| accumulateDerivative(const unsigned &ider, const double &df) | PLMD::vesselbase::ActionWithVessel | inlineprotected |
| Action(const ActionOptions &) | PLMD::Action | |
| ActionAtomistic(const ActionOptions &ao) | PLMD::ActionAtomistic | |
| ActionWithValue(const ActionOptions &ao) | PLMD::ActionWithValue | |
| ActionWithVessel(const ActionOptions &ao) | PLMD::vesselbase::ActionWithVessel | |
| activate() | PLMD::Action | virtual |
| addBridgingVessel(ActionWithVessel *tome) | PLMD::vesselbase::ActionWithVessel | protected |
| addColvar(const std::vector< unsigned > &newatoms) | PLMD::secondarystructure::SecondaryStructureRMSD | protected |
| addComponent(const std::string &name) | PLMD::ActionWithValue | |
| addComponentWithDerivatives(const std::string &name) | PLMD::ActionWithValue | |
| addDependency(Action *) | PLMD::Action | |
| addElementDerivative(const unsigned &, const double &) | PLMD::vesselbase::ActionWithVessel | inline |
| addValue() | PLMD::ActionWithValue | |
| addValueWithDerivatives() | PLMD::ActionWithValue | |
| addVessel(const std::string &name, const std::string &input, const int numlab=0, const std::string thislab="") | PLMD::vesselbase::ActionWithVessel | protected |
| addVessel(Vessel *vv) | PLMD::vesselbase::ActionWithVessel | protected |
| AlphaRMSD(const ActionOptions &) | PLMD::secondarystructure::AlphaRMSD | |
| apply() | PLMD::secondarystructure::SecondaryStructureRMSD | virtual |
| applyBridgeForces(const std::vector< double > &bb) | PLMD::vesselbase::ActionWithVessel | inlinevirtual |
| applyForces() | PLMD::ActionAtomistic | |
| atoms | PLMD::ActionAtomistic | protected |
| bridgeVariable | PLMD::vesselbase::ActionWithVessel | protected |
| calculate() | PLMD::secondarystructure::SecondaryStructureRMSD | virtual |
| calculateAllVessels() | PLMD::vesselbase::ActionWithVessel | protected |
| calculateAtomicNumericalDerivatives(ActionWithValue *a, const unsigned &startnum) | PLMD::ActionAtomistic | |
| calculateFromPDB(const PDB &) | PLMD::Action | |
| calculateNumericalDerivatives(ActionWithValue *a=NULL) | PLMD::ActionAtomistic | virtual |
| chainRuleForElementDerivatives(const unsigned &, const unsigned &, const double &, Vessel *) | PLMD::vesselbase::ActionWithVessel | |
| chainRuleForElementDerivatives(const unsigned &, const unsigned &, const unsigned &, const unsigned &, const double &, Vessel *) | PLMD::vesselbase::ActionWithVessel | |
| checkFieldsAllowed() | PLMD::ActionWithValue | inlinevirtual |
| checkNeedsGradients() const | PLMD::Action | inlinevirtual |
| PLMD::checkNumericalDerivatives() const | PLMD::Action | inlinevirtual |
| PLMD::ActionWithValue::checkNumericalDerivatives() const | PLMD::ActionWithValue | inlinevirtual |
| checkRead() | PLMD::Action | |
| cite(const std::string &s) | PLMD::Action | |
| clearAfterTask() | PLMD::vesselbase::ActionWithVessel | protected |
| clearDependencies() | PLMD::Action | |
| clearDerivatives() | PLMD::ActionWithValue | virtual |
| clearDerivativesAfterTask(const unsigned &) | PLMD::secondarystructure::SecondaryStructureRMSD | inlinevirtual |
| clearInputForces() | PLMD::ActionWithValue | |
| clearOptions() | PLMD::Action | virtual |
| clearOutputForces() | PLMD::ActionAtomistic | inline |
| comm | PLMD::Action | |
| componentIsNotPeriodic(const std::string &name) | PLMD::ActionWithValue | |
| componentIsPeriodic(const std::string &name, const std::string &min, const std::string &max) | PLMD::ActionWithValue | |
| componentsAreNotOptional(Keywords &keys) | PLMD::ActionWithValue | static |
| contributorsAreUnlocked | PLMD::vesselbase::ActionWithVessel | protected |
| copyOutput(const std::string &name) const | PLMD::ActionWithValue | |
| copyOutput(const unsigned &n) const | PLMD::ActionWithValue | |
| current | PLMD::vesselbase::ActionWithVessel | protected |
| deactivate() | PLMD::Action | inlinevirtual |
| deactivate_task() | PLMD::vesselbase::ActionWithVessel | virtual |
| Dependencies typedef | PLMD::Action | |
| doJobsRequiredBeforeTaskList() | PLMD::vesselbase::ActionWithVessel | virtual |
| error(const std::string &msg) const | PLMD::Action | |
| exists(const std::string &name) const | PLMD::ActionWithValue | |
| exit(int c=0) | PLMD::Action | |
| fclose(FILE *fp) | PLMD::Action | |
| fflush() | PLMD::Action | |
| files | PLMD::Action | |
| files_iterator typedef | PLMD::Action | |
| finishComputations() | PLMD::vesselbase::ActionWithVessel | protected |
| fopen(const char *path, const char *mode) | PLMD::Action | |
| getAbsoluteIndex(int i) const | PLMD::ActionAtomistic | inline |
| getAbsoluteIndexes() const | PLMD::ActionAtomistic | inline |
| getBox() const | PLMD::ActionAtomistic | inline |
| getCharge(int i) const | PLMD::ActionAtomistic | inline |
| getComponentsList() const | PLMD::ActionWithValue | |
| getComponentsVector() const | PLMD::ActionWithValue | |
| getDependencies() const | PLMD::Action | inline |
| getDocumentation() const | PLMD::Action | virtual |
| getElementDerivative(const unsigned &) const | PLMD::vesselbase::ActionWithVessel | inline |
| getElementValue(const unsigned &ival) const | PLMD::vesselbase::ActionWithVessel | inline |
| getEnergy() const | PLMD::ActionAtomistic | inline |
| getExchangeStep() const | PLMD::Action | |
| getForcesFromVessels(std::vector< double > &forcesToApply) | PLMD::vesselbase::ActionWithVessel | protected |
| getLabel() const | PLMD::Action | inline |
| getMass(int i) const | PLMD::ActionAtomistic | inline |
| getName() const | PLMD::Action | inline |
| getNLTolerance() const | PLMD::vesselbase::ActionWithVessel | inlineprotected |
| getNumberOfAtoms() const | PLMD::ActionAtomistic | inline |
| getNumberOfComponents() const | PLMD::ActionWithValue | inline |
| getNumberOfDerivatives() | PLMD::secondarystructure::SecondaryStructureRMSD | inlinevirtual |
| getNumberOfFunctionsInAction() | PLMD::secondarystructure::SecondaryStructureRMSD | inline |
| getNumberOfVessels() const | PLMD::vesselbase::ActionWithVessel | inlineprotected |
| getOutputQuantity(const unsigned j) const | PLMD::ActionWithValue | inline |
| getOutputQuantity(const std::string &name) const | PLMD::ActionWithValue | inline |
| getPbc() const | PLMD::ActionAtomistic | inline |
| getPntrToComponent(int i) | PLMD::ActionWithValue | protected |
| getPntrToComponent(const std::string &name) | PLMD::ActionWithValue | protected |
| getPntrToValue() | PLMD::ActionWithValue | protected |
| getPntrToVessel(const unsigned &i) | PLMD::vesselbase::ActionWithVessel | inlineprotected |
| getPosition(int) const | PLMD::ActionAtomistic | inline |
| getPositions() const | PLMD::ActionAtomistic | inline |
| getStep() const | PLMD::Action | |
| getTime() const | PLMD::Action | |
| getTimeStep() const | PLMD::Action | |
| getTolerance() const | PLMD::vesselbase::ActionWithVessel | inlineprotected |
| getUnique() const | PLMD::ActionAtomistic | inline |
| getVessel(const std::string &name) | PLMD::vesselbase::ActionWithVessel | |
| isActive() const | PLMD::Action | inline |
| isOptionOn(const std::string &s) const | PLMD::Action | inline |
| isPeriodic() | PLMD::secondarystructure::SecondaryStructureRMSD | inlinevirtual |
| keywords | PLMD::Action | |
| lockContributors() | PLMD::vesselbase::ActionWithVessel | inlinevirtual |
| lockRequests() | PLMD::ActionAtomistic | inlinevirtual |
| log | PLMD::Action | |
| mergeDerivatives(const unsigned &, const double &) | PLMD::secondarystructure::SecondaryStructureRMSD | virtual |
| mergeFieldDerivatives(const std::vector< double > &derivatives, Value *val_out) | PLMD::ActionWithValue | virtual |
| modifyForceOnEnergy() | PLMD::ActionAtomistic | inline |
| modifyForces() | PLMD::ActionAtomistic | inline |
| modifyVirial() | PLMD::ActionAtomistic | inline |
| multi_sim_comm | PLMD::Action | |
| noAnalyticalDerivatives(Keywords &keys) | PLMD::ActionWithValue | static |
| parse(const std::string &key, T &t) | PLMD::Action | |
| parseAtomList(const std::string &key, std::vector< AtomNumber > &t) | PLMD::ActionAtomistic | |
| parseAtomList(const std::string &key, const int num, std::vector< AtomNumber > &t) | PLMD::ActionAtomistic | |
| parseFlag(const std::string &key, bool &t) | PLMD::Action | |
| parseNumbered(const std::string &key, const int no, T &t) | PLMD::Action | |
| parseNumberedVector(const std::string &key, const int no, std::vector< T > &t) | PLMD::Action | |
| parseVector(const std::string &key, std::vector< T > &t) | PLMD::Action | |
| pbcDistance(const Vector &, const Vector &) const | PLMD::ActionAtomistic | |
| performTask(const unsigned &j) | PLMD::secondarystructure::SecondaryStructureRMSD | virtual |
| plumed | PLMD::Action | |
| prepare() | PLMD::secondarystructure::SecondaryStructureRMSD | virtual |
| readAtomsFromPDB(const PDB &pdb) | PLMD::ActionAtomistic | virtual |
| readBackboneAtoms(const std::vector< std::string > &backnames, std::vector< unsigned > &chain_lengths) | PLMD::secondarystructure::SecondaryStructureRMSD | protected |
| readVesselKeywords() | PLMD::vesselbase::ActionWithVessel | protected |
| registerKeywords(Keywords &keys) | PLMD::secondarystructure::AlphaRMSD | static |
| requestAtoms(const std::vector< AtomNumber > &a) | PLMD::ActionAtomistic | |
| resizeFunctions() | PLMD::vesselbase::ActionWithVessel | protected |
| retrieveAtoms() | PLMD::ActionAtomistic | |
| retrieveDomain(std::string &min, std::string &max) | PLMD::vesselbase::ActionWithVessel | virtual |
| runAllTasks() | PLMD::vesselbase::ActionWithVessel | protected |
| runFinalJobs() | PLMD::Action | inlinevirtual |
| SecondaryStructureRMSD(const ActionOptions &) | PLMD::secondarystructure::SecondaryStructureRMSD | |
| setAtomsFromStrands(const unsigned &atom1, const unsigned &atom2) | PLMD::secondarystructure::SecondaryStructureRMSD | protected |
| setElementDerivative(const unsigned &, const double &) | PLMD::vesselbase::ActionWithVessel | inlineprotected |
| setElementValue(const unsigned &, const double &) | PLMD::vesselbase::ActionWithVessel | inline |
| setForcesOnAtoms(const std::vector< double > &forcesToApply, unsigned ind=0) | PLMD::ActionAtomistic | |
| setGradientsIfNeeded() | PLMD::ActionWithValue | |
| setNotPeriodic() | PLMD::ActionWithValue | |
| setOption(const std::string &s) | PLMD::Action | virtual |
| setPeriodic(const std::string &min, const std::string &max) | PLMD::ActionWithValue | |
| setSecondaryStructure(std::vector< Vector > &structure, double bondlength, double units) | PLMD::secondarystructure::SecondaryStructureRMSD | protected |
| setValue(const double &d) | PLMD::ActionWithValue | inlineprotected |
| setValue(Value *, double) | PLMD::ActionWithValue | |
| taskList | PLMD::vesselbase::ActionWithVessel | protected |
| unlockContributors() | PLMD::vesselbase::ActionWithVessel | inlinevirtual |
| unlockRequests() | PLMD::ActionAtomistic | inlinevirtual |
| update() | PLMD::Action | inlinevirtual |
| useCustomisableComponents(Keywords &keys) | PLMD::ActionWithValue | static |
| useNumericalDerivatives() | PLMD::ActionWithValue | inline |
| warning(const std::string &msg) | PLMD::Action | |
| weightHasDerivatives | PLMD::vesselbase::ActionWithVessel | protected |
| ~Action() | PLMD::Action | virtual |
| ~ActionAtomistic() | PLMD::ActionAtomistic | |
| ~ActionWithValue() | PLMD::ActionWithValue | |
| ~ActionWithVessel() | PLMD::vesselbase::ActionWithVessel | |
| ~SecondaryStructureRMSD() | PLMD::secondarystructure::SecondaryStructureRMSD | virtual |
1.8.8