Inheritance diagram for PLMD::MahalanobisDistance:

Public Member Functions
	MahalanobisDistance (const ReferenceConfigurationOptions &ro)

double	calc (const std::vector< Vector > &pos, const Pbc &pbc, const std::vector< Value *> &vals, const std::vector< double > &arg, ReferenceValuePack &myder, const bool &squared) const
	Calculate the distance from the reference configuration. More...

double	calculate (const std::vector< Value *> &vals, ReferenceValuePack &myder, const bool &squared) const

double	calculate (const std::vector< Vector > &pos, const Pbc &pbc, const std::vector< Value *> &vals, ReferenceValuePack &myder, const bool &squared=false) const
	Calculate the distance from the reference configuration. More...

virtual double	calculateArgumentDistance (const std::vector< Value *> &vals, const std::vector< double > &arg, ReferenceValuePack &myder, const bool &squared) const
	Calculate the euclidean/malanobius distance the atoms have moved from the reference configuration in CV space. More...

void	copyDerivatives (const ReferenceConfiguration *)
	Parse something from the pdb remarks Copy derivatives from one frame to this frame. More...

void	displaceReferenceArguments (const double &weight, const std::vector< double > &displace)
	Displace the positions of the reference atoms. More...

void	displaceReferenceConfiguration (const double &weight, Direction &dir)
	Move the reference configuration by an ammount specified using a Direction. More...

virtual void	extractArgumentDisplacement (const std::vector< Value *> &vals, const std::vector< double > &arg, std::vector< double > &dirout) const
	Extract the displacement from a position in a space. More...

void	extractDisplacementVector (const std::vector< Vector > &pos, const std::vector< Value *> &vals, const std::vector< double > &arg, const bool &nflag, Direction &mydir) const
	Extract a Direction giving you the displacement from some position. More...

virtual const std::vector< AtomNumber > &	getAbsoluteIndexes ()
	These are overwritten in ReferenceArguments and ReferenceAtoms to make frame copying work. More...

const std::vector< std::string > &	getArgumentNames ()
	Return names. More...

void	getArgumentRequests (std::vector< std::string > &, bool disable_checks=false)
	Get the arguments required. More...

virtual void	getAtomRequests (std::vector< AtomNumber > &, bool disable_checks=false)
	Retrieve the atoms that are required for this guy. More...

std::string	getName () const
	Return the name of this metric. More...

unsigned	getNumberOfReferenceArguments () const
	Get the number of reference arguments. More...

virtual unsigned	getNumberOfReferencePositions () const

double	getReferenceArgument (const unsigned &i) const
	Get the value of the ith reference argument. More...

const std::vector< double > &	getReferenceArguments () const
	Return all the reference arguments. More...

const std::vector< double > &	getReferenceMetric ()

virtual const std::vector< Vector > &	getReferencePositions () const
	These are overwritten in ReferenceArguments and ReferenceAtoms but are required here to make PLMD::distance work. More...

void	moveReferenceArguments (const std::vector< double > &arg_vals)
	Set the positions of the reference arguments. More...

bool	pcaIsEnabledForThisReference ()
	Stuff for pca. More...

double	projectArgDisplacementOnVector (const std::vector< double > &eigv, const std::vector< Value *> &vals, const std::vector< double > &arg, ReferenceValuePack &mypack) const
	Project the displacement of the arguments on a vector. More...

double	projectDisplacementOnVector (const Direction &mydir, const std::vector< Value *> &vals, const std::vector< double > &arg, ReferenceValuePack &mypack) const

void	read (const PDB &pdb)
	Do all local business for setting the configuration. More...

void	setReferenceArguments (const std::vector< double > &arg_vals, const std::vector< double > &sigma)
	Set the positions of the refernce arguments. More...

void	setupPCAStorage (ReferenceValuePack &mypack)
	Stuff to setup pca. More...

Protected Member Functions
void	error (const std::string &msg)
	Crash with an error. More...

void	readArgumentsFromPDB (const PDB &pdb)
	Read in the atoms from the pdb file. More...

void	setReferenceArguments ()
	Set the values of the colvars based on their current instantanous values (used in Analysis) More...

Protected Attributes
bool	hasmetric
	Are we calculating a Malanobius distance. More...

bool	hasweights
	Are we reading weights from input. More...

Constructor & Destructor Documentation

◆ MahalanobisDistance()

PLMD::MahalanobisDistance::MahalanobisDistance ( const ReferenceConfigurationOptions & ro )

explicit

Member Function Documentation

◆ calc()

double PLMD::ArgumentOnlyDistance::calc	(	const std::vector< Vector > &	pos,
		const Pbc &	pbc,
		const std::vector< Value *> &	vals,
		const std::vector< double > &	args,
		ReferenceValuePack &	myder,
		const bool &	squared
	)		const

virtualinherited

Calculate the distance from the reference configuration.

Implements PLMD::ReferenceConfiguration.

◆ calculate() [1/2]

double PLMD::ArgumentOnlyDistance::calculate	(	const std::vector< Value *> &	vals,
		ReferenceValuePack &	myder,
		const bool &	squared
	)		const

inherited

◆ calculate() [2/2]

double PLMD::ReferenceConfiguration::calculate	(	const std::vector< Vector > &	pos,
		const Pbc &	pbc,
		const std::vector< Value *> &	vals,
		ReferenceValuePack &	myder,
		const bool &	squared = `false`
	)		const

inherited

Calculate the distance from the reference configuration.

◆ calculateArgumentDistance()

double PLMD::ReferenceArguments::calculateArgumentDistance	(	const std::vector< Value *> &	vals,
		const std::vector< double > &	arg,
		ReferenceValuePack &	myder,
		const bool &	squared
	)		const

virtualinherited

Calculate the euclidean/malanobius distance the atoms have moved from the reference configuration in CV space.

Reimplemented in PLMD::DotProductDistance.

◆ copyDerivatives()

void PLMD::ReferenceConfiguration::copyDerivatives ( const ReferenceConfiguration * )

inherited

Parse something from the pdb remarks Copy derivatives from one frame to this frame.

◆ displaceReferenceArguments()

void PLMD::ReferenceArguments::displaceReferenceArguments	(	const double &	weight,
		const std::vector< double > &	displace
	)

inherited

Displace the positions of the reference atoms.

◆ displaceReferenceConfiguration()

void PLMD::ReferenceConfiguration::displaceReferenceConfiguration	(	const double &	weight,
		Direction &	dir
	)

inherited

Move the reference configuration by an ammount specified using a Direction.

◆ error()

void PLMD::ReferenceConfiguration::error ( const std::string & msg )

protectedinherited

Crash with an error.

◆ extractArgumentDisplacement()

void PLMD::ReferenceArguments::extractArgumentDisplacement	(	const std::vector< Value *> &	vals,
		const std::vector< double > &	arg,
		std::vector< double > &	dirout
	)		const

virtualinherited

Extract the displacement from a position in a space.

Reimplemented in PLMD::Direction.

◆ extractDisplacementVector()

void PLMD::ReferenceConfiguration::extractDisplacementVector	(	const std::vector< Vector > &	pos,
		const std::vector< Value *> &	vals,
		const std::vector< double > &	arg,
		const bool &	nflag,
		Direction &	mydir
	)		const

inherited

Extract a Direction giving you the displacement from some position.

◆ getAbsoluteIndexes()

const std::vector< AtomNumber > & PLMD::ReferenceConfiguration::getAbsoluteIndexes ( )

inlinevirtualinherited

These are overwritten in ReferenceArguments and ReferenceAtoms to make frame copying work.

Reimplemented in PLMD::ReferenceAtoms.

◆ getArgumentNames()

const std::vector< std::string > & PLMD::ReferenceArguments::getArgumentNames ( )

inlinevirtualinherited

Return names.

Reimplemented from PLMD::ReferenceConfiguration.

◆ getArgumentRequests()

void PLMD::ReferenceArguments::getArgumentRequests	(	std::vector< std::string > &	argout,
		bool	disable_checks = `false`
	)

virtualinherited

Get the arguments required.

Reimplemented from PLMD::ReferenceConfiguration.

◆ getAtomRequests()

virtual void PLMD::ReferenceConfiguration::getAtomRequests	(	std::vector< AtomNumber > &	,
		bool	disable_checks = `false`
	)

inlinevirtualinherited

Retrieve the atoms that are required for this guy.

Reimplemented in PLMD::ReferenceAtoms.

◆ getName()

std::string PLMD::ReferenceConfiguration::getName ( ) const

inherited

Return the name of this metric.

◆ getNumberOfReferenceArguments()

unsigned PLMD::ReferenceArguments::getNumberOfReferenceArguments ( ) const

inlinevirtualinherited

Get the number of reference arguments.

Reimplemented from PLMD::ReferenceConfiguration.

◆ getNumberOfReferencePositions()

unsigned PLMD::ReferenceConfiguration::getNumberOfReferencePositions ( ) const

inlinevirtualinherited

Reimplemented in PLMD::ReferenceAtoms.

◆ getReferenceArgument()

double PLMD::ReferenceArguments::getReferenceArgument ( const unsigned & i ) const

inlinevirtualinherited

Get the value of the ith reference argument.

Reimplemented from PLMD::ReferenceConfiguration.

◆ getReferenceArguments()

const std::vector< double > & PLMD::ReferenceArguments::getReferenceArguments ( ) const

inlinevirtualinherited

Return all the reference arguments.

Reimplemented from PLMD::ReferenceConfiguration.

◆ getReferenceMetric()

const std::vector< double > & PLMD::ReferenceArguments::getReferenceMetric ( )

virtualinherited

Reimplemented from PLMD::ReferenceConfiguration.

◆ getReferencePositions()

const std::vector< Vector > & PLMD::ReferenceConfiguration::getReferencePositions ( ) const

inlinevirtualinherited

These are overwritten in ReferenceArguments and ReferenceAtoms but are required here to make PLMD::distance work.

Reimplemented in PLMD::ReferenceAtoms.

◆ moveReferenceArguments()

void PLMD::ReferenceArguments::moveReferenceArguments ( const std::vector< double > & arg_vals )

inherited

Set the positions of the reference arguments.

◆ pcaIsEnabledForThisReference()

bool PLMD::ArgumentOnlyDistance::pcaIsEnabledForThisReference ( )

inlinevirtualinherited

Stuff for pca.

Reimplemented from PLMD::ReferenceConfiguration.

◆ projectArgDisplacementOnVector()

double PLMD::ReferenceArguments::projectArgDisplacementOnVector	(	const std::vector< double > &	eigv,
		const std::vector< Value *> &	vals,
		const std::vector< double > &	arg,
		ReferenceValuePack &	mypack
	)		const

inherited

Project the displacement of the arguments on a vector.

◆ projectDisplacementOnVector()

double PLMD::ReferenceConfiguration::projectDisplacementOnVector	(	const Direction &	mydir,
		const std::vector< Value *> &	vals,
		const std::vector< double > &	arg,
		ReferenceValuePack &	mypack
	)		const

inherited

◆ read()

void PLMD::ArgumentOnlyDistance::read ( const PDB & )

virtualinherited

Do all local business for setting the configuration.

Implements PLMD::ReferenceConfiguration.

Reimplemented in PLMD::DotProductDistance.

◆ readArgumentsFromPDB()

void PLMD::ReferenceArguments::readArgumentsFromPDB ( const PDB & pdb )

protectedinherited

Read in the atoms from the pdb file.

◆ setReferenceArguments() [1/2]

void PLMD::ReferenceArguments::setReferenceArguments ( )

protectedinherited

Set the values of the colvars based on their current instantanous values (used in Analysis)

◆ setReferenceArguments() [2/2]

void PLMD::ReferenceArguments::setReferenceArguments	(	const std::vector< double > &	arg_vals,
		const std::vector< double > &	sigma
	)

inherited

Set the positions of the refernce arguments.

◆ setupPCAStorage()

void PLMD::ArgumentOnlyDistance::setupPCAStorage ( ReferenceValuePack & mypack )

inlinevirtualinherited

Stuff to setup pca.

Reimplemented from PLMD::ReferenceConfiguration.

Member Data Documentation

◆ hasmetric

bool PLMD::ReferenceArguments::hasmetric

protectedinherited

Are we calculating a Malanobius distance.

◆ hasweights

bool PLMD::ReferenceArguments::hasweights

protectedinherited

Are we reading weights from input.

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

reference/MahalanobisDistance.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Constructor & Destructor Documentation

◆ MahalanobisDistance()

Member Function Documentation

◆ calc()

◆ calculate() [1/2]

◆ calculate() [2/2]

◆ calculateArgumentDistance()

◆ copyDerivatives()

◆ displaceReferenceArguments()

◆ displaceReferenceConfiguration()

◆ error()

◆ extractArgumentDisplacement()

◆ extractDisplacementVector()

◆ getAbsoluteIndexes()

◆ getArgumentNames()

◆ getArgumentRequests()

◆ getAtomRequests()

◆ getName()

◆ getNumberOfReferenceArguments()

◆ getNumberOfReferencePositions()

◆ getReferenceArgument()

◆ getReferenceArguments()

◆ getReferenceMetric()

◆ getReferencePositions()

◆ moveReferenceArguments()

◆ pcaIsEnabledForThisReference()

◆ projectArgDisplacementOnVector()

◆ projectDisplacementOnVector()

◆ read()

◆ readArgumentsFromPDB()

◆ setReferenceArguments() [1/2]

◆ setReferenceArguments() [2/2]

◆ setupPCAStorage()

Member Data Documentation

◆ hasmetric

◆ hasweights