libpappsomspp
Library for mass spectrometry
peptiderawfragmentmasses.h
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1 /**
2  * \file pappsomspp/peptide/peptiderawfragmentmasses.h
3  * \date 16/7/2016
4  * \author Olivier Langella
5  * \brief class dedicated to raw mass computations of peptide products
6  * (fragments)
7  */
8 
9 /*******************************************************************************
10  * Copyright (c) 2016 Olivier Langella <Olivier.Langella@moulon.inra.fr>.
11  *
12  * This file is part of the PAPPSOms++ library.
13  *
14  * PAPPSOms++ is free software: you can redistribute it and/or modify
15  * it under the terms of the GNU General Public License as published by
16  * the Free Software Foundation, either version 3 of the License, or
17  * (at your option) any later version.
18  *
19  * PAPPSOms++ is distributed in the hope that it will be useful,
20  * but WITHOUT ANY WARRANTY; without even the implied warranty of
21  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
22  * GNU General Public License for more details.
23  *
24  * You should have received a copy of the GNU General Public License
25  * along with PAPPSOms++. If not, see <http://www.gnu.org/licenses/>.
26  *
27  * Contributors:
28  * Olivier Langella <Olivier.Langella@moulon.inra.fr> - initial API and
29  *implementation
30  ******************************************************************************/
31 
32 #pragma once
33 
34 
35 #include "peptide.h"
36 #include "../massspectrum/massspectrum.h"
37 
38 namespace pappso
39 {
40 
41 
42 enum class RawFragmentationMode : std::int8_t
43 {
44  full = 0,
45  proline_effect = 1
46 };
47 
48 
50 {
53  unsigned int ion_size;
54  unsigned int ion_charge;
56 };
57 
58 
60 {
62 
63  private:
65 
66  /** \brief cumulative Nter masses (without internal Nter modification)
67  * */
68  std::vector<pappso_double> m_cumulativeNterMasses;
69 
70  /** \brief cumulative Cter masses (without internal Cter modification)
71  * */
72  std::vector<pappso_double> m_cumulativeCterMasses;
73 
74  public:
77 
78  void pushBackIonMasses(std::vector<pappso_double> &mass_list,
79  PeptideIon ion_type) const;
80  void pushBackIonMz(std::vector<pappso_double> &mass_list,
81  PeptideIon ion_type,
82  unsigned int charge) const;
83 
84  void pushBackMatchSpectrum(std::vector<SimplePeakIonMatch> &peak_match_list,
85  const MassSpectrum &spectrum,
86  PrecisionPtr precision,
87  PeptideIon ion_type,
88  unsigned int charge) const;
89 
90  static pappso_double getDeltaMass(PeptideIon ion_type);
91 };
92 
93 
94 } // namespace pappso
pappso::pappso_double
double pappso_double
A type definition for doubles.
Definition: types.h:48
pappso::PeptideRawFragmentMasses::m_ionDeltaMz
static ionDeltatMzMassMap m_ionDeltaMz
Definition: peptiderawfragmentmasses.h:64
PMSPP_LIB_DECL
#define PMSPP_LIB_DECL
Definition: exportinmportconfig.h:14
pappso
tries to keep as much as possible monoisotopes, removing any possible C13 peaks
Definition: aa.cpp:39
pappso::MassSpectrum
Class to represent a mass spectrum.
Definition: massspectrum.h:71
pappso::PeptideRawFragmentMasses::m_cumulativeCterMasses
std::vector< pappso_double > m_cumulativeCterMasses
cumulative Cter masses (without internal Cter modification)
Definition: peptiderawfragmentmasses.h:72
pappso::DataPoint
Definition: datapoint.h:21
pappso::SimplePeakIonMatch::ion_charge
unsigned int ion_charge
Definition: peptiderawfragmentmasses.h:54
peptide.h
peptide model
pappso::PeptideIon
PeptideIon
PeptideIon enum defines all types of ions (Nter or Cter)
Definition: types.h:334
pappso::Peptide
Definition: peptide.h:93
pappso::RawFragmentationMode::full
@ full
pappso::SimplePeakIonMatch::peak
DataPoint peak
Definition: peptiderawfragmentmasses.h:51
pappso::PeptideRawFragmentMasses::ionDeltatMzMassMap
pappso_double[20] ionDeltatMzMassMap
Definition: peptiderawfragmentmasses.h:61
pappso::PeptideRawFragmentMasses::m_cumulativeNterMasses
std::vector< pappso_double > m_cumulativeNterMasses
cumulative Nter masses (without internal Nter modification)
Definition: peptiderawfragmentmasses.h:68
pappso::SimplePeakIonMatch::ion_mz
pappso_double ion_mz
Definition: peptiderawfragmentmasses.h:55
pappso::SimplePeakIonMatch::ion_type
PeptideIon ion_type
Definition: peptiderawfragmentmasses.h:52
pappso::PrecisionBase
Definition: precision.h:44
pappso::SimplePeakIonMatch::ion_size
unsigned int ion_size
Definition: peptiderawfragmentmasses.h:53
pappso::PeptideRawFragmentMasses
Definition: peptiderawfragmentmasses.h:60
pappso::RawFragmentationMode
RawFragmentationMode
Definition: peptiderawfragmentmasses.h:43
pappso::SimplePeakIonMatch
Definition: peptiderawfragmentmasses.h:50