| addAtomicDerivatives(const unsigned &, const Vector &) | PLMD::ReferenceAtoms | inlineprotected |
| addBoxDerivatives(const Tensor &) | PLMD::ReferenceAtoms | inlineprotected |
| align | PLMD::ReferenceAtoms | private |
| arg_ders | PLMD::ReferenceConfiguration | protected |
| atom_ders | PLMD::ReferenceConfiguration | protected |
| calc(const std::vector< Vector > &pos, const Pbc &pbc, const std::vector< Value * > &vals, const std::vector< double > &args, const bool &squared)=0 | PLMD::ReferenceConfiguration | pure virtual |
| calculate(const std::vector< Vector > &pos, const Pbc &pbc, const std::vector< Value * > &vals, const bool &squared=false) | PLMD::ReferenceConfiguration | |
| checkRead() | PLMD::ReferenceConfiguration | |
| checks_were_disabled | PLMD::ReferenceAtoms | private |
| clearDerivatives() | PLMD::ReferenceConfiguration | protected |
| copyDerivatives(const ReferenceConfiguration *) | PLMD::ReferenceConfiguration | |
| der_index | PLMD::ReferenceAtoms | private |
| displace | PLMD::ReferenceAtoms | private |
| error(const std::string &msg) | PLMD::ReferenceConfiguration | protected |
| getAbsoluteIndexes() | PLMD::ReferenceAtoms | inlinevirtual |
| getAlign() const | PLMD::ReferenceAtoms | inlineprotected |
| getArgumentDerivative(const unsigned &) const | PLMD::ReferenceConfiguration | inline |
| getArgumentNames() | PLMD::ReferenceConfiguration | inlinevirtual |
| getArgumentRequests(std::vector< std::string > &, bool disable_checks=false) | PLMD::ReferenceConfiguration | inlinevirtual |
| getAtomDerivative(const unsigned &) const | PLMD::ReferenceConfiguration | inline |
| getAtomIndex(const unsigned &) const | PLMD::ReferenceAtoms | inlineprotected |
| getAtomRequests(std::vector< AtomNumber > &, bool disable_checks=false) | PLMD::ReferenceAtoms | virtual |
| getDisplace() const | PLMD::ReferenceAtoms | inlineprotected |
| getName() const | PLMD::ReferenceConfiguration | |
| getNumberOfAtoms() const | PLMD::ReferenceAtoms | inlineprotected |
| getNumberOfReferencePositions() const | PLMD::ReferenceAtoms | inlineprotected |
| getReferenceArgument(const unsigned &i) | PLMD::ReferenceConfiguration | inlinevirtual |
| getReferenceArguments() | PLMD::ReferenceConfiguration | inlinevirtual |
| getReferenceMetric() | PLMD::ReferenceConfiguration | inlinevirtual |
| getReferencePosition(const unsigned &iatom) const | PLMD::ReferenceAtoms | inlineprotected |
| getReferencePositions() | PLMD::ReferenceAtoms | inlineprotectedvirtual |
| getVirial(Tensor &virout) const | PLMD::ReferenceConfiguration | |
| getWeight() const | PLMD::ReferenceConfiguration | inline |
| indices | PLMD::ReferenceAtoms | private |
| parse(const std::string &key, T &t, bool ignore_missing=false) | PLMD::ReferenceConfiguration | |
| parseAtomList(const std::string &, std::vector< unsigned > &) | PLMD::ReferenceAtoms | protected |
| parseFlag(const std::string &key, bool &t) | PLMD::ReferenceConfiguration | |
| parseVector(const std::string &key, std::vector< T > &t, bool ignore_missing=false) | PLMD::ReferenceConfiguration | |
| print(OFile &ofile, const double &time, const double &weight, const double &old_norm) | PLMD::ReferenceConfiguration | |
| print(OFile &ofile, const std::string &fmt) | PLMD::ReferenceConfiguration | |
| printAtoms(OFile &ofile) const | PLMD::ReferenceAtoms | |
| read(const PDB &)=0 | PLMD::ReferenceConfiguration | pure virtual |
| readAtomsFromPDB(const PDB &) | PLMD::ReferenceAtoms | protected |
| reference_atoms | PLMD::ReferenceAtoms | private |
| ReferenceAtoms(const ReferenceConfigurationOptions &ro) | PLMD::ReferenceAtoms | |
| ReferenceConfiguration(const ReferenceConfigurationOptions &ro) | PLMD::ReferenceConfiguration | |
| retrieveAtomicDerivatives(const unsigned &) const | PLMD::ReferenceAtoms | inlineprotected |
| set(const PDB &) | PLMD::ReferenceConfiguration | virtual |
| setAtomIndices(const std::vector< AtomNumber > &atomnumbers) | PLMD::ReferenceAtoms | protected |
| setAtomNumbers(const std::vector< AtomNumber > &numbers) | PLMD::ReferenceAtoms | |
| setNamesAndAtomNumbers(const std::vector< AtomNumber > &numbers, const std::vector< std::string > &arg) | PLMD::ReferenceConfiguration | |
| setNumberOfArguments(const unsigned &) | PLMD::ReferenceConfiguration | virtual |
| setNumberOfAtoms(const unsigned &) | PLMD::ReferenceConfiguration | virtual |
| setReferenceAtoms(const std::vector< Vector > &conf, const std::vector< double > &align_in, const std::vector< double > &displace_in)=0 | PLMD::ReferenceAtoms | pure virtual |
| setReferenceConfig(const std::vector< Vector > &pos, const std::vector< double > &arg, const std::vector< double > &metric) | PLMD::ReferenceConfiguration | |
| setWeight(const double &ww) | PLMD::ReferenceConfiguration | inline |
| singleDomainRequests(std::vector< AtomNumber > &, bool disable_checks) | PLMD::ReferenceAtoms | protected |
| SingleDomainRMSD class | PLMD::ReferenceAtoms | friend |
| virial | PLMD::ReferenceConfiguration | protected |
| virialWasSet | PLMD::ReferenceConfiguration | protected |
| ~ReferenceConfiguration() | PLMD::ReferenceConfiguration | virtual |
1.8.7