OpenMS  2.6.0
ResidueModification.h
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35 
36 #pragma once
37 
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 
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 
108  {
109  ARTIFACT = 0,
125  NUMBER_OF_SOURCE_CLASSIFICATIONS
126  };
128 
132 
135 
137  ResidueModification(const ResidueModification&) = default;
138 
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 setNeutralLossDiffFormulas(const std::vector<EmpiricalFormula>& diff_formulas);
313 
315  const std::vector<EmpiricalFormula>& getNeutralLossDiffFormulas() const;
316 
318  void setNeutralLossMonoMasses(std::vector<double> mono_masses);
319 
321  std::vector<double> getNeutralLossMonoMasses() const;
322 
324  void setNeutralLossAverageMasses(std::vector<double> average_masses);
325 
327  std::vector<double> getNeutralLossAverageMasses() 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;
347 
349 
352 
359  static const ResidueModification* createUnknownFromMassString(const String& mod,
360  const double mass,
361  const bool delta_mass,
362  const TermSpecificity specificity,
363  const Residue* residue = nullptr);
364 
381  static const ResidueModification* combineMods(const ResidueModification* base,
382  const std::set<const ResidueModification*>& addons,
383  bool allow_unknown_masses = false,
384  const Residue* residue = nullptr);
385 
393  String toString() const;
394 
397  static String getDiffMonoMassString(const double diff_mono_mass);
398 
400  static String getDiffMonoMassWithBracket(const double diff_mono_mass);
401 
403  static String getMonoMassWithBracket(const double mono_mass);
404 
405 protected:
407 
409 
411 
412  // The UniMod record id (an integer)
414 
416 
418 
420 
421  char origin_;
422 
424 
426 
427  double mono_mass_;
428 
430 
432 
434 
436 
437  std::set<String> synonyms_;
438 
439  std::vector<EmpiricalFormula> neutral_loss_diff_formulas_;
440 
441  std::vector<double> neutral_loss_mono_masses_;
442 
443  std::vector<double> neutral_loss_average_masses_;
444  };
445 }
OpenMS::ResidueModification::classification_
SourceClassification classification_
Definition: ResidueModification.h:423
OpenMS::ResidueModification::full_id_
String full_id_
Definition: ResidueModification.h:408
OpenMS::ResidueModification::OTHER_GLYCOSYLATION
Definition: ResidueModification.h:117
OpenMS::ResidueModification
Representation of a modification.
Definition: ResidueModification.h:76
OpenMS::ResidueModification::HYPOTHETICAL
Definition: ResidueModification.h:110
OpenMS::ResidueModification::ISOTOPIC_LABEL
Definition: ResidueModification.h:115
OpenMS::String
A more convenient string class.
Definition: String.h:59
OpenMS::ResidueModification::full_name_
String full_name_
Definition: ResidueModification.h:415
KDTree::operator!=
bool operator!=(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:824
OpenMS::ResidueModification::MULTIPLE
Definition: ResidueModification.h:113
OpenMS::ResidueModification::NATURAL
Definition: ResidueModification.h:111
OpenMS::ResidueModification::NONSTANDARD_RESIDUE
Definition: ResidueModification.h:121
OpenMS::ResidueModification::name_
String name_
Definition: ResidueModification.h:417
OpenMS::ResidueModification::UNKNOWN
Definition: ResidueModification.h:124
OpenMS::operator<
bool operator<(const QTCluster &q1, const QTCluster &q2)
OpenMS::ResidueModification::COTRANSLATIONAL
Definition: ResidueModification.h:122
OpenMS::ResidueModification::PRETRANSLATIONAL
Definition: ResidueModification.h:116
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::ResidueModification::neutral_loss_mono_masses_
std::vector< double > neutral_loss_mono_masses_
Definition: ResidueModification.h:441
OpenMS::ResidueModification::origin_
char origin_
Definition: ResidueModification.h:421
OpenMS::ResidueModification::CHEMICAL_DERIVATIVE
Definition: ResidueModification.h:114
OpenMS::Residue
Representation of a residue.
Definition: Residue.h:62
OpenMS::ResidueModification::TermSpecificity
TermSpecificity
Position where the modification is allowed to occur.
Definition: ResidueModification.h:95
int
OpenMS::ResidueModification::OTHER
Definition: ResidueModification.h:120
OpenMS::ResidueModification::AA_SUBSTITUTION
Definition: ResidueModification.h:119
OpenMS::ResidueModification::SourceClassification
SourceClassification
Classification of the modification.
Definition: ResidueModification.h:107
OpenMS::ResidueModification::synonyms_
std::set< String > synonyms_
Definition: ResidueModification.h:437
OpenMS::ResidueModification::average_mass_
double average_mass_
Definition: ResidueModification.h:425
OpenMS::StringConversions::toString
String toString(const T &i)
fallback template for general purpose using Boost::Karma; more specializations below
Definition: StringUtils.h:127
OpenMS::ResidueModification::neutral_loss_diff_formulas_
std::vector< EmpiricalFormula > neutral_loss_diff_formulas_
Definition: ResidueModification.h:439
OpenMS::ResidueModification::psi_mod_accession_
String psi_mod_accession_
Definition: ResidueModification.h:410
EmpiricalFormula.h
OpenMS::Internal::operator==
bool operator==(const IDBoostGraph::ProteinGroup &lhs, const IDBoostGraph::ProteinGroup &rhs)
OpenMS::ResidueModification::id_
String id_
Definition: ResidueModification.h:406
OpenMS::ResidueModification::NLINKED_GLYCOSYLATION
Definition: ResidueModification.h:118
OpenMS::EmpiricalFormula
Representation of an empirical formula.
Definition: EmpiricalFormula.h:82
OpenMS::ResidueModification::formula_
String formula_
Definition: ResidueModification.h:433
OpenMS::ResidueModification::diff_mono_mass_
double diff_mono_mass_
Definition: ResidueModification.h:431
OpenMS::ResidueModification::mono_mass_
double mono_mass_
Definition: ResidueModification.h:427
String.h
OpenMS::ResidueModification::diff_average_mass_
double diff_average_mass_
Definition: ResidueModification.h:429
OpenMS::ResidueModification::OLINKED_GLYCOSYLATION
Definition: ResidueModification.h:123
OpenMS::ResidueModification::unimod_record_id_
Int unimod_record_id_
Definition: ResidueModification.h:413
OpenMS::ResidueModification::neutral_loss_average_masses_
std::vector< double > neutral_loss_average_masses_
Definition: ResidueModification.h:443
OpenMS::ResidueModification::diff_formula_
EmpiricalFormula diff_formula_
Definition: ResidueModification.h:435
OpenMS::ResidueModification::POSTTRANSLATIONAL
Definition: ResidueModification.h:112
OpenMS::ResidueModification::term_spec_
TermSpecificity term_spec_
Definition: ResidueModification.h:419