Public Member Functions | |
IntramolecularDRMSD (const ReferenceConfigurationOptions &ro) | |
void | read (const PDB &pdb) |
Check that similar comparisons are being performed - perhaps this is needed ask Davide? GAT. More... | |
void | setup_targets () |
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. More... | |
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, 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, 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 | 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... | |
const std::vector< Vector > & | getReferencePositions () const |
Get the reference 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... | |
void | displaceReferenceAtoms (const double &weight, const std::vector< Vector > &dir) |
Displace the positions of the reference atoms a bit. More... | |
virtual void | extractAtomicDisplacement (const std::vector< Vector > &pos, std::vector< Vector > &direction) const |
Extract a displacement from a position in space. More... | |
virtual double | projectAtomicDisplacementOnVector (const bool &normalized, const std::vector< Vector > &eigv, ReferenceValuePack &mypack) const |
Project the displacement on a vector. 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... | |
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 () const |
virtual const std::vector< double > & | getReferenceMetric () |
virtual const std::vector< std::string > & | getArgumentNames () |
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... | |
virtual bool | pcaIsEnabledForThisReference () |
Stuff for pca. More... | |
double | projectDisplacementOnVector (const Direction &mydir, const std::vector< Value *> &vals, const std::vector< double > &arg, ReferenceValuePack &mypack) const |
virtual void | setupPCAStorage (ReferenceValuePack &mypack) |
Stuff to setup pca. More... | |
void | displaceReferenceConfiguration (const double &weight, Direction &dir) |
Move the reference configuration by an ammount specified using a Direction. More... | |
Protected Member Functions | |
void | readBounds () |
Read in NOPBC, LOWER_CUTOFF and UPPER_CUTOFF. More... | |
void | readReference (const PDB &pdb) |
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... | |
Vector | getReferencePosition (const unsigned &iatom) const |
Get the position of the ith atom. 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... | |
Protected Attributes | |
bool | bounds_were_set |
double | lower |
double | upper |
std::map< std::pair< unsigned, unsigned >, double > | targets |
Private Attributes | |
unsigned | nblocks |
std::vector< unsigned > | blocks |
|
explicit |
|
virtualinherited |
Calculate.
Implements PLMD::ReferenceConfiguration.
|
virtualinherited |
Calculate the distance using the input position.
Implements PLMD::SingleDomainRMSD.
|
inherited |
|
inherited |
Calculate the distance from the reference configuration.
|
inherited |
Check that all the remarks in the pdb have been read in.
|
inherited |
Copy derivatives from one frame to this frame.
|
inherited |
Displace the positions of the reference atoms a bit.
|
inherited |
Move the reference configuration by an ammount specified using a Direction.
|
protectedinherited |
Derivatives wrt to the arguments.
The virial contribution has to be stored Derivatives wrt to the atoms Crash with an error
|
inlinevirtualinherited |
Extract a displacement from a position in space.
Reimplemented in PLMD::MultiDomainRMSD, PLMD::Direction, PLMD::OptimalRMSD, and PLMD::SimpleRMSD.
|
inherited |
Extract a Direction giving you the displacement from some position.
|
inlinevirtualinherited |
Return all atom indexes.
Reimplemented from PLMD::ReferenceConfiguration.
|
inlineinherited |
Get the vector of alignment weights.
|
inlinevirtualinherited |
Reimplemented in PLMD::ReferenceArguments.
|
inlinevirtualinherited |
Retrieve the arguments that are required for this guy.
Reimplemented in PLMD::ReferenceArguments.
|
inlineinherited |
This allows us to use a single pos array with RMSD objects using different atom indexes.
|
virtualinherited |
Get the atoms required (additional checks are required when we have multiple domains)
Reimplemented from PLMD::ReferenceConfiguration.
|
inlineinherited |
Get the vector of displacement weights.
|
inherited |
Return the name of this metric.
|
inlineinherited |
This returns how many atoms there should be.
|
inlinevirtualinherited |
Reimplemented in PLMD::ReferenceArguments.
|
inlinevirtualinherited |
This returns the number of reference atom positions.
Reimplemented from PLMD::ReferenceConfiguration.
|
inlinevirtualinherited |
Get one of the referene arguments.
Reimplemented in PLMD::ReferenceArguments.
|
inlinevirtualinherited |
Reimplemented in PLMD::ReferenceArguments.
|
inlinevirtualinherited |
Reimplemented in PLMD::ReferenceArguments.
|
inlineprotectedinherited |
Get the position of the ith atom.
|
inlinevirtualinherited |
Get the reference positions.
Reimplemented from PLMD::ReferenceConfiguration.
|
inlineinherited |
Return the weight for this frame.
|
inherited |
|
protectedinherited |
Read a list of atoms from the pdb input file.
|
inherited |
Parse a flag.
|
inherited |
Parse vector from the pdb remarks.
|
inlinevirtualinherited |
Stuff for pca.
Reimplemented in PLMD::MultiDomainRMSD, PLMD::ArgumentOnlyDistance, PLMD::OptimalRMSD, and PLMD::SimpleRMSD.
|
inherited |
Print a pdb file containing the reference configuration.
|
inherited |
|
inherited |
Print the atomic positions.
|
inlinevirtualinherited |
Project the displacement on a vector.
Reimplemented in PLMD::MultiDomainRMSD, PLMD::OptimalRMSD, and PLMD::SimpleRMSD.
|
inherited |
|
virtual |
Check that similar comparisons are being performed - perhaps this is needed ask Davide? GAT.
Reimplemented from PLMD::DRMSD.
|
protectedinherited |
Read in the atoms from the pdb file.
|
protectedinherited |
Read in NOPBC, LOWER_CUTOFF and UPPER_CUTOFF.
|
protectedinherited |
|
virtualinherited |
Set the final number of arguments.
Set the final number of atoms Set the reference configuration using a PDB
|
protectedinherited |
Add atom indices to list.
|
inherited |
Set the indices of the reference atoms.
|
virtualinherited |
This sets upper and lower bounds on distances to be used in DRMSD.
Reimplemented from PLMD::SingleDomainRMSD.
|
inherited |
Set the atom numbers and the argument names.
|
virtualinherited |
Set the reference structure.
Reimplemented from PLMD::SingleDomainRMSD.
|
inherited |
Set the reference structure (perhaps should also pass the pbc and align and displace )
|
virtual |
Reimplemented from PLMD::DRMSD.
|
inlinevirtualinherited |
Stuff to setup pca.
Reimplemented in PLMD::MultiDomainRMSD, PLMD::ArgumentOnlyDistance, PLMD::OptimalRMSD, and PLMD::SimpleRMSD.
|
inlinevirtualinherited |
This is used by MultiDomainRMSD to setup the RMSD object in Optimal RMSD type.
Reimplemented in PLMD::OptimalRMSD.
|
inlineinherited |
Set the weight for this frame.
|
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
|
private |
|
protectedinherited |
|
protectedinherited |
|
private |
|
protectedinherited |
|
protectedinherited |
Hosted by GitHub | 1.8.14 |