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 
59  public:
60  AaModification(AaModification &&toCopy); // move constructor
61 
62  static AaModificationP getInstance(const QString &accession);
63  static AaModificationP getInstance(const OboPsiModTerm &oboterm);
64 
65  /** @brief get a fake modification coding a mutation from an amino acid to an
66  * other
67  * @param mut_from orginal amino acid
68  * @param mut_to targeted amino acid
69  */
70  static AaModificationP getInstanceMutation(const QChar &mut_from,
71  const QChar &mut_to);
72  static AaModificationP getInstanceXtandemMod(const QString &type,
73  pappso_double mass,
74  const PeptideSp &peptide_sp,
75  unsigned int position);
76  static AaModificationP
77  getInstanceCustomizedMod(pappso_double modificationMass);
78 
79  const QString &getAccession() const;
80  const QString &getName() const;
81 
82  ~AaModification();
83 
84  pappso_double getMass() const;
85  int getNumberOfAtom(AtomIsotopeSurvey atom) const override final;
86  int getNumberOfIsotope(Isotope isotope) const override final;
87  bool isInternal() const;
88 
89 
90  protected:
91  const QString m_accession;
92  QString m_name;
93 
94  protected:
95  void setDiffFormula(const QString &diff_formula);
96  /** @brief set list of amino acid on which this modification takes place
97  *
98  * @arg origin string of the form "S T" for Serine or Threonine, "X" for any
99  * amino acid (see OBO PSI format)
100  * */
101  void setXrefOrigin(const QString &origin);
102 
103 
104  private:
105  AaModification(const QString &accession, pappso_double mass);
106  static AaModificationP createInstance(const QString &saccession);
107  static AaModificationP createInstance(const OboPsiModTerm &term);
108  static AaModificationP createInstanceMutation(const Aa &aa_from,
109  const Aa &aa_to);
110  void calculateMassFromChemicalComponents();
111 
112  using MapAccessionModifications = std::map<QString, AaModificationP>;
113 
114 
115  private:
117  QString m_origin;
118  std::map<AtomIsotopeSurvey, int> m_atomCount;
119  std::map<Isotope, int> m_mapIsotope;
120 
121 
123 
124  static QMutex m_mutex;
125 };
126 
127 } // namespace pappso
std::map< Isotope, int > m_mapIsotope
std::map< AtomIsotopeSurvey, int > m_atomCount
std::map< QString, AaModificationP > MapAccessionModifications
const QString m_accession
static MapAccessionModifications m_mapAccessionModifications
Definition: aa.h:45
#define PMSPP_LIB_DECL
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
Definition: aa.cpp:39
std::shared_ptr< const Peptide > PeptideSp
const AaModification * AaModificationP
AtomIsotopeSurvey
Definition: types.h:77
double pappso_double
A type definition for doubles.
Definition: types.h:49
Isotope
Definition: types.h:92
std::unique_ptr< const AaModification > AaModificationUp