| OpenMS 2.5.0

ResidueModification.h
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1 // --------------------------------------------------------------------------
2 // OpenMS -- Open-Source Mass Spectrometry
3 // --------------------------------------------------------------------------
4 // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
5 // ETH Zurich, and Freie Universitaet Berlin 2002-2020.
6 //
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30 // --------------------------------------------------------------------------
31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Andreas Bertsch $
33 // --------------------------------------------------------------------------
34 //
35
36 #pragma once
37
38 #include <OpenMS/DATASTRUCTURES/String.h>
39 #include <OpenMS/CHEMISTRY/EmpiricalFormula.h>
40
41 #include <set>
42
43 namespace OpenMS
44 {
45 // forward declaration
46 class Residue;
47
76 class OPENMS_DLLAPI ResidueModification
77 {
78 public:
79
95 enum TermSpecificity
96 {
97 ANYWHERE = 0,
98 C_TERM = 1,
99 N_TERM = 2,
100 PROTEIN_C_TERM = 3,
101 PROTEIN_N_TERM = 4,
102 NUMBER_OF_TERM_SPECIFICITY
103 };
104
107 enum SourceClassification
108 {
109 ARTIFACT = 0,
110 HYPOTHETICAL,
111 NATURAL,
112 POSTTRANSLATIONAL,
113 MULTIPLE,
114 CHEMICAL_DERIVATIVE,
115 ISOTOPIC_LABEL,
116 PRETRANSLATIONAL,
117 OTHER_GLYCOSYLATION,
118 NLINKED_GLYCOSYLATION,
119 AA_SUBSTITUTION,
120 OTHER,
121 NONSTANDARD_RESIDUE,
122 COTRANSLATIONAL,
123 OLINKED_GLYCOSYLATION,
124 UNKNOWN,
125 NUMBER_OF_SOURCE_CLASSIFICATIONS
126 };
128
132
134 ResidueModification();
135
137 ResidueModification(const ResidueModification&) = default;
138
140 ResidueModification(ResidueModification&&) = default;
141
143 virtual ~ResidueModification();
145
149
151 ResidueModification& operator=(const ResidueModification&) = default;
152
154 ResidueModification& operator=(ResidueModification&&) & = default;
156
160 void setId(const String& id);
162
164 const String& getId() const;
165
173 void setFullId(const String& full_id = "");
174
176
185 const String& getFullId() const;
186
188 void setUniModRecordId(const Int& id);
189
191 const Int& getUniModRecordId() const;
192
194 const String getUniModAccession() const;
195
197 void setPSIMODAccession(const String& id);
198
200 const String& getPSIMODAccession() const;
201
203 void setFullName(const String& full_name);
204
206 const String& getFullName() const;
207
209 void setName(const String& name);
210
212 const String& getName() const;
213
219 void setTermSpecificity(TermSpecificity term_spec);
220
228 void setTermSpecificity(const String& name);
229
231 TermSpecificity getTermSpecificity() const;
232
239 String getTermSpecificityName(TermSpecificity term_spec = NUMBER_OF_TERM_SPECIFICITY) const;
240
249 void setOrigin(char origin);
250
252 char getOrigin() const;
253
255 void setSourceClassification(const String& classification);
256
258 void setSourceClassification(SourceClassification classification);
259
261 SourceClassification getSourceClassification() const;
262
264 String getSourceClassificationName(SourceClassification classification = NUMBER_OF_SOURCE_CLASSIFICATIONS) const;
265
267 void setAverageMass(double mass);
268
270 double getAverageMass() const;
271
273 void setMonoMass(double mass);
274
276 double getMonoMass() const;
277
279 void setDiffAverageMass(double mass);
280
282 double getDiffAverageMass() const;
283
285 void setDiffMonoMass(double mass);
286
288 double getDiffMonoMass() const;
289
291 void setFormula(const String& composition);
292
294 const String& getFormula() const;
295
297 void setDiffFormula(const EmpiricalFormula& diff_formula);
298
300 const EmpiricalFormula& getDiffFormula() const;
301
303 void setSynonyms(const std::set<String>& synonyms);
304
306 void addSynonym(const String& synonym);
307
309 const std::set<String>& getSynonyms() const;
310
312 void setNeutralLossDiffFormula(const EmpiricalFormula& loss);
313
315 const EmpiricalFormula& getNeutralLossDiffFormula() const;
316
318 void setNeutralLossMonoMass(double mono_mass);
319
321 double getNeutralLossMonoMass() const;
322
324 void setNeutralLossAverageMass(double average_mass);
325
327 double getNeutralLossAverageMass() const;
329
333 bool hasNeutralLoss() const;
335
337 bool isUserDefined() const;
338
340 bool operator==(const ResidueModification& modification) const;
341
343 bool operator!=(const ResidueModification& modification) const;
344
346 bool operator<(const ResidueModification& modification) const;
348
349 protected:
350
351 String id_;
352
353 String full_id_;
354
355 String psi_mod_accession_;
356
357 // The UniMod record id (an integer)
358 Int unimod_record_id_;
359
360 String full_name_;
361
362 String name_;
363
364 TermSpecificity term_spec_;
365
366 char origin_;
367
368 SourceClassification classification_;
369
370 double average_mass_;
371
372 double mono_mass_;
373
374 double diff_average_mass_;
375
376 double diff_mono_mass_;
377
378 String formula_;
379
380 EmpiricalFormula diff_formula_;
381
382 std::set<String> synonyms_;
383
384 EmpiricalFormula neutral_loss_diff_formula_;
385
386 double neutral_loss_mono_mass_;
387
388 double neutral_loss_average_mass_;
389 };
390 }
391
OpenMS::ResidueModification::synonyms_
std::set< String > synonyms_
Definition: ResidueModification.h:382
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::ResidueModification::psi_mod_accession_
String psi_mod_accession_
Definition: ResidueModification.h:355
OpenMS::operator<
bool operator<(const MultiplexDeltaMasses &dm1, const MultiplexDeltaMasses &dm2)
OpenMS::ResidueModification::name_
String name_
Definition: ResidueModification.h:362
OpenMS::ResidueModification::MULTIPLE
Definition: ResidueModification.h:113
OpenMS::ResidueModification::unimod_record_id_
Int unimod_record_id_
Definition: ResidueModification.h:358
OpenMS::ResidueModification::neutral_loss_diff_formula_
EmpiricalFormula neutral_loss_diff_formula_
Definition: ResidueModification.h:384
OpenMS::ResidueModification::neutral_loss_average_mass_
double neutral_loss_average_mass_
Definition: ResidueModification.h:388
KDTree::operator!=
bool operator!=(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:824
OpenMS::ResidueModification::diff_formula_
EmpiricalFormula diff_formula_
Definition: ResidueModification.h:380
OpenMS::ResidueModification::NLINKED_GLYCOSYLATION
Definition: ResidueModification.h:118
OpenMS::ResidueModification::neutral_loss_mono_mass_
double neutral_loss_mono_mass_
Definition: ResidueModification.h:386
OpenMS::ResidueModification::CHEMICAL_DERIVATIVE
Definition: ResidueModification.h:114
OpenMS::ResidueModification
Representation of a modification.
Definition: ResidueModification.h:76
OpenMS::ResidueModification::average_mass_
double average_mass_
Definition: ResidueModification.h:370
OpenMS::ResidueModification::AA_SUBSTITUTION
Definition: ResidueModification.h:119
OpenMS::ResidueModification::origin_
char origin_
Definition: ResidueModification.h:366
OpenMS::ResidueModification::PRETRANSLATIONAL
Definition: ResidueModification.h:116
OpenMS::ResidueModification::diff_average_mass_
double diff_average_mass_
Definition: ResidueModification.h:374
OpenMS::ResidueModification::POSTTRANSLATIONAL
Definition: ResidueModification.h:112
String.h
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::ResidueModification::NATURAL
Definition: ResidueModification.h:111
OpenMS::ResidueModification::term_spec_
TermSpecificity term_spec_
Definition: ResidueModification.h:364
OpenMS::EmpiricalFormula
Representation of an empirical formula.
Definition: EmpiricalFormula.h:82
OpenMS::ResidueModification::full_id_
String full_id_
Definition: ResidueModification.h:353
OpenMS::ResidueModification::full_name_
String full_name_
Definition: ResidueModification.h:360
OpenMS::ResidueModification::classification_
SourceClassification classification_
Definition: ResidueModification.h:368
OpenMS::ResidueModification::COTRANSLATIONAL
Definition: ResidueModification.h:122
OpenMS::ResidueModification::HYPOTHETICAL
Definition: ResidueModification.h:110
OpenMS::ResidueModification::SourceClassification
SourceClassification
Classification of the modification.
Definition: ResidueModification.h:107
EmpiricalFormula.h
OpenMS::ResidueModification::ISOTOPIC_LABEL
Definition: ResidueModification.h:115
int
OpenMS::ResidueModification::TermSpecificity
TermSpecificity
Position where the modification is allowed to occur.
Definition: ResidueModification.h:95
OpenMS::ResidueModification::UNKNOWN
Definition: ResidueModification.h:124
OpenMS::ResidueModification::OTHER
Definition: ResidueModification.h:120
OpenMS::ResidueModification::diff_mono_mass_
double diff_mono_mass_
Definition: ResidueModification.h:376
OpenMS::ResidueModification::NONSTANDARD_RESIDUE
Definition: ResidueModification.h:121
OpenMS::ResidueModification::id_
String id_
Definition: ResidueModification.h:351
OpenMS::ResidueModification::OLINKED_GLYCOSYLATION
Definition: ResidueModification.h:123
OpenMS::ResidueModification::mono_mass_
double mono_mass_
Definition: ResidueModification.h:372
OpenMS::ResidueModification::OTHER_GLYCOSYLATION
Definition: ResidueModification.h:117
OpenMS::ResidueModification::formula_
String formula_
Definition: ResidueModification.h:378
KDTree::operator==
bool operator==(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:806