174 static String getResidueTypeName(
const ResidueType res_type);
188 const String& three_letter_code,
189 const String& one_letter_code,
206 void setName(
const String& name);
210 const String& getName()
const;
213 void setShortName(
const String& short_name);
216 const String& getShortName()
const;
219 void setSynonyms(
const std::set<String>& synonyms);
222 void addSynonym(
const String& synonym);
225 const std::set<String>& getSynonyms()
const;
228 void setThreeLetterCode(
const String& three_letter_code);
231 const String& getThreeLetterCode()
const;
234 void setOneLetterCode(
const String& one_letter_code);
237 const String& getOneLetterCode()
const;
243 void setLossFormulas(
const std::vector<EmpiricalFormula>&);
249 void setNTermLossFormulas(
const std::vector<EmpiricalFormula>&);
252 const std::vector<EmpiricalFormula>& getLossFormulas()
const;
255 const std::vector<EmpiricalFormula>& getNTermLossFormulas()
const;
258 void setLossNames(
const std::vector<String>& name);
261 void setNTermLossNames(
const std::vector<String>& name);
264 void addLossName(
const String& name);
267 void addNTermLossName(
const String& name);
270 const std::vector<String>& getLossNames()
const;
273 const std::vector<String>& getNTermLossNames()
const;
282 void setAverageWeight(
double weight);
285 double getAverageWeight(ResidueType res_type = Full)
const;
288 void setMonoWeight(
double weight);
291 double getMonoWeight(ResidueType res_type = Full)
const;
300 const String& getModificationName()
const;
303 void setLowMassIons(
const std::vector<EmpiricalFormula>& low_mass_ions);
306 const std::vector<EmpiricalFormula>& getLowMassIons()
const;
309 void setResidueSets(
const std::set<String>& residues_sets);
312 void addResidueSet(
const String& residue_sets);
315 const std::set<String>& getResidueSets()
const;
318 double getPka()
const;
321 double getPkb()
const;
324 double getPkc()
const;
327 double getPiValue()
const;
330 void setPka(
double value);
333 void setPkb(
double value);
336 void setPkc(
double value);
339 double getSideChainBasicity()
const;
342 void setSideChainBasicity(
double gb_sc);
345 double getBackboneBasicityLeft()
const;
348 void setBackboneBasicityLeft(
double gb_bb_l);
351 double getBackboneBasicityRight()
const;
354 void setBackboneBasicityRight(
double gb_bb_r);
360 bool hasNeutralLoss()
const;
364 bool hasNTermNeutralLosses()
const;
379 bool isModified()
const;
382 bool isInResidueSet(
const String& residue_set);
386 friend OPENMS_DLLAPI std::ostream&
operator<<(std::ostream& os,
const Residue& residue);
451 OPENMS_DLLAPI std::ostream&
operator<<(std::ostream& os,
const Residue& residue);
MS:1001229 N-terminus up to the C-alpha/carbonyl carbon bond.
Definition: Residue.h:156
MS:1001220 peptide bond up to the C-terminus.
Definition: Residue.h:160
std::vector< String > loss_names_
Definition: Residue.h:413
A more convenient string class.
Definition: String.h:57
std::vector< String > NTerm_loss_names_
Definition: Residue.h:417
double pkc_
Definition: Residue.h:435
static const EmpiricalFormula & getInternalToNTerm()
Definition: Residue.h:87
internal, without any termini
Definition: Residue.h:153
only N-terminus
Definition: Residue.h:154
double gb_bb_r_
Definition: Residue.h:441
static const EmpiricalFormula & getInternalToFull()
Definition: Residue.h:81
Representation of a modification.
Definition: ResidueModification.h:76
only C-terminus
Definition: Residue.h:155
static const EmpiricalFormula & getInternalToAIon()
Definition: Residue.h:99
static const EmpiricalFormula & getInternalToBIon()
Definition: Residue.h:107
bool operator==(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:806
double pka_
Definition: Residue.h:429
static const EmpiricalFormula & getInternalToXIon()
Definition: Residue.h:122
double gb_sc_
Definition: Residue.h:437
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
MS:1001223 y ion without water.
Definition: Residue.h:164
Representation of a residue.
Definition: Residue.h:61
std::vector< EmpiricalFormula > loss_formulas_
Definition: Residue.h:415
double gb_bb_l_
Definition: Residue.h:439
double loss_mono_weight_
Definition: Residue.h:423
std::vector< EmpiricalFormula > low_mass_ions_
Definition: Residue.h:426
static const EmpiricalFormula & getInternalToCTerm()
Definition: Residue.h:93
static const EmpiricalFormula & getInternalToYIon()
Definition: Residue.h:130
MS:1001230 C-alpha/carbonyl carbon bond.
Definition: Residue.h:161
void setModification(int location, int max_size, String modification, OpenMS::AASequence &aas)
helper function that sets a modification on a AASequence object
const ResidueModification * modification_
Definition: Residue.h:410
static const EmpiricalFormula & getInternalToZIon()
Definition: Residue.h:137
MS:1001232 b ion without ammonia.
Definition: Residue.h:165
MS:1001233 y ion without ammonia.
Definition: Residue.h:166
std::ostream & operator<<(std::ostream &os, const AccurateMassSearchResult &amsr)
double average_weight_
Definition: Residue.h:405
String short_name_
Definition: Residue.h:393
MS:1001228 amide/C-alpha bond up to the C-terminus.
Definition: Residue.h:159
no stored annotation
Definition: Residue.h:168
EmpiricalFormula internal_formula_
Definition: Residue.h:403
double mono_weight_
Definition: Residue.h:407
MS:1001523 Precursor ion.
Definition: Residue.h:162
String name_
Definition: Residue.h:391
String three_letter_code_
Definition: Residue.h:397
MS:1001222 b ion without water.
Definition: Residue.h:163
bool operator!=(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:824
residue data base which holds residues
Definition: ResidueDB.h:60
ResidueType
Definition: Residue.h:150
MS:1001240 Non-identified ion.
Definition: Residue.h:167
double pkb_
Definition: Residue.h:432
MS:1001224 N-terminus up to the peptide bond.
Definition: Residue.h:157
std::set< String > synonyms_
Definition: Residue.h:395
EmpiricalFormula formula_
Definition: Residue.h:401
double loss_average_weight_
Definition: Residue.h:421
std::set< String > residue_sets_
Definition: Residue.h:444
std::vector< EmpiricalFormula > NTerm_loss_formulas_
Definition: Residue.h:419
String one_letter_code_
Definition: Residue.h:399
MS:1001231 N-terminus up to the amide/C-alpha bond.
Definition: Residue.h:158
static const EmpiricalFormula & getInternalToCIon()
Definition: Residue.h:115