Definition at line 67 of file RMSD.h.

AlignmentMethod PLMD::RMSD::alignmentMethod

private

Definition at line 65 of file RMSD.h.

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

private

Definition at line 68 of file RMSD.h.

Log* PLMD::RMSD::log

private

Definition at line 70 of file RMSD.h.

OptimalAlignment* PLMD::RMSD::myoptimalalignment

private

Definition at line 69 of file RMSD.h.

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

private

Definition at line 66 of file RMSD.h.

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

• tools/RMSD.h
• tools/RMSD.cpp