align | PLMD::ReferenceAtoms | private |
atom_der_index | PLMD::ReferenceAtoms | private |
bounds_were_set | PLMD::DRMSD | protected |
calc(const std::vector< Vector > &pos, const Pbc &pbc, ReferenceValuePack &myder, const bool &squared) const override | PLMD::DRMSD | virtual |
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 override | PLMD::SingleDomainRMSD | virtual |
calculate(const std::vector< Vector > &pos, const Pbc &pbc, ReferenceValuePack &myder, const bool &squared) const | PLMD::SingleDomainRMSD | |
PLMD::ReferenceAtoms::calculate(const std::vector< Vector > &pos, const Pbc &pbc, const std::vector< Value * > &vals, ReferenceValuePack &myder, const bool &squared=false) const | PLMD::ReferenceConfiguration | |
checks_were_disabled | PLMD::ReferenceAtoms | private |
copyDerivatives(const ReferenceConfiguration *) | PLMD::ReferenceConfiguration | |
displace | PLMD::ReferenceAtoms | private |
displaceReferenceAtoms(const double &weight, const std::vector< Vector > &dir) | PLMD::ReferenceAtoms | |
displaceReferenceConfiguration(const double &weight, Direction &dir) | PLMD::ReferenceConfiguration | |
DRMSD(const ReferenceConfigurationOptions &ro) | PLMD::DRMSD | explicit |
error(const std::string &msg) | PLMD::ReferenceConfiguration | protected |
extractAtomicDisplacement(const std::vector< Vector > &pos, std::vector< Vector > &direction) const | PLMD::ReferenceAtoms | inlinevirtual |
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() override | PLMD::ReferenceAtoms | inlinevirtual |
getAlign() const | PLMD::ReferenceAtoms | inline |
getArgumentNames() | PLMD::ReferenceConfiguration | inlinevirtual |
getArgumentRequests(std::vector< std::string > &, bool disable_checks=false) | PLMD::ReferenceConfiguration | inlinevirtual |
getAtomIndex(const unsigned &) const | PLMD::ReferenceAtoms | inline |
getAtomRequests(std::vector< AtomNumber > &, bool disable_checks=false) override | PLMD::ReferenceAtoms | virtual |
getDisplace() const | PLMD::ReferenceAtoms | inline |
getName() const | PLMD::ReferenceConfiguration | |
getNumberOfAtoms() const | PLMD::ReferenceAtoms | inline |
getNumberOfReferenceArguments() const | PLMD::ReferenceConfiguration | inlinevirtual |
getNumberOfReferencePositions() const override | PLMD::ReferenceAtoms | inlinevirtual |
getReferenceArgument(const unsigned &i) const | PLMD::ReferenceConfiguration | inlinevirtual |
getReferenceArguments() const | PLMD::ReferenceConfiguration | inlinevirtual |
getReferenceMetric() | PLMD::ReferenceConfiguration | inlinevirtual |
getReferencePosition(const unsigned &iatom) const | PLMD::ReferenceAtoms | inlineprotected |
getReferencePositions() const override | PLMD::ReferenceAtoms | inlinevirtual |
indices | PLMD::ReferenceAtoms | private |
line | PLMD::ReferenceConfiguration | private |
lower | PLMD::DRMSD | protected |
name | PLMD::ReferenceConfiguration | private |
nopbc | PLMD::DRMSD | private |
parseAtomList(const std::string &, std::vector< unsigned > &) | PLMD::ReferenceAtoms | protected |
pcaIsEnabledForThisReference() | PLMD::ReferenceConfiguration | inlinevirtual |
projectAtomicDisplacementOnVector(const bool &normalized, const std::vector< Vector > &eigv, ReferenceValuePack &mypack) const | PLMD::ReferenceAtoms | inlinevirtual |
projectDisplacementOnVector(const Direction &mydir, const std::vector< Value * > &vals, const std::vector< double > &arg, ReferenceValuePack &mypack) const | PLMD::ReferenceConfiguration | |
read(const PDB &) override | PLMD::DRMSD | virtual |
readAtomsFromPDB(const PDB &, const bool allowblocks=false) | PLMD::ReferenceAtoms | protected |
readBounds(const PDB &) | PLMD::DRMSD | protected |
readReference(const PDB &pdb) | PLMD::SingleDomainRMSD | protected |
reference_atoms | PLMD::ReferenceAtoms | private |
ReferenceAtoms(const ReferenceConfigurationOptions &ro) | PLMD::ReferenceAtoms | explicit |
PLMD::ReferenceConfiguration::ReferenceConfiguration(const ReferenceConfigurationOptions &ro) | PLMD::ReferenceConfiguration | explicit |
setAtomIndices(const std::vector< AtomNumber > &atomnumbers) | PLMD::ReferenceAtoms | protected |
setBoundsOnDistances(bool dopbc, double lbound=0.0, double ubound=std::numeric_limits< double >::max()) override | PLMD::DRMSD | virtual |
setReferenceAtoms(const std::vector< Vector > &conf, const std::vector< double > &align_in, const std::vector< double > &displace_in) override | PLMD::DRMSD | virtual |
setup_targets() | PLMD::DRMSD | virtual |
setupPCAStorage(ReferenceValuePack &mypack) | PLMD::ReferenceConfiguration | inlinevirtual |
setupRMSDObject() | PLMD::SingleDomainRMSD | inlinevirtual |
singleDomainRequests(std::vector< AtomNumber > &, bool disable_checks) | PLMD::ReferenceAtoms | protected |
SingleDomainRMSD(const ReferenceConfigurationOptions &ro) | PLMD::SingleDomainRMSD | explicit |
targets | PLMD::DRMSD | protected |
upper | PLMD::DRMSD | protected |
~ReferenceConfiguration() | PLMD::ReferenceConfiguration | virtual |