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OpenMS
2.4.0
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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);
@ Unannotated
no stored annotation
Definition: Residue.h:168
residue data base which holds residues
Definition: ResidueDB.h:60
Base class for TOPP applications.
Definition: TOPPBase.h:150
double gb_sc_
Definition: Residue.h:437
@ BIon
MS:1001224 N-terminus up to the peptide bond.
Definition: Residue.h:157
Representation of a modification.
Definition: ResidueModification.h:76
double pka_
Definition: Residue.h:429
@ DATA_PROCESSING
General data processing (if no other term applies)
Definition: DataProcessing.h:60
double loss_mono_weight_
Definition: Residue.h:423
double loss_average_weight_
Definition: Residue.h:421
static const EmpiricalFormula & getInternalToCIon()
Definition: Residue.h:115
void store(const String &filename, const PeakMap &map) const
Stores a map in an MzML file.
@ ZIon
MS:1001230 C-alpha/carbonyl carbon bond.
Definition: Residue.h:161
void setValue(const String &key, const DataValue &value, const String &description="", const StringList &tags=StringList())
Sets a value.
File adapter for MzML files.
Definition: MzMLFile.h:55
A more convenient string class.
Definition: String.h:57
bool operator!=(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:824
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
static const EmpiricalFormula & getInternalToCTerm()
Definition: Residue.h:93
Linear Resampling of raw data with alignment.
Definition: LinearResamplerAlign.h:57
@ CIon
MS:1001231 N-terminus up to the amide/C-alpha bond.
Definition: Residue.h:158
void raster_align(SpecT &container, double start_pos, double end_pos)
Applies the resampling algorithm to a container (MSSpectrum or MSChromatogram) with fixed coordinates...
Definition: LinearResamplerAlign.h:116
const ResidueModification * modification_
Definition: Residue.h:410
@ AIon
MS:1001229 N-terminus up to the C-alpha/carbonyl carbon bond.
Definition: Residue.h:156
bool clearMetaDataArrays()
Clears the meta data arrays of all contained spectra (float, integer and string arrays)
Size size() const
Definition: MSExperiment.h:127
std::vector< String > NTerm_loss_names_
Definition: Residue.h:417
double pkc_
Definition: Residue.h:435
EmpiricalFormula internal_formula_
Definition: Residue.h:403
Linear Resampling of raw data.
Definition: LinearResampler.h:61
@ Precursor
MS:1001523 Precursor ion.
Definition: Residue.h:162
static const EmpiricalFormula & getInternalToAIon()
Definition: Residue.h:99
@ YIonMinusNH3
MS:1001233 y ion without ammonia.
Definition: Residue.h:166
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
@ Internal
internal, without any termini
Definition: Residue.h:153
double gb_bb_r_
Definition: Residue.h:441
static const EmpiricalFormula & getInternalToBIon()
Definition: Residue.h:107
static const EmpiricalFormula & getInternalToFull()
Definition: Residue.h:81
Representation of a residue.
Definition: Residue.h:61
void load(const String &filename, PeakMap &map)
Loads a map from a MzML file. Spectra and chromatograms are sorted by default (this can be disabled u...
double mono_weight_
Definition: Residue.h:407
double gb_bb_l_
Definition: Residue.h:439
@ NTerminal
only N-terminus
Definition: Residue.h:154
static const EmpiricalFormula & getInternalToXIon()
Definition: Residue.h:122
@ NonIdentified
MS:1001240 Non-identified ion.
Definition: Residue.h:167
@ CTerminal
only C-terminus
Definition: Residue.h:155
double pkb_
Definition: Residue.h:432
std::vector< EmpiricalFormula > low_mass_ions_
Definition: Residue.h:426
std::set< String > synonyms_
Definition: Residue.h:395
static const EmpiricalFormula & getInternalToYIon()
Definition: Residue.h:130
@ BIonMinusH20
MS:1001222 b ion without water.
Definition: Residue.h:163
void clear(bool clear_meta_data)
Clears all data and meta data.
void setParameters(const Param ¶m)
Sets the parameters.
std::vector< EmpiricalFormula > loss_formulas_
Definition: Residue.h:415
ResidueType
Definition: Residue.h:150
EmpiricalFormula formula_
Definition: Residue.h:401
std::ostream & operator<<(std::ostream &os, const AccurateMassSearchResult &amsr)
void setModification(int location, int max_size, String modification, OpenMS::AASequence &aas)
helper function that sets a modification on a AASequence object
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:73
bool operator==(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:806
std::vector< EmpiricalFormula > NTerm_loss_formulas_
Definition: Residue.h:419
String one_letter_code_
Definition: Residue.h:399
double average_weight_
Definition: Residue.h:405
String short_name_
Definition: Residue.h:393
void raster(MSSpectrum &spectrum)
Applies the resampling algorithm to an MSSpectrum.
Definition: LinearResampler.h:84
static const EmpiricalFormula & getInternalToZIon()
Definition: Residue.h:137
std::set< String > residue_sets_
Definition: Residue.h:444
Management and storage of parameters / INI files.
Definition: Param.h:74
@ BIonMinusNH3
MS:1001232 b ion without ammonia.
Definition: Residue.h:165
String name_
Definition: Residue.h:391
@ YIon
MS:1001220 peptide bond up to the C-terminus.
Definition: Residue.h:160
@ XIon
MS:1001228 amide/C-alpha bond up to the C-terminus.
Definition: Residue.h:159
The representation of a 1D spectrum.
Definition: MSSpectrum.h:66
std::vector< String > loss_names_
Definition: Residue.h:413
@ YIonMinusH20
MS:1001223 y ion without water.
Definition: Residue.h:164
static const EmpiricalFormula & getInternalToNTerm()
Definition: Residue.h:87
void setLogType(LogType type) const
Sets the progress log that should be used. The default type is NONE!
String three_letter_code_
Definition: Residue.h:397