Abstract base class for calculating the distance from a reference configuration. More...

#include <ReferenceConfiguration.h>

Inheritance diagram for PLMD::ReferenceConfiguration:

[legend]

Public Member Functions
	ReferenceConfiguration (const ReferenceConfigurationOptions &ro)
	Clear the derivatives. More...

virtual	~ReferenceConfiguration ()
	Destructor. More...

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

virtual unsigned	getNumberOfReferencePositions () const

virtual unsigned	getNumberOfReferenceArguments () const

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

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...

virtual void	read (const PDB &)=0
	Do all local business for setting the configuration. 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...

virtual 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 =0
	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< Vector > &	getReferencePositions () const
	These are overwritten in ReferenceArguments and ReferenceAtoms but are required here to make PLMD::distance work. More...

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

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

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

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

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

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

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

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

Protected Member Functions
void	error (const std::string &msg)
	Derivatives wrt to the arguments. More...

Private Attributes
std::string	name
	The name of this particular config. More...

double	weight
	A weight assigned to this particular frame. More...

std::vector< std::string >	line
	A vector containing all the remarks from the pdb input. More...

std::vector< AtomNumber >	fake_atom_numbers
	This is used to store the values of arguments. More...

std::vector< std::string >	fake_arg_names

std::vector< Vector >	fake_refatoms
	These are use by the distance function above. More...

std::vector< double >	fake_refargs

std::vector< double >	fake_metric

Friends
class	SingleDomainRMSD

double	distance (const Pbc &pbc, const std::vector< Value > &vals, ReferenceConfiguration , ReferenceConfiguration *, const bool &squared)

Detailed Description

Abstract base class for calculating the distance from a reference configuration.

A reference configuration can either have a particular set of atoms in a particular given configuration or it can be that a particular set of colvars have a particular set of values. It could also be a combination of both. To allow all the posible permutations and in order make it easy to add new ways of calculating the distance we have implemented this using polymorphism and multiple inheritance. The following provides information on how to implement a new method for calculating the distance between a pair of configurations

Constructor & Destructor Documentation

◆ ReferenceConfiguration()

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

explicit

Clear the derivatives.

◆ ~ReferenceConfiguration()

PLMD::ReferenceConfiguration::~ReferenceConfiguration ( )

virtual

Destructor.

Member Function Documentation

◆ calc()

virtual double PLMD::ReferenceConfiguration::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

pure virtual

Calculate the distance from the reference configuration.

Implemented in PLMD::MultiDomainRMSD, PLMD::ArgumentOnlyDistance, PLMD::SingleDomainRMSD, PLMD::Direction, and PLMD::FakeFrame.

◆ 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

Calculate the distance from the reference configuration.

◆ checkRead()

void PLMD::ReferenceConfiguration::checkRead ( )

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

◆ copyDerivatives()

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

Copy derivatives from one frame to this frame.

◆ displaceReferenceConfiguration()

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

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

◆ error()

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

protected

Derivatives wrt to the arguments.

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

◆ 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

Extract a Direction giving you the displacement from some position.

◆ getAbsoluteIndexes()

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

inlinevirtual

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

Reimplemented in PLMD::ReferenceAtoms.

◆ getArgumentNames()

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

inlinevirtual

Reimplemented in PLMD::ReferenceArguments.

◆ getArgumentRequests()

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

inlinevirtual

Retrieve the arguments that are required for this guy.

Reimplemented in PLMD::ReferenceArguments.

◆ getAtomRequests()

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

inlinevirtual

Retrieve the atoms that are required for this guy.

Reimplemented in PLMD::ReferenceAtoms.

◆ getName()

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

Return the name of this metric.

◆ getNumberOfReferenceArguments()

unsigned PLMD::ReferenceConfiguration::getNumberOfReferenceArguments ( ) const

inlinevirtual

Reimplemented in PLMD::ReferenceArguments.

◆ getNumberOfReferencePositions()

unsigned PLMD::ReferenceConfiguration::getNumberOfReferencePositions ( ) const

inlinevirtual

Reimplemented in PLMD::ReferenceAtoms.

◆ getReferenceArgument()

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

inlinevirtual

Get one of the referene arguments.

Reimplemented in PLMD::ReferenceArguments.

◆ getReferenceArguments()

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

inlinevirtual

Reimplemented in PLMD::ReferenceArguments.

◆ getReferenceMetric()

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

inlinevirtual

Reimplemented in PLMD::ReferenceArguments.

◆ getReferencePositions()

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

inlinevirtual

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

Reimplemented in PLMD::ReferenceAtoms.

◆ getWeight()

double PLMD::ReferenceConfiguration::getWeight ( ) const

inline

Return the weight for this frame.

◆ parse()

template<class T >

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

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

◆ parseFlag()

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

Parse a flag.

◆ parseVector()

template<class T >

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

Parse vector from the pdb remarks.

◆ pcaIsEnabledForThisReference()

virtual bool PLMD::ReferenceConfiguration::pcaIsEnabledForThisReference ( )

inlinevirtual

Stuff for pca.

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

◆ print() [1/2]

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

Print a pdb file containing the reference configuration.

◆ print() [2/2]

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

◆ projectDisplacementOnVector()

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

◆ read()

virtual void PLMD::ReferenceConfiguration::read ( const PDB & )

pure virtual

Do all local business for setting the configuration.

Implemented in PLMD::DRMSD, PLMD::MultiDomainRMSD, PLMD::ArgumentOnlyDistance, PLMD::Direction, PLMD::OptimalRMSD, PLMD::FakeFrame, PLMD::IntermolecularDRMSD, PLMD::IntramolecularDRMSD, PLMD::SimpleRMSD, and PLMD::DotProductDistance.

◆ set()

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

virtual

Set the final number of arguments.

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

◆ setNamesAndAtomNumbers()

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

Set the atom numbers and the argument names.

◆ setReferenceConfig()

void PLMD::ReferenceConfiguration::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 )

◆ setupPCAStorage()

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

inlinevirtual

Stuff to setup pca.

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

◆ setWeight()

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

inline

Set the weight for this frame.

Friends And Related Function Documentation

◆ distance

double distance	(	const Pbc &	pbc,
		const std::vector< Value *> &	vals,
		ReferenceConfiguration *	ref1,
		ReferenceConfiguration *	ref2,
		const bool &	squared
	)

friend

◆ SingleDomainRMSD

friend class SingleDomainRMSD

friend

Member Data Documentation

◆ fake_arg_names

std::vector<std::string> PLMD::ReferenceConfiguration::fake_arg_names

private

◆ fake_atom_numbers

std::vector<AtomNumber> PLMD::ReferenceConfiguration::fake_atom_numbers

private

This is used to store the values of arguments.

These are used to do fake things when we copy frames

◆ fake_metric

std::vector<double> PLMD::ReferenceConfiguration::fake_metric

private

◆ fake_refargs

std::vector<double> PLMD::ReferenceConfiguration::fake_refargs

private

◆ fake_refatoms

std::vector<Vector> PLMD::ReferenceConfiguration::fake_refatoms

private

These are use by the distance function above.

◆ line

std::vector<std::string> PLMD::ReferenceConfiguration::line

private

A vector containing all the remarks from the pdb input.

◆ name

std::string PLMD::ReferenceConfiguration::name

private

The name of this particular config.

◆ weight

double PLMD::ReferenceConfiguration::weight

private

A weight assigned to this particular frame.

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

reference/ReferenceConfiguration.h
reference/ReferenceConfiguration.cpp

Public Member Functions

Protected Member Functions

Private Attributes

Friends

Detailed Description

Constructor & Destructor Documentation

◆ ReferenceConfiguration()

◆ ~ReferenceConfiguration()

Member Function Documentation

◆ calc()

◆ calculate()

◆ checkRead()

◆ copyDerivatives()

◆ displaceReferenceConfiguration()

◆ error()

◆ extractDisplacementVector()

◆ getAbsoluteIndexes()

◆ getArgumentNames()

◆ getArgumentRequests()

◆ getAtomRequests()

◆ getName()

◆ getNumberOfReferenceArguments()

◆ getNumberOfReferencePositions()

◆ getReferenceArgument()

◆ getReferenceArguments()

◆ getReferenceMetric()

◆ getReferencePositions()

◆ getWeight()

◆ parse()

◆ parseFlag()

◆ parseVector()

◆ pcaIsEnabledForThisReference()

◆ print() [1/2]

◆ print() [2/2]

◆ projectDisplacementOnVector()

◆ read()

◆ set()

◆ setNamesAndAtomNumbers()

◆ setReferenceConfig()

◆ setupPCAStorage()

◆ setWeight()

Friends And Related Function Documentation

◆ distance

◆ SingleDomainRMSD

Member Data Documentation

◆ fake_arg_names

◆ fake_atom_numbers

◆ fake_metric

◆ fake_refargs

◆ fake_refatoms

◆ line

◆ name

◆ weight