#include <ReferenceConfiguration.h>

Inheritance diagram for PLMD::ReferenceConfiguration:

Public Member Functions
	ReferenceConfiguration (const ReferenceConfigurationOptions &ro)

virtual	~ReferenceConfiguration ()
	Destructor. More...

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

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	setNumberOfArguments (const unsigned &)
	Set the final number of arguments. More...

virtual void	setNumberOfAtoms (const unsigned &)
	Set the final number of atoms. More...

virtual void	set (const PDB &)
	Set the reference configuration using a PDB. 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, const bool &squared=false)
	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, const bool &squared)=0
	Calculate the distance from the reference configuration. More...

Vector	getAtomDerivative (const unsigned &) const
	Return the derivative wrt to the ith atom. More...

double	getArgumentDerivative (const unsigned &) const
	Return the derivative wrt to the ith argument. More...

bool	getVirial (Tensor &virout) const
	Return the derivatives of the distance wrt the cell vectors. More...

template<class T >
bool	parse (const std::string &key, T &t, bool ignore_missing=false)
	Parse something from the pdb remarks. 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 &old_norm)
	Print a pdb file containing the reference configuration. More...

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

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

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

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

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 ()

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

void	clearDerivatives ()
	Clear the derivatives. More...

Protected Attributes
std::vector< double >	arg_ders
	Derivatives wrt to the arguments. More...

bool	virialWasSet
	The virial contribution has to be stored. More...

Tensor	virial

std::vector< Vector >	atom_ders
	Derivatives wrt to the atoms. 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< double >	tmparg
	This is used to store the values of arguments. More...

std::vector< AtomNumber >	fake_atom_numbers
	These are used to do fake things when we copy frames. 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)

Constructor & Destructor Documentation

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

PLMD::ReferenceConfiguration::~ReferenceConfiguration ( )

virtual

Destructor.

Member Function Documentation

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

pure virtual

Calculate the distance from the reference configuration.

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

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

Calculate the distance from the reference configuration.

void PLMD::ReferenceConfiguration::checkRead ( )

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

void PLMD::ReferenceConfiguration::clearDerivatives ( )

protected

Clear the derivatives.

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

Copy derivatives from one frame to this frame.

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

protected

Crash with an error.

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

inlinevirtual

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

Reimplemented in PLMD::ReferenceAtoms.

double PLMD::ReferenceConfiguration::getArgumentDerivative ( const unsigned & ider ) const

inline

Return the derivative wrt to the ith argument.

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

inlinevirtual

Reimplemented in PLMD::ReferenceArguments.

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.

Vector PLMD::ReferenceConfiguration::getAtomDerivative ( const unsigned & ider ) const

inline

Return the derivative wrt to the ith atom.

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.

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

Return the name of this metric.

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

inlinevirtual

Get one of the referene arguments.

Reimplemented in PLMD::ReferenceArguments.

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

inlinevirtual

Reimplemented in PLMD::ReferenceArguments.

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

inlinevirtual

Reimplemented in PLMD::ReferenceArguments.

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

inlinevirtual

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

Reimplemented in PLMD::ReferenceAtoms.

bool PLMD::ReferenceConfiguration::getVirial ( Tensor & virout ) const

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

double PLMD::ReferenceConfiguration::getWeight ( ) const

inline

Return the weight for this frame.

template<class T >

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

Parse something from the pdb remarks.

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

Parse a flag.

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.

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

Print a pdb file containing the reference configuration.

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

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

pure virtual

Do all local business for setting the configuration.

Implemented in PLMD::DRMSD, PLMD::MultiDomainRMSD, PLMD::SimpleRMSD, PLMD::OptimalRMSD, PLMD::FakeFrame, PLMD::SimpleRMSD, PLMD::EuclideanDistance, and PLMD::NormalizedEuclideanDistance.

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

virtual

Set the reference configuration using a PDB.

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

Set the atom numbers and the argument names.

void PLMD::ReferenceConfiguration::setNumberOfArguments ( const unsigned & n )

virtual

Set the final number of arguments.

void PLMD::ReferenceConfiguration::setNumberOfAtoms ( const unsigned & n )

virtual

Set the final number of atoms.

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 )

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

inline

Set the weight for this frame.

Friends And Related Function Documentation

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

friend

friend class SingleDomainRMSD

friend

Member Data Documentation

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

protected

Derivatives wrt to the arguments.

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

protected

Derivatives wrt to the atoms.

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

private

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

private

These are used to do fake things when we copy frames.

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

private

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

private

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

private

These are use by the distance function above.

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

private

A vector containing all the remarks from the pdb input.

std::string PLMD::ReferenceConfiguration::name

private

The name of this particular config.

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

private

This is used to store the values of arguments.

Tensor PLMD::ReferenceConfiguration::virial

protected

bool PLMD::ReferenceConfiguration::virialWasSet

protected

The virial contribution has to be stored.

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

Protected Attributes

Private Attributes

Friends

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation