| 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 | |
| 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 |
| 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() | PLMD::ReferenceConfiguration | inlinevirtual |
| getReferenceMetric() | PLMD::ReferenceConfiguration | inlinevirtual |
| getReferencePositions() const | PLMD::ReferenceConfiguration | inlinevirtual |
| getWeight() const | PLMD::ReferenceConfiguration | inline |
| isDirection() const | PLMD::ReferenceConfiguration | |
| 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 | |
| projectAtomicDisplacementOnVector(const unsigned &i, const Matrix< Vector > &eigv, const std::vector< Vector > &pos, ReferenceValuePack &mypack) const | PLMD::ReferenceConfiguration | inlinevirtual |
| 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 |
1.8.14