#include <MultiDomainRMSD.h>

Inheritance diagram for PLMD::MultiDomainRMSD:

Public Member Functions
	MultiDomainRMSD (const ReferenceConfigurationOptions &ro)

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, 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...

void	copyDerivatives (const ReferenceConfiguration *)
	Parse something from the pdb remarks Copy derivatives from one frame to this frame. 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	extractAtomicDisplacement (const std::vector< Vector > &pos, std::vector< Vector > &direction) 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...

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

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...

virtual unsigned	getNumberOfReferenceArguments () const

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

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

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

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

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

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

double	projectAtomicDisplacementOnVector (const bool &normalized, const std::vector< Vector > &vecs, 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 &)
	Read in the input from a pdb. More...

void	setReferenceAtoms (const std::vector< Vector > &conf, const std::vector< double > &align_in, const std::vector< double > &displace_in)
	Set the input from an analysis object (don't know how this will work yet so currently just a plumed_error) More...

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

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

Private Attributes
std::vector< unsigned >	blocks
	Blocks containing start and end points for all the domains. More...

std::vector< std::unique_ptr< SingleDomainRMSD > >	domains
	Each of the domains we are calculating the distance from. More...

std::string	ftype
	The type of RMSD we are using. More...

std::vector< double >	weights
	The weight of a block. More...

Constructor & Destructor Documentation

◆ MultiDomainRMSD()

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

explicit

Member Function Documentation

◆ calc()

double PLMD::MultiDomainRMSD::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

virtual

Calculate.

Implements PLMD::ReferenceConfiguration.

◆ calculate() [1/2]

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

◆ calculate() [2/2]

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.

◆ copyDerivatives()

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

inherited

Parse something from the pdb remarks Copy derivatives from one frame to this frame.

◆ 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.

◆ extractAtomicDisplacement()

void PLMD::MultiDomainRMSD::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()

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

inlinevirtualinherited

Reimplemented in PLMD::ReferenceArguments.

◆ getArgumentRequests()

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()

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()

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

inlinevirtualinherited

Get one of the referene arguments.

Reimplemented in PLMD::ReferenceArguments.

◆ getReferenceArguments()

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

inlinevirtualinherited

Reimplemented in PLMD::ReferenceArguments.

◆ getReferenceMetric()

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.

◆ parseAtomList()

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

protectedinherited

Read a list of atoms from the pdb input file.

◆ pcaIsEnabledForThisReference()

bool PLMD::MultiDomainRMSD::pcaIsEnabledForThisReference ( )

virtual

Stuff for pca.

Reimplemented from PLMD::ReferenceConfiguration.

◆ projectAtomicDisplacementOnVector()

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

virtual

Project the displacement on a vector.

Reimplemented from PLMD::ReferenceAtoms.

◆ 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::MultiDomainRMSD::read ( const PDB & pdb )

virtual

Read in the input from a pdb.

Implements PLMD::ReferenceConfiguration.

◆ 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.

◆ setReferenceAtoms()

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

virtual

Set the input from an analysis object (don't know how this will work yet so currently just a plumed_error)

Implements PLMD::ReferenceAtoms.

◆ setupPCAStorage()

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

virtual

Stuff to setup pca.

Reimplemented from PLMD::ReferenceConfiguration.

◆ 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

Member Data Documentation

◆ blocks

std::vector<unsigned> PLMD::MultiDomainRMSD::blocks

private

Blocks containing start and end points for all the domains.

◆ domains

std::vector<std::unique_ptr<SingleDomainRMSD> > PLMD::MultiDomainRMSD::domains

private

Each of the domains we are calculating the distance from.

◆ ftype

std::string PLMD::MultiDomainRMSD::ftype

private

The type of RMSD we are using.

◆ weights

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

private

The weight of a block.

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

reference/MultiDomainRMSD.h
reference/MultiDomainRMSD.cpp

Public Member Functions

Protected Member Functions

Private Attributes

Constructor & Destructor Documentation

◆ MultiDomainRMSD()

Member Function Documentation

◆ calc()

◆ calculate() [1/2]

◆ calculate() [2/2]

◆ copyDerivatives()

◆ displaceReferenceAtoms()

◆ displaceReferenceConfiguration()

◆ error()

◆ extractAtomicDisplacement()

◆ extractDisplacementVector()

◆ getAbsoluteIndexes()

◆ getAlign()

◆ getArgumentNames()

◆ getArgumentRequests()

◆ getAtomIndex()

◆ getAtomRequests()

◆ getDisplace()

◆ getName()

◆ getNumberOfAtoms()

◆ getNumberOfReferenceArguments()

◆ getNumberOfReferencePositions()

◆ getReferenceArgument()

◆ getReferenceArguments()

◆ getReferenceMetric()

◆ getReferencePosition()

◆ getReferencePositions()

◆ parseAtomList()

◆ pcaIsEnabledForThisReference()

◆ projectAtomicDisplacementOnVector()

◆ projectDisplacementOnVector()

◆ read()

◆ readAtomsFromPDB()

◆ setAtomIndices()

◆ setReferenceAtoms()

◆ setupPCAStorage()

◆ singleDomainRequests()

Member Data Documentation

◆ blocks

◆ domains

◆ ftype

◆ weights