| bb_charge_ | ProtonDistributionModel | protected | 
  | bb_charge_full_ | ProtonDistributionModel | protected | 
  | bb_charge_ion_c_term_ | ProtonDistributionModel | protected | 
  | bb_charge_ion_n_term_ | ProtonDistributionModel | protected | 
  | calcChargeStateIntensities_(const AASequence &peptide, const AASequence &n_term_ion, const AASequence &c_term_ion, Int charge, Residue::ResidueType n_term_type, std::vector< DoubleReal > &n_term_intensities, std::vector< DoubleReal > &c_term_intensities, FragmentationType type) | ProtonDistributionModel | protected | 
  | calcChargeStateIntensities_(const AASequence &peptide, const AASequence &n_term_ion, const AASequence &c_term_ion, Int charge, Residue::ResidueType n_term_type, DoubleReal &n_term1, DoubleReal &c_term1, DoubleReal &n_term2, DoubleReal &c_term2, FragmentationType type) | ProtonDistributionModel | protected | 
  | calculateProtonDistribution_(const AASequence &peptide, Int charge, Residue::ResidueType res_type=Residue::YIon, bool fixed_proton=false, Size cleavage_site=0, bool use_most_basic_site=false) | ProtonDistributionModel | protected | 
  | calculateProtonDistributionCharge1_(const AASequence &peptide, Residue::ResidueType res_type) | ProtonDistributionModel | protected | 
  | calculateProtonDistributionCharge2_(const AASequence &peptide, Residue::ResidueType res_type, bool fixed_proton, Size cleavage_site, bool use_most_basic_site) | ProtonDistributionModel | protected | 
  | calculateProtonDistributionGreater2_(const AASequence &peptide, Int charge, Residue::ResidueType res_type) | ProtonDistributionModel | protected | 
  | calculateProtonDistributionIonPair_(const AASequence &peptide, Residue::ResidueType type, Size cleavage_site) | ProtonDistributionModel | protected | 
  | ChargeDirected enum value | ProtonDistributionModel |  | 
  | ChargeRemote enum value | ProtonDistributionModel |  | 
  | check_defaults_ | DefaultParamHandler | protected | 
  | DefaultParamHandler(const String &name) | DefaultParamHandler |  | 
  | DefaultParamHandler(const DefaultParamHandler &rhs) | DefaultParamHandler |  | 
  | defaults_ | DefaultParamHandler | protected | 
  | defaultsToParam_() | DefaultParamHandler | protected | 
  | E_ | ProtonDistributionModel | protected | 
  | E_c_term_ | ProtonDistributionModel | protected | 
  | E_n_term_ | ProtonDistributionModel | protected | 
  | error_name_ | DefaultParamHandler | protected | 
  | FragmentationType enum name | ProtonDistributionModel |  | 
  | getChargeStateIntensities(const AASequence &peptide, const AASequence &n_term_ion, const AASequence &c_term_ion, Int charge, Residue::ResidueType n_term_type, std::vector< DoubleReal > &n_term_intensities, std::vector< DoubleReal > &c_term_intensities, FragmentationType type) | ProtonDistributionModel |  | 
  | getDefaults() const | DefaultParamHandler |  | 
  | getLeftAndRightGBValues_(const AASequence &peptide, DoubleReal &left_gb, DoubleReal &right_gb, Size position) | ProtonDistributionModel | protected | 
  | getName() const | DefaultParamHandler |  | 
  | getParameters() const | DefaultParamHandler |  | 
  | getProtonDistribution(std::vector< DoubleReal > &bb_charges, std::vector< DoubleReal > &sc_charges, const AASequence &peptide, Int charge, Residue::ResidueType res_type=Residue::YIon) | ProtonDistributionModel |  | 
  | getSubsections() const | DefaultParamHandler |  | 
  | operator=(const ProtonDistributionModel &pdm) | ProtonDistributionModel |  | 
  | OpenMS::DefaultParamHandler::operator=(const DefaultParamHandler &rhs) | DefaultParamHandler | virtual | 
  | operator==(const DefaultParamHandler &rhs) const | DefaultParamHandler | virtual | 
  | param_ | DefaultParamHandler | protected | 
  | ProtonDistributionModel() | ProtonDistributionModel |  | 
  | ProtonDistributionModel(const ProtonDistributionModel &model) | ProtonDistributionModel |  | 
  | sc_charge_ | ProtonDistributionModel | protected | 
  | sc_charge_full_ | ProtonDistributionModel | protected | 
  | sc_charge_ion_c_term_ | ProtonDistributionModel | protected | 
  | sc_charge_ion_n_term_ | ProtonDistributionModel | protected | 
  | setName(const String &name) | DefaultParamHandler |  | 
  | setParameters(const Param ¶m) | DefaultParamHandler |  | 
  | setPeptideProtonDistribution(const std::vector< DoubleReal > &bb_charge, const std::vector< DoubleReal > &sc_charge) | ProtonDistributionModel |  | 
  | SideChain enum value | ProtonDistributionModel |  | 
  | subsections_ | DefaultParamHandler | protected | 
  | updateMembers_() | DefaultParamHandler | protectedvirtual | 
  | warn_empty_defaults_ | DefaultParamHandler | protected | 
  | ~DefaultParamHandler() | DefaultParamHandler | virtual | 
  | ~ProtonDistributionModel() | ProtonDistributionModel | virtual |