OpenMS
SimpleTSGXLMS.h
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31 // $Maintainer: Eugen Netz $
32 // $Authors: Eugen Netz $
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34 
35 
36 #pragma once
37 
43 
44 
45 namespace OpenMS
46 {
47  class AASequence;
48 
62  class OPENMS_DLLAPI SimpleTSGXLMS :
63  public DefaultParamHandler
64  {
65  public:
66 
70  struct SimplePeak
71  {
72  double mz;
73  int charge;
74 
75  SimplePeak(double mz, int charge)
76  : mz(mz), charge(charge)
77  {}
78 
80  : mz(0.0), charge(0)
81  {}
82  };
83 
88  {
89  bool operator() (const SimplePeak& a, const SimplePeak& b)
90  {
91  return a.mz < b.mz;
92  }
93  };
94 
95  struct LossIndex
96  {
97  bool has_H2O_loss = false;
98  bool has_NH3_loss = false;
99  };
100 
106 
108  SimpleTSGXLMS(const SimpleTSGXLMS & source);
109 
111  ~SimpleTSGXLMS() override;
113 
116 
132  virtual void getLinearIonSpectrum(std::vector< SimplePeak >& spectrum, AASequence& peptide, Size link_pos, int charge = 1, Size link_pos_2 = 0) const;
133 
156  virtual void getXLinkIonSpectrum(std::vector< SimplePeak >& spectrum, AASequence& peptide, Size link_pos, double precursor_mass, int mincharge, int maxcharge, Size link_pos_2 = 0) const;
157 
177  virtual void getXLinkIonSpectrum(std::vector< SimplePeak >& spectrum, OPXLDataStructs::ProteinProteinCrossLink& crosslink, bool frag_alpha, int mincharge, int maxcharge) const;
178 
180  void updateMembers_() override;
181 
182  protected:
183 
195  virtual void addLinearPeaks_(std::vector< SimplePeak >& spectrum, AASequence& peptide, Size link_pos, Residue::ResidueType res_type, std::vector< LossIndex >& forward_losses, std::vector< LossIndex >& backward_losses, int charge = 1, Size link_pos_2 = 0) const;
196 
204  virtual void addPrecursorPeaks_(std::vector< SimplePeak >& spectrum, double precursor_mass, int charge) const;
205 
214  virtual void addLosses_(std::vector< SimplePeak >& spectrum, double mono_weight, int charge, LossIndex & losses) const;
215 
229  virtual void addKLinkedIonPeaks_(std::vector< SimplePeak >& spectrum, AASequence & peptide, Size link_pos, double precursor_mass, int charge) const;
230 
246  virtual void addXLinkIonPeaks_(std::vector< SimplePeak >& spectrum, AASequence & peptide, Size link_pos, double precursor_mass, Residue::ResidueType res_type, std::vector< LossIndex > & forward_losses, std::vector< LossIndex > & backward_losses, int charge, Size link_pos_2 = 0) const;
247 
264  virtual void addXLinkIonPeaks_(std::vector< SimplePeak >& spectrum, 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;
265 
273  std::vector< LossIndex > getForwardLosses_(AASequence & peptide) const;
274 
282  std::vector< LossIndex > getBackwardLosses_(AASequence & peptide) const;
283 
297  double pre_int_;
298  double pre_int_H2O_;
299  double pre_int_NH3_;
301 
302  std::map< String, LossIndex > loss_db_;
303  double loss_H2O_ = 0;
304  double loss_NH3_ = 0;
305  };
306 }
Representation of a peptide/protein sequence.
Definition: AASequence.h:112
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92
ResidueType
Definition: Residue.h:152
Generates theoretical spectra for cross-linked peptides.
Definition: SimpleTSGXLMS.h:64
bool add_x_ions_
Definition: SimpleTSGXLMS.h:288
bool add_precursor_peaks_
Definition: SimpleTSGXLMS.h:294
bool add_charges_
Definition: SimpleTSGXLMS.h:292
std::vector< LossIndex > getForwardLosses_(AASequence &peptide) const
Calculates sets of possible neutral losses for each position in the given peptide.
bool add_losses_
Definition: SimpleTSGXLMS.h:291
virtual void addLinearPeaks_(std::vector< SimplePeak > &spectrum, AASequence &peptide, Size link_pos, 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.
bool add_a_ions_
Definition: SimpleTSGXLMS.h:286
bool add_b_ions_
Definition: SimpleTSGXLMS.h:284
bool add_abundant_immonium_ions_
Definition: SimpleTSGXLMS.h:295
virtual void addPrecursorPeaks_(std::vector< SimplePeak > &spectrum, double precursor_mass, int charge) const
Adds precursor masses including neutral losses for the given charge.
SimpleTSGXLMS()
default constructor
SimpleTSGXLMS & operator=(const SimpleTSGXLMS &tsg)
assignment operator
bool add_y_ions_
Definition: SimpleTSGXLMS.h:285
bool add_isotopes_
Definition: SimpleTSGXLMS.h:293
SimpleTSGXLMS(const SimpleTSGXLMS &source)
copy constructor
double pre_int_NH3_
Definition: SimpleTSGXLMS.h:299
virtual void addKLinkedIonPeaks_(std::vector< SimplePeak > &spectrum, AASequence &peptide, Size link_pos, double precursor_mass, int charge) const
Adds one-residue-linked ion peaks, that are specific to XLMS.
virtual void getXLinkIonSpectrum(std::vector< SimplePeak > &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 addLosses_(std::vector< SimplePeak > &spectrum, double mono_weight, int charge, LossIndex &losses) const
Adds neutral losses for an ion to a spectrum.
bool add_k_linked_ions_
Definition: SimpleTSGXLMS.h:300
bool add_first_prefix_ion_
Definition: SimpleTSGXLMS.h:290
~SimpleTSGXLMS() override
destructor
virtual void getXLinkIonSpectrum(std::vector< SimplePeak > &spectrum, AASequence &peptide, Size link_pos, double precursor_mass, int mincharge, int maxcharge, Size link_pos_2=0) const
Generates fragment ions containing the cross-linker for one peptide.
void updateMembers_() override
overwrite
virtual void addXLinkIonPeaks_(std::vector< SimplePeak > &spectrum, AASequence &peptide, Size link_pos, double precursor_mass, 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.
std::map< String, LossIndex > loss_db_
Definition: SimpleTSGXLMS.h:302
double pre_int_
Definition: SimpleTSGXLMS.h:297
virtual void getLinearIonSpectrum(std::vector< SimplePeak > &spectrum, AASequence &peptide, Size link_pos, int charge=1, Size link_pos_2=0) const
Generates fragment ions not containing the cross-linker for one peptide.
Int max_isotope_
Definition: SimpleTSGXLMS.h:296
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: SimpleTSGXLMS.h:287
virtual void addXLinkIonPeaks_(std::vector< SimplePeak > &spectrum, 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.
bool add_z_ions_
Definition: SimpleTSGXLMS.h:289
double pre_int_H2O_
Definition: SimpleTSGXLMS.h:298
Definition: SimpleTSGXLMS.h:96
int Int
Signed integer type.
Definition: Types.h:102
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:48
Comparator to sort SimplePeaks by mz.
Definition: SimpleTSGXLMS.h:88
A simple struct to represent peaks with mz and charge and sort them easily.
Definition: SimpleTSGXLMS.h:71
SimplePeak(double mz, int charge)
Definition: SimpleTSGXLMS.h:75
double mz
Definition: SimpleTSGXLMS.h:72
SimplePeak()
Definition: SimpleTSGXLMS.h:79
int charge
Definition: SimpleTSGXLMS.h:73