| aa_t enum name | PLMD::isdb::CS2Backbone | private |
| Action(const ActionOptions &) | PLMD::Action | explicit |
| ActionAtomistic(const ActionOptions &ao) | PLMD::ActionAtomistic | explicit |
| ActionWithArguments(const ActionOptions &) | PLMD::ActionWithArguments | explicit |
| ActionWithValue(const ActionOptions &ao) | PLMD::ActionWithValue | explicit |
| activate() | PLMD::Action | virtual |
| addComponent(const std::string &name) | PLMD::ActionWithValue | |
| addComponentWithDerivatives(const std::string &name) | PLMD::ActionWithValue | |
| addDependency(Action *) | PLMD::Action | |
| addForcesOnArguments(const std::vector< double > &forces) | PLMD::ActionWithArguments | |
| addValue() | PLMD::ActionWithValue | |
| addValueWithDerivatives() | PLMD::ActionWithValue | |
| ALA enum value | PLMD::isdb::CS2Backbone | private |
| allowToAccessGlobalForces() | PLMD::ActionAtomistic | inline |
| apply() | PLMD::isdb::MetainferenceBase | inlinevirtual |
| applyForces() | PLMD::ActionAtomistic | |
| ARG enum value | PLMD::isdb::CS2Backbone | private |
| ASN enum value | PLMD::isdb::CS2Backbone | private |
| ASP enum value | PLMD::isdb::CS2Backbone | private |
| atom | PLMD::isdb::CS2Backbone | private |
| atom_t enum name | PLMD::isdb::CS2Backbone | private |
| atoms | PLMD::ActionAtomistic | protected |
| beforeUpdate() | PLMD::Action | inlinevirtual |
| box_count | PLMD::isdb::CS2Backbone | private |
| box_nupdate | PLMD::isdb::CS2Backbone | private |
| bringBackInPbc(int i, double d1) const | PLMD::ActionWithArguments | inline |
| calculate() | PLMD::isdb::CS2Backbone | virtual |
| calculateAtomicNumericalDerivatives(ActionWithValue *a, const unsigned &startnum) | PLMD::ActionAtomistic | |
| calculateFromPDB(const PDB &) | PLMD::Action | |
| calculateNumericalDerivatives(ActionWithValue *a) | PLMD::isdb::MetainferenceBase | inlinevirtual |
| camshift | PLMD::isdb::CS2Backbone | private |
| changeBox(const Tensor &newbox) | PLMD::ActionAtomistic | |
| 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 | |
| checkUpdate() const | PLMD::Action | |
| cite(const std::string &s) | PLMD::Action | |
| clearDependencies() | PLMD::Action | |
| clearDerivatives() | PLMD::ActionWithValue | virtual |
| clearInputForces() | PLMD::ActionWithValue | |
| clearOptions() | PLMD::Action | virtual |
| clearOutputForces() | PLMD::ActionAtomistic | |
| 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 |
| compute_dihedrals() | PLMD::isdb::CS2Backbone | private |
| compute_ring_parameters() | PLMD::isdb::CS2Backbone | private |
| copyOutput(const std::string &name) const | PLMD::ActionWithValue | |
| copyOutput(const unsigned &n) const | PLMD::ActionWithValue | |
| CS2Backbone(const ActionOptions &) | PLMD::isdb::CS2Backbone | explicit |
| CYS enum value | PLMD::isdb::CS2Backbone | private |
| D_C enum value | PLMD::isdb::CS2Backbone | private |
| D_C2 enum value | PLMD::isdb::CS2Backbone | private |
| D_H enum value | PLMD::isdb::CS2Backbone | private |
| D_N enum value | PLMD::isdb::CS2Backbone | private |
| D_N2 enum value | PLMD::isdb::CS2Backbone | private |
| D_O enum value | PLMD::isdb::CS2Backbone | private |
| D_O2 enum value | PLMD::isdb::CS2Backbone | private |
| D_S enum value | PLMD::isdb::CS2Backbone | private |
| db | PLMD::isdb::CS2Backbone | private |
| deactivate() | PLMD::Action | inlinevirtual |
| debug_report() | PLMD::isdb::CS2Backbone | private |
| Dependencies typedef | PLMD::Action | |
| difference(int, double, double) const | PLMD::ActionWithArguments | inline |
| doNotCalculateDerivatives() const | PLMD::ActionWithValue | inlinevirtual |
| doNotForce() | PLMD::ActionAtomistic | inline |
| doNotRetrieve() | PLMD::ActionAtomistic | inline |
| error(const std::string &msg) const | PLMD::Action | |
| exists(const std::string &name) const | PLMD::ActionWithValue | |
| exit(int c=0) | PLMD::Action | |
| expandArgKeywordInPDB(PDB &pdb) | PLMD::ActionWithArguments | protected |
| fclose(FILE *fp) | PLMD::Action | |
| fflush() | PLMD::Action | |
| files | PLMD::Action | |
| fopen(const char *path, const char *mode) | PLMD::Action | |
| frag2enum(const string &aa) | PLMD::isdb::CS2Backbone | private |
| frag_relitive_index(const unsigned p, const unsigned s) | PLMD::isdb::CS2Backbone | private |
| frag_segment(const unsigned p) | PLMD::isdb::CS2Backbone | private |
| getAbsoluteIndex(int i) const | PLMD::ActionAtomistic | inline |
| getAbsoluteIndexes() const | PLMD::ActionAtomistic | inlinevirtual |
| getArgument(const unsigned n) const | PLMD::ActionWithArguments | inline |
| getArguments() const | PLMD::ActionWithArguments | inline |
| getBox() const | PLMD::ActionAtomistic | inline |
| getCharge(int i) const | PLMD::ActionAtomistic | inline |
| getComponentsList() const | PLMD::ActionWithValue | |
| getComponentsVector() const | PLMD::ActionWithValue | |
| getCPT() const | PLMD::Action | |
| getDependencies() const | PLMD::Action | inline |
| getDocumentation() const | PLMD::Action | virtual |
| getDoScore() | PLMD::isdb::MetainferenceBase | inline |
| getEnergy() const | PLMD::ActionAtomistic | inline |
| getExchangeStep() const | PLMD::Action | |
| getKeyword(const std::string &key) | PLMD::Action | |
| getLabel() const | PLMD::Action | inline |
| getMass(int i) const | PLMD::ActionAtomistic | inline |
| getMetaDer(const unsigned index) | PLMD::isdb::MetainferenceBase | inline |
| getName() const | PLMD::Action | inline |
| getNarg() | PLMD::isdb::MetainferenceBase | inline |
| getNumberOfArguments() const | PLMD::ActionWithArguments | inlinevirtual |
| getNumberOfAtoms() const | PLMD::ActionAtomistic | inline |
| getNumberOfComponents() const | PLMD::ActionWithValue | inline |
| getNumberOfDerivatives() | PLMD::isdb::MetainferenceBase | inlinevirtual |
| getOutputQuantity(const unsigned j) const | PLMD::ActionWithValue | inline |
| getOutputQuantity(const std::string &name) const | PLMD::ActionWithValue | inline |
| getPbc() const | PLMD::ActionAtomistic | inline |
| getPntrToArgument(const unsigned n) | PLMD::ActionWithArguments | inline |
| getPntrToComponent(int i) | PLMD::ActionWithValue | protected |
| getPntrToComponent(const std::string &name) | PLMD::ActionWithValue | protected |
| getPntrToValue() | PLMD::ActionWithValue | protected |
| getPosition(int) const | PLMD::ActionAtomistic | inline |
| getPosition(AtomNumber) const | PLMD::ActionAtomistic | inline |
| getPositions() const | PLMD::ActionAtomistic | inline |
| getProjection(unsigned i, unsigned j) const | PLMD::ActionWithArguments | |
| getRestart() const | PLMD::Action | inline |
| getScore() | PLMD::isdb::MetainferenceBase | |
| getStep() const | PLMD::Action | |
| getTime() const | PLMD::Action | |
| getTimeStep() const | PLMD::Action | |
| getTotAtoms() const | PLMD::ActionAtomistic | inline |
| getUnique() const | PLMD::ActionAtomistic | inline |
| getUniqueLocal() const | PLMD::ActionAtomistic | inline |
| getWstride() | PLMD::isdb::MetainferenceBase | inline |
| GLN enum value | PLMD::isdb::CS2Backbone | private |
| GLU enum value | PLMD::isdb::CS2Backbone | private |
| GLY enum value | PLMD::isdb::CS2Backbone | private |
| HIS enum value | PLMD::isdb::CS2Backbone | private |
| ILE enum value | PLMD::isdb::CS2Backbone | private |
| index_cs | PLMD::isdb::CS2Backbone | private |
| init_backbone(const PDB &pdb) | PLMD::isdb::CS2Backbone | private |
| init_rings(const PDB &pdb) | PLMD::isdb::CS2Backbone | private |
| init_sidechain(const PDB &pdb) | PLMD::isdb::CS2Backbone | private |
| init_types(const PDB &pdb) | PLMD::isdb::CS2Backbone | private |
| init_xdist(const PDB &pdb) | PLMD::isdb::CS2Backbone | private |
| Initialise(const unsigned input) | PLMD::isdb::MetainferenceBase | |
| interpretArgumentList(const std::vector< std::string > &c, std::vector< Value *> &arg) | PLMD::ActionWithArguments | |
| interpretAtomList(std::vector< std::string > &strings, std::vector< AtomNumber > &t) | PLMD::ActionAtomistic | |
| is_chi1_cx(const string &frg, const string &atm) | PLMD::isdb::CS2Backbone | private |
| isActive() const | PLMD::Action | inline |
| isOptionOn(const std::string &s) const | PLMD::Action | inline |
| isSP2(const string &resType, const string &atomName) | PLMD::isdb::CS2Backbone | private |
| keywords | PLMD::Action | |
| LEU enum value | PLMD::isdb::CS2Backbone | private |
| lockRequests() | PLMD::isdb::MetainferenceBase | inlinevirtual |
| log | PLMD::Action | |
| LYS enum value | PLMD::isdb::CS2Backbone | private |
| makeWhole() | PLMD::ActionAtomistic | |
| MET enum value | PLMD::isdb::CS2Backbone | private |
| MetainferenceBase(const ActionOptions &) | PLMD::isdb::MetainferenceBase | explicit |
| modifyForceOnEnergy() | PLMD::ActionAtomistic | inline |
| modifyForces() | PLMD::ActionAtomistic | inline |
| modifyGlobalForce(AtomNumber) | PLMD::ActionAtomistic | inline |
| modifyGlobalPbc() | PLMD::ActionAtomistic | inline |
| modifyGlobalVirial() | PLMD::ActionAtomistic | inline |
| modifyPosition(AtomNumber) | 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 | |
| parseArgumentList(const std::string &key, std::vector< Value *> &args) | PLMD::ActionWithArguments | |
| parseArgumentList(const std::string &key, int i, std::vector< Value *> &args) | PLMD::ActionWithArguments | |
| 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 | |
| pbc | PLMD::isdb::CS2Backbone | private |
| pbcApply(std::vector< Vector > &dlist, unsigned max_index=0) const | PLMD::ActionAtomistic | |
| pbcDistance(const Vector &, const Vector &) const | PLMD::ActionAtomistic | |
| PHE enum value | PLMD::isdb::CS2Backbone | private |
| plumed | PLMD::Action | |
| prepare() | PLMD::Action | virtual |
| PRO enum value | PLMD::isdb::CS2Backbone | private |
| read_cs(const string &file, const string &k) | PLMD::isdb::CS2Backbone | private |
| readAtomsFromPDB(const PDB &pdb) | PLMD::ActionAtomistic | virtual |
| registerKeywords(Keywords &keys) | PLMD::isdb::CS2Backbone | static |
| remove_problematic(const string &res, const string &nucl) | PLMD::isdb::CS2Backbone | private |
| requestArguments(const std::vector< Value *> &arg) | PLMD::ActionWithArguments | |
| requestAtoms(const std::vector< AtomNumber > &a) | PLMD::ActionAtomistic | |
| res_num | PLMD::isdb::CS2Backbone | private |
| retrieveAtoms() | PLMD::ActionAtomistic | virtual |
| ringInfo | PLMD::isdb::CS2Backbone | private |
| runFinalJobs() | PLMD::Action | inlinevirtual |
| seg_last | PLMD::isdb::CS2Backbone | private |
| Selector() | PLMD::isdb::MetainferenceBase | |
| SER enum value | PLMD::isdb::CS2Backbone | private |
| setArgDerivatives(Value *v, const double &d) | PLMD::isdb::MetainferenceBase | inline |
| setAtomsDerivatives(Value *v, const unsigned i, const Vector &d) | PLMD::isdb::MetainferenceBase | inline |
| setBoxDerivatives(Value *v, const Tensor &d) | PLMD::isdb::MetainferenceBase | inline |
| setCalcData(const unsigned index, const double datum) | PLMD::isdb::MetainferenceBase | inline |
| setCalcData(const std::vector< double > &data) | PLMD::isdb::MetainferenceBase | inline |
| setDerivatives() | PLMD::isdb::MetainferenceBase | inline |
| setForcesOnAtoms(const std::vector< double > &forcesToApply, unsigned ind=0) | PLMD::ActionAtomistic | |
| setGradientsIfNeeded() | PLMD::ActionWithValue | |
| setNarg(const unsigned input) | PLMD::isdb::MetainferenceBase | inline |
| setNotPeriodic() | PLMD::ActionWithValue | |
| setOption(const std::string &s) | PLMD::Action | virtual |
| setParameter(const double input) | PLMD::isdb::MetainferenceBase | inline |
| setParameters(const std::vector< double > &input) | PLMD::isdb::MetainferenceBase | inline |
| setPeriodic(const std::string &min, const std::string &max) | PLMD::ActionWithValue | |
| setScore(const double score) | PLMD::isdb::MetainferenceBase | inline |
| setValue(const double &d) | PLMD::ActionWithValue | inlineprotected |
| setValue(Value *, double) | PLMD::ActionWithValue | |
| side_chain_atoms(const string &s) | PLMD::isdb::CS2Backbone | private |
| THR enum value | PLMD::isdb::CS2Backbone | private |
| TRP enum value | PLMD::isdb::CS2Backbone | private |
| turnOnDerivatives() | PLMD::isdb::MetainferenceBase | inlinevirtual |
| type | PLMD::isdb::CS2Backbone | private |
| TYR enum value | PLMD::isdb::CS2Backbone | private |
| UNK enum value | PLMD::isdb::CS2Backbone | private |
| unlockRequests() | PLMD::isdb::MetainferenceBase | inlinevirtual |
| update() | PLMD::isdb::CS2Backbone | virtual |
| update_neighb() | PLMD::isdb::CS2Backbone | private |
| updateUniqueLocal() | PLMD::ActionAtomistic | |
| useCustomisableComponents(Keywords &keys) | PLMD::ActionWithValue | static |
| useNumericalDerivatives() | PLMD::ActionWithValue | inline |
| VAL enum value | PLMD::isdb::CS2Backbone | private |
| warning(const std::string &msg) | PLMD::Action | |
| writeStatus() | PLMD::isdb::MetainferenceBase | |
| xdist_name_map(string &name) | PLMD::isdb::CS2Backbone | private |
| ~Action() | PLMD::Action | virtual |
| ~ActionAtomistic() | PLMD::ActionAtomistic | |
| ~ActionWithArguments() | PLMD::ActionWithArguments | inlinevirtual |
| ~ActionWithValue() | PLMD::ActionWithValue | |
| ~MetainferenceBase() | PLMD::isdb::MetainferenceBase | |
1.8.14