Inheritance diagram for PLMD::Direction:

Public Member Functions
	Direction (const ReferenceConfigurationOptions &ro)

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

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...

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...

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

void	setAtomNumbers (const std::vector< AtomNumber > &numbers)
	Set the indices of the reference atoms. More...

void	printAtoms (OFile &ofile, const double &lunits) const
	Print the atomic positions. More...

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

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

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

virtual unsigned	getNumberOfReferenceArguments () const

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

virtual void	set (const PDB &)
	Set the final number of arguments. More...

void	setWeight (const double &ww)
	Set the weight for this frame. More...

double	getWeight () const
	Return the weight for this frame. 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...

template<class T >
bool	parse (const std::string &key, T &t, bool ignore_missing=false)
	Return the derivatives of the distance wrt the cell vectors. More...

template<class T >
bool	parseVector (const std::string &key, std::vector< T > &t, bool ignore_missing=false)
	Parse vector from the pdb remarks. More...

void	parseFlag (const std::string &key, bool &t)
	Parse a flag. More...

void	checkRead ()
	Check that all the remarks in the pdb have been read in. More...

void	copyDerivatives (const ReferenceConfiguration *)
	Copy derivatives from one frame to this frame. More...

void	setNamesAndAtomNumbers (const std::vector< AtomNumber > &numbers, const std::vector< std::string > &arg)
	Set the atom numbers and the argument names. More...

void	setReferenceConfig (const std::vector< Vector > &pos, const std::vector< double > &arg, const std::vector< double > &metric)
	Set the reference structure (perhaps should also pass the pbc and align and displace ) More...

void	print (OFile &ofile, const double &time, const double &weight, const double &lunits, const double &old_norm)
	Print a pdb file containing the reference configuration. More...

void	print (OFile &ofile, const std::string &fmt, const double &lunits)

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

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

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

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

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

virtual double	projectAtomicDisplacementOnVector (const unsigned &i, const Matrix< Vector > &eigv, const std::vector< Vector > &pos, ReferenceValuePack &mypack) const

bool	isDirection () const
	Stuff for sanity checks on distance. More...

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

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

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

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

void	setArgumentNames (const std::vector< std::string > &arg_vals)
	Set the names of the arguments. More...

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

void	printArguments (OFile &ofile, const std::string &fmt) const
	Print the arguments out. More...

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

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

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

Protected Member Functions
void	readAtomsFromPDB (const PDB &)
	Read in the atoms from the pdb file. More...

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

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

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

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

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

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

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

void	error (const std::string &msg)
	Derivatives wrt to the arguments. 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	hasweights
	Are we reading weights from input. More...

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

Constructor & Destructor Documentation

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

explicit

Member Function Documentation

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.

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.

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.

void PLMD::ReferenceConfiguration::checkRead ( )

inherited

Check that all the remarks in the pdb have been read in.

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

inherited

Copy derivatives from one frame to this frame.

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

protectedinherited

Derivatives wrt to the arguments.

The virial contribution has to be stored Derivatives wrt to the atoms Crash with an error

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

inlinevirtualinherited

Return all atom indexes.

Reimplemented from PLMD::ReferenceConfiguration.

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

inlineprotectedinherited

Get the vector of alignment weights.

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

inlinevirtualinherited

Return names.

Reimplemented from PLMD::ReferenceConfiguration.

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

inlinevirtualinherited

Reimplemented in PLMD::ReferenceArguments.

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

virtualinherited

Get the arguments required.

Reimplemented from PLMD::ReferenceConfiguration.

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.

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.

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.

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

inlineprotectedinherited

Get the vector of displacement weights.

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

inherited

Return the name of this metric.

unsigned PLMD::ReferenceAtoms::getNumberOfAtoms ( ) const

inlineinherited

This returns how many atoms there should be.

unsigned PLMD::ReferenceArguments::getNumberOfReferenceArguments ( ) const

inlinevirtualinherited

Get the number of reference arguments.

Reimplemented from PLMD::ReferenceConfiguration.

unsigned PLMD::ReferenceConfiguration::getNumberOfReferenceArguments ( ) const

inlinevirtualinherited

Reimplemented in PLMD::ReferenceArguments.

unsigned PLMD::ReferenceAtoms::getNumberOfReferencePositions ( ) const

inlinevirtualinherited

This returns the number of reference atom positions.

Reimplemented from PLMD::ReferenceConfiguration.

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

inlinevirtualinherited

Get the value of the ith reference argument.

Reimplemented from PLMD::ReferenceConfiguration.

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

inlinevirtualinherited

Get one of the referene arguments.

Reimplemented in PLMD::ReferenceArguments.

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

inlinevirtualinherited

Return all the reference arguments.

Reimplemented from PLMD::ReferenceConfiguration.

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

inlinevirtualinherited

Reimplemented in PLMD::ReferenceArguments.

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

virtualinherited

Reimplemented from PLMD::ReferenceConfiguration.

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

inlinevirtualinherited

Reimplemented in PLMD::ReferenceArguments.

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

inlineprotectedinherited

Get the position of the ith atom.

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

inlineprotectedvirtualinherited

Get the reference positions.

Reimplemented from PLMD::ReferenceConfiguration.

double PLMD::ReferenceConfiguration::getWeight ( ) const

inlineinherited

Return the weight for this frame.

bool PLMD::ReferenceConfiguration::isDirection ( ) const

inherited

Stuff for sanity checks on distance.

template<class T >

bool PLMD::ReferenceConfiguration::parse	(	const std::string &	key,
		T &	t,
		bool	ignore_missing = `false`
	)

inherited

Return the derivatives of the distance wrt the cell vectors.

This returns false for everything other than DRMSD as these sort of calculations have to be done separately when you use RMSD Parse something from the pdb remarks

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

protectedinherited

Read a list of atoms from the pdb input file.

void PLMD::ReferenceConfiguration::parseFlag	(	const std::string &	key,
		bool &	t
	)

inherited

Parse a flag.

template<class T >

bool PLMD::ReferenceConfiguration::parseVector	(	const std::string &	key,
		std::vector< T > &	t,
		bool	ignore_missing = `false`
	)

inherited

Parse vector from the pdb remarks.

virtual bool PLMD::ReferenceConfiguration::pcaIsEnabledForThisReference ( )

inlinevirtualinherited

Stuff for pca.

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

void PLMD::ReferenceConfiguration::print	(	OFile &	ofile,
		const double &	time,
		const double &	weight,
		const double &	lunits,
		const double &	old_norm
	)

inherited

Print a pdb file containing the reference configuration.

void PLMD::ReferenceConfiguration::print	(	OFile &	ofile,
		const std::string &	fmt,
		const double &	lunits
	)

inherited

void PLMD::ReferenceArguments::printArguments	(	OFile &	ofile,
		const std::string &	fmt
	)		const

inherited

Print the arguments out.

void PLMD::ReferenceAtoms::printAtoms	(	OFile &	ofile,
		const double &	lunits
	)		const

inherited

Print the atomic positions.

virtual double PLMD::ReferenceConfiguration::projectAtomicDisplacementOnVector	(	const unsigned &	i,
		const Matrix< Vector > &	eigv,
		const std::vector< Vector > &	pos,
		ReferenceValuePack &	mypack
	)		const

inlinevirtualinherited

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

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

virtual

Do all local business for setting the configuration.

Implements PLMD::ReferenceConfiguration.

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

protectedinherited

Read in the atoms from the pdb file.

void PLMD::ReferenceAtoms::readAtomsFromPDB ( const PDB & pdb )

protectedinherited

Read in the atoms from the pdb file.

void PLMD::ReferenceConfiguration::set ( const PDB & pdb )

virtualinherited

Set the final number of arguments.

Set the final number of atoms Set the reference configuration using a PDB

void PLMD::ReferenceArguments::setArgumentNames ( const std::vector< std::string > & arg_vals )

inherited

Set the names of the arguments.

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

protectedinherited

Add atom indices to list.

void PLMD::ReferenceAtoms::setAtomNumbers ( const std::vector< AtomNumber > & numbers )

inherited

Set the indices of the reference atoms.

void PLMD::ReferenceConfiguration::setNamesAndAtomNumbers	(	const std::vector< AtomNumber > &	numbers,
		const std::vector< std::string > &	arg
	)

inherited

Set the atom numbers and the argument names.

void PLMD::ReferenceArguments::setReferenceArguments ( )

protectedinherited

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

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

inherited

Set the positions of the refernce arguments.

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.

void PLMD::ReferenceConfiguration::setReferenceConfig	(	const std::vector< Vector > &	pos,
		const std::vector< double > &	arg,
		const std::vector< double > &	metric
	)

inherited

Set the reference structure (perhaps should also pass the pbc and align and displace )

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

inlinevirtualinherited

Stuff to setup pca.

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

void PLMD::ReferenceConfiguration::setWeight ( const double & ww )

inlineinherited

Set the weight for this frame.

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

Member Data Documentation

bool PLMD::ReferenceArguments::hasmetric

protectedinherited

Are we calculating a Malanobius distance.

bool PLMD::ReferenceArguments::hasweights

protectedinherited

Are we reading weights from input.

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

reference/Direction.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation