#include <aabase.h>

Inheritance diagram for pappso::AaBase:

Public Member Functions
virtual pappso_double	getMass () const

virtual const char &	getLetter () const

const Enums::AminoAcidChar &	getAminoAcidChar () const

virtual void	replaceLeucineIsoleucine ()

Public Member Functions inherited from pappso::AtomNumberInterface
virtual const ChemicalFormula	getChemicalFormula () const

Static Public Member Functions
static const std::vector< Enums::AminoAcidChar > &	getAminoAcidCharList ()

Protected Member Functions
	AaBase (char aa_letter)

	AaBase (Enums::AminoAcidChar aa_char)

	AaBase (const AaBase &aabase)

virtual	~AaBase ()

virtual int	getNumberOfAtom (Enums::AtomIsotopeSurvey atom) const override
	get the number of atom C, O, N, H in the molecule

int	getNumberOfIsotope (Enums::Isotope isotope) const override
	get the number of isotopes C13, H2, O17, O18, N15, S33, S34, S36 in the molecule

Static Protected Member Functions
static pappso_double	getAaMass (char aa_letter)

Protected Attributes
char	m_aaLetter

Private Types
using	AaMassMap = std::map<char, pappso_double>

using	AaIntMap = std::map<char, unsigned int>

using	AminoAcidCharList = std::vector<Enums::AminoAcidChar>

Static Private Attributes
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

Friends
class	AaModification

Detailed Description

Definition at line 43 of file aabase.h.

Member Typedef Documentation

◆ AaIntMap

using pappso::AaBase::AaIntMap = std::map<char, unsigned int>

private

Definition at line 72 of file aabase.h.

◆ AaMassMap

using pappso::AaBase::AaMassMap = std::map<char, pappso_double>

private

Definition at line 71 of file aabase.h.

◆ AminoAcidCharList

using pappso::AaBase::AminoAcidCharList = std::vector<Enums::AminoAcidChar>

private

Definition at line 73 of file aabase.h.

Constructor & Destructor Documentation

◆ AaBase() [1/3]

pappso::AaBase::AaBase ( char aa_letter )

protected

Definition at line 43 of file aabase.cpp.

                             : m_aaLetter(aa_letter)
{
  /*
   if (AaBase::_aa_mass_map.empty()) {
   AaBase::static_builder();
   }
   */
  qDebug() << aa_letter;
  if(m_aaMassMap.find(aa_letter) == m_aaMassMap.end())
    {
      qDebug() << "error";
      if((int)aa_letter == 0)
        {
          throw ExceptionNotPossible(QObject::tr("amino acid letter is void"));
        }
      else
        {
          throw ExceptionNotFound(QObject::tr("amino acid %1 not found").arg(aa_letter));
        }
    }
  qDebug();
}

References m_aaLetter, and m_aaMassMap.

Referenced by pappso::Aa::Aa(), pappso::Aa::Aa(), pappso::Aa::Aa(), pappso::Aa::Aa(), AaBase(), and AaModification.

◆ AaBase() [2/3]

pappso::AaBase::AaBase ( Enums::AminoAcidChar aa_char )

protected

Definition at line 66 of file aabase.cpp.

                                         : m_aaLetter((char)aa_char)
{
}

References m_aaLetter.

◆ AaBase() [3/3]

pappso::AaBase::AaBase ( const AaBase & aabase )

protected

Definition at line 71 of file aabase.cpp.

                               : m_aaLetter(aa.m_aaLetter)
{
}

References AaBase(), and m_aaLetter.

◆ ~AaBase()

pappso::AaBase::~AaBase ( )

protectedvirtual

Definition at line 75 of file aabase.cpp.

{
  // TODO Auto-generated destructor stub
}

Member Function Documentation

◆ getAaMass()

pappso_double pappso::AaBase::getAaMass ( char aa_letter )

staticprotected

Definition at line 349 of file aabase.cpp.

{
  return m_aaMassMap.at(aa_letter);
}

References m_aaMassMap.

Referenced by AaModification.

◆ getAminoAcidChar()

const Enums::AminoAcidChar & pappso::AaBase::getAminoAcidChar ( ) const

Definition at line 409 of file aabase.cpp.

{
  return (Enums::AminoAcidChar &)m_aaLetter;
}

References m_aaLetter.

Referenced by AaModification, and pappso::PeptideProFormaParser::parseStringToPeptide().

◆ getAminoAcidCharList()

const std::vector< Enums::AminoAcidChar > & pappso::AaBase::getAminoAcidCharList ( )

static

Definition at line 415 of file aabase.cpp.

{
  return m_aminoAcidCharList;
}

References m_aminoAcidCharList.

Referenced by AaModification.

◆ getLetter()

const char & pappso::AaBase::getLetter ( ) const

virtual

Definition at line 403 of file aabase.cpp.

{
  return m_aaLetter;
}

References m_aaLetter.

Referenced by AaModification, pappso::specglob::PeptideModel::checkForAaModification(), pappso::specglob::PeptideModel::checkForMutation(), pappso::AaModification::createInstanceMutation(), pappso::Aa::toAbsoluteString(), pappso::Aa::toProForma(), and pappso::Aa::toString().

◆ getMass()

pappso_double pappso::AaBase::getMass ( ) const

virtual

Reimplemented in pappso::Aa.

Definition at line 356 of file aabase.cpp.

{
  return m_aaMassMap.at(m_aaLetter);
}

References m_aaLetter, and m_aaMassMap.

Referenced by AaModification, and pappso::Aa::getMass().

◆ getNumberOfAtom()

int pappso::AaBase::getNumberOfAtom ( Enums::AtomIsotopeSurvey atom ) const

overrideprotectedvirtual

get the number of atom C, O, N, H in the molecule

Implements pappso::AtomNumberInterface.

Reimplemented in pappso::Aa.

Definition at line 363 of file aabase.cpp.

{
  switch(atom)
    {
      case Enums::AtomIsotopeSurvey::C:
        return this->m_aaNumberOfCarbonMap.at(m_aaLetter);
      case Enums::AtomIsotopeSurvey::H:
        return this->m_aaNumberOfHydrogenMap.at(m_aaLetter);
      case Enums::AtomIsotopeSurvey::N:
        return this->m_aaNumberOfNitrogenMap.at(m_aaLetter);
      case Enums::AtomIsotopeSurvey::O:
        return this->m_aaNumberOfOxygenMap.at(m_aaLetter);
      case Enums::AtomIsotopeSurvey::S:
        return this->m_aaNumberOfSulfurMap.at(m_aaLetter);
      default:
        return 0;
    }
  // selenium (U) is not taken into account to compute isotopes
  // it has 5 stable isotopes and the most abundant is 80Se (49,61%)
  qDebug() << "AaBase::getNumberOfAtom(Enums::AtomIsotopeSurvey atom) NOT IMPLEMENTED";
  return 0;
}

References pappso::Enums::C, pappso::Enums::H, m_aaLetter, m_aaNumberOfCarbonMap, m_aaNumberOfHydrogenMap, m_aaNumberOfNitrogenMap, m_aaNumberOfOxygenMap, m_aaNumberOfSulfurMap, pappso::Enums::N, pappso::Enums::O, and pappso::Enums::S.

Referenced by AaModification, and pappso::Aa::getNumberOfAtom().

◆ getNumberOfIsotope()

int pappso::AaBase::getNumberOfIsotope ( Enums::Isotope isotope ) const

overrideprotectedvirtual

get the number of isotopes C13, H2, O17, O18, N15, S33, S34, S36 in the molecule

Implements pappso::AtomNumberInterface.

Definition at line 396 of file aabase.cpp.

{
  return 0;
}

Referenced by AaModification.

◆ replaceLeucineIsoleucine()

void pappso::AaBase::replaceLeucineIsoleucine ( )

virtual

Definition at line 388 of file aabase.cpp.

{
  if(m_aaLetter == 'L')
    m_aaLetter = 'I';
}

References m_aaLetter.

Referenced by AaModification.

Friends And Related Symbol Documentation

◆ AaModification

friend class AaModification

friend

Definition at line 45 of file aabase.h.

References AaBase(), AaModification, getAaMass(), getAminoAcidChar(), getAminoAcidCharList(), getLetter(), getMass(), getNumberOfAtom(), getNumberOfIsotope(), and replaceLeucineIsoleucine().

Referenced by AaModification.

Member Data Documentation

◆ m_aaLetter

char pappso::AaBase::m_aaLetter

protected

Definition at line 68 of file aabase.h.

Referenced by AaBase(), AaBase(), AaBase(), getAminoAcidChar(), getLetter(), getMass(), getNumberOfAtom(), pappso::Aa::isAaEqual(), pappso::Aa::isLesser(), pappso::Aa::operator=(), and replaceLeucineIsoleucine().

◆ m_aaMassMap

AaBase::AaMassMap pappso::AaBase::m_aaMassMap

staticprivate

Definition at line 75 of file aabase.h.

Referenced by AaBase(), getAaMass(), and getMass().

◆ m_aaNumberOfCarbonMap

AaBase::AaIntMap pappso::AaBase::m_aaNumberOfCarbonMap

staticprivate

Initial value:

= [] {
  AaIntMap ret;
  
 
  ret.insert(std::pair<char, unsigned int>('W', 11));
  ret.insert(std::pair<char, unsigned int>('G', 2));
  ret.insert(std::pair<char, unsigned int>('A', 3));
  ret.insert(std::pair<char, unsigned int>('S', 3));
  ret.insert(std::pair<char, unsigned int>('P', 5));
  ret.insert(std::pair<char, unsigned int>('V', 5));
  ret.insert(std::pair<char, unsigned int>('T', 4));
  ret.insert(std::pair<char, unsigned int>('L', 6));
  ret.insert(std::pair<char, unsigned int>('I', 6));
  ret.insert(std::pair<char, unsigned int>('N', 4));
  ret.insert(std::pair<char, unsigned int>('D', 4));
  ret.insert(std::pair<char, unsigned int>('K', 6));
  ret.insert(std::pair<char, unsigned int>('Q', 5));
  ret.insert(std::pair<char, unsigned int>('E', 5));
  ret.insert(std::pair<char, unsigned int>('M', 5));
  ret.insert(std::pair<char, unsigned int>('H', 6));
  ret.insert(std::pair<char, unsigned int>('F', 9));
  ret.insert(std::pair<char, unsigned int>('R', 6));
  ret.insert(std::pair<char, unsigned int>('C', 3));
  ret.insert(std::pair<char, unsigned int>('Y', 9));
  
  ret.insert(std::pair<char, unsigned int>('U', 3));
  
  ret.insert(std::pair<char, unsigned int>('O', 12));
  return ret;
}()

Definition at line 76 of file aabase.h.

Referenced by getNumberOfAtom().

◆ m_aaNumberOfHydrogenMap

AaBase::AaIntMap pappso::AaBase::m_aaNumberOfHydrogenMap

staticprivate

Initial value:

= [] {
  AaIntMap ret;
  
 
  ret.insert(std::pair<char, unsigned int>('A', 5));
  ret.insert(std::pair<char, unsigned int>('C', 5));
  ret.insert(std::pair<char, unsigned int>('D', 5));
  ret.insert(std::pair<char, unsigned int>('E', 7));
  ret.insert(std::pair<char, unsigned int>('F', 9));
  ret.insert(std::pair<char, unsigned int>('G', 3));
  ret.insert(std::pair<char, unsigned int>('H', 7));
  ret.insert(std::pair<char, unsigned int>('I', 11));
  ret.insert(std::pair<char, unsigned int>('K', 12));
  ret.insert(std::pair<char, unsigned int>('L', 11));
  ret.insert(std::pair<char, unsigned int>('M', 9));
  ret.insert(std::pair<char, unsigned int>('N', 6));
  ret.insert(std::pair<char, unsigned int>('P', 7));
  ret.insert(std::pair<char, unsigned int>('Q', 8));
  ret.insert(std::pair<char, unsigned int>('R', 12));
  ret.insert(std::pair<char, unsigned int>('S', 5));
  ret.insert(std::pair<char, unsigned int>('T', 7));
  ret.insert(std::pair<char, unsigned int>('V', 9));
  ret.insert(std::pair<char, unsigned int>('W', 10));
  ret.insert(std::pair<char, unsigned int>('Y', 9));
  
  ret.insert(std::pair<char, unsigned int>('U', 7));
  
  ret.insert(std::pair<char, unsigned int>('O', 21));
  return ret;
}()

Definition at line 78 of file aabase.h.

Referenced by getNumberOfAtom().

◆ m_aaNumberOfNitrogenMap

AaBase::AaIntMap pappso::AaBase::m_aaNumberOfNitrogenMap

staticprivate

Initial value:

= [] {
  AaIntMap ret;
  
 
  ret.insert(std::pair<char, unsigned int>('A', 1));
  ret.insert(std::pair<char, unsigned int>('C', 1));
  ret.insert(std::pair<char, unsigned int>('D', 1));
  ret.insert(std::pair<char, unsigned int>('E', 1));
  ret.insert(std::pair<char, unsigned int>('F', 1));
  ret.insert(std::pair<char, unsigned int>('G', 1));
  ret.insert(std::pair<char, unsigned int>('H', 3));
  ret.insert(std::pair<char, unsigned int>('I', 1));
  ret.insert(std::pair<char, unsigned int>('K', 2));
  ret.insert(std::pair<char, unsigned int>('L', 1));
  ret.insert(std::pair<char, unsigned int>('M', 1));
  ret.insert(std::pair<char, unsigned int>('N', 2));
  ret.insert(std::pair<char, unsigned int>('P', 1));
  ret.insert(std::pair<char, unsigned int>('Q', 2));
  ret.insert(std::pair<char, unsigned int>('R', 4));
  ret.insert(std::pair<char, unsigned int>('S', 1));
  ret.insert(std::pair<char, unsigned int>('T', 1));
  ret.insert(std::pair<char, unsigned int>('V', 1));
  ret.insert(std::pair<char, unsigned int>('W', 2));
  ret.insert(std::pair<char, unsigned int>('Y', 1));
  
  ret.insert(std::pair<char, unsigned int>('U', 1));
  
  ret.insert(std::pair<char, unsigned int>('O', 3));
  return ret;
}()

Definition at line 79 of file aabase.h.

Referenced by getNumberOfAtom().

◆ m_aaNumberOfOxygenMap

AaBase::AaIntMap pappso::AaBase::m_aaNumberOfOxygenMap

staticprivate

Initial value:

= [] {
  AaIntMap ret;
  
 
  ret.insert(std::pair<char, unsigned int>('A', 1));
  ret.insert(std::pair<char, unsigned int>('C', 1));
  ret.insert(std::pair<char, unsigned int>('D', 3));
  ret.insert(std::pair<char, unsigned int>('E', 3));
  ret.insert(std::pair<char, unsigned int>('F', 1));
  ret.insert(std::pair<char, unsigned int>('G', 1));
  ret.insert(std::pair<char, unsigned int>('H', 1));
  ret.insert(std::pair<char, unsigned int>('I', 1));
  ret.insert(std::pair<char, unsigned int>('K', 1));
  ret.insert(std::pair<char, unsigned int>('L', 1));
  ret.insert(std::pair<char, unsigned int>('M', 1));
  ret.insert(std::pair<char, unsigned int>('N', 2));
  ret.insert(std::pair<char, unsigned int>('P', 1));
  ret.insert(std::pair<char, unsigned int>('Q', 2));
  ret.insert(std::pair<char, unsigned int>('R', 1));
  ret.insert(std::pair<char, unsigned int>('S', 2));
  ret.insert(std::pair<char, unsigned int>('T', 2));
  ret.insert(std::pair<char, unsigned int>('V', 1));
  ret.insert(std::pair<char, unsigned int>('W', 1));
  ret.insert(std::pair<char, unsigned int>('Y', 2));
  
  ret.insert(std::pair<char, unsigned int>('U', 2));
  
  ret.insert(std::pair<char, unsigned int>('O', 3));
  return ret;
}()

Definition at line 80 of file aabase.h.

Referenced by getNumberOfAtom().

◆ m_aaNumberOfSulfurMap

AaBase::AaIntMap pappso::AaBase::m_aaNumberOfSulfurMap

staticprivate

Initial value:

= [] {
  AaIntMap ret;
  
 
  ret.insert(std::pair<char, unsigned int>('A', 0));
  ret.insert(std::pair<char, unsigned int>('C', 1));
  ret.insert(std::pair<char, unsigned int>('D', 0));
  ret.insert(std::pair<char, unsigned int>('E', 0));
  ret.insert(std::pair<char, unsigned int>('F', 0));
  ret.insert(std::pair<char, unsigned int>('G', 0));
  ret.insert(std::pair<char, unsigned int>('H', 0));
  ret.insert(std::pair<char, unsigned int>('I', 0));
  ret.insert(std::pair<char, unsigned int>('K', 0));
  ret.insert(std::pair<char, unsigned int>('L', 0));
  ret.insert(std::pair<char, unsigned int>('M', 1));
  ret.insert(std::pair<char, unsigned int>('N', 0));
  ret.insert(std::pair<char, unsigned int>('P', 0));
  ret.insert(std::pair<char, unsigned int>('Q', 0));
  ret.insert(std::pair<char, unsigned int>('R', 0));
  ret.insert(std::pair<char, unsigned int>('S', 0));
  ret.insert(std::pair<char, unsigned int>('T', 0));
  ret.insert(std::pair<char, unsigned int>('V', 0));
  ret.insert(std::pair<char, unsigned int>('W', 0));
  ret.insert(std::pair<char, unsigned int>('Y', 0));
  
  ret.insert(std::pair<char, unsigned int>('U', 0));
  
  ret.insert(std::pair<char, unsigned int>('O', 0));
  return ret;
}()

Definition at line 77 of file aabase.h.

Referenced by getNumberOfAtom().

◆ m_aminoAcidCharList

AaBase::AminoAcidCharList pappso::AaBase::m_aminoAcidCharList

staticprivate

Initial value:

= [] {
  AminoAcidCharList ret = {
    Enums::AminoAcidChar::alanine,        Enums::AminoAcidChar::arginine,
    Enums::AminoAcidChar::cysteine,       Enums::AminoAcidChar::aspartic_acid,
    Enums::AminoAcidChar::glutamic_acid,  Enums::AminoAcidChar::phenylalanine,
    Enums::AminoAcidChar::glycine,        Enums::AminoAcidChar::histidine,
    Enums::AminoAcidChar::isoleucine,     Enums::AminoAcidChar::lysine,
    Enums::AminoAcidChar::leucine,        Enums::AminoAcidChar::methionine,
    Enums::AminoAcidChar::asparagine,     Enums::AminoAcidChar::proline,
    Enums::AminoAcidChar::glutamine,      Enums::AminoAcidChar::serine,
    Enums::AminoAcidChar::threonine,      Enums::AminoAcidChar::valine,
    Enums::AminoAcidChar::tryptophan,     Enums::AminoAcidChar::tyrosine,
    Enums::AminoAcidChar::selenocysteine, Enums::AminoAcidChar::pyrrolysine,
  };
 
 
  return ret;
}()

Definition at line 81 of file aabase.h.

Referenced by getAminoAcidCharList().

The documentation for this class was generated from the following files:

pappsomspp/core/amino_acid/aabase.h
pappsomspp/core/amino_acid/aabase.cpp

Public Member Functions

Static Public Member Functions

Protected Member Functions

Static Protected Member Functions

Protected Attributes

Private Types

Static Private Attributes

Friends

Detailed Description

Member Typedef Documentation

◆ AaIntMap

◆ AaMassMap

◆ AminoAcidCharList

Constructor & Destructor Documentation

◆ AaBase() [1/3]

◆ AaBase() [2/3]

◆ AaBase() [3/3]

◆ ~AaBase()

Member Function Documentation

◆ getAaMass()

◆ getAminoAcidChar()

◆ getAminoAcidCharList()

◆ getLetter()

◆ getMass()

◆ getNumberOfAtom()

◆ getNumberOfIsotope()

◆ replaceLeucineIsoleucine()

Friends And Related Symbol Documentation

◆ AaModification

Member Data Documentation

◆ m_aaLetter

◆ m_aaMassMap

◆ m_aaNumberOfCarbonMap

◆ m_aaNumberOfHydrogenMap

◆ m_aaNumberOfNitrogenMap

◆ m_aaNumberOfOxygenMap

◆ m_aaNumberOfSulfurMap

◆ m_aminoAcidCharList