#include <SingleDomainRMSD.h>
Public Member Functions | |
SingleDomainRMSD (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... | |
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, 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 |
virtual void | read (const PDB &)=0 |
Do all local business for setting the 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... | |
void | setReferenceAtoms (const std::vector< Vector > &conf, const std::vector< double > &align_in, const std::vector< double > &displace_in) override |
Set the reference structure. More... | |
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 | 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... | |
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... | |
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... | |
std::vector< Vector > | reference_atoms |
The positions of the atoms in the reference configuration. More... | |
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explicit |
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overridevirtual |
Calculate.
Implements PLMD::ReferenceConfiguration.
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pure virtual |
Calculate the distance using the input position.
Implemented in PLMD::DRMSD, and PLMD::RMSDBase.
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inherited |
Calculate the distance from the reference configuration.
double PLMD::SingleDomainRMSD::calculate | ( | const std::vector< Vector > & | pos, |
const Pbc & | pbc, | ||
ReferenceValuePack & | myder, | ||
const bool & | squared | ||
) | const |
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inherited |
Parse something from the pdb remarks Copy derivatives from one frame to this frame.
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inherited |
Displace the positions of the reference atoms a bit.
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inherited |
Move the reference configuration by an amount specified using a Direction.
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protectedinherited |
Crash with an error.
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inlinevirtualinherited |
Extract a displacement from a position in space.
Reimplemented in PLMD::Direction, PLMD::MultiDomainRMSD, PLMD::OptimalRMSD, and PLMD::SimpleRMSD.
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inherited |
Extract a Direction giving you the displacement from some position.
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inlineoverridevirtualinherited |
Return all atom indexes.
Reimplemented from PLMD::ReferenceConfiguration.
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inlineinherited |
Get the vector of alignment weights.
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inlinevirtualinherited |
Reimplemented in PLMD::ReferenceArguments.
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inlinevirtualinherited |
Retrieve the arguments that are required for this guy.
Reimplemented in PLMD::ReferenceArguments.
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inlineinherited |
This allows us to use a single pos array with RMSD objects using different atom indexes.
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overridevirtualinherited |
Get the atoms required (additional checks are required when we have multiple domains)
Reimplemented from PLMD::ReferenceConfiguration.
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inlineinherited |
Get the vector of displacement weights.
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inherited |
Return the name of this metric.
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inlineinherited |
This returns how many atoms there should be.
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inlinevirtualinherited |
Reimplemented in PLMD::ReferenceArguments.
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inlineoverridevirtualinherited |
This returns the number of reference atom positions.
Reimplemented from PLMD::ReferenceConfiguration.
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inlinevirtualinherited |
Get one of the referene arguments.
Reimplemented in PLMD::ReferenceArguments.
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inlinevirtualinherited |
Reimplemented in PLMD::ReferenceArguments.
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inlinevirtualinherited |
Reimplemented in PLMD::ReferenceArguments.
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inlineprotectedinherited |
Get the position of the ith atom.
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inlineoverridevirtualinherited |
Get the reference positions.
Reimplemented from PLMD::ReferenceConfiguration.
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protectedinherited |
Read a list of atoms from the pdb input file.
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inlinevirtualinherited |
Stuff for pca.
Reimplemented in PLMD::MultiDomainRMSD, PLMD::ArgumentOnlyDistance, PLMD::OptimalRMSD, and PLMD::SimpleRMSD.
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inlinevirtualinherited |
Project the displacement on a vector.
Reimplemented in PLMD::MultiDomainRMSD, PLMD::OptimalRMSD, and PLMD::SimpleRMSD.
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inherited |
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pure virtualinherited |
Do all local business for setting the configuration.
Implemented in PLMD::ArgumentOnlyDistance, PLMD::IntermolecularDRMSD, PLMD::IntramolecularDRMSD, PLMD::DRMSD, PLMD::MultiDomainRMSD, PLMD::Direction, PLMD::OptimalRMSD, PLMD::FakeFrame, PLMD::SimpleRMSD, and PLMD::DotProductDistance.
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protectedinherited |
Read in the atoms from the pdb file.
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protected |
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protectedinherited |
Add atom indices to list.
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inlinevirtual |
This sets upper and lower bounds on distances to be used in DRMSD (here it does nothing)
Reimplemented in PLMD::DRMSD.
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overridevirtual |
Set the reference structure.
Implements PLMD::ReferenceAtoms.
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inlinevirtualinherited |
Stuff to setup pca.
Reimplemented in PLMD::MultiDomainRMSD, PLMD::ArgumentOnlyDistance, PLMD::OptimalRMSD, and PLMD::SimpleRMSD.
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inlinevirtual |
This is used by MultiDomainRMSD to setup the RMSD object in Optimal RMSD type.
Reimplemented in PLMD::OptimalRMSD.
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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
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privateinherited |
The atoms to be used to align the instantaneous atomic positions to the reference configuration.
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privateinherited |
The indeces for setting derivatives.
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privateinherited |
This flag tells us if the user has disabled checking of the input in order to do fancy paths with weird inputs.
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privateinherited |
The atoms to be used to calculate the distance the atoms have moved from the reference configuration.
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privateinherited |
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privateinherited |
These are used to do fake things when we copy frames.
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privateinherited |
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privateinherited |
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privateinherited |
These are use by the distance function above.
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privateinherited |
The indices of the atoms in the pdb file.
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privateinherited |
A vector containing all the remarks from the pdb input.
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privateinherited |
The name of this particular config.
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privateinherited |
The positions of the atoms in the reference configuration.
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