Inheritance diagram for PLMD::IntramolecularDRMSD:

[legend]

Public Member Functions
	IntramolecularDRMSD (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 override
	Calculate. More...

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

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

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 amount specified using a Direction. More...

virtual 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 () override
	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...

void	getAtomRequests (std::vector< AtomNumber > &, bool disable_checks=false) override
	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 override
	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 override
	Get the reference positions. More...

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

virtual double	projectAtomicDisplacementOnVector (const bool &normalized, const std::vector< Vector > &eigv, 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 &pdb) override
	Check that similar comparisons are being performed - perhaps this is needed ask Davide? GAT. More...

void	setBoundsOnDistances (bool dopbc, double lbound=0.0, double ubound=std::numeric_limits< double >::max()) override
	This sets upper and lower bounds on distances to be used in DRMSD. More...

void	setReferenceAtoms (const std::vector< Vector > &conf, const std::vector< double > &align_in, const std::vector< double > &displace_in) override
	Set the positions of the reference atoms. More...

void	setup_targets () override

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

virtual void	setupRMSDObject ()
	This is used by MultiDomainRMSD to setup the RMSD object in Optimal RMSD type. 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	readBounds (const PDB &)
	Read in NOPBC, LOWER_CUTOFF and UPPER_CUTOFF. More...

void	readReference (const PDB &pdb)

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...

Protected Attributes
bool	bounds_were_set

double	lower

std::map< std::pair< unsigned, unsigned >, double >	targets

double	upper

Private Attributes
std::vector< double >	align
	The atoms to be used to align the instantaneous atomic positions to the reference configuration. More...

std::vector< unsigned >	atom_der_index
	The indeces for setting derivatives. More...

std::vector< unsigned >	blocks

bool	checks_were_disabled
	This flag tells us if the user has disabled checking of the input in order to do fancy paths with weird inputs. More...

std::vector< double >	displace
	The atoms to be used to calculate the distance the atoms have moved from the reference configuration. More...

std::vector< std::string >	fake_arg_names

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

std::vector< double >	fake_metric

std::vector< double >	fake_refargs

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

std::vector< AtomNumber >	indices
	The indices of the atoms in the pdb file. More...

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

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

unsigned	nblocks

bool	nopbc

std::vector< Vector >	reference_atoms
	The positions of the atoms in the reference configuration. More...

Constructor & Destructor Documentation

◆ IntramolecularDRMSD()

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

explicit

Member Function Documentation

◆ calc() [1/2]

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

overridevirtualinherited

Calculate.

Implements PLMD::ReferenceConfiguration.

◆ calc() [2/2]

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

overridevirtualinherited

Calculate the distance using the input position.

Implements PLMD::SingleDomainRMSD.

◆ calculate() [1/2]

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.

◆ calculate() [2/2]

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

inherited

◆ 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 amount specified using a Direction.

◆ error()

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

protectedinherited

Crash with an error.

◆ extractAtomicDisplacement()

virtual void PLMD::ReferenceAtoms::extractAtomicDisplacement	(	const std::vector< Vector > &	pos,
		std::vector< Vector > &	direction
	)		const

inlinevirtualinherited

Extract a displacement from a position in space.

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

◆ 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 ( )

inlineoverridevirtualinherited

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`
	)

overridevirtualinherited

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

inlineoverridevirtualinherited

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

inlineoverridevirtualinherited

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()

virtual bool PLMD::ReferenceConfiguration::pcaIsEnabledForThisReference ( )

inlinevirtualinherited

Stuff for pca.

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

◆ projectAtomicDisplacementOnVector()

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

inlinevirtualinherited

Project the displacement on a vector.

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

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

overridevirtual

Check that similar comparisons are being performed - perhaps this is needed ask Davide? GAT.

Reimplemented from PLMD::DRMSD.

◆ readAtomsFromPDB()

void PLMD::ReferenceAtoms::readAtomsFromPDB	(	const PDB &	pdb,
		const bool	allowblocks = `false`
	)

protectedinherited

Read in the atoms from the pdb file.

◆ readBounds()

void PLMD::DRMSD::readBounds ( const PDB & pdb )

protectedinherited

Read in NOPBC, LOWER_CUTOFF and UPPER_CUTOFF.

◆ readReference()

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

protectedinherited

◆ setAtomIndices()

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

protectedinherited

Add atom indices to list.

◆ setBoundsOnDistances()

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

overridevirtualinherited

This sets upper and lower bounds on distances to be used in DRMSD.

Reimplemented from PLMD::SingleDomainRMSD.

◆ setReferenceAtoms()

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

overridevirtualinherited

Set the positions of the reference atoms.

Implements PLMD::ReferenceAtoms.

◆ setup_targets()

void PLMD::IntramolecularDRMSD::setup_targets ( )

overridevirtual

Reimplemented from PLMD::DRMSD.

◆ setupPCAStorage()

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

inlinevirtualinherited

Stuff to setup pca.

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

◆ setupRMSDObject()

virtual void PLMD::SingleDomainRMSD::setupRMSDObject ( )

inlinevirtualinherited

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

Reimplemented in PLMD::OptimalRMSD.

◆ 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

◆ align

std::vector<double> PLMD::ReferenceAtoms::align

privateinherited

The atoms to be used to align the instantaneous atomic positions to the reference configuration.

◆ atom_der_index

std::vector<unsigned> PLMD::ReferenceAtoms::atom_der_index

privateinherited

The indeces for setting derivatives.

◆ blocks

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

private

◆ bounds_were_set

bool PLMD::DRMSD::bounds_were_set

protectedinherited

◆ checks_were_disabled

bool PLMD::ReferenceAtoms::checks_were_disabled

privateinherited

This flag tells us if the user has disabled checking of the input in order to do fancy paths with weird inputs.

◆ displace

std::vector<double> PLMD::ReferenceAtoms::displace

privateinherited

The atoms to be used to calculate the distance the atoms have moved from the reference configuration.

◆ fake_arg_names

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

privateinherited

◆ fake_atom_numbers

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

privateinherited

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

◆ fake_metric

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

privateinherited

◆ fake_refargs

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

privateinherited

◆ fake_refatoms

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

privateinherited

These are use by the distance function above.

◆ indices

std::vector<AtomNumber> PLMD::ReferenceAtoms::indices

privateinherited

The indices of the atoms in the pdb file.

◆ line

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

privateinherited

A vector containing all the remarks from the pdb input.

◆ lower

double PLMD::DRMSD::lower

protectedinherited

◆ name

std::string PLMD::ReferenceConfiguration::name

privateinherited

The name of this particular config.

◆ nblocks

unsigned PLMD::IntramolecularDRMSD::nblocks

private

◆ nopbc

bool PLMD::DRMSD::nopbc

privateinherited

◆ reference_atoms

std::vector<Vector> PLMD::ReferenceAtoms::reference_atoms

privateinherited

The positions of the atoms in the reference configuration.

◆ targets

std::map< std::pair <unsigned,unsigned>, double> PLMD::DRMSD::targets

protectedinherited

◆ upper

double PLMD::DRMSD::upper

protectedinherited

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

reference/IntramolecularDRMSD.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Private Attributes

Constructor & Destructor Documentation

◆ IntramolecularDRMSD()

Member Function Documentation

◆ calc() [1/2]

◆ calc() [2/2]

◆ 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()

◆ readBounds()

◆ readReference()

◆ setAtomIndices()

◆ setBoundsOnDistances()

◆ setReferenceAtoms()

◆ setup_targets()

◆ setupPCAStorage()

◆ setupRMSDObject()

◆ singleDomainRequests()

Member Data Documentation

◆ align

◆ atom_der_index

◆ blocks

◆ bounds_were_set

◆ checks_were_disabled

◆ displace

◆ fake_arg_names

◆ fake_atom_numbers

◆ fake_metric

◆ fake_refargs

◆ fake_refatoms

◆ indices

◆ line

◆ lower

◆ name

◆ nblocks

◆ nopbc

◆ reference_atoms

◆ targets

◆ upper