36 #ifndef OPENMS_CHEMISTRY_RESIDUE_H
37 #define OPENMS_CHEMISTRY_RESIDUE_H
73 return internal_to_full;
78 static const double internal_to_full_average_weight = getInternalToFull().getAverageWeight();
79 return internal_to_full_average_weight;
84 static const double internal_to_full_mono_weight = getInternalToFull().getMonoWeight();
85 return internal_to_full_mono_weight;
92 return Nterminal_to_full;
97 static const double Nterminal_to_full_average_weight = getNTerminalToFull().getAverageWeight();
98 return Nterminal_to_full_average_weight;
103 static const double Nterminal_to_full_mono_weight = getNTerminalToFull().getMonoWeight();
104 return Nterminal_to_full_mono_weight;
111 return Cterminal_to_full;
116 static const double Cterminal_to_full_average_weight = getCTerminalToFull().getAverageWeight();
117 return Cterminal_to_full_average_weight;
122 static const double Cterminal_to_full_mono_weight = getCTerminalToFull().getMonoWeight();
123 return Cterminal_to_full_mono_weight;
130 return b_ion_to_full;
135 static const double b_ion_to_full_average_weight = getBIonToFull().getAverageWeight();
136 return b_ion_to_full_average_weight;
141 static const double b_ion_to_full_mono_weight = getBIonToFull().getMonoWeight();
142 return b_ion_to_full_mono_weight;
149 return a_ion_to_full;
154 static const double a_ion_to_full_average_weight = getAIonToFull().getAverageWeight();
155 return a_ion_to_full_average_weight;
160 static const double a_ion_to_full_mono_weight = getAIonToFull().getMonoWeight();
161 return a_ion_to_full_mono_weight;
168 return y_ion_to_full;
173 static const double y_ion_to_full_average_weight = getYIonToFull().getAverageWeight();
174 return y_ion_to_full_average_weight;
179 static const double y_ion_to_full_mono_weight = getYIonToFull().getMonoWeight();
180 return y_ion_to_full_mono_weight;
187 return c_ion_to_full;
192 static const double c_ion_to_full_average_weight = getCIonToFull().getAverageWeight();
193 return c_ion_to_full_average_weight;
198 static const double c_ion_to_full_mono_weight = getCIonToFull().getMonoWeight();
199 return c_ion_to_full_mono_weight;
206 return c_ion_to_full;
211 static const double c_ion_to_full_average_weight = getCIonMinusOneToFull().getAverageWeight();
212 return c_ion_to_full_average_weight;
217 static const double c_ion_to_full_mono_weight = getCIonMinusOneToFull().getMonoWeight();
218 return c_ion_to_full_mono_weight;
225 return c_ion_to_full;
230 static const double c_ion_to_full_average_weight = getCIonPlusOneToFull().getAverageWeight();
231 return c_ion_to_full_average_weight;
236 static const double c_ion_to_full_mono_weight = getCIonPlusOneToFull().getMonoWeight();
237 return c_ion_to_full_mono_weight;
244 return c_ion_to_full;
249 static const double c_ion_to_full_average_weight = getCIonPlusTwoToFull().getAverageWeight();
250 return c_ion_to_full_average_weight;
255 static const double c_ion_to_full_mono_weight = getCIonPlusTwoToFull().getMonoWeight();
256 return c_ion_to_full_mono_weight;
263 return x_ion_to_full;
268 static const double x_ion_to_full_average_weight = getXIonToFull().getAverageWeight();
269 return x_ion_to_full_average_weight;
274 static const double x_ion_to_full_mono_weight = getXIonToFull().getMonoWeight();
275 return x_ion_to_full_mono_weight;
282 return z_ion_to_full;
287 static const double z_ion_to_full_average_weight = getZIonToFull().getAverageWeight();
288 return z_ion_to_full_average_weight;
293 static const double z_ion_to_full_mono_weight = getZIonToFull().getMonoWeight();
294 return z_ion_to_full_mono_weight;
301 return z_ion_to_full;
306 static const double z_ion_to_full_average_weight = getZIonMinusOneToFull().getAverageWeight();
307 return z_ion_to_full_average_weight;
312 static const double z_ion_to_full_mono_weight = getZIonMinusOneToFull().getMonoWeight();
313 return z_ion_to_full_mono_weight;
320 return z_ion_to_full;
325 static const double z_ion_to_full_average_weight = getZIonPlusOneToFull().getAverageWeight();
326 return z_ion_to_full_average_weight;
331 static const double z_ion_to_full_mono_weight = getZIonPlusOneToFull().getMonoWeight();
332 return z_ion_to_full_mono_weight;
339 return z_ion_to_full;
344 static const double z_ion_to_full_average_weight = getZIonPlusTwoToFull().getAverageWeight();
345 return z_ion_to_full_average_weight;
350 static const double z_ion_to_full_mono_weight = getZIonPlusTwoToFull().getMonoWeight();
351 return z_ion_to_full_mono_weight;
384 static String getResidueTypeName(
const ResidueType res_type);
398 const String & three_letter_code,
399 const String & one_letter_code,
416 void setName(
const String & name);
420 const String & getName()
const;
423 void setShortName(
const String & short_name);
426 const String & getShortName()
const;
429 void setSynonyms(
const std::set<String> & synonyms);
432 void addSynonym(
const String & synonym);
435 const std::set<String> & getSynonyms()
const;
438 void setThreeLetterCode(
const String & three_letter_code);
441 const String & getThreeLetterCode()
const;
444 void setOneLetterCode(
const String & one_letter_code);
447 const String & getOneLetterCode()
const;
453 void setLossFormulas(
const std::vector<EmpiricalFormula> &);
459 void setNTermLossFormulas(
const std::vector<EmpiricalFormula> &);
462 const std::vector<EmpiricalFormula> & getLossFormulas()
const;
465 const std::vector<EmpiricalFormula> & getNTermLossFormulas()
const;
468 void setLossNames(
const std::vector<String> & name);
471 void setNTermLossNames(
const std::vector<String> & name);
474 void addLossName(
const String & name);
477 void addNTermLossName(
const String & name);
480 const std::vector<String> & getLossNames()
const;
483 const std::vector<String> & getNTermLossNames()
const;
492 void setAverageWeight(
double weight);
495 double getAverageWeight(ResidueType res_type = Full)
const;
498 void setMonoWeight(
double weight);
501 double getMonoWeight(ResidueType res_type = Full)
const;
507 const String & getModification()
const;
510 void setLowMassIons(
const std::vector<EmpiricalFormula> & low_mass_ions);
513 const std::vector<EmpiricalFormula> & getLowMassIons()
const;
516 void setResidueSets(
const std::set<String> & residues_sets);
519 void addResidueSet(
const String & residue_sets);
522 const std::set<String> & getResidueSets()
const;
528 bool hasNeutralLoss()
const;
532 bool hasNTermNeutralLosses()
const;
535 bool operator==(
const Residue & residue)
const;
538 bool operator!=(
const Residue & residue)
const;
541 bool operator==(
char one_letter_code)
const;
544 bool operator!=(
char one_letter_code)
const;
547 double getPka()
const;
550 double getPkb()
const;
553 double getPkc()
const;
556 double getPiValue()
const;
559 void setPka(
double value);
562 void setPkb(
double value);
565 void setPkc(
double value);
568 double getSideChainBasicity()
const;
571 void setSideChainBasicity(
double gb_sc);
574 double getBackboneBasicityLeft()
const;
577 void setBackboneBasicityLeft(
double gb_bb_l);
580 double getBackboneBasicityRight()
const;
583 void setBackboneBasicityRight(
double gb_bb_r);
586 bool isModified()
const;
589 bool isInResidueSet(
const String & residue_set);
593 friend OPENMS_DLLAPI std::ostream &
operator<<(std::ostream & os,
const Residue & residue);
659 OPENMS_DLLAPI std::ostream &
operator<<(std::ostream & os,
const Residue & residue);
static const EmpiricalFormula & getZIonPlusTwoToFull()
Definition: Residue.h:336
static const EmpiricalFormula & getBIonToFull()
Definition: Residue.h:127
static double getBIonToFullMonoWeight()
Definition: Residue.h:139
static double getYIonToFullMonoWeight()
Definition: Residue.h:177
static double getCIonToFullMonoWeight()
Definition: Residue.h:196
Definition: Residue.h:372
std::vector< String > loss_names_
Definition: Residue.h:624
A more convenient string class.
Definition: String.h:57
std::vector< String > NTerm_loss_names_
Definition: Residue.h:628
double pkc_
Definition: Residue.h:646
Definition: Residue.h:373
static double getYIonToFullAverageWeight()
Definition: Residue.h:171
static double getCIonPlusTwoToFullMonoWeight()
Definition: Residue.h:253
double gb_bb_r_
Definition: Residue.h:652
Definition: Residue.h:369
static const EmpiricalFormula & getInternalToFull()
Definition: Residue.h:70
static double getCIonPlusOneToFullMonoWeight()
Definition: Residue.h:234
static const EmpiricalFormula & getYIonToFull()
Definition: Residue.h:165
Definition: Residue.h:363
Definition: Residue.h:362
static double getNTerminalToFullMonoWeight()
Definition: Residue.h:101
double pka_
Definition: Residue.h:640
Definition: Residue.h:375
static const EmpiricalFormula & getCIonPlusOneToFull()
Definition: Residue.h:222
double gb_sc_
Definition: Residue.h:648
static const EmpiricalFormula & getCIonToFull()
Definition: Residue.h:184
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
static const EmpiricalFormula & getZIonMinusOneToFull()
Definition: Residue.h:298
static double getCIonMinusOneToFullMonoWeight()
Definition: Residue.h:215
Representation of a residue.
Definition: Residue.h:62
std::vector< EmpiricalFormula > loss_formulas_
Definition: Residue.h:626
double gb_bb_l_
Definition: Residue.h:650
static double getCIonToFullAverageWeight()
Definition: Residue.h:190
static double getCTerminalToFullMonoWeight()
Definition: Residue.h:120
double loss_mono_weight_
Definition: Residue.h:634
static double getZIonPlusOneToFullMonoWeight()
Definition: Residue.h:329
static double getZIonToFullAverageWeight()
Definition: Residue.h:285
std::vector< EmpiricalFormula > low_mass_ions_
Definition: Residue.h:637
static double getCIonPlusOneToFullAverageWeight()
Definition: Residue.h:228
static double getZIonToFullMonoWeight()
Definition: Residue.h:291
Definition: Residue.h:370
static double getXIonToFullMonoWeight()
Definition: Residue.h:272
void setModification(int location, int max_size, String modification, OpenMS::AASequence &aas)
helper function that sets a modification on a AASequence object
Definition: Residue.h:364
static const EmpiricalFormula & getZIonToFull()
Definition: Residue.h:279
static double getCIonPlusTwoToFullAverageWeight()
Definition: Residue.h:247
static double getZIonPlusTwoToFullAverageWeight()
Definition: Residue.h:342
static const EmpiricalFormula & getZIonPlusOneToFull()
Definition: Residue.h:317
static const EmpiricalFormula & getAIonToFull()
Definition: Residue.h:146
static const EmpiricalFormula & getCIonMinusOneToFull()
Definition: Residue.h:203
static double getZIonMinusOneToFullMonoWeight()
Definition: Residue.h:310
static double getXIonToFullAverageWeight()
Definition: Residue.h:266
std::ostream & operator<<(std::ostream &os, const AccurateMassSearchResult &amsr)
static const EmpiricalFormula & getCIonPlusTwoToFull()
Definition: Residue.h:241
double average_weight_
Definition: Residue.h:612
String short_name_
Definition: Residue.h:600
Definition: Residue.h:374
static const EmpiricalFormula & getCTerminalToFull()
Definition: Residue.h:108
EmpiricalFormula internal_formula_
Definition: Residue.h:610
double mono_weight_
Definition: Residue.h:614
static double getZIonPlusTwoToFullMonoWeight()
Definition: Residue.h:348
static double getCIonMinusOneToFullAverageWeight()
Definition: Residue.h:209
static double getAIonToFullAverageWeight()
Definition: Residue.h:152
ResidueType
Definition: Residue.h:359
Definition: Residue.h:376
static double getAIonToFullMonoWeight()
Definition: Residue.h:158
Definition: Residue.h:365
String name_
Definition: Residue.h:598
static double getZIonMinusOneToFullAverageWeight()
Definition: Residue.h:304
String three_letter_code_
Definition: Residue.h:604
static double getBIonToFullAverageWeight()
Definition: Residue.h:133
double pkb_
Definition: Residue.h:643
bool is_modified_
Definition: Residue.h:617
static double getZIonPlusOneToFullAverageWeight()
Definition: Residue.h:323
Definition: Residue.h:367
static const EmpiricalFormula & getXIonToFull()
Definition: Residue.h:260
std::set< String > synonyms_
Definition: Residue.h:602
Definition: Residue.h:366
String pre_mod_name_
Definition: Residue.h:619
EmpiricalFormula formula_
Definition: Residue.h:608
double loss_average_weight_
Definition: Residue.h:632
String modification_
Definition: Residue.h:621
static double getNTerminalToFullAverageWeight()
Definition: Residue.h:95
static const EmpiricalFormula & getNTerminalToFull()
Definition: Residue.h:89
Definition: Residue.h:368
Definition: Residue.h:371
static double getInternalToFullMonoWeight()
Definition: Residue.h:82
static double getCTerminalToFullAverageWeight()
Definition: Residue.h:114
static double getInternalToFullAverageWeight()
Definition: Residue.h:76
std::set< String > residue_sets_
Definition: Residue.h:655
std::vector< EmpiricalFormula > NTerm_loss_formulas_
Definition: Residue.h:630
String one_letter_code_
Definition: Residue.h:606