| A | PLMD::isdb::SAXS | private |
| 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 |
| absolute | PLMD::isdb::SAXS | private |
| Action(const ActionOptions &) | PLMD::Action | explicit |
| Action(const Action &a)=delete | PLMD::Action | private |
| ActionAtomistic(const ActionOptions &ao) | PLMD::ActionAtomistic | explicit |
| actionHasForces() | PLMD::ActionAtomistic | virtual |
| PLMD::ActionWithArguments(const ActionOptions &) | PLMD::ActionWithArguments | explicit |
| ActionWithValue(const ActionOptions &ao) | PLMD::ActionWithValue | explicit |
| activate() | PLMD::Action | virtual |
| active | PLMD::Action | private |
| addComponent(const std::string &name, const std::vector< unsigned > &shape=std::vector< unsigned >()) | PLMD::ActionWithValue | |
| addComponentWithDerivatives(const std::string &name, const std::vector< unsigned > &shape=std::vector< unsigned >()) | PLMD::ActionWithValue | virtual |
| addDependency(Action *) | PLMD::Action | |
| addForce(const std::pair< std::size_t, std::size_t > &a, const Vector &f) | PLMD::ActionAtomistic | inline |
| addForcesOnArguments(const unsigned &argstart, const std::vector< double > &forces, unsigned &ind, const std::string &c) | PLMD::ActionWithArguments | |
| addValue(const std::vector< unsigned > &shape=std::vector< unsigned >()) | PLMD::ActionWithValue | |
| addValueWithDerivatives(const std::vector< unsigned > &shape=std::vector< unsigned >()) | PLMD::ActionWithValue | virtual |
| after | PLMD::Action | private |
| ALA enum value | PLMD::isdb::SAXS | private |
| ALA_BB enum value | PLMD::isdb::SAXS | private |
| apply() override | PLMD::isdb::MetainferenceBase | inlinevirtual |
| ARG enum value | PLMD::isdb::SAXS | private |
| ARG_BB enum value | PLMD::isdb::SAXS | private |
| ARG_SC1 enum value | PLMD::isdb::SAXS | private |
| ARG_SC2 enum value | PLMD::isdb::SAXS | private |
| arguments | PLMD::ActionWithArguments | private |
| ASN enum value | PLMD::isdb::SAXS | private |
| ASN_BB enum value | PLMD::isdb::SAXS | private |
| ASN_SC1 enum value | PLMD::isdb::SAXS | private |
| ASP 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 |
| atom_value_ind | PLMD::ActionAtomistic | private |
| atom_value_ind_grouped | PLMD::ActionAtomistic | private |
| atoms_masses | PLMD::isdb::SAXS | private |
| atoms_per_bead | PLMD::isdb::SAXS | private |
| average_weights_ | PLMD::isdb::MetainferenceBase | private |
| B | PLMD::isdb::SAXS | private |
| BASE_A enum value | PLMD::isdb::SAXS | private |
| BASE_C enum value | PLMD::isdb::SAXS | private |
| BASE_G enum value | PLMD::isdb::SAXS | private |
| BASE_T enum value | PLMD::isdb::SAXS | private |
| BASE_U enum value | PLMD::isdb::SAXS | private |
| BB_DNA enum value | PLMD::isdb::SAXS | private |
| BB_DNA_3 enum value | PLMD::isdb::SAXS | private |
| BB_DNA_5 enum value | PLMD::isdb::SAXS | private |
| BB_PO2 enum value | PLMD::isdb::SAXS | private |
| BB_RNA enum value | PLMD::isdb::SAXS | private |
| BB_RNA_3 enum value | PLMD::isdb::SAXS | private |
| BB_RNA_5 enum value | PLMD::isdb::SAXS | private |
| beforeUpdate() | PLMD::Action | inlinevirtual |
| boxValue | PLMD::ActionAtomistic | private |
| 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 |
| calc_data_ | PLMD::isdb::MetainferenceBase | private |
| calcNlist(std::vector< std::vector< int > > &Nlist) | PLMD::isdb::SAXS | private |
| calculate() override | PLMD::isdb::SAXS | virtual |
| calculate_cpu(std::vector< Vector > &pos, std::vector< Vector > &deriv) | PLMD::isdb::SAXS | private |
| calculate_gpu(std::vector< Vector > &pos, std::vector< Vector > &deriv) | PLMD::isdb::SAXS | private |
| calculateAFF(const std::vector< AtomNumber > &atoms, std::vector< std::vector< long double > > &FF_tmp, const double rho) | PLMD::isdb::SAXS | private |
| calculateAFFsans(const std::vector< AtomNumber > &atoms, std::vector< std::vector< long double > > &FF_tmp, const double deuter_conc) | PLMD::isdb::SAXS | private |
| calculateAtomicNumericalDerivatives(ActionWithValue *a, const unsigned &startnum) | PLMD::ActionAtomistic | |
| calculateConstantValues(const bool &have_atoms) | PLMD::ActionWithArguments | virtual |
| calculateFromPDB(const PDB &) | PLMD::Action | |
| calculateNumericalDerivatives(ActionWithValue *a) override | PLMD::isdb::MetainferenceBase | inlinevirtual |
| calculateOnUpdate() | PLMD::ActionWithValue | virtual |
| castToActionAtomistic() noexcept final | PLMD::ActionAtomistic | inlinevirtual |
| castToActionForInterface() noexcept | PLMD::Action | inlinevirtual |
| castToActionShortcut() noexcept | PLMD::Action | inlinevirtual |
| castToActionToGetData() noexcept | PLMD::Action | inlinevirtual |
| castToActionToPutData() noexcept | PLMD::Action | inlinevirtual |
| PLMD::castToActionWithArguments() noexcept | PLMD::Action | inlinevirtual |
| PLMD::ActionWithArguments::castToActionWithArguments() noexcept final | PLMD::ActionWithArguments | inlinevirtual |
| PLMD::castToActionWithValue() noexcept | PLMD::Action | inlinevirtual |
| PLMD::ActionWithValue::castToActionWithValue() noexcept final | PLMD::ActionWithValue | inlinevirtual |
| castToActionWithVirtualAtom() noexcept | PLMD::Action | inlinevirtual |
| castToDomainDecomposition() noexcept | PLMD::Action | inlinevirtual |
| castToPbcAction() noexcept | PLMD::Action | inlinevirtual |
| changeBox(const Tensor &newbox) | PLMD::ActionAtomistic | |
| charges | PLMD::ActionAtomistic | private |
| chargesWereSet | PLMD::ActionAtomistic | protected |
| chargev | PLMD::ActionAtomistic | private |
| chbevl(double x, const std::vector< double > &coeffs) | PLMD::isdb::SAXS | private |
| checkFieldsAllowed() | PLMD::ActionWithValue | inlinevirtual |
| checkForDependency(Action *) | PLMD::Action | |
| checkForForces() | PLMD::ActionWithValue | protected |
| 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(const bool &force=false) | PLMD::ActionWithValue | virtual |
| clearInputForces(const bool &force=false) | PLMD::ActionWithValue | virtual |
| clearOptions() | PLMD::Action | virtual |
| 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 | |
| copyOutput(const std::string &name) const | PLMD::ActionWithValue | |
| copyOutput(const unsigned &n) const | PLMD::ActionWithValue | |
| CYS enum value | PLMD::isdb::SAXS | private |
| 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 |
| decay_w_ | PLMD::isdb::MetainferenceBase | private |
| defaults | PLMD::Action | private |
| Dependencies typedef | PLMD::Action | |
| deuter_conc | PLMD::isdb::SAXS | private |
| deviceid | PLMD::isdb::SAXS | private |
| Dftilde_ | PLMD::isdb::MetainferenceBase | 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 |
| do_optsigmamean_ | PLMD::isdb::MetainferenceBase | private |
| do_regression_zero(const std::vector< double > &mean) | PLMD::isdb::MetainferenceBase | private |
| do_reweight_ | PLMD::isdb::MetainferenceBase | private |
| doCheckPoint | PLMD::Action | private |
| Doffset_ | PLMD::isdb::MetainferenceBase | private |
| doMonteCarlo(const std::vector< double > &mean) | PLMD::isdb::MetainferenceBase | private |
| doNotCalculateDerivatives() const | PLMD::ActionWithValue | inlinevirtual |
| donotforce | PLMD::ActionAtomistic | private |
| doNotForce() | PLMD::ActionAtomistic | inline |
| donotretrieve | PLMD::ActionAtomistic | private |
| doNotRetrieve() | PLMD::ActionAtomistic | inline |
| dooffset_ | PLMD::isdb::MetainferenceBase | private |
| doregres_zero_ | PLMD::isdb::MetainferenceBase | private |
| doscale_ | PLMD::isdb::MetainferenceBase | private |
| doscore_ | PLMD::isdb::MetainferenceBase | private |
| Dscale_ | PLMD::isdb::MetainferenceBase | private |
| Dsigma_ | PLMD::isdb::MetainferenceBase | private |
| 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 |
| energy | PLMD::ActionAtomistic | 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 |
| FF_value_mixed | PLMD::isdb::SAXS | private |
| FF_value_mixed_D | PLMD::isdb::SAXS | private |
| FF_value_mixed_H | PLMD::isdb::SAXS | private |
| FF_value_solv | PLMD::isdb::SAXS | private |
| FF_value_solv_H | PLMD::isdb::SAXS | private |
| FF_value_vacuum | PLMD::isdb::SAXS | private |
| FF_value_vacuum_D | PLMD::isdb::SAXS | private |
| FF_value_vacuum_H | PLMD::isdb::SAXS | private |
| FFf_value | PLMD::isdb::SAXS | private |
| fflush() | PLMD::Action | |
| files | PLMD::Action | |
| firststep | PLMD::ActionWithValue | private |
| firstTime | PLMD::isdb::MetainferenceBase | private |
| firstTimeW | PLMD::isdb::MetainferenceBase | private |
| fopen(const char *path, const char *mode) | PLMD::Action | |
| forceOnEnergy | PLMD::ActionAtomistic | private |
| forceOnExtraCV | PLMD::ActionAtomistic | private |
| forces | PLMD::isdb::MetainferenceBase | private |
| forcesForApply | PLMD::ActionWithValue | private |
| forcesToApply | PLMD::isdb::MetainferenceBase | private |
| ftilde_ | PLMD::isdb::MetainferenceBase | private |
| 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 |
| GAUSS enum value | PLMD::isdb::MetainferenceBase | private |
| gen_likelihood_ | PLMD::isdb::MetainferenceBase | private |
| GENERIC enum value | PLMD::isdb::MetainferenceBase | private |
| get_sigma_mean(const double weight, const double norm, const double neff, const std::vector< double > &mean) | PLMD::isdb::MetainferenceBase | private |
| get_weights(double &weight, double &norm, double &neff) | PLMD::isdb::MetainferenceBase | 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 |
| getAtomValuesFromPlumedObject(const PlumedMain &plumed, std::vector< Value * > &xpos, std::vector< Value * > &ypos, std::vector< Value * > &zpos, std::vector< Value * > &masv, std::vector< Value * > &chargev) | PLMD::ActionAtomistic | static |
| getBox() const | PLMD::ActionAtomistic | inline |
| getCalcData(const unsigned index) | PLMD::isdb::MetainferenceBase | inlineprivate |
| getCharge(int i) const | PLMD::ActionAtomistic | inline |
| getComponent(const std::string &name) const | PLMD::ActionWithValue | private |
| getComponentsList() const | PLMD::ActionWithValue | |
| getComponentsVector() const | PLMD::ActionWithValue | |
| getConstPntrToComponent(int i) const | PLMD::ActionWithValue | protected |
| getCPT() const | PLMD::Action | |
| getDefaultString() const | PLMD::Action | inline |
| getDependencies() const | PLMD::Action | inline |
| getDoScore() | PLMD::isdb::MetainferenceBase | inline |
| getEnergy() const | PLMD::ActionAtomistic | inline |
| getEnergyForceGJ(const std::vector< double > &mean, const std::vector< double > &dmean_x, const std::vector< double > &dmean_b) | PLMD::isdb::MetainferenceBase | private |
| getEnergyForceGJE(const std::vector< double > &mean, const std::vector< double > &dmean_x, const std::vector< double > &dmean_b) | PLMD::isdb::MetainferenceBase | private |
| getEnergyForceMIGEN(const std::vector< double > &mean, const std::vector< double > &dmean_x, const std::vector< double > &dmean_b) | PLMD::isdb::MetainferenceBase | private |
| getEnergyForceSP(const std::vector< double > &mean, const std::vector< double > &dmean_x, const std::vector< double > &dmean_b) | PLMD::isdb::MetainferenceBase | private |
| getEnergyForceSPE(const std::vector< double > &mean, const std::vector< double > &dmean_x, const std::vector< double > &dmean_b) | PLMD::isdb::MetainferenceBase | private |
| getEnergyGJ(const std::vector< double > &mean, const std::vector< double > &sigma, const double scale, const double offset) | PLMD::isdb::MetainferenceBase | private |
| getEnergyGJE(const std::vector< double > &mean, const std::vector< double > &sigma, const double scale, const double offset) | PLMD::isdb::MetainferenceBase | private |
| getEnergyMIGEN(const std::vector< double > &mean, const std::vector< double > &ftilde, const std::vector< double > &sigma, const double scale, const double offset) | PLMD::isdb::MetainferenceBase | private |
| getEnergySP(const std::vector< double > &mean, const std::vector< double > &sigma, const double scale, const double offset) | PLMD::isdb::MetainferenceBase | private |
| getEnergySPE(const std::vector< double > &mean, const std::vector< double > &sigma, const double scale, const double offset) | PLMD::isdb::MetainferenceBase | private |
| getExchangeStep() const | PLMD::Action | |
| getForce(const std::pair< std::size_t, std::size_t > &a) const | PLMD::ActionAtomistic | inline |
| getForcesToApply() const | PLMD::ActionWithValue | inlineprotected |
| getGlobalPosition(const std::pair< std::size_t, std::size_t > &) const | PLMD::ActionAtomistic | inline |
| getGradient(const unsigned &ind, Vector &deriv, std::map< AtomNumber, Vector > &gradients) const | PLMD::ActionAtomistic | |
| getKBoltzmann() const | PLMD::Action | protected |
| getkBT() | PLMD::Action | |
| getKeyword(const std::string &key) | PLMD::Action | |
| getLabel() const | PLMD::Action | inline |
| getMartiniFFparam(const std::vector< AtomNumber > &atoms, std::vector< std::vector< long double > > ¶meter) | PLMD::isdb::SAXS | private |
| getMass(int i) const | PLMD::ActionAtomistic | inline |
| getMatrixColumnTitles(std::vector< std::string > &argnames) const | PLMD::ActionWithValue | virtual |
| 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 |
| getOnebeadMapping(const PDB &pdb, const std::vector< AtomNumber > &atoms) | PLMD::isdb::SAXS | private |
| getOnebeadparam(const PDB &pdb, const std::vector< AtomNumber > &atoms, std::vector< std::vector< long double > > ¶meter_vac, std::vector< std::vector< long double > > ¶meter_mix, std::vector< std::vector< long double > > ¶meter_solv, const std::vector< unsigned > &residue_atom) | PLMD::isdb::SAXS | private |
| getOnebeadparam_sansD(const PDB &pdb, const std::vector< AtomNumber > &atoms, std::vector< std::vector< long double > > ¶meter_vac_D, std::vector< std::vector< long double > > ¶meter_mix_D) | PLMD::isdb::SAXS | private |
| getOnebeadparam_sansH(const PDB &pdb, const std::vector< AtomNumber > &atoms, std::vector< std::vector< long double > > ¶meter_vac_H, std::vector< std::vector< long double > > ¶meter_mix_H, std::vector< std::vector< long double > > ¶meter_solv_H) | PLMD::isdb::SAXS | private |
| getOutputComponentDescription(const std::string &cname, const Keywords &keys) const | PLMD::ActionWithValue | virtual |
| 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) const | PLMD::ActionWithArguments | inline |
| getPntrToComponent(int i) | PLMD::ActionWithValue | protected |
| getPntrToComponent(const std::string &name) | PLMD::ActionWithValue | protected |
| getPntrToValue() | PLMD::ActionWithValue | inlineprotected |
| 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 | |
| getUnique() const | PLMD::ActionAtomistic | inline |
| getUniqueLocal() const | PLMD::ActionAtomistic | inline |
| getUnits() const | PLMD::Action | protected |
| getValueIndices(const AtomNumber &i) const | PLMD::ActionAtomistic | protected |
| getVirial() const | PLMD::ActionAtomistic | |
| getWstride() | PLMD::isdb::MetainferenceBase | inline |
| GLN enum value | PLMD::isdb::SAXS | private |
| GLN_BB enum value | PLMD::isdb::SAXS | private |
| GLN_SC1 enum value | PLMD::isdb::SAXS | private |
| GLU enum value | PLMD::isdb::SAXS | private |
| GLU_BB enum value | PLMD::isdb::SAXS | private |
| GLU_SC1 enum value | PLMD::isdb::SAXS | private |
| GLY 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 |
| HIP enum value | PLMD::isdb::SAXS | private |
| HIS 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 |
| i0e(double x) | PLMD::isdb::SAXS | inlineprivate |
| ILE enum value | PLMD::isdb::SAXS | private |
| ILE_BB enum value | PLMD::isdb::SAXS | private |
| ILE_SC1 enum value | PLMD::isdb::SAXS | private |
| indexes | PLMD::ActionAtomistic | private |
| Initialise(const unsigned input) | PLMD::isdb::MetainferenceBase | |
| interpolation(std::vector< SplineCoeffs > &coeffs, double x) | PLMD::isdb::SAXS | inlineprivate |
| interpretArgumentList(const std::vector< std::string > &c, const ActionSet &as, Action *action, std::vector< Value * > &arg) | PLMD::ActionWithArguments | static |
| interpretAtomList(std::vector< std::string > &strings, std::vector< AtomNumber > &t) | PLMD::ActionAtomistic | |
| interpretAtomList(std::vector< std::string > &strings, const std::vector< Value * > &xpos, Action *action, std::vector< AtomNumber > &t) | PLMD::ActionAtomistic | static |
| Iq0 | PLMD::isdb::SAXS | private |
| Iq0_mix | PLMD::isdb::SAXS | private |
| Iq0_mix_D | PLMD::isdb::SAXS | private |
| Iq0_mix_H | PLMD::isdb::SAXS | private |
| Iq0_solv | PLMD::isdb::SAXS | private |
| Iq0_solv_H | PLMD::isdb::SAXS | private |
| Iq0_vac | PLMD::isdb::SAXS | private |
| Iq0_vac_D | PLMD::isdb::SAXS | private |
| Iq0_vac_H | PLMD::isdb::SAXS | private |
| isActive() const | PLMD::Action | inline |
| iselect | PLMD::isdb::MetainferenceBase | private |
| isFirstStep | PLMD::isdb::SAXS | private |
| isOptionOn(const std::string &s) const | PLMD::Action | inline |
| kbt_ | PLMD::isdb::MetainferenceBase | private |
| keywords | PLMD::Action | |
| label | PLMD::Action | private |
| LCPOparam | PLMD::isdb::SAXS | private |
| LEU enum value | PLMD::isdb::SAXS | private |
| LEU_BB enum value | PLMD::isdb::SAXS | private |
| LEU_SC1 enum value | PLMD::isdb::SAXS | private |
| LIKE_GAUSS enum value | PLMD::isdb::MetainferenceBase | private |
| LIKE_LOGN enum value | PLMD::isdb::MetainferenceBase | private |
| line | PLMD::Action | private |
| lockRequestArguments | PLMD::ActionWithArguments | private |
| lockRequestAtoms | PLMD::ActionAtomistic | private |
| lockRequests() override | PLMD::isdb::MetainferenceBase | inlinevirtual |
| log | PLMD::Action | |
| LYS enum value | PLMD::isdb::SAXS | private |
| 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 | |
| masses | PLMD::ActionAtomistic | private |
| master | PLMD::isdb::MetainferenceBase | private |
| masv | PLMD::ActionAtomistic | private |
| MCaccept_ | PLMD::isdb::MetainferenceBase | private |
| MCacceptFT_ | PLMD::isdb::MetainferenceBase | private |
| MCacceptScale_ | PLMD::isdb::MetainferenceBase | private |
| MCchunksize_ | PLMD::isdb::MetainferenceBase | private |
| MCsteps_ | PLMD::isdb::MetainferenceBase | private |
| MCtrial_ | PLMD::isdb::MetainferenceBase | private |
| MET enum value | PLMD::isdb::SAXS | private |
| MET_BB enum value | PLMD::isdb::SAXS | private |
| MET_SC1 enum value | PLMD::isdb::SAXS | private |
| metader_ | PLMD::isdb::MetainferenceBase | private |
| MetainferenceBase(const ActionOptions &) | PLMD::isdb::MetainferenceBase | explicit |
| MGAUSS enum value | PLMD::isdb::MetainferenceBase | private |
| modifyForceOnEnergy() | PLMD::ActionAtomistic | inline |
| MOUTLIERS enum value | PLMD::isdb::MetainferenceBase | private |
| moveScaleOffset(const std::vector< double > &mean_, double &old_energy) | PLMD::isdb::MetainferenceBase | private |
| moveSigmas(const std::vector< double > &mean_, double &old_energy, const unsigned i, const std::vector< unsigned > &indices, bool &breaknow) | PLMD::isdb::MetainferenceBase | private |
| moveTilde(const std::vector< double > &mean_, double &old_energy) | PLMD::isdb::MetainferenceBase | private |
| multi_sim_comm | PLMD::Action | |
| N enum value | PLMD::isdb::SAXS | private |
| N_optimized_step_ | PLMD::isdb::MetainferenceBase | private |
| name | PLMD::Action | private |
| narg | PLMD::isdb::MetainferenceBase | private |
| never_activate | PLMD::Action | private |
| Nj | PLMD::isdb::SAXS | private |
| NMARTINI enum value | PLMD::isdb::SAXS | private |
| noAnalyticalDerivatives(Keywords &keys) | PLMD::ActionWithValue | static |
| noderiv | PLMD::ActionWithValue | private |
| noise_type_ | PLMD::isdb::MetainferenceBase | private |
| NONEBEAD enum value | PLMD::isdb::SAXS | private |
| nregres_zero_ | PLMD::isdb::MetainferenceBase | private |
| nrep_ | PLMD::isdb::MetainferenceBase | private |
| nres | PLMD::isdb::SAXS | private |
| nsel_ | PLMD::isdb::MetainferenceBase | private |
| NTT enum value | PLMD::isdb::SAXS | private |
| numericalDerivatives | PLMD::ActionWithValue | private |
| O enum value | PLMD::isdb::SAXS | private |
| offset_ | PLMD::isdb::MetainferenceBase | private |
| offset_max_ | PLMD::isdb::MetainferenceBase | private |
| offset_min_ | PLMD::isdb::MetainferenceBase | private |
| offset_mu_ | PLMD::isdb::MetainferenceBase | private |
| offset_prior_ | PLMD::isdb::MetainferenceBase | private |
| onebead | PLMD::isdb::SAXS | private |
| operator=(const Action &a)=delete | PLMD::Action | private |
| optimized_step_ | PLMD::isdb::MetainferenceBase | private |
| options | PLMD::Action | private |
| optsigmamean_stride_ | PLMD::isdb::MetainferenceBase | private |
| OUTLIERS enum value | PLMD::isdb::MetainferenceBase | private |
| P enum value | PLMD::isdb::SAXS | private |
| parameters | PLMD::isdb::MetainferenceBase | 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 |
| pbc_fwd | PLMD::ActionAtomistic | private |
| pbcApply(std::vector< Vector > &dlist, unsigned max_index=0) const | PLMD::ActionAtomistic | |
| pbcDistance(const Vector &, const Vector &) const | PLMD::ActionAtomistic | inline |
| PHE enum value | PLMD::isdb::SAXS | private |
| 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 | |
| positions | PLMD::ActionAtomistic | private |
| prepare() | PLMD::Action | virtual |
| PRO enum value | PLMD::isdb::SAXS | private |
| PRO_BB enum value | PLMD::isdb::SAXS | private |
| PRO_SC1 enum value | PLMD::isdb::SAXS | private |
| q_list | PLMD::isdb::SAXS | private |
| qj_list | PLMD::isdb::SAXS | private |
| random | PLMD::isdb::MetainferenceBase | private |
| readAtomsFromPDB(const PDB &pdb) override | PLMD::ActionAtomistic | virtual |
| readLCPOparam(const std::vector< std::vector< std::string > > &AtomResidueName, unsigned natoms) | PLMD::isdb::SAXS | private |
| registerKeywords(Keywords &keys) | PLMD::isdb::SAXS | static |
| replica_ | PLMD::isdb::MetainferenceBase | private |
| replica_averaging(const double weight, const double norm, std::vector< double > &mean, std::vector< double > &dmean_b) | PLMD::isdb::MetainferenceBase | private |
| replica_index | PLMD::Action | private |
| 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 | |
| residue_atom | PLMD::isdb::SAXS | private |
| resolution | PLMD::isdb::SAXS | private |
| resolution_function() | PLMD::isdb::SAXS | private |
| restart | PLMD::Action | private |
| retrieveAtoms(const bool &force=false) | PLMD::ActionAtomistic | virtual |
| rho | PLMD::isdb::SAXS | private |
| rho_corr | PLMD::isdb::SAXS | private |
| Rij | PLMD::isdb::SAXS | private |
| runFinalJobs() | PLMD::Action | inlinevirtual |
| S enum value | PLMD::isdb::SAXS | private |
| sasa_calculate(std::vector< bool > &solv_res) | PLMD::isdb::SAXS | private |
| sasa_cutoff | PLMD::isdb::SAXS | private |
| SAXS(const ActionOptions &) | PLMD::isdb::SAXS | explicit |
| saxs | PLMD::isdb::SAXS | private |
| SC_FLAT enum value | PLMD::isdb::MetainferenceBase | private |
| SC_GAUSS enum value | PLMD::isdb::MetainferenceBase | private |
| scale_ | PLMD::isdb::MetainferenceBase | private |
| scale_max_ | PLMD::isdb::MetainferenceBase | private |
| scale_min_ | PLMD::isdb::MetainferenceBase | private |
| scale_mu_ | PLMD::isdb::MetainferenceBase | private |
| scale_prior_ | PLMD::isdb::MetainferenceBase | private |
| Selector() | PLMD::isdb::MetainferenceBase | |
| selector_ | PLMD::isdb::MetainferenceBase | private |
| SER enum value | PLMD::isdb::SAXS | private |
| 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 | protected |
| setForcesOnAtoms(const std::vector< double > &forcesToApply, unsigned &ind) | PLMD::ActionAtomistic | |
| setForcesOnCell(const std::vector< double > &forcesToApply, unsigned &ind) | PLMD::ActionAtomistic | |
| setForcesOnCell(const double *forcesToApply, std::size_t size, unsigned &ind) | PLMD::ActionAtomistic | |
| setGlobalPosition(const std::pair< std::size_t, std::size_t > &, const Vector &pos) | PLMD::ActionAtomistic | inline |
| setGradients(Value *myval, unsigned &start) const | PLMD::ActionWithArguments | |
| setGradientsIfNeeded() | PLMD::ActionWithValue | virtual |
| setMetaDer(const unsigned index, const double der) | PLMD::isdb::MetainferenceBase | inlineprivate |
| 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 |
| setupConstantValues(const bool &have_atoms) | PLMD::Action | |
| setupLCPOparam() | PLMD::isdb::SAXS | private |
| setValue(const double &d) | PLMD::ActionWithValue | inlineprotected |
| setValue(Value *, double) | PLMD::ActionWithValue | |
| sfile_ | PLMD::isdb::MetainferenceBase | private |
| sigma_ | PLMD::isdb::MetainferenceBase | private |
| sigma_max_ | PLMD::isdb::MetainferenceBase | private |
| sigma_max_est_ | PLMD::isdb::MetainferenceBase | private |
| sigma_mean2_ | PLMD::isdb::MetainferenceBase | private |
| sigma_mean2_last_ | PLMD::isdb::MetainferenceBase | private |
| sigma_min_ | PLMD::isdb::MetainferenceBase | private |
| sigma_res | PLMD::isdb::SAXS | private |
| sigmamax_opt_done_ | PLMD::isdb::MetainferenceBase | private |
| solv_stride | PLMD::isdb::SAXS | private |
| spline_coeffs(std::vector< double > &x, std::vector< double > &y) | PLMD::isdb::SAXS | private |
| status_file_name_ | PLMD::isdb::MetainferenceBase | private |
| THR enum value | PLMD::isdb::SAXS | private |
| THR_BB enum value | PLMD::isdb::SAXS | private |
| THR_SC1 enum value | PLMD::isdb::SAXS | private |
| timestep | PLMD::Action | private |
| TRP 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 enum value | PLMD::isdb::SAXS | private |
| 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 |
| unique | PLMD::ActionAtomistic | private |
| unique_local | PLMD::ActionAtomistic | private |
| unique_local_needs_update | PLMD::ActionAtomistic | private |
| unlockRequests() override | PLMD::isdb::MetainferenceBase | inlinevirtual |
| update() override | PLMD::isdb::SAXS | virtual |
| update_from | PLMD::Action | private |
| update_until | PLMD::Action | private |
| updateUniqueLocal(const bool &useunique, const std::vector< int > &g2l) | PLMD::ActionAtomistic | private |
| useCustomisableComponents(Keywords &keys) | PLMD::ActionWithValue | static |
| useNumericalDerivatives() | PLMD::ActionWithValue | inline |
| usingNaturalUnits() const | PLMD::Action | protected |
| VAL enum value | PLMD::isdb::SAXS | private |
| VAL_BB enum value | PLMD::isdb::SAXS | private |
| VAL_SC1 enum value | PLMD::isdb::SAXS | private |
| valsToForce | PLMD::ActionWithValue | private |
| value_depends | PLMD::ActionAtomistic | private |
| valueAccept | PLMD::isdb::MetainferenceBase | private |
| valueAcceptFT | PLMD::isdb::MetainferenceBase | private |
| valueAcceptScale | PLMD::isdb::MetainferenceBase | private |
| valueFtilde | PLMD::isdb::MetainferenceBase | private |
| valueOffset | PLMD::isdb::MetainferenceBase | private |
| values | PLMD::ActionWithValue | private |
| valueScale | PLMD::isdb::MetainferenceBase | private |
| valueScore | PLMD::isdb::MetainferenceBase | private |
| valueSigma | PLMD::isdb::MetainferenceBase | private |
| valueSigmaMean | PLMD::isdb::MetainferenceBase | private |
| warning(const std::string &msg) | PLMD::Action | |
| write_stride_ | PLMD::isdb::MetainferenceBase | private |
| writeInGraph() const | PLMD::Action | virtual |
| writeStatus() | PLMD::isdb::MetainferenceBase | |
| xpos | PLMD::ActionAtomistic | private |
| ypos | PLMD::ActionAtomistic | private |
| zpos | PLMD::ActionAtomistic | private |
| ~Action() | PLMD::Action | virtual |
| ~ActionAtomistic() | PLMD::ActionAtomistic | |
| ~ActionWithArguments() | PLMD::ActionWithArguments | inlinevirtual |
| ~ActionWithValue() | PLMD::ActionWithValue | |
| ~MetainferenceBase() | PLMD::isdb::MetainferenceBase | |
1.8.17