OpenMS
TheoreticalSpectrumGeneratorXLMS.h
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1 // Copyright (c) 2002-2023, The OpenMS Team -- EKU Tuebingen, ETH Zurich, and FU Berlin
2 // SPDX-License-Identifier: BSD-3-Clause
3 //
4 // --------------------------------------------------------------------------
5 // $Maintainer: Eugen Netz $
6 // $Authors: Eugen Netz $
7 // --------------------------------------------------------------------------
8 
9 
10 #pragma once
11 
17 
18 
19 namespace OpenMS
20 {
21  class AASequence;
22 
39  class OPENMS_DLLAPI TheoreticalSpectrumGeneratorXLMS :
40  public DefaultParamHandler
41  {
42  public:
43 
44  struct LossIndex
45  {
46  bool has_H2O_loss = false;
47  bool has_NH3_loss = false;
48  };
49 
55 
58 
62 
65 
82  virtual void getLinearIonSpectrum(PeakSpectrum & spectrum, AASequence & peptide, Size link_pos, bool frag_alpha, int charge = 1, Size link_pos_2 = 0) const;
83 
107  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;
108 
126  virtual void getXLinkIonSpectrum(PeakSpectrum & spectrum, OPXLDataStructs::ProteinProteinCrossLink & crosslink, bool frag_alpha, int mincharge, int maxcharge) const;
127 
129  void updateMembers_() override;
130 
131  protected:
132 
147  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;
148 
166  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;
167 
177  virtual void addPrecursorPeaks_(PeakSpectrum & spectrum, DataArrays::IntegerDataArray & charges, DataArrays::StringDataArray & ion_names, double precursor_mass, int charge) const;
178 
193  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;
194 
209  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;
210 
227  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;
228 
247  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;
248 
265  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;
266 
274  std::vector< LossIndex > getForwardLosses_(AASequence & peptide) const;
275 
283  std::vector< LossIndex > getBackwardLosses_(AASequence & peptide) const;
284 
298  double a_intensity_;
299  double b_intensity_;
300  double c_intensity_;
301  double x_intensity_;
302  double y_intensity_;
303  double z_intensity_;
306  double pre_int_;
307  double pre_int_H2O_;
308  double pre_int_NH3_;
310 
311  std::map< String, LossIndex > loss_db_;
312  double loss_H2O_ = 0;
313  double loss_NH3_ = 0;
314  };
315 }
Representation of a peptide/protein sequence.
Definition: AASequence.h:86
Integer data array class.
Definition: DataArrays.h:29
String data array class.
Definition: DataArrays.h:36
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:66
The representation of a 1D spectrum.
Definition: MSSpectrum.h:44
ResidueType
Definition: Residue.h:126
A more convenient string class.
Definition: String.h:34
Generates theoretical spectra for cross-linked peptides.
Definition: TheoreticalSpectrumGeneratorXLMS.h:41
virtual void getLinearIonSpectrum(PeakSpectrum &spectrum, AASequence &peptide, Size link_pos, bool frag_alpha, int charge=1, Size link_pos_2=0) const
Generates fragment ions not containing the cross-linker for one peptide.
bool add_x_ions_
Definition: TheoreticalSpectrumGeneratorXLMS.h:289
bool add_precursor_peaks_
Definition: TheoreticalSpectrumGeneratorXLMS.h:296
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
Adds losses for a cross-linked ion.
double rel_loss_intensity_
Definition: TheoreticalSpectrumGeneratorXLMS.h:305
bool add_charges_
Definition: TheoreticalSpectrumGeneratorXLMS.h:294
std::vector< LossIndex > getForwardLosses_(AASequence &peptide) const
Calculates sets of possible neutral losses for each position in the given peptide.
bool add_losses_
Definition: TheoreticalSpectrumGeneratorXLMS.h:292
bool add_a_ions_
Definition: TheoreticalSpectrumGeneratorXLMS.h:287
double c_intensity_
Definition: TheoreticalSpectrumGeneratorXLMS.h:300
bool add_b_ions_
Definition: TheoreticalSpectrumGeneratorXLMS.h:285
double z_intensity_
Definition: TheoreticalSpectrumGeneratorXLMS.h:303
bool add_abundant_immonium_ions_
Definition: TheoreticalSpectrumGeneratorXLMS.h:297
virtual void getXLinkIonSpectrum(PeakSpectrum &spectrum, OPXLDataStructs::ProteinProteinCrossLink &crosslink, bool frag_alpha, int mincharge, int maxcharge) const
Generates fragment ions containing the cross-linker for a pair of peptides.
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
Generates fragment ions containing the cross-linker for one peptide.
bool add_y_ions_
Definition: TheoreticalSpectrumGeneratorXLMS.h:286
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
Adds a single peak to a spectrum and its charge and ion name to the given DataArrays.
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
Adds losses for a linear ion.
~TheoreticalSpectrumGeneratorXLMS() override
destructor
bool add_isotopes_
Definition: TheoreticalSpectrumGeneratorXLMS.h:295
double pre_int_NH3_
Definition: TheoreticalSpectrumGeneratorXLMS.h:308
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
Adds cross-linked ions of a specific ion type and charge to a spectrum and adds ion name and charge a...
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
Adds one-residue-linked ion peaks, that are specific to XLMS.
TheoreticalSpectrumGeneratorXLMS & operator=(const TheoreticalSpectrumGeneratorXLMS &tsg)
assignment operator
double x_intensity_
Definition: TheoreticalSpectrumGeneratorXLMS.h:301
bool add_k_linked_ions_
Definition: TheoreticalSpectrumGeneratorXLMS.h:309
virtual void addPrecursorPeaks_(PeakSpectrum &spectrum, DataArrays::IntegerDataArray &charges, DataArrays::StringDataArray &ion_names, double precursor_mass, int charge) const
Adds precursor masses including neutral losses for the given charge and adds charge and ion name to t...
double a_intensity_
Definition: TheoreticalSpectrumGeneratorXLMS.h:298
bool add_first_prefix_ion_
Definition: TheoreticalSpectrumGeneratorXLMS.h:291
TheoreticalSpectrumGeneratorXLMS(const TheoreticalSpectrumGeneratorXLMS &source)
copy constructor
double b_intensity_
Definition: TheoreticalSpectrumGeneratorXLMS.h:299
void updateMembers_() override
overwrite
TheoreticalSpectrumGeneratorXLMS()
default constructor
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
Adds cross-link-less ions of a specific ion type and charge to a spectrum and adds ion name and charg...
std::map< String, LossIndex > loss_db_
Definition: TheoreticalSpectrumGeneratorXLMS.h:311
double pre_int_
Definition: TheoreticalSpectrumGeneratorXLMS.h:306
double y_intensity_
Definition: TheoreticalSpectrumGeneratorXLMS.h:302
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
Adds cross-linked ions of a specific ion type and charge to a spectrum and adds ion name and charge a...
Int max_isotope_
Definition: TheoreticalSpectrumGeneratorXLMS.h:304
std::vector< LossIndex > getBackwardLosses_(AASequence &peptide) const
Calculates sets of possible neutral losses for each position in the given peptide.
bool add_c_ions_
Definition: TheoreticalSpectrumGeneratorXLMS.h:288
bool add_z_ions_
Definition: TheoreticalSpectrumGeneratorXLMS.h:290
bool add_metainfo_
Definition: TheoreticalSpectrumGeneratorXLMS.h:293
double pre_int_H2O_
Definition: TheoreticalSpectrumGeneratorXLMS.h:307
Definition: TheoreticalSpectrumGeneratorXLMS.h:45
int Int
Signed integer type.
Definition: Types.h:76
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:101
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:22