this is a class which is needed to share information across the various non-threadsafe routines so that the public function of rmsd are threadsafe while the inner core can safely share information More...

#include <RMSD.h>

Public Member Functions
	RMSDCoreData (const std::vector< double > &a, const std::vector< double > &d, const std::vector< Vector > &p, const std::vector< Vector > &r, Vector &cp, Vector &cr)
	the constructor (note: only references are passed, therefore is rather fast) note: this aligns the reference onto the positions More...

	RMSDCoreData (const std::vector< double > &a, const std::vector< double > &d, const std::vector< Vector > &p, const std::vector< Vector > &r)

void	calcPositionsCenter ()

void	calcReferenceCenter ()

void	setPositionsCenter (Vector v)

void	setReferenceCenter (Vector v)

void	setPositionsCenterIsRemoved (bool t)

void	setReferenceCenterIsRemoved (bool t)

bool	getPositionsCenterIsRemoved ()

bool	getReferenceCenterIsRemoved ()

void	doCoreCalc (bool safe, bool alEqDis, bool only_rotation=false)
	This calculates the elements needed by the quaternion to calculate everything that is needed additional calls retrieve different components note that this considers that the centers of both reference and positions are already setted but automatically should properly account for non removed components: if not removed then it removes prior to calculation of the alignment. More...

double	getDistance (bool squared)
	just retrieve the distance already calculated More...

std::vector< Vector >	getDDistanceDPositions ()

std::vector< Vector >	getDDistanceDReference ()

std::vector< Vector >	getDDistanceDReferenceSOMA ()
	this version does not calculate the derivative of rotation matrix as needed for SOMA More...

std::vector< Vector >	getAlignedReferenceToPositions ()

std::vector< Vector >	getAlignedPositionsToReference ()

std::vector< Vector >	getCenteredPositions ()

std::vector< Vector >	getCenteredReference ()

Vector	getPositionsCenter ()

Vector	getReferenceCenter ()

Tensor	getRotationMatrixReferenceToPositions ()

Tensor	getRotationMatrixPositionsToReference ()

Matrix< std::vector< Vector > >	getDRotationDPositions (bool inverseTransform=false)

Matrix< std::vector< Vector > >	getDRotationDReference (bool inverseTransform=false)

Private Attributes
bool	alEqDis

bool	distanceIsMSD

bool	hasDistance

bool	isInitialized

bool	safe

Vector	creference

bool	creference_is_calculated

bool	creference_is_removed

Vector	cpositions

bool	cpositions_is_calculated

bool	cpositions_is_removed

bool	retrieve_only_rotation

const std::vector< Vector > &	positions

const std::vector< Vector > &	reference

const std::vector< double > &	align

const std::vector< double > &	displace

double	dist

std::vector< double >	eigenvals

Matrix< double >	eigenvecs

double	rr00

double	rr11

Tensor	rotation

Tensor	drotation_drr01 [3][3]

Tensor	ddist_drr01

Tensor	ddist_drotation

std::vector< Vector >	d

Detailed Description

this is a class which is needed to share information across the various non-threadsafe routines so that the public function of rmsd are threadsafe while the inner core can safely share information

Constructor & Destructor Documentation

PLMD::RMSDCoreData::RMSDCoreData	(	const std::vector< double > &	a,
		const std::vector< double > &	d,
		const std::vector< Vector > &	p,
		const std::vector< Vector > &	r,
		Vector &	cp,
		Vector &	cr
	)

inline

the constructor (note: only references are passed, therefore is rather fast) note: this aligns the reference onto the positions

this method assumes that the centers are already calculated and subtracted

PLMD::RMSDCoreData::RMSDCoreData	(	const std::vector< double > &	a,
		const std::vector< double > &	d,
		const std::vector< Vector > &	p,
		const std::vector< Vector > &	r
	)

inline

Member Function Documentation

void PLMD::RMSDCoreData::calcPositionsCenter ( )

inline

void PLMD::RMSDCoreData::calcReferenceCenter ( )

inline

void PLMD::RMSDCoreData::doCoreCalc	(	bool	safe,
		bool	alEqDis,
		bool	only_rotation = `false`
	)

This calculates the elements needed by the quaternion to calculate everything that is needed additional calls retrieve different components note that this considers that the centers of both reference and positions are already setted but automatically should properly account for non removed components: if not removed then it removes prior to calculation of the alignment.

std::vector< Vector > PLMD::RMSDCoreData::getAlignedPositionsToReference ( )

std::vector< Vector > PLMD::RMSDCoreData::getAlignedReferenceToPositions ( )

std::vector< Vector > PLMD::RMSDCoreData::getCenteredPositions ( )

std::vector< Vector > PLMD::RMSDCoreData::getCenteredReference ( )

std::vector< Vector > PLMD::RMSDCoreData::getDDistanceDPositions ( )

std::vector< Vector > PLMD::RMSDCoreData::getDDistanceDReference ( )

std::vector< Vector > PLMD::RMSDCoreData::getDDistanceDReferenceSOMA ( )

this version does not calculate the derivative of rotation matrix as needed for SOMA

double PLMD::RMSDCoreData::getDistance ( bool squared )

just retrieve the distance already calculated

Matrix< std::vector< Vector > > PLMD::RMSDCoreData::getDRotationDPositions ( bool inverseTransform = false )

Matrix< std::vector< Vector > > PLMD::RMSDCoreData::getDRotationDReference ( bool inverseTransform = false )

Vector PLMD::RMSDCoreData::getPositionsCenter ( )

bool PLMD::RMSDCoreData::getPositionsCenterIsRemoved ( )

inline

Vector PLMD::RMSDCoreData::getReferenceCenter ( )

bool PLMD::RMSDCoreData::getReferenceCenterIsRemoved ( )

inline

Tensor PLMD::RMSDCoreData::getRotationMatrixPositionsToReference ( )

Tensor PLMD::RMSDCoreData::getRotationMatrixReferenceToPositions ( )

void PLMD::RMSDCoreData::setPositionsCenter ( Vector v )

inline

void PLMD::RMSDCoreData::setPositionsCenterIsRemoved ( bool t )

inline

void PLMD::RMSDCoreData::setReferenceCenter ( Vector v )

inline

void PLMD::RMSDCoreData::setReferenceCenterIsRemoved ( bool t )

inline

Member Data Documentation

bool PLMD::RMSDCoreData::alEqDis

private

const std::vector<double>& PLMD::RMSDCoreData::align

private

Vector PLMD::RMSDCoreData::cpositions

private

bool PLMD::RMSDCoreData::cpositions_is_calculated

private

bool PLMD::RMSDCoreData::cpositions_is_removed

private

Vector PLMD::RMSDCoreData::creference

private

bool PLMD::RMSDCoreData::creference_is_calculated

private

bool PLMD::RMSDCoreData::creference_is_removed

private

std::vector<Vector> PLMD::RMSDCoreData::d

private

Tensor PLMD::RMSDCoreData::ddist_drotation

private

Tensor PLMD::RMSDCoreData::ddist_drr01

private

const std::vector<double>& PLMD::RMSDCoreData::displace

private

double PLMD::RMSDCoreData::dist

private

bool PLMD::RMSDCoreData::distanceIsMSD

private

Tensor PLMD::RMSDCoreData::drotation_drr01[3][3]

private

std::vector<double> PLMD::RMSDCoreData::eigenvals

private

Matrix<double> PLMD::RMSDCoreData::eigenvecs

private

bool PLMD::RMSDCoreData::hasDistance

private

bool PLMD::RMSDCoreData::isInitialized

private

const std::vector<Vector>& PLMD::RMSDCoreData::positions

private

const std::vector<Vector>& PLMD::RMSDCoreData::reference

private

bool PLMD::RMSDCoreData::retrieve_only_rotation

private

Tensor PLMD::RMSDCoreData::rotation

private

double PLMD::RMSDCoreData::rr00

private

double PLMD::RMSDCoreData::rr11

private

bool PLMD::RMSDCoreData::safe

private

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

tools/RMSD.h
tools/RMSD.cpp

Public Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation