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)

	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...

void	calcPositionsCenter ()

void	calcReferenceCenter ()

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...

void	doCoreCalcWithCloseStructure (bool safe, bool alEqDis, const Tensor &rotationPosClose, const Tensor &rotationRefClose, std::array< std::array< Tensor, 3 >, 3 > &drotationPosCloseDrr01)

std::vector< Vector >	getAlignedPositionsToReference ()

std::vector< Vector >	getAlignedReferenceToPositions ()

std::vector< Vector >	getCenteredPositions ()

std::vector< Vector >	getCenteredReference ()

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...

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

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

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

const std::array< std::array< Tensor, 3 >, 3 > &	getDRotationDRr01 () const

Vector	getPositionsCenter ()

bool	getPositionsCenterIsRemoved ()

Vector	getReferenceCenter ()

bool	getReferenceCenterIsRemoved ()

Tensor	getRotationMatrixPositionsToReference ()

Tensor	getRotationMatrixReferenceToPositions ()

void	setPositionsCenter (Vector v)

void	setPositionsCenterIsRemoved (bool t)

void	setReferenceCenter (Vector v)

void	setReferenceCenterIsRemoved (bool t)

Private Attributes
bool	alEqDis

const std::vector< double > &	align

Vector	cpositions

bool	cpositions_is_calculated

bool	cpositions_is_removed

Vector	creference

bool	creference_is_calculated

bool	creference_is_removed

std::vector< Vector >	d

Tensor	ddist_drotation

Tensor	ddist_drr01

const std::vector< double > &	displace

double	dist

bool	distanceIsMSD

std::array< std::array< Tensor, 3 >, 3 >	drotation_drr01

Vector4d	eigenvals

Tensor4d	eigenvecs

bool	hasDistance

bool	isInitialized

const std::vector< Vector > &	positions

const std::vector< Vector > &	reference

bool	retrieve_only_rotation

Tensor	rotation

double	rr00

double	rr11

bool	safe

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

◆ RMSDCoreData() [1/2]

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

◆ RMSDCoreData() [2/2]

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

◆ calcPositionsCenter()

void PLMD::RMSDCoreData::calcPositionsCenter ( )

inline

◆ calcReferenceCenter()

void PLMD::RMSDCoreData::calcReferenceCenter ( )

inline

◆ doCoreCalc()

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.

◆ doCoreCalcWithCloseStructure()

void PLMD::RMSDCoreData::doCoreCalcWithCloseStructure	(	bool	safe,
		bool	alEqDis,
		const Tensor &	rotationPosClose,
		const Tensor &	rotationRefClose,
		std::array< std::array< Tensor, 3 >, 3 > &	drotationPosCloseDrr01
	)

◆ getAlignedPositionsToReference()

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

◆ getAlignedReferenceToPositions()

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

◆ getCenteredPositions()

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

◆ getCenteredReference()

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

◆ getDDistanceDPositions()

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

◆ getDDistanceDReference()

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

◆ getDDistanceDReferenceSOMA()

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

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

◆ getDistance()

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

just retrieve the distance already calculated

◆ getDRotationDPositions()

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

◆ getDRotationDReference()

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

◆ getDRotationDRr01()

const std::array< std::array< Tensor, 3 >, 3 > & PLMD::RMSDCoreData::getDRotationDRr01 ( ) const

◆ getPositionsCenter()

Vector PLMD::RMSDCoreData::getPositionsCenter ( )

◆ getPositionsCenterIsRemoved()

bool PLMD::RMSDCoreData::getPositionsCenterIsRemoved ( )

inline

◆ getReferenceCenter()

Vector PLMD::RMSDCoreData::getReferenceCenter ( )

◆ getReferenceCenterIsRemoved()

bool PLMD::RMSDCoreData::getReferenceCenterIsRemoved ( )

inline

◆ getRotationMatrixPositionsToReference()

Tensor PLMD::RMSDCoreData::getRotationMatrixPositionsToReference ( )

◆ getRotationMatrixReferenceToPositions()

Tensor PLMD::RMSDCoreData::getRotationMatrixReferenceToPositions ( )

◆ setPositionsCenter()

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

inline

◆ setPositionsCenterIsRemoved()

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

inline

◆ setReferenceCenter()

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

inline

◆ setReferenceCenterIsRemoved()

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

inline

Member Data Documentation

◆ alEqDis

bool PLMD::RMSDCoreData::alEqDis

private

◆ align

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

private

◆ cpositions

Vector PLMD::RMSDCoreData::cpositions

private

◆ cpositions_is_calculated

bool PLMD::RMSDCoreData::cpositions_is_calculated

private

◆ cpositions_is_removed

bool PLMD::RMSDCoreData::cpositions_is_removed

private

◆ creference

Vector PLMD::RMSDCoreData::creference

private

◆ creference_is_calculated

bool PLMD::RMSDCoreData::creference_is_calculated

private

◆ creference_is_removed

bool PLMD::RMSDCoreData::creference_is_removed

private

◆ d

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

private

◆ ddist_drotation

Tensor PLMD::RMSDCoreData::ddist_drotation

private

◆ ddist_drr01

Tensor PLMD::RMSDCoreData::ddist_drr01

private

◆ displace

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

private

◆ dist

double PLMD::RMSDCoreData::dist

private

◆ distanceIsMSD

bool PLMD::RMSDCoreData::distanceIsMSD

private

◆ drotation_drr01

std::array<std::array<Tensor,3>,3> PLMD::RMSDCoreData::drotation_drr01

private

◆ eigenvals

Vector4d PLMD::RMSDCoreData::eigenvals

private

◆ eigenvecs

Tensor4d PLMD::RMSDCoreData::eigenvecs

private

◆ hasDistance

bool PLMD::RMSDCoreData::hasDistance

private

◆ isInitialized

bool PLMD::RMSDCoreData::isInitialized

private

◆ positions

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

private

◆ reference

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

private

◆ retrieve_only_rotation

bool PLMD::RMSDCoreData::retrieve_only_rotation

private

◆ rotation

Tensor PLMD::RMSDCoreData::rotation

private

◆ rr00

double PLMD::RMSDCoreData::rr00

private

◆ rr11

double PLMD::RMSDCoreData::rr11

private

◆ safe

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

◆ RMSDCoreData() [1/2]

◆ RMSDCoreData() [2/2]

Member Function Documentation

◆ calcPositionsCenter()

◆ calcReferenceCenter()

◆ doCoreCalc()

◆ doCoreCalcWithCloseStructure()

◆ getAlignedPositionsToReference()

◆ getAlignedReferenceToPositions()

◆ getCenteredPositions()

◆ getCenteredReference()

◆ getDDistanceDPositions()

◆ getDDistanceDReference()

◆ getDDistanceDReferenceSOMA()

◆ getDistance()

◆ getDRotationDPositions()

◆ getDRotationDReference()

◆ getDRotationDRr01()

◆ getPositionsCenter()

◆ getPositionsCenterIsRemoved()

◆ getReferenceCenter()

◆ getReferenceCenterIsRemoved()

◆ getRotationMatrixPositionsToReference()

◆ getRotationMatrixReferenceToPositions()

◆ setPositionsCenter()

◆ setPositionsCenterIsRemoved()

◆ setReferenceCenter()

◆ setReferenceCenterIsRemoved()

Member Data Documentation

◆ alEqDis

◆ align

◆ cpositions

◆ cpositions_is_calculated

◆ cpositions_is_removed

◆ creference

◆ creference_is_calculated

◆ creference_is_removed

◆ d

◆ ddist_drotation

◆ ddist_drr01

◆ displace

◆ dist

◆ distanceIsMSD

◆ drotation_drr01

◆ eigenvals

◆ eigenvecs

◆ hasDistance

◆ isInitialized

◆ positions

◆ reference

◆ retrieve_only_rotation

◆ rotation

◆ rr00

◆ rr11

◆ safe