Public Member Functions | Protected Member Functions | Protected Attributes | List of all members
PLMD::Direction Class Reference

#include <Direction.h>

Inheritance diagram for PLMD::Direction:
Inheritance graph
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Public Member Functions

 Direction (const ReferenceConfigurationOptions &ro)
 
void read (const PDB &)
 Do all local business for setting the configuration. More...
 
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
 Calculate the distance from the reference configuration. More...
 
void setDirection (const std::vector< Vector > &conf, const std::vector< double > &args)
 
void setReferenceAtoms (const std::vector< Vector > &conf, const std::vector< double > &align_in, const std::vector< double > &displace_in)
 Set the positions of the reference atoms. 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...
 
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...
 
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 ()
 
virtual bool pcaIsEnabledForThisReference ()
 Stuff for pca. More...
 
virtual double projectAtomicDisplacementOnVector (const unsigned &i, const Matrix< Vector > &eigv, const std::vector< Vector > &pos, ReferenceValuePack &mypack) const
 
bool isDirection () const
 Stuff for sanity checks on distance. More...
 
virtual void setupPCAStorage (ReferenceValuePack &mypack)
 Stuff to setup pca. More...
 
void setReferenceArguments (const std::vector< double > &arg_vals, const std::vector< double > &sigma)
 Set the positions of the refernce arguments. More...
 
unsigned getNumberOfReferenceArguments () const
 Get the number of reference arguments. More...
 
void getArgumentRequests (std::vector< std::string > &, bool disable_checks=false)
 Get the arguments required. More...
 
void setArgumentNames (const std::vector< std::string > &arg_vals)
 Set the names of the arguments. More...
 
double getReferenceArgument (const unsigned &i) const
 Get the value of the ith reference argument. More...
 
void printArguments (OFile &ofile, const std::string &fmt) const
 Print the arguments out. More...
 
const std::vector< double > & getReferenceArguments ()
 Return all the reference arguments. More...
 
const std::vector< double > & getReferenceMetric ()
 
const std::vector< std::string > & getArgumentNames ()
 Return names. More...
 
virtual double calculateArgumentDistance (const std::vector< Value *> &vals, const std::vector< double > &arg, ReferenceValuePack &myder, const bool &squared) const
 Calculate the euclidean/malanobius distance the atoms have moved from the reference configuration in CV space. More...
 

Protected Member Functions

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...
 
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 readArgumentsFromPDB (const PDB &pdb)
 Read in the atoms from the pdb file. More...
 
void setReferenceArguments ()
 Set the values of the colvars based on their current instantanous values (used in Analysis) More...
 

Protected Attributes

bool hasweights
 Are we reading weights from input. More...
 
bool hasmetric
 Are we calculating a Malanobius distance. More...
 

Constructor & Destructor Documentation

◆ Direction()

PLMD::Direction::Direction ( const ReferenceConfigurationOptions &  ro)
explicit

Member Function Documentation

◆ calc()

double PLMD::Direction::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
virtual

Calculate the distance from the reference configuration.

Implements PLMD::ReferenceConfiguration.

◆ 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
inherited

Calculate the distance from the reference configuration.

◆ calculateArgumentDistance()

double PLMD::ReferenceArguments::calculateArgumentDistance ( const std::vector< Value *> &  vals,
const std::vector< double > &  arg,
ReferenceValuePack &  myder,
const bool &  squared 
) const
virtualinherited

Calculate the euclidean/malanobius distance the atoms have moved from the reference configuration in CV space.

Reimplemented in PLMD::DotProductDistance.

◆ checkRead()

void PLMD::ReferenceConfiguration::checkRead ( )
inherited

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

◆ copyDerivatives()

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

Copy derivatives from one frame to this frame.

◆ error()

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

◆ 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
inlineprotectedinherited

Get the vector of alignment weights.

◆ getArgumentNames() [1/2]

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

Return names.

Reimplemented from PLMD::ReferenceConfiguration.

◆ getArgumentNames() [2/2]

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

Reimplemented in PLMD::ReferenceArguments.

◆ getArgumentRequests() [1/2]

void PLMD::ReferenceArguments::getArgumentRequests ( std::vector< std::string > &  argout,
bool  disable_checks = false 
)
virtualinherited

Get the arguments required.

Reimplemented from PLMD::ReferenceConfiguration.

◆ getArgumentRequests() [2/2]

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
inlineprotectedinherited

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() [1/2]

unsigned PLMD::ReferenceArguments::getNumberOfReferenceArguments ( ) const
inlinevirtualinherited

Get the number of reference arguments.

Reimplemented from PLMD::ReferenceConfiguration.

◆ getNumberOfReferenceArguments() [2/2]

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() [1/2]

double PLMD::ReferenceArguments::getReferenceArgument ( const unsigned &  i) const
inlinevirtualinherited

Get the value of the ith reference argument.

Reimplemented from PLMD::ReferenceConfiguration.

◆ getReferenceArgument() [2/2]

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

Get one of the referene arguments.

Reimplemented in PLMD::ReferenceArguments.

◆ getReferenceArguments() [1/2]

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

Return all the reference arguments.

Reimplemented from PLMD::ReferenceConfiguration.

◆ getReferenceArguments() [2/2]

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

Reimplemented in PLMD::ReferenceArguments.

◆ getReferenceMetric() [1/2]

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

Reimplemented from PLMD::ReferenceConfiguration.

◆ getReferenceMetric() [2/2]

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
inlineprotectedvirtualinherited

Get the reference positions.

Reimplemented from PLMD::ReferenceConfiguration.

◆ getWeight()

double PLMD::ReferenceConfiguration::getWeight ( ) const
inlineinherited

Return the weight for this frame.

◆ isDirection()

bool PLMD::ReferenceConfiguration::isDirection ( ) const
inherited

Stuff for sanity checks on distance.

◆ parse()

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

◆ parseAtomList()

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

Read a list of atoms from the pdb input file.

◆ parseFlag()

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

Parse a flag.

◆ parseVector()

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.

◆ pcaIsEnabledForThisReference()

virtual bool PLMD::ReferenceConfiguration::pcaIsEnabledForThisReference ( )
inlinevirtualinherited

Stuff for pca.

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

◆ print() [1/2]

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.

◆ print() [2/2]

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

◆ printArguments()

void PLMD::ReferenceArguments::printArguments ( OFile &  ofile,
const std::string &  fmt 
) const
inherited

Print the arguments out.

◆ printAtoms()

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

Print the atomic positions.

◆ projectAtomicDisplacementOnVector()

virtual double PLMD::ReferenceConfiguration::projectAtomicDisplacementOnVector ( const unsigned &  i,
const Matrix< Vector > &  eigv,
const std::vector< Vector > &  pos,
ReferenceValuePack &  mypack 
) const
inlinevirtualinherited

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

◆ read()

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

Do all local business for setting the configuration.

Implements PLMD::ReferenceConfiguration.

◆ readArgumentsFromPDB()

void PLMD::ReferenceArguments::readArgumentsFromPDB ( const PDB &  pdb)
protectedinherited

Read in the atoms from the pdb file.

◆ readAtomsFromPDB()

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

Read in the atoms from the pdb file.

◆ set()

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

◆ setArgumentNames()

void PLMD::ReferenceArguments::setArgumentNames ( const std::vector< std::string > &  arg_vals)
inherited

Set the names of the arguments.

◆ setAtomIndices()

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

Add atom indices to list.

◆ setAtomNumbers()

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

Set the indices of the reference atoms.

◆ setDirection()

void PLMD::Direction::setDirection ( const std::vector< Vector > &  conf,
const std::vector< double > &  args 
)

◆ setNamesAndAtomNumbers()

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

Set the atom numbers and the argument names.

◆ setReferenceArguments() [1/2]

void PLMD::ReferenceArguments::setReferenceArguments ( )
protectedinherited

Set the values of the colvars based on their current instantanous values (used in Analysis)

◆ setReferenceArguments() [2/2]

void PLMD::ReferenceArguments::setReferenceArguments ( const std::vector< double > &  arg_vals,
const std::vector< double > &  sigma 
)
inherited

Set the positions of the refernce arguments.

◆ setReferenceAtoms()

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

Set the positions of the reference atoms.

Implements PLMD::ReferenceAtoms.

◆ setReferenceConfig()

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 )

◆ setupPCAStorage()

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

Stuff to setup pca.

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

◆ setWeight()

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

Set the weight for this frame.

◆ 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

◆ hasmetric

bool PLMD::ReferenceArguments::hasmetric
protectedinherited

Are we calculating a Malanobius distance.

◆ hasweights

bool PLMD::ReferenceArguments::hasweights
protectedinherited

Are we reading weights from input.

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