36 #ifndef OPENMS_CHEMISTRY_RESIDUE_H
37 #define OPENMS_CHEMISTRY_RESIDUE_H
50 class ResidueModification;
75 return internal_to_full;
80 static const DoubleReal internal_to_full_average_weight = getInternalToFull().getAverageWeight();
81 return internal_to_full_average_weight;
86 static const DoubleReal internal_to_full_mono_weight = getInternalToFull().getMonoWeight();
87 return internal_to_full_mono_weight;
94 return Nterminal_to_full;
99 static const DoubleReal Nterminal_to_full_average_weight = getNTerminalToFull().getAverageWeight();
100 return Nterminal_to_full_average_weight;
105 static const DoubleReal Nterminal_to_full_mono_weight = getNTerminalToFull().getMonoWeight();
106 return Nterminal_to_full_mono_weight;
113 return Cterminal_to_full;
118 static const DoubleReal Cterminal_to_full_average_weight = getCTerminalToFull().getAverageWeight();
119 return Cterminal_to_full_average_weight;
124 static const DoubleReal Cterminal_to_full_mono_weight = getCTerminalToFull().getMonoWeight();
125 return Cterminal_to_full_mono_weight;
132 return b_ion_to_full;
137 static const DoubleReal b_ion_to_full_average_weight = getBIonToFull().getAverageWeight();
138 return b_ion_to_full_average_weight;
143 static const DoubleReal b_ion_to_full_mono_weight = getBIonToFull().getMonoWeight();
144 return b_ion_to_full_mono_weight;
151 return a_ion_to_full;
156 static const DoubleReal a_ion_to_full_average_weight = getAIonToFull().getAverageWeight();
157 return a_ion_to_full_average_weight;
162 static const DoubleReal a_ion_to_full_mono_weight = getAIonToFull().getMonoWeight();
163 return a_ion_to_full_mono_weight;
170 return y_ion_to_full;
175 static const DoubleReal y_ion_to_full_average_weight = getYIonToFull().getAverageWeight();
176 return y_ion_to_full_average_weight;
181 static const DoubleReal y_ion_to_full_mono_weight = getYIonToFull().getMonoWeight();
182 return y_ion_to_full_mono_weight;
189 return c_ion_to_full;
194 static const DoubleReal c_ion_to_full_average_weight = getCIonToFull().getAverageWeight();
195 return c_ion_to_full_average_weight;
200 static const DoubleReal c_ion_to_full_mono_weight = getCIonToFull().getMonoWeight();
201 return c_ion_to_full_mono_weight;
208 return c_ion_to_full;
213 static const DoubleReal c_ion_to_full_average_weight = getCIonMinusOneToFull().getAverageWeight();
214 return c_ion_to_full_average_weight;
219 static const DoubleReal c_ion_to_full_mono_weight = getCIonMinusOneToFull().getMonoWeight();
220 return c_ion_to_full_mono_weight;
227 return c_ion_to_full;
232 static const DoubleReal c_ion_to_full_average_weight = getCIonPlusOneToFull().getAverageWeight();
233 return c_ion_to_full_average_weight;
238 static const DoubleReal c_ion_to_full_mono_weight = getCIonPlusOneToFull().getMonoWeight();
239 return c_ion_to_full_mono_weight;
246 return c_ion_to_full;
251 static const DoubleReal c_ion_to_full_average_weight = getCIonPlusTwoToFull().getAverageWeight();
252 return c_ion_to_full_average_weight;
257 static const DoubleReal c_ion_to_full_mono_weight = getCIonPlusTwoToFull().getMonoWeight();
258 return c_ion_to_full_mono_weight;
265 return x_ion_to_full;
270 static const DoubleReal x_ion_to_full_average_weight = getXIonToFull().getAverageWeight();
271 return x_ion_to_full_average_weight;
276 static const DoubleReal x_ion_to_full_mono_weight = getXIonToFull().getMonoWeight();
277 return x_ion_to_full_mono_weight;
284 return z_ion_to_full;
289 static const DoubleReal z_ion_to_full_average_weight = getZIonToFull().getAverageWeight();
290 return z_ion_to_full_average_weight;
295 static const DoubleReal z_ion_to_full_mono_weight = getZIonToFull().getMonoWeight();
296 return z_ion_to_full_mono_weight;
303 return z_ion_to_full;
308 static const DoubleReal z_ion_to_full_average_weight = getZIonMinusOneToFull().getAverageWeight();
309 return z_ion_to_full_average_weight;
314 static const DoubleReal z_ion_to_full_mono_weight = getZIonMinusOneToFull().getMonoWeight();
315 return z_ion_to_full_mono_weight;
322 return z_ion_to_full;
327 static const DoubleReal z_ion_to_full_average_weight = getZIonPlusOneToFull().getAverageWeight();
328 return z_ion_to_full_average_weight;
333 static const DoubleReal z_ion_to_full_mono_weight = getZIonPlusOneToFull().getMonoWeight();
334 return z_ion_to_full_mono_weight;
341 return z_ion_to_full;
346 static const DoubleReal z_ion_to_full_average_weight = getZIonPlusTwoToFull().getAverageWeight();
347 return z_ion_to_full_average_weight;
352 static const DoubleReal z_ion_to_full_mono_weight = getZIonPlusTwoToFull().getMonoWeight();
353 return z_ion_to_full_mono_weight;
386 static String getResidueTypeName(
const ResidueType res_type);
400 const String & three_letter_code,
401 const String & one_letter_code,
418 void setName(
const String & name);
422 const String & getName()
const;
425 void setShortName(
const String & short_name);
428 const String & getShortName()
const;
431 void setSynonyms(
const std::set<String> & synonyms);
434 void addSynonym(
const String & synonym);
437 const std::set<String> & getSynonyms()
const;
440 void setThreeLetterCode(
const String & three_letter_code);
443 const String & getThreeLetterCode()
const;
446 void setOneLetterCode(
const String & one_letter_code);
449 const String & getOneLetterCode()
const;
455 void setLossFormulas(
const std::vector<EmpiricalFormula> &);
461 void setNTermLossFormulas(
const std::vector<EmpiricalFormula> &);
464 const std::vector<EmpiricalFormula> & getLossFormulas()
const;
467 const std::vector<EmpiricalFormula> & getNTermLossFormulas()
const;
470 void setLossNames(
const std::vector<String> & name);
473 void setNTermLossNames(
const std::vector<String> & name);
476 void addLossName(
const String & name);
479 void addNTermLossName(
const String & name);
482 const std::vector<String> & getLossNames()
const;
485 const std::vector<String> & getNTermLossNames()
const;
497 DoubleReal getAverageWeight(ResidueType res_type = Full)
const;
503 DoubleReal getMonoWeight(ResidueType res_type = Full)
const;
509 const String & getModification()
const;
512 void setLowMassIons(
const std::vector<EmpiricalFormula> & low_mass_ions);
515 const std::vector<EmpiricalFormula> & getLowMassIons()
const;
518 void setResidueSets(
const std::set<String> & residues_sets);
521 void addResidueSet(
const String & residue_sets);
524 const std::set<String> & getResidueSets()
const;
530 bool hasNeutralLoss()
const;
534 bool hasNTermNeutralLosses()
const;
537 bool operator==(
const Residue & residue)
const;
540 bool operator!=(
const Residue & residue)
const;
543 bool operator==(
char one_letter_code)
const;
546 bool operator!=(
char one_letter_code)
const;
579 void setBackboneBasicityLeft(
DoubleReal gb_bb_l);
585 void setBackboneBasicityRight(
DoubleReal gb_bb_r);
588 bool isModified()
const;
591 bool isInResidueSet(
const String & residue_set);
595 friend OPENMS_DLLAPI std::ostream &
operator<<(std::ostream & os,
const Residue & residue);
661 OPENMS_DLLAPI std::ostream &
operator<<(std::ostream & os,
const Residue & residue);
Definition: Residue.h:367
static const EmpiricalFormula & getZIonPlusTwoToFull()
Definition: Residue.h:338
static const EmpiricalFormula & getBIonToFull()
Definition: Residue.h:129
static DoubleReal getCIonToFullAverageWeight()
Definition: Residue.h:192
Definition: Residue.h:374
DoubleReal pka_
Definition: Residue.h:642
std::vector< String > loss_names_
Definition: Residue.h:626
static DoubleReal getCIonMinusOneToFullMonoWeight()
Definition: Residue.h:217
A more convenient string class.
Definition: String.h:56
static DoubleReal getZIonToFullAverageWeight()
Definition: Residue.h:287
static DoubleReal getNTerminalToFullMonoWeight()
Definition: Residue.h:103
std::vector< String > NTerm_loss_names_
Definition: Residue.h:630
static DoubleReal getAIonToFullMonoWeight()
Definition: Residue.h:160
Definition: Residue.h:364
DoubleReal pkb_
Definition: Residue.h:645
Definition: Residue.h:365
DoubleReal loss_average_weight_
Definition: Residue.h:634
DoubleReal gb_bb_r_
Definition: Residue.h:654
static const EmpiricalFormula & getInternalToFull()
Definition: Residue.h:72
static const EmpiricalFormula & getYIonToFull()
Definition: Residue.h:167
DoubleReal average_weight_
Definition: Residue.h:614
static DoubleReal getZIonMinusOneToFullMonoWeight()
Definition: Residue.h:312
static DoubleReal getCIonPlusTwoToFullMonoWeight()
Definition: Residue.h:255
std::ostream & operator<<(std::ostream &os, const ItraqQuantifier::ItraqQuantifierStats &stats)
Definition: Residue.h:366
static const EmpiricalFormula & getCIonPlusOneToFull()
Definition: Residue.h:224
static const EmpiricalFormula & getCIonToFull()
Definition: Residue.h:186
static const EmpiricalFormula & getZIonMinusOneToFull()
Definition: Residue.h:300
Representation of a residue.
Definition: Residue.h:64
std::vector< EmpiricalFormula > loss_formulas_
Definition: Residue.h:628
static DoubleReal getZIonPlusOneToFullMonoWeight()
Definition: Residue.h:331
DoubleReal gb_sc_
Definition: Residue.h:650
static DoubleReal getCTerminalToFullAverageWeight()
Definition: Residue.h:116
std::vector< EmpiricalFormula > low_mass_ions_
Definition: Residue.h:639
Definition: Residue.h:378
DoubleReal pkc_
Definition: Residue.h:648
Definition: Residue.h:376
Definition: Residue.h:372
void setModification(int location, int max_size, String modification, OpenMS::AASequence &aas)
helper function that sets a modifiction on a AASequence object
static DoubleReal getCIonPlusTwoToFullAverageWeight()
Definition: Residue.h:249
static const EmpiricalFormula & getZIonToFull()
Definition: Residue.h:281
static DoubleReal getZIonPlusTwoToFullAverageWeight()
Definition: Residue.h:344
static const EmpiricalFormula & getZIonPlusOneToFull()
Definition: Residue.h:319
static const EmpiricalFormula & getAIonToFull()
Definition: Residue.h:148
static const EmpiricalFormula & getCIonMinusOneToFull()
Definition: Residue.h:205
DoubleReal loss_mono_weight_
Definition: Residue.h:636
static DoubleReal getYIonToFullAverageWeight()
Definition: Residue.h:173
static DoubleReal getAIonToFullAverageWeight()
Definition: Residue.h:154
static const EmpiricalFormula & getCIonPlusTwoToFull()
Definition: Residue.h:243
String short_name_
Definition: Residue.h:602
Definition: Residue.h:373
Definition: Residue.h:377
static DoubleReal getXIonToFullAverageWeight()
Definition: Residue.h:268
static const EmpiricalFormula & getCTerminalToFull()
Definition: Residue.h:110
EmpiricalFormula internal_formula_
Definition: Residue.h:612
static DoubleReal getZIonToFullMonoWeight()
Definition: Residue.h:293
static DoubleReal getCIonMinusOneToFullAverageWeight()
Definition: Residue.h:211
String name_
Definition: Residue.h:600
String three_letter_code_
Definition: Residue.h:606
static DoubleReal getZIonPlusTwoToFullMonoWeight()
Definition: Residue.h:350
static DoubleReal getInternalToFullMonoWeight()
Definition: Residue.h:84
ResidueType
Definition: Residue.h:361
bool is_modified_
Definition: Residue.h:619
static DoubleReal getInternalToFullAverageWeight()
Definition: Residue.h:78
Definition: Residue.h:368
Definition: Residue.h:369
static const EmpiricalFormula & getXIonToFull()
Definition: Residue.h:262
std::set< String > synonyms_
Definition: Residue.h:604
static DoubleReal getCIonPlusOneToFullMonoWeight()
Definition: Residue.h:236
static DoubleReal getCIonToFullMonoWeight()
Definition: Residue.h:198
String pre_mod_name_
Definition: Residue.h:621
static DoubleReal getCTerminalToFullMonoWeight()
Definition: Residue.h:122
EmpiricalFormula formula_
Definition: Residue.h:610
static DoubleReal getBIonToFullAverageWeight()
Definition: Residue.h:135
String modification_
Definition: Residue.h:623
static DoubleReal getXIonToFullMonoWeight()
Definition: Residue.h:274
static DoubleReal getBIonToFullMonoWeight()
Definition: Residue.h:141
static const EmpiricalFormula & getNTerminalToFull()
Definition: Residue.h:91
DoubleReal gb_bb_l_
Definition: Residue.h:652
static DoubleReal getZIonMinusOneToFullAverageWeight()
Definition: Residue.h:306
DoubleReal mono_weight_
Definition: Residue.h:616
Definition: Residue.h:375
std::set< String > residue_sets_
Definition: Residue.h:657
Definition: Residue.h:371
std::vector< EmpiricalFormula > NTerm_loss_formulas_
Definition: Residue.h:632
static DoubleReal getCIonPlusOneToFullAverageWeight()
Definition: Residue.h:230
String one_letter_code_
Definition: Residue.h:608
static DoubleReal getYIonToFullMonoWeight()
Definition: Residue.h:179
static DoubleReal getNTerminalToFullAverageWeight()
Definition: Residue.h:97
Definition: Residue.h:370
static DoubleReal getZIonPlusOneToFullAverageWeight()
Definition: Residue.h:325