| 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::FakeFrame | inlinevirtual |
| calculate(const std::vector< Vector > &pos, const Pbc &pbc, const std::vector< Value *> &vals, ReferenceValuePack &myder, const bool &squared=false) const | PLMD::ReferenceConfiguration | |
| copyDerivatives(const ReferenceConfiguration *) | PLMD::ReferenceConfiguration | |
| displaceReferenceConfiguration(const double &weight, Direction &dir) | PLMD::ReferenceConfiguration | |
| 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 | |
| FakeFrame(const ReferenceConfigurationOptions &ro) | PLMD::FakeFrame | inlineexplicit |
| 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 |
| pcaIsEnabledForThisReference() | PLMD::ReferenceConfiguration | 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::FakeFrame | inlinevirtual |
| ReferenceConfiguration(const ReferenceConfigurationOptions &ro) | PLMD::ReferenceConfiguration | explicit |
| setupPCAStorage(ReferenceValuePack &mypack) | PLMD::ReferenceConfiguration | inlinevirtual |
| ~ReferenceConfiguration() | PLMD::ReferenceConfiguration | virtual |