| align | PLMD::ReferenceAtoms | private |
| atom_der_index | PLMD::ReferenceAtoms | private |
| calc(const std::vector< Vector > &pos, ReferenceValuePack &myder, const bool &squared) const override | PLMD::SimpleRMSD | virtual |
| PLMD::RMSDBase::calc(const std::vector< Vector > &pos, const Pbc &pbc, ReferenceValuePack &myder, const bool &squared) const override | PLMD::RMSDBase | 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, ReferenceValuePack &myder, const bool &squared) const | PLMD::RMSDBase | |
| PLMD::SingleDomainRMSD::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 | |
| error(const std::string &msg) | PLMD::ReferenceConfiguration | protected |
| extractAtomicDisplacement(const std::vector< Vector > &pos, std::vector< Vector > &direction) const override | PLMD::SimpleRMSD | virtual |
| 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 |
| myrmsd | PLMD::SimpleRMSD | private |
| name | PLMD::ReferenceConfiguration | private |
| parseAtomList(const std::string &, std::vector< unsigned > &) | PLMD::ReferenceAtoms | protected |
| pcaIsEnabledForThisReference() override | PLMD::SimpleRMSD | inlinevirtual |
| projectAtomicDisplacementOnVector(const bool &normalized, const std::vector< Vector > &vecs, ReferenceValuePack &mypack) const override | PLMD::SimpleRMSD | virtual |
| projectDisplacementOnVector(const Direction &mydir, const std::vector< Value * > &vals, const std::vector< double > &arg, ReferenceValuePack &mypack) const | PLMD::ReferenceConfiguration | |
| read(const PDB &) override | PLMD::SimpleRMSD | virtual |
| readAtomsFromPDB(const PDB &, const bool allowblocks=false) | PLMD::ReferenceAtoms | 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 |
| RMSDBase(const ReferenceConfigurationOptions &ro) | PLMD::RMSDBase | explicit |
| setAtomIndices(const std::vector< AtomNumber > &atomnumbers) | PLMD::ReferenceAtoms | protected |
| setBoundsOnDistances(bool dopbc, double lbound=0.0, double ubound=std::numeric_limits< double >::max()) | PLMD::SingleDomainRMSD | inlinevirtual |
| setReferenceAtoms(const std::vector< Vector > &conf, const std::vector< double > &align_in, const std::vector< double > &displace_in) override | PLMD::SingleDomainRMSD | virtual |
| setupPCAStorage(ReferenceValuePack &mypack) override | PLMD::SimpleRMSD | inlinevirtual |
| setupRMSDObject() | PLMD::SingleDomainRMSD | inlinevirtual |
| SimpleRMSD(const ReferenceConfigurationOptions &ro) | PLMD::SimpleRMSD | explicit |
| singleDomainRequests(std::vector< AtomNumber > &, bool disable_checks) | PLMD::ReferenceAtoms | protected |
| SingleDomainRMSD(const ReferenceConfigurationOptions &ro) | PLMD::SingleDomainRMSD | explicit |
| ~ReferenceConfiguration() | PLMD::ReferenceConfiguration | virtual |
1.8.17