libpappsomspp
Library for mass spectrometry
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aabase.h
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1/**
2 * \file pappsomspp/amino_acid/aabase.h
3 * \date 7/3/2015
4 * \author Olivier Langella
5 * \brief private amino acid 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 <map>
35
36#include "../types.h"
37#include "atomnumberinterface.h"
38#include "../exportinmportconfig.h"
39
40namespace pappso
41{
42
44{
45 friend class AaModification;
46
47 public:
48 virtual pappso_double getMass() const;
49 virtual const char &getLetter() const;
50 const AminoAcidChar &getAminoAcidChar() const;
51
52 virtual void replaceLeucineIsoleucine();
53
54 static const std::vector<AminoAcidChar> &getAminoAcidCharList();
55
56
57 protected:
58 AaBase(char aa_letter);
59 AaBase(AminoAcidChar aa_char);
60 AaBase(const AaBase &aabase);
61 virtual ~AaBase();
62
63 virtual int getNumberOfAtom(AtomIsotopeSurvey atom) const override;
64 int getNumberOfIsotope(Isotope isotope) const override;
65 static pappso_double getAaMass(char aa_letter);
66
67 protected:
69
70 private:
71 using AaMassMap = std::map<char, pappso_double>;
72 using AaIntMap = std::map<char, unsigned int>;
73 using AminoAcidCharList = std::vector<AminoAcidChar>;
74
82};
83
84} /* namespace pappso */
std::vector< AminoAcidChar > AminoAcidCharList
Definition aabase.h:73
static AaMassMap m_aaMassMap
Definition aabase.h:75
std::map< char, unsigned int > AaIntMap
Definition aabase.h:72
static AaIntMap m_aaNumberOfSulfurMap
Definition aabase.h:77
static AaIntMap m_aaNumberOfCarbonMap
Definition aabase.h:76
static AaIntMap m_aaNumberOfOxygenMap
Definition aabase.h:80
char m_aaLetter
Definition aabase.h:68
std::map< char, pappso_double > AaMassMap
Definition aabase.h:71
static AminoAcidCharList m_aminoAcidCharList
Definition aabase.h:81
static AaIntMap m_aaNumberOfNitrogenMap
Definition aabase.h:79
static AaIntMap m_aaNumberOfHydrogenMap
Definition aabase.h:78
#define PMSPP_LIB_DECL
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
Definition aa.cpp:39
AminoAcidChar
Definition types.h:166
AtomIsotopeSurvey
Definition types.h:89
double pappso_double
A type definition for doubles.
Definition types.h:50
Isotope
Definition types.h:104