| 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< double > &n_term_intensities, std::vector< double > &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, double &n_term1, double &c_term1, double &n_term2, double &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< double > &n_term_intensities, std::vector< double > &c_term_intensities, FragmentationType type) | ProtonDistributionModel | |
| getDefaults() const | DefaultParamHandler | |
| getLeftAndRightGBValues_(const AASequence &peptide, double &left_gb, double &right_gb, Size position) | ProtonDistributionModel | protected |
| getName() const | DefaultParamHandler | |
| getParameters() const | DefaultParamHandler | |
| getProtonDistribution(std::vector< double > &bb_charges, std::vector< double > &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< double > &bb_charge, const std::vector< double > &sc_charge) | ProtonDistributionModel | |
| SideChain enum value | ProtonDistributionModel | |
| subsections_ | DefaultParamHandler | protected |
| updateMembers_() | DefaultParamHandler | protectedvirtual |
| warn_empty_defaults_ | DefaultParamHandler | protected |
| ~DefaultParamHandler() | DefaultParamHandler | virtual |
| ~ProtonDistributionModel() | ProtonDistributionModel | virtual |