#include <SimpleRMSD.h>

Inheritance diagram for PLMD::SimpleRMSD:

[legend]

Public Member Functions
	SimpleRMSD (const ReferenceConfigurationOptions &ro)

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

double	calc (const std::vector< Vector > &pos, ReferenceValuePack &myder, const bool &squared) const

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

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

double	projectAtomicDisplacementOnVector (const unsigned &iv, const Matrix< Vector > &vecs, const std::vector< Vector > &pos, ReferenceValuePack &mypack) const

	SimpleRMSD (const std::string &thisname, Action *)

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

double	dist (const std::vector< Vector > &pos, const bool &squared)

double	calc (const bool &squared)

double	simpleAlignment (const std::vector< double > &align, const std::vector< double > &displace, const std::vector< Vector > &positions, bool squared)

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

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. More...

virtual double	calc (const std::vector< Vector > &pos, const Pbc &pbc, ReferenceValuePack &myder, const bool &squared) const =0
	Calculate the distance using the input position. More...

double	calculate (const std::vector< Vector > &pos, const Pbc &pbc, 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 void	setBoundsOnDistances (bool dopbc, double lbound=0.0, double ubound=std::numeric_limits< double >::max())
	This sets upper and lower bounds on distances to be used in DRMSD (here it does nothing) More...

virtual void	setupRMSDObject ()
	This is used by MultiDomainRMSD to setup the RMSD object in Optimal RMSD type. 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...

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 ()

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

double	calc (const std::vector< Vector > &pos, const Pbc &pbc, ReferenceValuePack &myder, const bool &squared) const
	Calculate the distance using the input position. More...

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. More...

double	calculate (const std::vector< Vector > &pos, ReferenceValuePack &myder, const bool &squared) const

double	calculate (const std::vector< Vector > &pos, const Pbc &pbc, ReferenceValuePack &myder, const bool &squared) const

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...

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...

Protected Member Functions
void	readReference (const PDB &pdb)

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	readReference (const PDB &pdb)

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...

Private Attributes
RMSD	myrmsd

std::vector< double >	weights

Constructor & Destructor Documentation

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

explicit

PLMD::SimpleRMSD::SimpleRMSD	(	const std::string &	thisname,
		Action *
	)

Member Function Documentation

double PLMD::SimpleRMSD::calc	(	const std::vector< Vector > &	pos,
		ReferenceValuePack &	myder,
		const bool &	squared
	)		const

virtual

Implements PLMD::RMSDBase.

double PLMD::SimpleRMSD::calc ( const bool & squared )

double PLMD::RMSDBase::calc	(	const std::vector< Vector > &	pos,
		const Pbc &	pbc,
		ReferenceValuePack &	myder,
		const bool &	squared
	)		const

virtualinherited

Calculate the distance using the input position.

Implements PLMD::SingleDomainRMSD.

double PLMD::SingleDomainRMSD::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

virtualinherited

Calculate.

Implements PLMD::ReferenceConfiguration.

double PLMD::SingleDomainRMSD::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

virtualinherited

Calculate.

Implements PLMD::ReferenceConfiguration.

virtual double PLMD::SingleDomainRMSD::calc	(	const std::vector< Vector > &	pos,
		const Pbc &	pbc,
		ReferenceValuePack &	myder,
		const bool &	squared
	)		const

pure virtualinherited

Calculate the distance using the input position.

Implemented in PLMD::DRMSD, and PLMD::RMSDBase.

double PLMD::RMSDBase::calculate	(	const std::vector< Vector > &	pos,
		ReferenceValuePack &	myder,
		const bool &	squared
	)		const

inherited

double PLMD::SingleDomainRMSD::calculate	(	const std::vector< Vector > &	pos,
		const Pbc &	pbc,
		ReferenceValuePack &	myder,
		const bool &	squared
	)		const

inherited

double PLMD::SingleDomainRMSD::calculate	(	const std::vector< Vector > &	pos,
		const Pbc &	pbc,
		ReferenceValuePack &	myder,
		const bool &	squared
	)		const

inherited

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.

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.

double PLMD::SimpleRMSD::dist	(	const std::vector< Vector > &	pos,
		const bool &	squared
	)

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

inlineprotectedinherited

Get the vector of alignment weights.

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

inlinevirtualinherited

Reimplemented in PLMD::ReferenceArguments.

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.

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.

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::ReferenceAtoms::getNumberOfAtoms ( ) const

inlineinherited

This returns how many atoms there should be.

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.

unsigned PLMD::ReferenceAtoms::getNumberOfReferencePositions ( ) const

inlinevirtualinherited

This returns the number of reference atom positions.

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::ReferenceConfiguration::getReferenceArguments ( )

inlinevirtualinherited

Reimplemented in PLMD::ReferenceArguments.

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.

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.

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.

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.

bool PLMD::SimpleRMSD::pcaIsEnabledForThisReference ( )

inlinevirtual

Stuff for pca.

Reimplemented from PLMD::ReferenceConfiguration.

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

inherited

Print the atomic positions.

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

inherited

Print the atomic positions.

double PLMD::SimpleRMSD::projectAtomicDisplacementOnVector	(	const unsigned &	iv,
		const Matrix< Vector > &	vecs,
		const std::vector< Vector > &	pos,
		ReferenceValuePack &	mypack
	)		const

virtual

Reimplemented from PLMD::ReferenceConfiguration.

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

virtual

Do all local business for setting the configuration.

Implements PLMD::ReferenceConfiguration.

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

virtual

Do all local business for setting the configuration.

Implements PLMD::ReferenceConfiguration.

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

protectedinherited

void PLMD::SingleDomainRMSD::readReference ( const PDB & pdb )

protectedinherited

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

protectedinherited

Add atom indices to list.

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

inherited

Set the indices of the reference atoms.

virtual void PLMD::SingleDomainRMSD::setBoundsOnDistances	(	bool	dopbc,
		double	lbound = `0.0`,
		double	ubound = `std::numeric_limits<double>::max( )`
	)

inlinevirtualinherited

This sets upper and lower bounds on distances to be used in DRMSD (here it does nothing)

Reimplemented in PLMD::DRMSD.

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

virtualinherited

Set the reference structure.

Implements PLMD::ReferenceAtoms.

Reimplemented in PLMD::DRMSD.

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 )

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

inlinevirtual

Stuff to setup pca.

Reimplemented from PLMD::ReferenceConfiguration.

virtual void PLMD::SingleDomainRMSD::setupRMSDObject ( )

inlinevirtualinherited

This is used by MultiDomainRMSD to setup the RMSD object in Optimal RMSD type.

Reimplemented in PLMD::OptimalRMSD.

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

inlineinherited

Set the weight for this frame.

double PLMD::SimpleRMSD::simpleAlignment	(	const std::vector< double > &	align,
		const std::vector< double > &	displace,
		const std::vector< Vector > &	positions,
		bool	squared
	)

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

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

RMSD PLMD::SimpleRMSD::myrmsd

private

std::vector<double> PLMD::SimpleRMSD::weights

private

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

reference/SimpleRMSD.cpp
reference/SimpleRMSD.h

Public Member Functions

Protected Member Functions

Private Attributes

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation