, including all inherited members.
| addLossFormula(const EmpiricalFormula &) | Residue | |
| addLossName(const String &name) | Residue | |
| addNTermLossFormula(const EmpiricalFormula &) | Residue | |
| addNTermLossName(const String &name) | Residue | |
| addResidueSet(const String &residue_sets) | Residue | |
| addSynonym(const String &synonym) | Residue | |
| AIon enum value | Residue | |
| average_weight_ | Residue | [protected] |
| BIon enum value | Residue | |
| CIon enum value | Residue | |
| CIonMinusOne enum value | Residue | |
| CIonPlusOne enum value | Residue | |
| CIonPlusTwo enum value | Residue | |
| CTerminal enum value | Residue | |
| formula_ | Residue | [protected] |
| Full enum value | Residue | |
| gb_bb_l_ | Residue | [protected] |
| gb_bb_r_ | Residue | [protected] |
| gb_sc_ | Residue | [protected] |
| getAIonToFull() | Residue | [inline, static] |
| getAIonToFullAverageWeight() | Residue | [inline, static] |
| getAIonToFullMonoWeight() | Residue | [inline, static] |
| getAverageWeight(ResidueType res_type=Full) const | Residue | |
| getBackboneBasicityLeft() const | Residue | |
| getBackboneBasicityRight() const | Residue | |
| getBIonToFull() | Residue | [inline, static] |
| getBIonToFullAverageWeight() | Residue | [inline, static] |
| getBIonToFullMonoWeight() | Residue | [inline, static] |
| getCIonMinusOneToFull() | Residue | [inline, static] |
| getCIonMinusOneToFullAverageWeight() | Residue | [inline, static] |
| getCIonMinusOneToFullMonoWeight() | Residue | [inline, static] |
| getCIonPlusOneToFull() | Residue | [inline, static] |
| getCIonPlusOneToFullAverageWeight() | Residue | [inline, static] |
| getCIonPlusOneToFullMonoWeight() | Residue | [inline, static] |
| getCIonPlusTwoToFull() | Residue | [inline, static] |
| getCIonPlusTwoToFullAverageWeight() | Residue | [inline, static] |
| getCIonPlusTwoToFullMonoWeight() | Residue | [inline, static] |
| getCIonToFull() | Residue | [inline, static] |
| getCIonToFullAverageWeight() | Residue | [inline, static] |
| getCIonToFullMonoWeight() | Residue | [inline, static] |
| getCTerminalToFull() | Residue | [inline, static] |
| getCTerminalToFullAverageWeight() | Residue | [inline, static] |
| getCTerminalToFullMonoWeight() | Residue | [inline, static] |
| getFormula(ResidueType res_type=Full) const | Residue | |
| getInternalToFull() | Residue | [inline, static] |
| getInternalToFullAverageWeight() | Residue | [inline, static] |
| getInternalToFullMonoWeight() | Residue | [inline, static] |
| getLossFormulas() const | Residue | |
| getLossNames() const | Residue | |
| getLowMassIons() const | Residue | |
| getModification() const | Residue | |
| getMonoWeight(ResidueType res_type=Full) const | Residue | |
| getName() const | Residue | |
| getNTerminalToFull() | Residue | [inline, static] |
| getNTerminalToFullAverageWeight() | Residue | [inline, static] |
| getNTerminalToFullMonoWeight() | Residue | [inline, static] |
| getNTermLossFormulas() const | Residue | |
| getNTermLossNames() const | Residue | |
| getOneLetterCode() const | Residue | |
| getPiValue() const | Residue | |
| getPka() const | Residue | |
| getPkb() const | Residue | |
| getPkc() const | Residue | |
| getResidueSets() const | Residue | |
| getResidueTypeName(const ResidueType res_type) | Residue | [static] |
| getShortName() const | Residue | |
| getSideChainBasicity() const | Residue | |
| getSynonyms() const | Residue | |
| getThreeLetterCode() const | Residue | |
| getXIonToFull() | Residue | [inline, static] |
| getXIonToFullAverageWeight() | Residue | [inline, static] |
| getXIonToFullMonoWeight() | Residue | [inline, static] |
| getYIonToFull() | Residue | [inline, static] |
| getYIonToFullAverageWeight() | Residue | [inline, static] |
| getYIonToFullMonoWeight() | Residue | [inline, static] |
| getZIonMinusOneToFull() | Residue | [inline, static] |
| getZIonMinusOneToFullAverageWeight() | Residue | [inline, static] |
| getZIonMinusOneToFullMonoWeight() | Residue | [inline, static] |
| getZIonPlusOneToFull() | Residue | [inline, static] |
| getZIonPlusOneToFullAverageWeight() | Residue | [inline, static] |
| getZIonPlusOneToFullMonoWeight() | Residue | [inline, static] |
| getZIonPlusTwoToFull() | Residue | [inline, static] |
| getZIonPlusTwoToFullAverageWeight() | Residue | [inline, static] |
| getZIonPlusTwoToFullMonoWeight() | Residue | [inline, static] |
| getZIonToFull() | Residue | [inline, static] |
| getZIonToFullAverageWeight() | Residue | [inline, static] |
| getZIonToFullMonoWeight() | Residue | [inline, static] |
| hasNeutralLoss() const | Residue | |
| hasNTermNeutralLosses() const | Residue | |
| Internal enum value | Residue | |
| internal_formula_ | Residue | [protected] |
| is_modified_ | Residue | [protected] |
| isInResidueSet(const String &residue_set) | Residue | |
| isModified() const | Residue | |
| loss_average_weight_ | Residue | [protected] |
| loss_formulas_ | Residue | [protected] |
| loss_mono_weight_ | Residue | [protected] |
| loss_names_ | Residue | [protected] |
| low_mass_ions_ | Residue | [protected] |
| modification_ | Residue | [protected] |
| mono_weight_ | Residue | [protected] |
| name_ | Residue | [protected] |
| NTerm_loss_formulas_ | Residue | [protected] |
| NTerm_loss_names_ | Residue | [protected] |
| NTerminal enum value | Residue | |
| one_letter_code_ | Residue | [protected] |
| operator!=(const Residue &residue) const | Residue | |
| operator!=(char one_letter_code) const | Residue | |
| operator<<(std::ostream &os, const Residue &residue) | Residue | [friend] |
| operator=(const Residue &residue) | Residue | |
| operator==(const Residue &residue) const | Residue | |
| operator==(char one_letter_code) const | Residue | |
| pka_ | Residue | [protected] |
| pkb_ | Residue | [protected] |
| pkc_ | Residue | [protected] |
| pre_mod_name_ | Residue | [protected] |
| Residue() | Residue | |
| Residue(const Residue &residue) | Residue | |
| Residue(const String &name, const String &three_letter_code, const String &one_letter_code, const EmpiricalFormula &formula) | Residue | |
| residue_sets_ | Residue | [protected] |
| ResidueType enum name | Residue | |
| setAverageWeight(DoubleReal weight) | Residue | |
| setBackboneBasicityLeft(DoubleReal gb_bb_l) | Residue | |
| setBackboneBasicityRight(DoubleReal gb_bb_r) | Residue | |
| setFormula(const EmpiricalFormula &formula) | Residue | |
| setLossFormulas(const std::vector< EmpiricalFormula > &) | Residue | |
| setLossNames(const std::vector< String > &name) | Residue | |
| setLowMassIons(const std::vector< EmpiricalFormula > &low_mass_ions) | Residue | |
| setModification(const String &name) | Residue | |
| setMonoWeight(DoubleReal weight) | Residue | |
| setName(const String &name) | Residue | |
| setNTermLossFormulas(const std::vector< EmpiricalFormula > &) | Residue | |
| setNTermLossNames(const std::vector< String > &name) | Residue | |
| setOneLetterCode(const String &one_letter_code) | Residue | |
| setPka(DoubleReal value) | Residue | |
| setPkb(DoubleReal value) | Residue | |
| setPkc(DoubleReal value) | Residue | |
| setResidueSets(const std::set< String > &residues_sets) | Residue | |
| setShortName(const String &short_name) | Residue | |
| setSideChainBasicity(DoubleReal gb_sc) | Residue | |
| setSynonyms(const std::set< String > &synonyms) | Residue | |
| setThreeLetterCode(const String &three_letter_code) | Residue | |
| short_name_ | Residue | [protected] |
| SizeOfResidueType enum value | Residue | |
| synonyms_ | Residue | [protected] |
| three_letter_code_ | Residue | [protected] |
| XIon enum value | Residue | |
| YIon enum value | Residue | |
| ZIon enum value | Residue | |
| ZIonMinusOne enum value | Residue | |
| ZIonPlusOne enum value | Residue | |
| ZIonPlusTwo enum value | Residue | |
| ~Residue() | Residue | [virtual] |