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aabase.h
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/**
* \file pappsomspp/amino_acid/aabase.h
* \date 7/3/2015
* \author Olivier Langella
* \brief private amino acid model
*/
/*******************************************************************************
* Copyright (c) 2015 Olivier Langella <Olivier.Langella@moulon.inra.fr>.
*
* This file is part of the PAPPSOms++ library.
*
* PAPPSOms++ is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* PAPPSOms++ is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with PAPPSOms++. If not, see <http://www.gnu.org/licenses/>.
*
* Contributors:
* Olivier Langella <Olivier.Langella@moulon.inra.fr> - initial API and
*implementation
******************************************************************************/
#pragma once
#include <map>
#include "../types.h"
#include "atomnumberinterface.h"
#include "../exportinmportconfig.h"
namespace pappso
{
class PMSPP_LIB_DECL AaBase : public AtomNumberInterface
{
friend class AaModification;
public:
virtual pappso_double getMass() const;
virtual const char &getLetter() const;
const AminoAcidChar &getAminoAcidChar() const;
virtual void replaceLeucineIsoleucine();
static const std::vector<AminoAcidChar> &getAminoAcidCharList();
protected:
AaBase(char aa_letter);
AaBase(AminoAcidChar aa_char);
AaBase(const AaBase &aabase);
virtual ~AaBase();
virtual int getNumberOfAtom(AtomIsotopeSurvey atom) const override;
int getNumberOfIsotope(Isotope isotope) const override;
static pappso_double getAaMass(char aa_letter);
protected:
char m_aaLetter;
private:
using AaMassMap = std::map<char, pappso_double>;
using AaIntMap = std::map<char, unsigned int>;
using AminoAcidCharList = std::vector<AminoAcidChar>;
static AaMassMap m_aaMassMap;
static AaIntMap m_aaNumberOfCarbonMap;
static AaIntMap m_aaNumberOfSulfurMap;
static AaIntMap m_aaNumberOfHydrogenMap;
static AaIntMap m_aaNumberOfNitrogenMap;
static AaIntMap m_aaNumberOfOxygenMap;
static AminoAcidCharList m_aminoAcidCharList;
};
} /* namespace pappso */
atomnumberinterface.h
pappso::AaBase
Definition aabase.h:44
pappso::AaBase::AminoAcidCharList
std::vector< AminoAcidChar > AminoAcidCharList
Definition aabase.h:73
pappso::AaBase::m_aaMassMap
static AaMassMap m_aaMassMap
Definition aabase.h:75
pappso::AaBase::AaIntMap
std::map< char, unsigned int > AaIntMap
Definition aabase.h:72
pappso::AaBase::m_aaNumberOfSulfurMap
static AaIntMap m_aaNumberOfSulfurMap
Definition aabase.h:77
pappso::AaBase::m_aaNumberOfCarbonMap
static AaIntMap m_aaNumberOfCarbonMap
Definition aabase.h:76
pappso::AaBase::m_aaNumberOfOxygenMap
static AaIntMap m_aaNumberOfOxygenMap
Definition aabase.h:80
pappso::AaBase::m_aaLetter
char m_aaLetter
Definition aabase.h:68
pappso::AaBase::AaMassMap
std::map< char, pappso_double > AaMassMap
Definition aabase.h:71
pappso::AaBase::m_aminoAcidCharList
static AminoAcidCharList m_aminoAcidCharList
Definition aabase.h:81
pappso::AaBase::m_aaNumberOfNitrogenMap
static AaIntMap m_aaNumberOfNitrogenMap
Definition aabase.h:79
pappso::AaBase::m_aaNumberOfHydrogenMap
static AaIntMap m_aaNumberOfHydrogenMap
Definition aabase.h:78
pappso::AaModification
Definition aamodification.h:57
pappso::AtomNumberInterface
Definition atomnumberinterface.h:31
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 and changes multichar...
Definition aa.cpp:39
pappso::AminoAcidChar
AminoAcidChar
Definition types.h:159
pappso::AtomIsotopeSurvey
AtomIsotopeSurvey
Definition types.h:89
pappso::pappso_double
double pappso_double
A type definition for doubles.
Definition types.h:50
pappso::Isotope
Isotope
Definition types.h:104