libpappsomspp
Library for mass spectrometry
aamodification.h
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1 /**
2  * \file pappsomspp/amino_acid/aamodification.h
3  * \date 7/3/2015
4  * \author Olivier Langella
5  * \brief amino acid modification model
6  */
7 
8 /*******************************************************************************
9  * Copyright (c) 2015 Olivier Langella <Olivier.Langella@moulon.inra.fr>.
10  *
11  * This file is part of the PAPPSOms++ library.
12  *
13  * PAPPSOms++ is free software: you can redistribute it and/or modify
14  * it under the terms of the GNU General Public License as published by
15  * the Free Software Foundation, either version 3 of the License, or
16  * (at your option) any later version.
17  *
18  * PAPPSOms++ is distributed in the hope that it will be useful,
19  * but WITHOUT ANY WARRANTY; without even the implied warranty of
20  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
21  * GNU General Public License for more details.
22  *
23  * You should have received a copy of the GNU General Public License
24  * along with PAPPSOms++. If not, see <http://www.gnu.org/licenses/>.
25  *
26  * Contributors:
27  * Olivier Langella <Olivier.Langella@moulon.inra.fr> - initial API and
28  *implementation
29  ******************************************************************************/
30 
31 
32 #pragma once
33 
34 #include <QDebug>
35 #include <QString>
36 #include <QMutex>
37 #include <memory>
38 #include <map>
39 #include "../types.h"
40 #include "atomnumberinterface.h"
41 #include "../obo/obopsimod.h"
42 
43 namespace pappso
44 {
45 
46 
47 class Peptide;
48 typedef std::shared_ptr<const Peptide> PeptideSp;
49 
50 class AaModification;
51 typedef std::unique_ptr<const AaModification> AaModificationUp;
53 
54 class Aa;
55 
57 {
58  private:
60  QString m_origin;
61  std::map<AtomIsotopeSurvey, int> m_atomCount;
62  std::map<Isotope, int> m_mapIsotope;
63 
64  AaModification(const QString &accession, pappso_double mass);
65  static AaModificationP createInstance(const QString &saccession);
66  static AaModificationP createInstance(const OboPsiModTerm &term);
67  static AaModificationP createInstanceMutation(const Aa &aa_from,
68  const Aa &aa_to);
69  void calculateMassFromChemicalComponents();
70 
71  using MapAccessionModifications = std::map<QString, AaModificationP>;
73 
74  static QMutex m_mutex;
75 
76  protected:
77  const QString m_accession;
78  QString m_name;
79  void setDiffFormula(const QString &diff_formula);
80  /** @brief set list of amino acid on which this modification takes place
81  *
82  * @arg origin string of the form "S T" for Serine or Threonine, "X" for any
83  * amino acid (see OBO PSI format)
84  * */
85  void setXrefOrigin(const QString &origin);
86 
87 
88  public:
89  AaModification(AaModification &&toCopy); // move constructor
90 
91  static AaModificationP getInstance(const QString &accession);
92  static AaModificationP getInstance(const OboPsiModTerm &oboterm);
93 
94  /** @brief get a fake modification coding a mutation from an amino acid to an
95  * other
96  * @param mut_from orginal amino acid
97  * @param mut_to targeted amino acid
98  */
99  static AaModificationP getInstanceMutation(const QChar &mut_from,
100  const QChar &mut_to);
101  static AaModificationP getInstanceXtandemMod(const QString &type,
102  pappso_double mass,
103  const PeptideSp &peptide_sp,
104  unsigned int position);
105  static AaModificationP
106  getInstanceCustomizedMod(pappso_double modificationMass);
107 
108  const QString &getAccession() const;
109  const QString &getName() const;
110 
111  ~AaModification();
112 
113  pappso_double getMass() const;
114  int getNumberOfAtom(AtomIsotopeSurvey atom) const override final;
115  int getNumberOfIsotope(Isotope isotope) const override final;
116  bool isInternal() const;
117 };
118 
119 } // namespace pappso
pappso::pappso_double
double pappso_double
A type definition for doubles.
Definition: types.h:48
pappso::AtomNumberInterface
Definition: atomnumberinterface.h:31
pappso::AaModification::m_mass
pappso_double m_mass
Definition: aamodification.h:59
pappso::OboPsiModTerm
Definition: obopsimod.h:36
pappso::AaModification::m_accession
const QString m_accession
Definition: aamodification.h:77
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::Isotope
Isotope
Definition: types.h:91
pappso::AaModificationP
const AaModification * AaModificationP
Definition: aamodification.h:52
pappso::AaModification::m_mapAccessionModifications
static MapAccessionModifications m_mapAccessionModifications
Definition: aamodification.h:72
pappso::AaModificationUp
std::unique_ptr< const AaModification > AaModificationUp
Definition: aamodification.h:50
pappso::AaModification::m_mapIsotope
std::map< Isotope, int > m_mapIsotope
Definition: aamodification.h:62
pappso::AaModification::MapAccessionModifications
std::map< QString, AaModificationP > MapAccessionModifications
Definition: aamodification.h:71
pappso::AaModification::m_atomCount
std::map< AtomIsotopeSurvey, int > m_atomCount
Definition: aamodification.h:61
atomnumberinterface.h
pappso::AaModification::m_mutex
static QMutex m_mutex
Definition: aamodification.h:74
pappso::AaModification::m_name
QString m_name
Definition: aamodification.h:78
pappso::PeptideSp
std::shared_ptr< const Peptide > PeptideSp
Definition: aamodification.h:47
pappso::Aa
Definition: aa.h:45
pappso::AaModification
Definition: aamodification.h:57
pappso::AtomIsotopeSurvey
AtomIsotopeSurvey
Definition: types.h:76
pappso::AaModification::m_origin
QString m_origin
Definition: aamodification.h:60