PLMD::ReferenceConfiguration Member List

This is the complete list of members for PLMD::ReferenceConfiguration, including all inherited members.

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 =0	PLMD::ReferenceConfiguration	pure virtual
calculate(const std::vector< Vector > &pos, const Pbc &pbc, const std::vector< Value *> &vals, ReferenceValuePack &myder, const bool &squared=false) const	PLMD::ReferenceConfiguration
checkRead()	PLMD::ReferenceConfiguration
copyDerivatives(const ReferenceConfiguration *)	PLMD::ReferenceConfiguration
displaceReferenceConfiguration(const double &weight, Direction &dir)	PLMD::ReferenceConfiguration
distance(const Pbc &pbc, const std::vector< Value *> &vals, ReferenceConfiguration *, ReferenceConfiguration *, const bool &squared)	PLMD::ReferenceConfiguration	friend
error(const std::string &msg)	PLMD::ReferenceConfiguration	protected
extractDisplacementVector(const std::vector< Vector > &pos, const std::vector< Value *> &vals, const std::vector< double > &arg, const bool &nflag, Direction &mydir) const	PLMD::ReferenceConfiguration
fake_arg_names	PLMD::ReferenceConfiguration	private
fake_atom_numbers	PLMD::ReferenceConfiguration	private
fake_metric	PLMD::ReferenceConfiguration	private
fake_refargs	PLMD::ReferenceConfiguration	private
fake_refatoms	PLMD::ReferenceConfiguration	private
getAbsoluteIndexes()	PLMD::ReferenceConfiguration	inlinevirtual
getArgumentNames()	PLMD::ReferenceConfiguration	inlinevirtual
getArgumentRequests(std::vector< std::string > &, bool disable_checks=false)	PLMD::ReferenceConfiguration	inlinevirtual
getAtomRequests(std::vector< AtomNumber > &, bool disable_checks=false)	PLMD::ReferenceConfiguration	inlinevirtual
getName() const	PLMD::ReferenceConfiguration
getNumberOfReferenceArguments() const	PLMD::ReferenceConfiguration	inlinevirtual
getNumberOfReferencePositions() const	PLMD::ReferenceConfiguration	inlinevirtual
getReferenceArgument(const unsigned &i) const	PLMD::ReferenceConfiguration	inlinevirtual
getReferenceArguments() const	PLMD::ReferenceConfiguration	inlinevirtual
getReferenceMetric()	PLMD::ReferenceConfiguration	inlinevirtual
getReferencePositions() const	PLMD::ReferenceConfiguration	inlinevirtual
getWeight() const	PLMD::ReferenceConfiguration	inline
line	PLMD::ReferenceConfiguration	private
name	PLMD::ReferenceConfiguration	private
parse(const std::string &key, T &t, bool ignore_missing=false)	PLMD::ReferenceConfiguration
parseFlag(const std::string &key, bool &t)	PLMD::ReferenceConfiguration
parseVector(const std::string &key, std::vector< T > &t, bool ignore_missing=false)	PLMD::ReferenceConfiguration
pcaIsEnabledForThisReference()	PLMD::ReferenceConfiguration	inlinevirtual
print(OFile &ofile, const double &time, const double &weight, const double &lunits, const double &old_norm)	PLMD::ReferenceConfiguration
print(OFile &ofile, const std::string &fmt, const double &lunits)	PLMD::ReferenceConfiguration
projectDisplacementOnVector(const Direction &mydir, const std::vector< Value *> &vals, const std::vector< double > &arg, ReferenceValuePack &mypack) const	PLMD::ReferenceConfiguration
read(const PDB &)=0	PLMD::ReferenceConfiguration	pure virtual
ReferenceConfiguration(const ReferenceConfigurationOptions &ro)	PLMD::ReferenceConfiguration	explicit
set(const PDB &)	PLMD::ReferenceConfiguration	virtual
setNamesAndAtomNumbers(const std::vector< AtomNumber > &numbers, const std::vector< std::string > &arg)	PLMD::ReferenceConfiguration
setReferenceConfig(const std::vector< Vector > &pos, const std::vector< double > &arg, const std::vector< double > &metric)	PLMD::ReferenceConfiguration
setupPCAStorage(ReferenceValuePack &mypack)	PLMD::ReferenceConfiguration	inlinevirtual
setWeight(const double &ww)	PLMD::ReferenceConfiguration	inline
SingleDomainRMSD class	PLMD::ReferenceConfiguration	friend
weight	PLMD::ReferenceConfiguration	private
~ReferenceConfiguration()	PLMD::ReferenceConfiguration	virtual