| A_3TE enum value | PLMD::isdb::SAXS | private |
| A_5TE enum value | PLMD::isdb::SAXS | private |
| A_BB1 enum value | PLMD::isdb::SAXS | private |
| A_BB2 enum value | PLMD::isdb::SAXS | private |
| A_BB3 enum value | PLMD::isdb::SAXS | private |
| A_SC1 enum value | PLMD::isdb::SAXS | private |
| A_SC2 enum value | PLMD::isdb::SAXS | private |
| A_SC3 enum value | PLMD::isdb::SAXS | private |
| A_SC4 enum value | PLMD::isdb::SAXS | private |
| A_TE3 enum value | PLMD::isdb::SAXS | private |
| A_TE5 enum value | PLMD::isdb::SAXS | 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_BB enum value | PLMD::isdb::SAXS | private |
| allowToAccessGlobalForces() | PLMD::ActionAtomistic | inline |
| apply() override | PLMD::isdb::MetainferenceBase | inlinevirtual |
| applyForces() | PLMD::ActionAtomistic | |
| ARG_BB enum value | PLMD::isdb::SAXS | private |
| ARG_SC1 enum value | PLMD::isdb::SAXS | private |
| ARG_SC2 enum value | PLMD::isdb::SAXS | private |
| ASN_BB enum value | PLMD::isdb::SAXS | private |
| ASN_SC1 enum value | PLMD::isdb::SAXS | private |
| ASP_BB enum value | PLMD::isdb::SAXS | private |
| ASP_SC1 enum value | PLMD::isdb::SAXS | private |
| atoi | PLMD::isdb::SAXS | private |
| atoms | PLMD::ActionAtomistic | protected |
| beforeUpdate() | PLMD::Action | inlinevirtual |
| bringBackInPbc(int i, double d1) const | PLMD::ActionWithArguments | inline |
| C enum value | PLMD::isdb::SAXS | private |
| C_3TE enum value | PLMD::isdb::SAXS | private |
| C_5TE enum value | PLMD::isdb::SAXS | private |
| C_BB1 enum value | PLMD::isdb::SAXS | private |
| C_BB2 enum value | PLMD::isdb::SAXS | private |
| C_BB3 enum value | PLMD::isdb::SAXS | private |
| C_SC1 enum value | PLMD::isdb::SAXS | private |
| C_SC2 enum value | PLMD::isdb::SAXS | private |
| C_SC3 enum value | PLMD::isdb::SAXS | private |
| C_TE3 enum value | PLMD::isdb::SAXS | private |
| C_TE5 enum value | PLMD::isdb::SAXS | private |
| calculate() override | PLMD::isdb::SAXS | virtual |
| calculate_cpu(std::vector< Vector > &deriv) | PLMD::isdb::SAXS | private |
| calculate_gpu(std::vector< Vector > &deriv) | PLMD::isdb::SAXS | private |
| calculateASF(const std::vector< AtomNumber > &atoms, std::vector< std::vector< long double > > &FF_tmp, const double rho) | PLMD::isdb::SAXS | private |
| calculateAtomicNumericalDerivatives(ActionWithValue *a, const unsigned &startnum) | PLMD::ActionAtomistic | |
| calculateFromPDB(const PDB &) | PLMD::Action | |
| calculateNumericalDerivatives(ActionWithValue *a) override | PLMD::isdb::MetainferenceBase | inlinevirtual |
| 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 override | 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 |
| copyOutput(const std::string &name) const | PLMD::ActionWithValue | |
| copyOutput(const unsigned &n) const | PLMD::ActionWithValue | |
| CYS_BB enum value | PLMD::isdb::SAXS | private |
| CYS_SC1 enum value | PLMD::isdb::SAXS | private |
| DA_3TE enum value | PLMD::isdb::SAXS | private |
| DA_5TE enum value | PLMD::isdb::SAXS | private |
| DA_BB1 enum value | PLMD::isdb::SAXS | private |
| DA_BB2 enum value | PLMD::isdb::SAXS | private |
| DA_BB3 enum value | PLMD::isdb::SAXS | private |
| DA_SC1 enum value | PLMD::isdb::SAXS | private |
| DA_SC2 enum value | PLMD::isdb::SAXS | private |
| DA_SC3 enum value | PLMD::isdb::SAXS | private |
| DA_SC4 enum value | PLMD::isdb::SAXS | private |
| DA_TE3 enum value | PLMD::isdb::SAXS | private |
| DA_TE5 enum value | PLMD::isdb::SAXS | private |
| DC_3TE enum value | PLMD::isdb::SAXS | private |
| DC_5TE enum value | PLMD::isdb::SAXS | private |
| DC_BB1 enum value | PLMD::isdb::SAXS | private |
| DC_BB2 enum value | PLMD::isdb::SAXS | private |
| DC_BB3 enum value | PLMD::isdb::SAXS | private |
| DC_SC1 enum value | PLMD::isdb::SAXS | private |
| DC_SC2 enum value | PLMD::isdb::SAXS | private |
| DC_SC3 enum value | PLMD::isdb::SAXS | private |
| DC_TE3 enum value | PLMD::isdb::SAXS | private |
| DC_TE5 enum value | PLMD::isdb::SAXS | private |
| deactivate() | PLMD::Action | inlinevirtual |
| Dependencies typedef | PLMD::Action | |
| deviceid | PLMD::isdb::SAXS | private |
| DG_3TE enum value | PLMD::isdb::SAXS | private |
| DG_5TE enum value | PLMD::isdb::SAXS | private |
| DG_BB1 enum value | PLMD::isdb::SAXS | private |
| DG_BB2 enum value | PLMD::isdb::SAXS | private |
| DG_BB3 enum value | PLMD::isdb::SAXS | private |
| DG_SC1 enum value | PLMD::isdb::SAXS | private |
| DG_SC2 enum value | PLMD::isdb::SAXS | private |
| DG_SC3 enum value | PLMD::isdb::SAXS | private |
| DG_SC4 enum value | PLMD::isdb::SAXS | private |
| DG_TE3 enum value | PLMD::isdb::SAXS | private |
| DG_TE5 enum value | PLMD::isdb::SAXS | private |
| difference(int, double, double) const | PLMD::ActionWithArguments | inline |
| doNotCalculateDerivatives() const | PLMD::ActionWithValue | inlinevirtual |
| doNotForce() | PLMD::ActionAtomistic | inline |
| doNotRetrieve() | PLMD::ActionAtomistic | inline |
| DT_3TE enum value | PLMD::isdb::SAXS | private |
| DT_5TE enum value | PLMD::isdb::SAXS | private |
| DT_BB1 enum value | PLMD::isdb::SAXS | private |
| DT_BB2 enum value | PLMD::isdb::SAXS | private |
| DT_BB3 enum value | PLMD::isdb::SAXS | private |
| DT_SC1 enum value | PLMD::isdb::SAXS | private |
| DT_SC2 enum value | PLMD::isdb::SAXS | private |
| DT_SC3 enum value | PLMD::isdb::SAXS | private |
| DT_TE3 enum value | PLMD::isdb::SAXS | private |
| DT_TE5 enum value | PLMD::isdb::SAXS | private |
| error(const std::string &msg) const | PLMD::Action | |
| exists(const std::string &name) const | PLMD::ActionWithValue | |
| exit(int c=0) | PLMD::Action | |
| expandArgKeywordInPDB(const PDB &pdb) | PLMD::ActionWithArguments | protected |
| fclose(FILE *fp) | PLMD::Action | |
| FF_rank | PLMD::isdb::SAXS | private |
| FF_value | PLMD::isdb::SAXS | private |
| FFf_value | PLMD::isdb::SAXS | private |
| fflush() | PLMD::Action | |
| files | PLMD::Action | |
| fopen(const char *path, const char *mode) | PLMD::Action | |
| G_3TE enum value | PLMD::isdb::SAXS | private |
| G_5TE enum value | PLMD::isdb::SAXS | private |
| G_BB1 enum value | PLMD::isdb::SAXS | private |
| G_BB2 enum value | PLMD::isdb::SAXS | private |
| G_BB3 enum value | PLMD::isdb::SAXS | private |
| G_SC1 enum value | PLMD::isdb::SAXS | private |
| G_SC2 enum value | PLMD::isdb::SAXS | private |
| G_SC3 enum value | PLMD::isdb::SAXS | private |
| G_SC4 enum value | PLMD::isdb::SAXS | private |
| G_TE3 enum value | PLMD::isdb::SAXS | private |
| G_TE5 enum value | PLMD::isdb::SAXS | 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 | inlinevirtual |
| 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 | |
| getGlobalPosition(AtomNumber) const | PLMD::ActionAtomistic | inline |
| getKeyword(const std::string &key) | PLMD::Action | |
| getLabel() const | PLMD::Action | inline |
| getMartiniSFparam(const std::vector< AtomNumber > &atoms, std::vector< std::vector< long double > > ¶meter) | PLMD::isdb::SAXS | private |
| 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() override | 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 |
| 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_BB enum value | PLMD::isdb::SAXS | private |
| GLN_SC1 enum value | PLMD::isdb::SAXS | private |
| GLU_BB enum value | PLMD::isdb::SAXS | private |
| GLU_SC1 enum value | PLMD::isdb::SAXS | private |
| GLY_BB enum value | PLMD::isdb::SAXS | private |
| gpu | PLMD::isdb::SAXS | private |
| H enum value | PLMD::isdb::SAXS | private |
| HIS_BB enum value | PLMD::isdb::SAXS | private |
| HIS_SC1 enum value | PLMD::isdb::SAXS | private |
| HIS_SC2 enum value | PLMD::isdb::SAXS | private |
| HIS_SC3 enum value | PLMD::isdb::SAXS | private |
| ILE_BB enum value | PLMD::isdb::SAXS | private |
| ILE_SC1 enum value | PLMD::isdb::SAXS | 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 | |
| isActive() const | PLMD::Action | inline |
| isOptionOn(const std::string &s) const | PLMD::Action | inline |
| keywords | PLMD::Action | |
| LEU_BB enum value | PLMD::isdb::SAXS | private |
| LEU_SC1 enum value | PLMD::isdb::SAXS | private |
| lockRequests() override | PLMD::isdb::MetainferenceBase | inlinevirtual |
| log | PLMD::Action | |
| LYS_BB enum value | PLMD::isdb::SAXS | private |
| LYS_SC1 enum value | PLMD::isdb::SAXS | private |
| LYS_SC2 enum value | PLMD::isdb::SAXS | private |
| makeWhole() | PLMD::ActionAtomistic | |
| MET_BB enum value | PLMD::isdb::SAXS | private |
| MET_SC1 enum value | PLMD::isdb::SAXS | private |
| MetainferenceBase(const ActionOptions &) | PLMD::isdb::MetainferenceBase | explicit |
| modifyForceOnEnergy() | PLMD::ActionAtomistic | inline |
| modifyForceOnExtraCV() | PLMD::ActionAtomistic | inline |
| modifyForces() | PLMD::ActionAtomistic | inline |
| modifyGlobalForce(AtomNumber) | PLMD::ActionAtomistic | inline |
| modifyGlobalPbc() | PLMD::ActionAtomistic | inline |
| modifyGlobalPosition(AtomNumber) | PLMD::ActionAtomistic | inline |
| modifyGlobalVirial() | PLMD::ActionAtomistic | inline |
| modifyVirial() | PLMD::ActionAtomistic | inline |
| multi_sim_comm | PLMD::Action | |
| N enum value | PLMD::isdb::SAXS | private |
| NMARTINI enum value | PLMD::isdb::SAXS | private |
| noAnalyticalDerivatives(Keywords &keys) | PLMD::ActionWithValue | static |
| NTT enum value | PLMD::isdb::SAXS | private |
| O enum value | PLMD::isdb::SAXS | private |
| P enum value | PLMD::isdb::SAXS | private |
| 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::SAXS | private |
| pbcApply(std::vector< Vector > &dlist, unsigned max_index=0) const | PLMD::ActionAtomistic | |
| pbcDistance(const Vector &, const Vector &) const | PLMD::ActionAtomistic | |
| PHE_BB enum value | PLMD::isdb::SAXS | private |
| PHE_SC1 enum value | PLMD::isdb::SAXS | private |
| PHE_SC2 enum value | PLMD::isdb::SAXS | private |
| PHE_SC3 enum value | PLMD::isdb::SAXS | private |
| plumed | PLMD::Action | |
| prepare() | PLMD::Action | virtual |
| PRO_BB enum value | PLMD::isdb::SAXS | private |
| PRO_SC1 enum value | PLMD::isdb::SAXS | private |
| q_list | PLMD::isdb::SAXS | private |
| readAtomsFromPDB(const PDB &pdb) override | PLMD::ActionAtomistic | virtual |
| registerKeywords(Keywords &keys) | PLMD::isdb::SAXS | static |
| requestArguments(const std::vector< Value *> &arg) | PLMD::ActionWithArguments | |
| requestAtoms(const std::vector< AtomNumber > &a, const bool clearDep=true) | PLMD::ActionAtomistic | |
| requestExtraDependencies(const std::vector< Value *> &extra) | PLMD::ActionWithArguments | |
| retrieveAtoms() | PLMD::ActionAtomistic | virtual |
| runFinalJobs() | PLMD::Action | inlinevirtual |
| S enum value | PLMD::isdb::SAXS | private |
| SAXS(const ActionOptions &) | PLMD::isdb::SAXS | explicit |
| Selector() | PLMD::isdb::MetainferenceBase | |
| SER_BB enum value | PLMD::isdb::SAXS | private |
| SER_SC1 enum value | PLMD::isdb::SAXS | private |
| serial | PLMD::isdb::SAXS | 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 |
| setExtraCV(const std::string &name) | PLMD::ActionAtomistic | inlineprotected |
| 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 | |
| THR_BB enum value | PLMD::isdb::SAXS | private |
| THR_SC1 enum value | PLMD::isdb::SAXS | private |
| TRP_BB enum value | PLMD::isdb::SAXS | private |
| TRP_SC1 enum value | PLMD::isdb::SAXS | private |
| TRP_SC2 enum value | PLMD::isdb::SAXS | private |
| TRP_SC3 enum value | PLMD::isdb::SAXS | private |
| TRP_SC4 enum value | PLMD::isdb::SAXS | private |
| turnOnDerivatives() override | PLMD::isdb::MetainferenceBase | inlinevirtual |
| TYR_BB enum value | PLMD::isdb::SAXS | private |
| TYR_SC1 enum value | PLMD::isdb::SAXS | private |
| TYR_SC2 enum value | PLMD::isdb::SAXS | private |
| TYR_SC3 enum value | PLMD::isdb::SAXS | private |
| U_3TE enum value | PLMD::isdb::SAXS | private |
| U_5TE enum value | PLMD::isdb::SAXS | private |
| U_BB1 enum value | PLMD::isdb::SAXS | private |
| U_BB2 enum value | PLMD::isdb::SAXS | private |
| U_BB3 enum value | PLMD::isdb::SAXS | private |
| U_SC1 enum value | PLMD::isdb::SAXS | private |
| U_SC2 enum value | PLMD::isdb::SAXS | private |
| U_SC3 enum value | PLMD::isdb::SAXS | private |
| U_TE3 enum value | PLMD::isdb::SAXS | private |
| U_TE5 enum value | PLMD::isdb::SAXS | private |
| unlockRequests() override | PLMD::isdb::MetainferenceBase | inlinevirtual |
| update() override | PLMD::isdb::SAXS | virtual |
| updateUniqueLocal() | PLMD::ActionAtomistic | |
| useCustomisableComponents(Keywords &keys) | PLMD::ActionWithValue | static |
| useNumericalDerivatives() | PLMD::ActionWithValue | inline |
| VAL_BB enum value | PLMD::isdb::SAXS | private |
| VAL_SC1 enum value | PLMD::isdb::SAXS | private |
| warning(const std::string &msg) | PLMD::Action | |
| writeStatus() | PLMD::isdb::MetainferenceBase | |
| ~Action() | PLMD::Action | virtual |
| ~ActionAtomistic() | PLMD::ActionAtomistic | |
| ~ActionWithArguments() | PLMD::ActionWithArguments | inlinevirtual |
| ~ActionWithValue() | PLMD::ActionWithValue | |
| ~MetainferenceBase() | PLMD::isdb::MetainferenceBase | |
1.8.14