OpenMS  2.8.0
TheoreticalSpectrumGeneratorXLMS.h
Go to the documentation of this file.
1 // --------------------------------------------------------------------------
2 // OpenMS -- Open-Source Mass Spectrometry
3 // --------------------------------------------------------------------------
4 // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
5 // ETH Zurich, and Freie Universitaet Berlin 2002-2021.
6 //
7 // This software is released under a three-clause BSD license:
8 // * Redistributions of source code must retain the above copyright
9 // notice, this list of conditions and the following disclaimer.
10 // * Redistributions in binary form must reproduce the above copyright
11 // notice, this list of conditions and the following disclaimer in the
12 // documentation and/or other materials provided with the distribution.
13 // * Neither the name of any author or any participating institution
14 // may be used to endorse or promote products derived from this software
15 // without specific prior written permission.
16 // For a full list of authors, refer to the file AUTHORS.
17 // --------------------------------------------------------------------------
18 // THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
19 // AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
20 // IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
21 // ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
22 // INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
23 // EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
24 // PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
25 // OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
26 // WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
27 // OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
28 // ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
29 //
30 // --------------------------------------------------------------------------
31 // $Maintainer: Eugen Netz $
32 // $Authors: Eugen Netz $
33 // --------------------------------------------------------------------------
34 
35 
36 #pragma once
37 
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 
81 
84 
88 
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 
152  virtual void getXLinkIonSpectrum(PeakSpectrum & spectrum, OPXLDataStructs::ProteinProteinCrossLink & crosslink, bool frag_alpha, int mincharge, int maxcharge) const;
153 
155  void updateMembers_() override;
156 
157  protected:
158 
173  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;
174 
192  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;
193 
203  virtual void addPrecursorPeaks_(PeakSpectrum & spectrum, DataArrays::IntegerDataArray & charges, DataArrays::StringDataArray & ion_names, double precursor_mass, int charge) const;
204 
219  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;
220 
235  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;
236 
253  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;
254 
273  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;
274 
291  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;
292 
300  std::vector< LossIndex > getForwardLosses_(AASequence & peptide) const;
301 
309  std::vector< LossIndex > getBackwardLosses_(AASequence & peptide) const;
310 
324  double a_intensity_;
325  double b_intensity_;
326  double c_intensity_;
327  double x_intensity_;
328  double y_intensity_;
329  double z_intensity_;
332  double pre_int_;
333  double pre_int_H2O_;
334  double pre_int_NH3_;
336 
337  std::map< String, LossIndex > loss_db_;
338  double loss_H2O_ = 0;
339  double loss_NH3_ = 0;
340  };
341 }
Representation of a peptide/protein sequence.
Definition: AASequence.h:112
Integer data array class.
Definition: DataArrays.h:55
String data array class.
Definition: DataArrays.h:62
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:93
The representation of a 1D spectrum.
Definition: MSSpectrum.h:70
ResidueType
Definition: Residue.h:152
A more convenient string class.
Definition: String.h:60
Generates theoretical spectra for cross-linked peptides.
Definition: TheoreticalSpectrumGeneratorXLMS.h:67
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:315
bool add_precursor_peaks_
Definition: TheoreticalSpectrumGeneratorXLMS.h:322
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:331
bool add_charges_
Definition: TheoreticalSpectrumGeneratorXLMS.h:320
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:318
bool add_a_ions_
Definition: TheoreticalSpectrumGeneratorXLMS.h:313
double c_intensity_
Definition: TheoreticalSpectrumGeneratorXLMS.h:326
bool add_b_ions_
Definition: TheoreticalSpectrumGeneratorXLMS.h:311
double z_intensity_
Definition: TheoreticalSpectrumGeneratorXLMS.h:329
bool add_abundant_immonium_ions_
Definition: TheoreticalSpectrumGeneratorXLMS.h:323
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:312
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:321
double pre_int_NH3_
Definition: TheoreticalSpectrumGeneratorXLMS.h:334
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:327
bool add_k_linked_ions_
Definition: TheoreticalSpectrumGeneratorXLMS.h:335
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:324
bool add_first_prefix_ion_
Definition: TheoreticalSpectrumGeneratorXLMS.h:317
TheoreticalSpectrumGeneratorXLMS(const TheoreticalSpectrumGeneratorXLMS &source)
copy constructor
double b_intensity_
Definition: TheoreticalSpectrumGeneratorXLMS.h:325
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:337
double pre_int_
Definition: TheoreticalSpectrumGeneratorXLMS.h:332
double y_intensity_
Definition: TheoreticalSpectrumGeneratorXLMS.h:328
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:330
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:314
bool add_z_ions_
Definition: TheoreticalSpectrumGeneratorXLMS.h:316
bool add_metainfo_
Definition: TheoreticalSpectrumGeneratorXLMS.h:319
double pre_int_H2O_
Definition: TheoreticalSpectrumGeneratorXLMS.h:333
Definition: TheoreticalSpectrumGeneratorXLMS.h:71
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:47