| OpenMS 2.5.0

SimpleTSGXLMS.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 2002-2020.
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
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
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
79 SimplePeak()
80 : mz(0.0), charge(0)
81 {}
82 };
83
87 struct SimplePeakComparator
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
284 bool add_b_ions_;
285 bool add_y_ions_;
286 bool add_a_ions_;
287 bool add_c_ions_;
288 bool add_x_ions_;
289 bool add_z_ions_;
290 bool add_first_prefix_ion_;
291 bool add_losses_;
292 bool add_charges_;
293 bool add_isotopes_;
294 bool add_precursor_peaks_;
295 bool add_abundant_immonium_ions_;
296 Int max_isotope_;
297 double pre_int_;
298 double pre_int_H2O_;
299 double pre_int_NH3_;
300 bool add_k_linked_ions_;
301
302 std::map< String, LossIndex > loss_db_;
303 double loss_H2O_ = 0;
304 double loss_NH3_ = 0;
305 };
306 }
OpenMS::SimpleTSGXLMS::SimplePeak::charge
int charge
Definition: SimpleTSGXLMS.h:73
OpenMS::SimpleTSGXLMS::pre_int_H2O_
double pre_int_H2O_
Definition: SimpleTSGXLMS.h:298
OpenMS::SimpleTSGXLMS::add_c_ions_
bool add_c_ions_
Definition: SimpleTSGXLMS.h:287
OpenMS::SimpleTSGXLMS::SimplePeak
A simple struct to represent peaks with mz and charge and sort them easily.
Definition: SimpleTSGXLMS.h:70
OpenMS::SimpleTSGXLMS::SimplePeak::SimplePeak
SimplePeak(double mz, int charge)
Definition: SimpleTSGXLMS.h:75
OpenMS::DefaultParamHandler
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:91
OPXLDataStructs.h
OpenMS::SimpleTSGXLMS::add_isotopes_
bool add_isotopes_
Definition: SimpleTSGXLMS.h:293
OpenMS::SimpleTSGXLMS::add_losses_
bool add_losses_
Definition: SimpleTSGXLMS.h:291
Residue.h
StandardTypes.h
OpenMS::SimpleTSGXLMS::SimplePeak::SimplePeak
SimplePeak()
Definition: SimpleTSGXLMS.h:79
DataArrays.h
OpenMS::SimpleTSGXLMS::loss_db_
std::map< String, LossIndex > loss_db_
Definition: SimpleTSGXLMS.h:302
OpenMS::OPXLDataStructs::ProteinProteinCrossLink
The ProteinProteinCrossLink struct represents a cross-link between two peptides in OpenPepXL...
Definition: OPXLDataStructs.h:72
OpenMS::SimpleTSGXLMS::pre_int_
double pre_int_
Definition: SimpleTSGXLMS.h:297
OpenMS::SimpleTSGXLMS
Generates theoretical spectra for cross-linked peptides.
Definition: SimpleTSGXLMS.h:62
OpenMS::AASequence
Representation of a peptide/protein sequence.
Definition: AASequence.h:113
OpenMS::SimpleTSGXLMS::add_abundant_immonium_ions_
bool add_abundant_immonium_ions_
Definition: SimpleTSGXLMS.h:295
OpenMS::SimpleTSGXLMS::SimplePeak::mz
double mz
Definition: SimpleTSGXLMS.h:72
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::SimpleTSGXLMS::SimplePeakComparator
Comparator to sort SimplePeaks by mz.
Definition: SimpleTSGXLMS.h:87
OpenMS::SimpleTSGXLMS::add_b_ions_
bool add_b_ions_
Definition: SimpleTSGXLMS.h:284
OpenMS::SimpleTSGXLMS::LossIndex
Definition: SimpleTSGXLMS.h:95
OpenMS::SimpleTSGXLMS::add_y_ions_
bool add_y_ions_
Definition: SimpleTSGXLMS.h:285
OpenMS::SimpleTSGXLMS::add_a_ions_
bool add_a_ions_
Definition: SimpleTSGXLMS.h:286
DefaultParamHandler.h
OpenMS::SimpleTSGXLMS::add_precursor_peaks_
bool add_precursor_peaks_
Definition: SimpleTSGXLMS.h:294
OpenMS::SimpleTSGXLMS::add_x_ions_
bool add_x_ions_
Definition: SimpleTSGXLMS.h:288
OpenMS::SimpleTSGXLMS::add_z_ions_
bool add_z_ions_
Definition: SimpleTSGXLMS.h:289
OpenMS::SimpleTSGXLMS::pre_int_NH3_
double pre_int_NH3_
Definition: SimpleTSGXLMS.h:299
int
OpenMS::SimpleTSGXLMS::add_k_linked_ions_
bool add_k_linked_ions_
Definition: SimpleTSGXLMS.h:300
OpenMS::SimpleTSGXLMS::add_first_prefix_ion_
bool add_first_prefix_ion_
Definition: SimpleTSGXLMS.h:290
OpenMS::SimpleTSGXLMS::add_charges_
bool add_charges_
Definition: SimpleTSGXLMS.h:292
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::SimpleTSGXLMS::max_isotope_
Int max_isotope_
Definition: SimpleTSGXLMS.h:296