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TheoreticalSpectrumGeneratorXLMS.h
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2 // OpenMS -- Open-Source Mass Spectrometry
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4 // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
5 // ETH Zurich, and Freie Universitaet Berlin 2002-2020.
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30 // --------------------------------------------------------------------------
31 // $Maintainer: Eugen Netz $
32 // $Authors: Eugen Netz $
33 // --------------------------------------------------------------------------
34
35
36 #pragma once
37
38 #include <OpenMS/CHEMISTRY/Residue.h>
39 #include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
40 #include <OpenMS/KERNEL/StandardTypes.h>
41 #include <OpenMS/METADATA/DataArrays.h>
42 #include <OpenMS/ANALYSIS/XLMS/OPXLDataStructs.h>
43
44
45 namespace OpenMS
46 {
47 class AASequence;
48
65 class OPENMS_DLLAPI TheoreticalSpectrumGeneratorXLMS :
66 public DefaultParamHandler
67 {
68 public:
69
70 struct LossIndex
71 {
72 bool has_H2O_loss = false;
73 bool has_NH3_loss = false;
74 };
75
79 TheoreticalSpectrumGeneratorXLMS();
81
83 TheoreticalSpectrumGeneratorXLMS(const TheoreticalSpectrumGeneratorXLMS & source);
84
86 ~TheoreticalSpectrumGeneratorXLMS() override;
88
90 TheoreticalSpectrumGeneratorXLMS & operator=(const TheoreticalSpectrumGeneratorXLMS & tsg);
91
108 virtual void getLinearIonSpectrum(PeakSpectrum & spectrum, AASequence & peptide, Size link_pos, bool frag_alpha, int charge = 1, Size link_pos_2 = 0) const;
109
133 virtual void getXLinkIonSpectrum(PeakSpectrum & spectrum, AASequence & peptide, Size link_pos, double precursor_mass, bool frag_alpha, int mincharge, int maxcharge, Size link_pos_2 = 0) const;
134
154 virtual void getXLinkIonSpectrum(PeakSpectrum & spectrum, OPXLDataStructs::ProteinProteinCrossLink & crosslink, bool frag_alpha, int mincharge, int maxcharge) const;
155
157 void updateMembers_() override;
158
159 protected:
160
175 virtual void addLinearPeaks_(PeakSpectrum & spectrum, DataArrays::IntegerDataArray & charges, DataArrays::StringDataArray & ion_names, AASequence & peptide, Size link_pos, bool frag_alpha, Residue::ResidueType res_type, std::vector< LossIndex > & forward_losses, std::vector< LossIndex > & backward_losses, int charge = 1, Size link_pos_2 = 0) const;
176
194 virtual void addPeak_(PeakSpectrum & spectrum, DataArrays::IntegerDataArray & charges, DataArrays::StringDataArray & ion_names, double pos, double intensity, Residue::ResidueType res_type, Size ion_index, int charge, String ion_type) const;
195
205 virtual void addPrecursorPeaks_(PeakSpectrum & spectrum, DataArrays::IntegerDataArray & charges, DataArrays::StringDataArray & ion_names, double precursor_mass, int charge) const;
206
221 virtual void addLinearIonLosses_(PeakSpectrum & spectrum, DataArrays::IntegerDataArray& charges, DataArrays::StringDataArray& ion_names, double mono_weight, Residue::ResidueType res_type, Size frag_index, double intensity, int charge, String ion_type, LossIndex & losses) const;
222
237 virtual void addXLinkIonLosses_(PeakSpectrum & spectrum, DataArrays::IntegerDataArray& charges, DataArrays::StringDataArray& ion_names, double mono_weight, double intensity, int charge, String ion_name, LossIndex & losses) const;
238
255 virtual void addKLinkedIonPeaks_(PeakSpectrum & spectrum, DataArrays::IntegerDataArray & charges, DataArrays::StringDataArray & ion_names, AASequence & peptide, Size link_pos, double precursor_mass, bool frag_alpha, int charge) const;
256
275 virtual void addXLinkIonPeaks_(PeakSpectrum& spectrum, DataArrays::IntegerDataArray & charges, DataArrays::StringDataArray & ion_names, AASequence & peptide, Size link_pos, double precursor_mass, bool frag_alpha, Residue::ResidueType res_type, std::vector< LossIndex > & forward_losses, std::vector< LossIndex > & backward_losses, int charge, Size link_pos_2 = 0) const;
276
295 virtual void addXLinkIonPeaks_(PeakSpectrum & spectrum, DataArrays::IntegerDataArray & charges, DataArrays::StringDataArray & ion_names, OPXLDataStructs::ProteinProteinCrossLink & crosslink, bool frag_alpha, Residue::ResidueType res_type, std::vector< LossIndex > & forward_losses, std::vector< LossIndex > & backward_losses, LossIndex & losses_peptide2, int charge) const;
296
304 std::vector< LossIndex > getForwardLosses_(AASequence & peptide) const;
305
313 std::vector< LossIndex > getBackwardLosses_(AASequence & peptide) const;
314
315 bool add_b_ions_;
316 bool add_y_ions_;
317 bool add_a_ions_;
318 bool add_c_ions_;
319 bool add_x_ions_;
320 bool add_z_ions_;
321 bool add_first_prefix_ion_;
322 bool add_losses_;
323 bool add_metainfo_;
324 bool add_charges_;
325 bool add_isotopes_;
326 bool add_precursor_peaks_;
327 bool add_abundant_immonium_ions_;
328 double a_intensity_;
329 double b_intensity_;
330 double c_intensity_;
331 double x_intensity_;
332 double y_intensity_;
333 double z_intensity_;
334 Int max_isotope_;
335 double rel_loss_intensity_;
336 double pre_int_;
337 double pre_int_H2O_;
338 double pre_int_NH3_;
339 bool add_k_linked_ions_;
340
341 std::map< String, LossIndex > loss_db_;
342 double loss_H2O_ = 0;
343 double loss_NH3_ = 0;
344 };
345 }
OpenMS::TheoreticalSpectrumGeneratorXLMS::add_x_ions_
bool add_x_ions_
Definition: TheoreticalSpectrumGeneratorXLMS.h:319
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::TheoreticalSpectrumGeneratorXLMS::z_intensity_
double z_intensity_
Definition: TheoreticalSpectrumGeneratorXLMS.h:333
OpenMS::TheoreticalSpectrumGeneratorXLMS::add_precursor_peaks_
bool add_precursor_peaks_
Definition: TheoreticalSpectrumGeneratorXLMS.h:326
OpenMS::TheoreticalSpectrumGeneratorXLMS::y_intensity_
double y_intensity_
Definition: TheoreticalSpectrumGeneratorXLMS.h:332
OpenMS::TheoreticalSpectrumGeneratorXLMS::add_a_ions_
bool add_a_ions_
Definition: TheoreticalSpectrumGeneratorXLMS.h:317
OpenMS::DefaultParamHandler
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:91
OpenMS::TheoreticalSpectrumGeneratorXLMS::rel_loss_intensity_
double rel_loss_intensity_
Definition: TheoreticalSpectrumGeneratorXLMS.h:335
OpenMS::TheoreticalSpectrumGeneratorXLMS::add_c_ions_
bool add_c_ions_
Definition: TheoreticalSpectrumGeneratorXLMS.h:318
OPXLDataStructs.h
Residue.h
StandardTypes.h
DataArrays.h
OpenMS::OPXLDataStructs::ProteinProteinCrossLink
The ProteinProteinCrossLink struct represents a cross-link between two peptides in OpenPepXL...
Definition: OPXLDataStructs.h:72
OpenMS::TheoreticalSpectrumGeneratorXLMS::add_first_prefix_ion_
bool add_first_prefix_ion_
Definition: TheoreticalSpectrumGeneratorXLMS.h:321
OpenMS::TheoreticalSpectrumGeneratorXLMS::add_b_ions_
bool add_b_ions_
Definition: TheoreticalSpectrumGeneratorXLMS.h:315
OpenMS::TheoreticalSpectrumGeneratorXLMS::add_isotopes_
bool add_isotopes_
Definition: TheoreticalSpectrumGeneratorXLMS.h:325
OpenMS::DataArrays::StringDataArray
String data array class.
Definition: DataArrays.h:59
OpenMS::AASequence
Representation of a peptide/protein sequence.
Definition: AASequence.h:113
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:67
OpenMS::TheoreticalSpectrumGeneratorXLMS::LossIndex
Definition: TheoreticalSpectrumGeneratorXLMS.h:70
OpenMS::TheoreticalSpectrumGeneratorXLMS::add_k_linked_ions_
bool add_k_linked_ions_
Definition: TheoreticalSpectrumGeneratorXLMS.h:339
OpenMS::TheoreticalSpectrumGeneratorXLMS::add_z_ions_
bool add_z_ions_
Definition: TheoreticalSpectrumGeneratorXLMS.h:320
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::DataArrays::IntegerDataArray
Integer data array class.
Definition: DataArrays.h:52
OpenMS::TheoreticalSpectrumGeneratorXLMS::pre_int_H2O_
double pre_int_H2O_
Definition: TheoreticalSpectrumGeneratorXLMS.h:337
OpenMS::TheoreticalSpectrumGeneratorXLMS
Generates theoretical spectra for cross-linked peptides.
Definition: TheoreticalSpectrumGeneratorXLMS.h:65
OpenMS::TheoreticalSpectrumGeneratorXLMS::add_charges_
bool add_charges_
Definition: TheoreticalSpectrumGeneratorXLMS.h:324
DefaultParamHandler.h
OpenMS::TheoreticalSpectrumGeneratorXLMS::loss_db_
std::map< String, LossIndex > loss_db_
Definition: TheoreticalSpectrumGeneratorXLMS.h:341
OpenMS::TheoreticalSpectrumGeneratorXLMS::c_intensity_
double c_intensity_
Definition: TheoreticalSpectrumGeneratorXLMS.h:330
OpenMS::TheoreticalSpectrumGeneratorXLMS::pre_int_
double pre_int_
Definition: TheoreticalSpectrumGeneratorXLMS.h:336
int
OpenMS::TheoreticalSpectrumGeneratorXLMS::x_intensity_
double x_intensity_
Definition: TheoreticalSpectrumGeneratorXLMS.h:331
OpenMS::TheoreticalSpectrumGeneratorXLMS::max_isotope_
Int max_isotope_
Definition: TheoreticalSpectrumGeneratorXLMS.h:334
OpenMS::TheoreticalSpectrumGeneratorXLMS::add_abundant_immonium_ions_
bool add_abundant_immonium_ions_
Definition: TheoreticalSpectrumGeneratorXLMS.h:327
OpenMS::TheoreticalSpectrumGeneratorXLMS::b_intensity_
double b_intensity_
Definition: TheoreticalSpectrumGeneratorXLMS.h:329
OpenMS::TheoreticalSpectrumGeneratorXLMS::a_intensity_
double a_intensity_
Definition: TheoreticalSpectrumGeneratorXLMS.h:328
OpenMS::TheoreticalSpectrumGeneratorXLMS::add_y_ions_
bool add_y_ions_
Definition: TheoreticalSpectrumGeneratorXLMS.h:316
OpenMS::TheoreticalSpectrumGeneratorXLMS::pre_int_NH3_
double pre_int_NH3_
Definition: TheoreticalSpectrumGeneratorXLMS.h:338
OpenMS::TheoreticalSpectrumGeneratorXLMS::add_losses_
bool add_losses_
Definition: TheoreticalSpectrumGeneratorXLMS.h:322
OpenMS::Residue::ResidueType
ResidueType
Definition: Residue.h:150
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
OpenMS::TheoreticalSpectrumGeneratorXLMS::add_metainfo_
bool add_metainfo_
Definition: TheoreticalSpectrumGeneratorXLMS.h:323