#include <Direction.h>

Inheritance diagram for PLMD::Direction:

Public Member Functions
	Direction (const ReferenceConfigurationOptions &ro)

void	addDirection (const double &weight, const Direction &dir)

double	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
	Calculate the distance from the reference configuration. More...

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	displaceReferenceAtoms (const double &weight, const std::vector< Vector > &dir)
	Displace the positions of the reference atoms a bit. More...

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

void	extractArgumentDisplacement (const std::vector< Value *> &vals, const std::vector< double > &arg, std::vector< double > &dirout) const
	This allows us to extract the reference positions, which are the direction in this case. More...

void	extractAtomicDisplacement (const std::vector< Vector > &pos, std::vector< Vector > &dirout) const
	Extract a displacement from a position in 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...

const std::vector< AtomNumber > &	getAbsoluteIndexes ()
	Return all atom indexes. More...

const std::vector< double > &	getAlign () const
	Get the vector of alignment weights. More...

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

virtual const std::vector< std::string > &	getArgumentNames ()

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

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

unsigned	getAtomIndex (const unsigned &) const
	This allows us to use a single pos array with RMSD objects using different atom indexes. More...

virtual void	getAtomRequests (std::vector< AtomNumber > &, bool disable_checks=false)
	Get the atoms required (additional checks are required when we have multiple domains) More...

const std::vector< double > &	getDisplace () const
	Get the vector of displacement weights. More...

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

unsigned	getNumberOfAtoms () const
	This returns how many atoms there should be. More...

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

virtual unsigned	getNumberOfReferenceArguments () const

unsigned	getNumberOfReferencePositions () const
	This returns the number of reference atom positions. More...

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

virtual double	getReferenceArgument (const unsigned &i) const
	Get one of the referene arguments. More...

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

virtual const std::vector< double > &	getReferenceArguments () const

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

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

const std::vector< Vector > &	getReferencePositions () const
	Get the reference positions. More...

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

virtual 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...

virtual double	projectAtomicDisplacementOnVector (const bool &normalized, const std::vector< Vector > &eigv, ReferenceValuePack &mypack) const
	Project the displacement 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 &)
	Do all local business for setting the configuration. More...

void	setDirection (const std::vector< Vector > &conf, const std::vector< double > &args)

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

void	setReferenceAtoms (const std::vector< Vector > &conf, const std::vector< double > &align_in, const std::vector< double > &displace_in)
	Set the positions of the reference atoms. More...

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

void	zeroDirection ()

Public Attributes
bool	normalized

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

Vector	getReferencePosition (const unsigned &iatom) const
	Get the position of the ith atom. More...

bool	parseAtomList (const std::string &, std::vector< unsigned > &)
	Read a list of atoms from the pdb input file. More...

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

void	readAtomsFromPDB (const PDB &, const bool allowblocks=false)
	Read in the atoms from the pdb file. More...

void	setAtomIndices (const std::vector< AtomNumber > &atomnumbers)
	Add atom indices to list. More...

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

void	singleDomainRequests (std::vector< AtomNumber > &, bool disable_checks)
	Add derivatives to iatom th atom in list. More...

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

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

Constructor & Destructor Documentation

◆ Direction()

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

explicit

Member Function Documentation

◆ addDirection()

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

◆ calc()

double PLMD::Direction::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

virtual

Calculate the distance from the reference configuration.

Implements PLMD::ReferenceConfiguration.

◆ calculate()

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.

◆ displaceReferenceAtoms()

void PLMD::ReferenceAtoms::displaceReferenceAtoms	(	const double &	weight,
		const std::vector< Vector > &	dir
	)

inherited

Displace the positions of the reference atoms a bit.

◆ 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::Direction::extractArgumentDisplacement	(	const std::vector< Value *> &	vals,
		const std::vector< double > &	arg,
		std::vector< double > &	dirout
	)		const

virtual

This allows us to extract the reference positions, which are the direction in this case.

Reimplemented from PLMD::ReferenceArguments.

◆ extractAtomicDisplacement()

void PLMD::Direction::extractAtomicDisplacement	(	const std::vector< Vector > &	pos,
		std::vector< Vector > &	direction
	)		const

virtual

Extract a displacement from a position in space.

Reimplemented from PLMD::ReferenceAtoms.

◆ 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::ReferenceAtoms::getAbsoluteIndexes ( )

inlinevirtualinherited

Return all atom indexes.

Reimplemented from PLMD::ReferenceConfiguration.

◆ getAlign()

const std::vector< double > & PLMD::ReferenceAtoms::getAlign ( ) const

inlineinherited

Get the vector of alignment weights.

◆ getArgumentNames() [1/2]

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

inlinevirtualinherited

Return names.

Reimplemented from PLMD::ReferenceConfiguration.

◆ getArgumentNames() [2/2]

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

inlinevirtualinherited

Reimplemented in PLMD::ReferenceArguments.

◆ getArgumentRequests() [1/2]

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

virtualinherited

Get the arguments required.

Reimplemented from PLMD::ReferenceConfiguration.

◆ getArgumentRequests() [2/2]

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

inlinevirtualinherited

Retrieve the arguments that are required for this guy.

Reimplemented in PLMD::ReferenceArguments.

◆ getAtomIndex()

unsigned PLMD::ReferenceAtoms::getAtomIndex ( const unsigned & iatom ) const

inlineinherited

This allows us to use a single pos array with RMSD objects using different atom indexes.

◆ getAtomRequests()

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

virtualinherited

Get the atoms required (additional checks are required when we have multiple domains)

Reimplemented from PLMD::ReferenceConfiguration.

◆ getDisplace()

const std::vector< double > & PLMD::ReferenceAtoms::getDisplace ( ) const

inlineinherited

Get the vector of displacement weights.

◆ getName()

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

inherited

Return the name of this metric.

◆ getNumberOfAtoms()

unsigned PLMD::ReferenceAtoms::getNumberOfAtoms ( ) const

inlineinherited

This returns how many atoms there should be.

◆ getNumberOfReferenceArguments() [1/2]

unsigned PLMD::ReferenceArguments::getNumberOfReferenceArguments ( ) const

inlinevirtualinherited

Get the number of reference arguments.

Reimplemented from PLMD::ReferenceConfiguration.

◆ getNumberOfReferenceArguments() [2/2]

unsigned PLMD::ReferenceConfiguration::getNumberOfReferenceArguments ( ) const

inlinevirtualinherited

Reimplemented in PLMD::ReferenceArguments.

◆ getNumberOfReferencePositions()

unsigned PLMD::ReferenceAtoms::getNumberOfReferencePositions ( ) const

inlinevirtualinherited

This returns the number of reference atom positions.

Reimplemented from PLMD::ReferenceConfiguration.

◆ getReferenceArgument() [1/2]

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

inlinevirtualinherited

Get the value of the ith reference argument.

Reimplemented from PLMD::ReferenceConfiguration.

◆ getReferenceArgument() [2/2]

virtual double PLMD::ReferenceConfiguration::getReferenceArgument ( const unsigned & i ) const

inlinevirtualinherited

Get one of the referene arguments.

Reimplemented in PLMD::ReferenceArguments.

◆ getReferenceArguments() [1/2]

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

inlinevirtualinherited

Return all the reference arguments.

Reimplemented from PLMD::ReferenceConfiguration.

◆ getReferenceArguments() [2/2]

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

inlinevirtualinherited

Reimplemented in PLMD::ReferenceArguments.

◆ getReferenceMetric() [1/2]

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

virtualinherited

Reimplemented from PLMD::ReferenceConfiguration.

◆ getReferenceMetric() [2/2]

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

inlinevirtualinherited

Reimplemented in PLMD::ReferenceArguments.

◆ getReferencePosition()

Vector PLMD::ReferenceAtoms::getReferencePosition ( const unsigned & iatom ) const

inlineprotectedinherited

Get the position of the ith atom.

◆ getReferencePositions()

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

inlinevirtualinherited

Get the reference positions.

Reimplemented from PLMD::ReferenceConfiguration.

◆ moveReferenceArguments()

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

inherited

Set the positions of the reference arguments.

◆ parseAtomList()

bool PLMD::ReferenceAtoms::parseAtomList	(	const std::string &	,
		std::vector< unsigned > &
	)

protectedinherited

Read a list of atoms from the pdb input file.

◆ pcaIsEnabledForThisReference()

virtual bool PLMD::ReferenceConfiguration::pcaIsEnabledForThisReference ( )

inlinevirtualinherited

Stuff for pca.

Reimplemented in PLMD::MultiDomainRMSD, PLMD::ArgumentOnlyDistance, PLMD::OptimalRMSD, and PLMD::SimpleRMSD.

◆ 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.

◆ projectAtomicDisplacementOnVector()

virtual double PLMD::ReferenceAtoms::projectAtomicDisplacementOnVector	(	const bool &	normalized,
		const std::vector< Vector > &	eigv,
		ReferenceValuePack &	mypack
	)		const

inlinevirtualinherited

Project the displacement on a vector.

Reimplemented in PLMD::MultiDomainRMSD, PLMD::OptimalRMSD, and PLMD::SimpleRMSD.

◆ 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::Direction::read ( const PDB & )

virtual

Do all local business for setting the configuration.

Implements PLMD::ReferenceConfiguration.

◆ readArgumentsFromPDB()

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

protectedinherited

Read in the atoms from the pdb file.

◆ readAtomsFromPDB()

void PLMD::ReferenceAtoms::readAtomsFromPDB	(	const PDB &	pdb,
		const bool	allowblocks = `false`
	)

protectedinherited

Read in the atoms from the pdb file.

◆ setAtomIndices()

void PLMD::ReferenceAtoms::setAtomIndices ( const std::vector< AtomNumber > & atomnumbers )

protectedinherited

Add atom indices to list.

◆ setDirection()

void PLMD::Direction::setDirection	(	const std::vector< Vector > &	conf,
		const std::vector< double > &	args
	)

◆ 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.

◆ setReferenceAtoms()

void PLMD::Direction::setReferenceAtoms	(	const std::vector< Vector > &	conf,
		const std::vector< double > &	align_in,
		const std::vector< double > &	displace_in
	)

inlinevirtual

Set the positions of the reference atoms.

Implements PLMD::ReferenceAtoms.

◆ setupPCAStorage()

virtual void PLMD::ReferenceConfiguration::setupPCAStorage ( ReferenceValuePack & mypack )

inlinevirtualinherited

Stuff to setup pca.

Reimplemented in PLMD::MultiDomainRMSD, PLMD::ArgumentOnlyDistance, PLMD::OptimalRMSD, and PLMD::SimpleRMSD.

◆ singleDomainRequests()

void PLMD::ReferenceAtoms::singleDomainRequests	(	std::vector< AtomNumber > &	numbers,
		bool	disable_checks
	)

protectedinherited

Add derivatives to iatom th atom in list.

Get the atomic derivatives on the ith atom in the list Add derivatives to the viral This does the checks that are always required

◆ zeroDirection()

void PLMD::Direction::zeroDirection ( )

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.

◆ normalized

bool PLMD::Direction::normalized

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

reference/Direction.h
reference/Direction.cpp

Public Member Functions

Public Attributes

Protected Member Functions

Protected Attributes

Constructor & Destructor Documentation

◆ Direction()

Member Function Documentation

◆ addDirection()

◆ calc()

◆ calculate()

◆ calculateArgumentDistance()

◆ copyDerivatives()

◆ displaceReferenceArguments()

◆ displaceReferenceAtoms()

◆ displaceReferenceConfiguration()

◆ error()

◆ extractArgumentDisplacement()

◆ extractAtomicDisplacement()

◆ extractDisplacementVector()

◆ getAbsoluteIndexes()

◆ getAlign()

◆ getArgumentNames() [1/2]

◆ getArgumentNames() [2/2]

◆ getArgumentRequests() [1/2]

◆ getArgumentRequests() [2/2]

◆ getAtomIndex()

◆ getAtomRequests()

◆ getDisplace()

◆ getName()

◆ getNumberOfAtoms()

◆ getNumberOfReferenceArguments() [1/2]

◆ getNumberOfReferenceArguments() [2/2]

◆ getNumberOfReferencePositions()

◆ getReferenceArgument() [1/2]

◆ getReferenceArgument() [2/2]

◆ getReferenceArguments() [1/2]

◆ getReferenceArguments() [2/2]

◆ getReferenceMetric() [1/2]

◆ getReferenceMetric() [2/2]

◆ getReferencePosition()

◆ getReferencePositions()

◆ moveReferenceArguments()

◆ parseAtomList()

◆ pcaIsEnabledForThisReference()

◆ projectArgDisplacementOnVector()

◆ projectAtomicDisplacementOnVector()

◆ projectDisplacementOnVector()

◆ read()

◆ readArgumentsFromPDB()

◆ readAtomsFromPDB()

◆ setAtomIndices()

◆ setDirection()

◆ setReferenceArguments() [1/2]

◆ setReferenceArguments() [2/2]

◆ setReferenceAtoms()

◆ setupPCAStorage()

◆ singleDomainRequests()

◆ zeroDirection()

Member Data Documentation

◆ hasmetric

◆ hasweights

◆ normalized