OpenMS  3.0.0
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 
104  SimpleTSGXLMS();
106 
108  SimpleTSGXLMS(const SimpleTSGXLMS & source);
109 
111  ~SimpleTSGXLMS() override;
113 
115  SimpleTSGXLMS & operator=(const SimpleTSGXLMS & tsg);
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 }
DefaultParamHandler.h
OpenMS::SimpleTSGXLMS::pre_int_NH3_
double pre_int_NH3_
Definition: SimpleTSGXLMS.h:299
OpenMS::SimpleTSGXLMS::SimplePeak::SimplePeak
SimplePeak(double mz, int charge)
Definition: SimpleTSGXLMS.h:75
DataArrays.h
OpenMS::SimpleTSGXLMS::pre_int_H2O_
double pre_int_H2O_
Definition: SimpleTSGXLMS.h:298
OpenMS::SimpleTSGXLMS::add_charges_
bool add_charges_
Definition: SimpleTSGXLMS.h:292
OpenMS::SimpleTSGXLMS::add_y_ions_
bool add_y_ions_
Definition: SimpleTSGXLMS.h:285
OpenMS::SimpleTSGXLMS::add_b_ions_
bool add_b_ions_
Definition: SimpleTSGXLMS.h:284
OpenMS::SimpleTSGXLMS::add_a_ions_
bool add_a_ions_
Definition: SimpleTSGXLMS.h:286
OpenMS::SimpleTSGXLMS::SimplePeak::mz
double mz
Definition: SimpleTSGXLMS.h:72
OpenMS::SimpleTSGXLMS::add_z_ions_
bool add_z_ions_
Definition: SimpleTSGXLMS.h:289
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
OpenMS::SimpleTSGXLMS::SimplePeakComparator
Comparator to sort SimplePeaks by mz.
Definition: SimpleTSGXLMS.h:87
OpenMS::SimpleTSGXLMS::LossIndex
Definition: SimpleTSGXLMS.h:95
OpenMS::SimpleTSGXLMS
Generates theoretical spectra for cross-linked peptides.
Definition: SimpleTSGXLMS.h:62
OpenMS::SimpleTSGXLMS::add_c_ions_
bool add_c_ions_
Definition: SimpleTSGXLMS.h:287
OpenMS::DefaultParamHandler
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92
OPXLDataStructs.h
OpenMS::Int
int Int
Signed integer type.
Definition: Types.h:102
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::SimpleTSGXLMS::add_precursor_peaks_
bool add_precursor_peaks_
Definition: SimpleTSGXLMS.h:294
OpenMS::SimpleTSGXLMS::add_losses_
bool add_losses_
Definition: SimpleTSGXLMS.h:291
OpenMS::SimpleTSGXLMS::pre_int_
double pre_int_
Definition: SimpleTSGXLMS.h:297
OpenMS::SimpleTSGXLMS::add_abundant_immonium_ions_
bool add_abundant_immonium_ions_
Definition: SimpleTSGXLMS.h:295
OpenMS::SimpleTSGXLMS::add_k_linked_ions_
bool add_k_linked_ions_
Definition: SimpleTSGXLMS.h:300
OpenMS::Residue::ResidueType
ResidueType
Definition: Residue.h:151
OpenMS::SimpleTSGXLMS::loss_db_
std::map< String, LossIndex > loss_db_
Definition: SimpleTSGXLMS.h:302
OpenMS::SimpleTSGXLMS::SimplePeak::charge
int charge
Definition: SimpleTSGXLMS.h:73
OpenMS::SimpleTSGXLMS::SimplePeak
A simple struct to represent peaks with mz and charge and sort them easily.
Definition: SimpleTSGXLMS.h:70
Residue.h
OpenMS::SimpleTSGXLMS::add_isotopes_
bool add_isotopes_
Definition: SimpleTSGXLMS.h:293
OpenMS::SimpleTSGXLMS::SimplePeak::SimplePeak
SimplePeak()
Definition: SimpleTSGXLMS.h:79
OpenMS::AASequence
Representation of a peptide/protein sequence.
Definition: AASequence.h:111
OpenMS::SimpleTSGXLMS::add_x_ions_
bool add_x_ions_
Definition: SimpleTSGXLMS.h:288
StandardTypes.h
OpenMS::SimpleTSGXLMS::max_isotope_
Int max_isotope_
Definition: SimpleTSGXLMS.h:296
OpenMS::SimpleTSGXLMS::add_first_prefix_ion_
bool add_first_prefix_ion_
Definition: SimpleTSGXLMS.h:290