pappso::PeptideNaturalIsotope Class Reference

#include <peptidenaturalisotope.h>

Inheritance diagram for pappso::PeptideNaturalIsotope:

Public Member Functions
	PeptideNaturalIsotope (const PeptideInterfaceSp &peptide, const std::map< Enums::Isotope, int > &map_isotope)
	PeptideNaturalIsotope (const PeptideNaturalIsotope &other)
virtual	~PeptideNaturalIsotope ()
virtual unsigned int	size () const override
virtual const QString	getSequence () const override
	amino acid sequence without modification
pappso_double	getMass () const override
virtual int	getNumberOfAtom (Enums::AtomIsotopeSurvey atom) const override
	get the number of atom C, O, N, H in the molecule
virtual int	getNumberOfIsotope (Enums::Isotope isotope) const override
	get the number of isotopes C13, H2, O17, O18, N15, S33, S34, S36 in the molecule
pappso_double	getIntensityRatio (unsigned int charge) const
const std::map< Enums::Isotope, int > &	getIsotopeMap () const
virtual unsigned int	getIsotopeNumber () const
virtual bool	isPalindrome () const override
	tells if the peptide sequence is a palindrome
Public Member Functions inherited from pappso::PeptideInterface
virtual const QString	getSequenceLi () const
	amino acid sequence without modification where L are replaced by I
virtual const QString	getName () const
virtual const ChemicalFormula	getChemicalFormulaCharge (unsigned int charge) const
virtual const QString	getFormula (unsigned int charge) const final
virtual bool	matchPeak (PrecisionPtr precision, pappso_double peak_mz, unsigned int charge) const final
	tells if the peptide m/z matches a given experimental mass
Public Member Functions inherited from pappso::Ion
	Ion ()
	~Ion ()
virtual pappso_double	getMz (unsigned int charge) const final
Public Member Functions inherited from pappso::AtomNumberInterface
virtual const ChemicalFormula	getChemicalFormula () const

Private Attributes
const PeptideInterfaceSp	m_peptide
const std::map< Enums::Isotope, int >	m_mapIsotope
pappso_double	m_ratio
pappso_double	m_mass

Detailed Description

Definition at line 45 of file peptidenaturalisotope.h.

Constructor & Destructor Documentation

PeptideNaturalIsotope() [1/2]

pappso::PeptideNaturalIsotope::PeptideNaturalIsotope	(	const PeptideInterfaceSp &	peptide,
		const std::map< Enums::Isotope, int > &	map_isotope )

Definition at line 195 of file peptidenaturalisotope.cpp.

  : m_peptide(peptide), m_mapIsotope(map_isotope)
{
  //_abundance = ((_number_of_carbon - number_of_C13) * ABUNDANCEC12) +
  //(number_of_C13 * ABUNDANCEC13); p = pow(0.01, i)*pow(0.99, (c-i))*comb(c,i)
  // qDebug()<< "pow" << pow(ABUNDANCEC13, number_of_C13)*pow(1-ABUNDANCEC13,
  // (_number_of_carbon-number_of_C13));
  // qDebug() <<"conb" << Combinations(_number_of_carbon,number_of_C13);
 
  // CHNO
  //_probC13 = pow(ABUNDANCEC13, number_of_C13)*pow((double)1-ABUNDANCEC13,
  //(_number_of_carbon-number_of_C13))* (double)
  // Combinations(_number_of_carbon,number_of_C13);
  // qDebug() <<"_probC13" <<_probC13;
 
  // number of fixed Oxygen atoms (already labelled, not natural) :
  int number_of_fixed_oxygen = m_peptide.get()->getNumberOfIsotope(Enums::Isotope::O18) +
                               m_peptide.get()->getNumberOfIsotope(Enums::Isotope::O17);
  int number_of_fixed_sulfur = m_peptide.get()->getNumberOfIsotope(Enums::Isotope::S33) +
                               m_peptide.get()->getNumberOfIsotope(Enums::Isotope::S34) +
                               m_peptide.get()->getNumberOfIsotope(Enums::Isotope::S36);
 
  m_ratio = isotopem_ratio_cache(Enums::Isotope::C13,
                                 m_peptide.get()->getNumberOfAtom(Enums::AtomIsotopeSurvey::C) -
                                   m_peptide.get()->getNumberOfIsotope(Enums::Isotope::C13),
                                 m_mapIsotope.at(Enums::Isotope::C13));
  m_ratio *= isotopem_ratio_cache(Enums::Isotope::N15,
                                  m_peptide.get()->getNumberOfAtom(Enums::AtomIsotopeSurvey::N) -
                                    m_peptide.get()->getNumberOfIsotope(Enums::Isotope::N15),
                                  m_mapIsotope.at(Enums::Isotope::N15));
  m_ratio *= isotopem_ratio_cache(Enums::Isotope::O18,
                                  m_peptide.get()->getNumberOfAtom(Enums::AtomIsotopeSurvey::O) -
                                    number_of_fixed_oxygen,
                                  m_mapIsotope.at(Enums::Isotope::O18));
  m_ratio *= isotopem_ratio_cache(Enums::Isotope::O17,
                                  m_peptide.get()->getNumberOfAtom(Enums::AtomIsotopeSurvey::O) -
                                    number_of_fixed_oxygen,
                                  m_mapIsotope.at(Enums::Isotope::O17));
  m_ratio *= isotopem_ratio_cache(Enums::Isotope::S33,
                                  m_peptide.get()->getNumberOfAtom(Enums::AtomIsotopeSurvey::S) -
                                    number_of_fixed_sulfur,
                                  m_mapIsotope.at(Enums::Isotope::S33));
  m_ratio *= isotopem_ratio_cache(Enums::Isotope::S34,
                                  m_peptide.get()->getNumberOfAtom(Enums::AtomIsotopeSurvey::S) -
                                    number_of_fixed_sulfur,
                                  m_mapIsotope.at(Enums::Isotope::S34));
  m_ratio *= isotopem_ratio_cache(Enums::Isotope::S36,
                                  m_peptide.get()->getNumberOfAtom(Enums::AtomIsotopeSurvey::S) -
                                    number_of_fixed_sulfur,
                                  m_mapIsotope.at(Enums::Isotope::S36));
 
 
  // qDebug() << "Aa::getMass() begin";
  m_mass = m_peptide.get()->getMass();
  m_mass += (DIFFC12C13 * m_mapIsotope.at(Enums::Isotope::C13));
  m_mass += (DIFFS32S33 * m_mapIsotope.at(Enums::Isotope::S33));
  m_mass += (DIFFS32S34 * m_mapIsotope.at(Enums::Isotope::S34));
  m_mass += (DIFFS32S36 * m_mapIsotope.at(Enums::Isotope::S36));
  m_mass += (DIFFH1H2 * m_mapIsotope.at(Enums::Isotope::H2));
  m_mass += (DIFFO16O18 * m_mapIsotope.at(Enums::Isotope::O18));
  m_mass += (DIFFN14N15 * m_mapIsotope.at(Enums::Isotope::N15));
  m_mass += (DIFFO16O17 * m_mapIsotope.at(Enums::Isotope::O17));
 
 
  // qDebug() << "Aa::getMass() end " << mass;
}

References pappso::Enums::C, pappso::Enums::C13, pappso::DIFFC12C13(), pappso::DIFFH1H2(), pappso::DIFFN14N15(), pappso::DIFFO16O17(), pappso::DIFFO16O18(), pappso::DIFFS32S33(), pappso::DIFFS32S34(), pappso::DIFFS32S36(), getNumberOfIsotope(), pappso::Enums::H2, pappso::isotopem_ratio_cache(), m_mapIsotope, m_mass, m_peptide, m_ratio, pappso::Enums::N, pappso::Enums::N15, pappso::Enums::O, pappso::Enums::O17, pappso::Enums::O18, pappso::Enums::S, pappso::Enums::S33, pappso::Enums::S34, and pappso::Enums::S36.

Referenced by PeptideNaturalIsotope().

PeptideNaturalIsotope() [2/2]

pappso::PeptideNaturalIsotope::PeptideNaturalIsotope

(

const PeptideNaturalIsotope &

other

)

Definition at line 263 of file peptidenaturalisotope.cpp.

  : m_peptide(other.m_peptide), m_mapIsotope(other.m_mapIsotope)
{
  m_ratio = other.m_ratio;
}

References PeptideNaturalIsotope(), m_mapIsotope, m_peptide, and m_ratio.

~PeptideNaturalIsotope()

pappso::PeptideNaturalIsotope::~PeptideNaturalIsotope ( )

virtual

Definition at line 269 of file peptidenaturalisotope.cpp.

{
}

Member Function Documentation

getIntensityRatio()

pappso_double pappso::PeptideNaturalIsotope::getIntensityRatio

(

unsigned int

charge

)

const

Definition at line 283 of file peptidenaturalisotope.cpp.

{
 
  return m_ratio *
         isotopem_ratio_cache(Enums::Isotope::H2,
                              (m_peptide.get()->getNumberOfAtom(Enums::AtomIsotopeSurvey::H) + charge) -
                                m_peptide.get()->getNumberOfIsotope(Enums::Isotope::H2),
                              m_mapIsotope.at(Enums::Isotope::H2));
}

References pappso::Enums::H, pappso::Enums::H2, pappso::isotopem_ratio_cache(), m_mapIsotope, m_peptide, and m_ratio.

getIsotopeMap()

const std::map< Enums::Isotope, int > & pappso::PeptideNaturalIsotope::getIsotopeMap

(

)

const

Definition at line 307 of file peptidenaturalisotope.cpp.

{
  return m_mapIsotope;
}

References m_mapIsotope.

getIsotopeNumber()

unsigned int pappso::PeptideNaturalIsotope::getIsotopeNumber ( ) const

virtual

Definition at line 333 of file peptidenaturalisotope.cpp.

{
  // only count variable (natural) isotope
  return m_mapIsotope.at(Enums::Isotope::C13) + m_mapIsotope.at(Enums::Isotope::H2) +
         m_mapIsotope.at(Enums::Isotope::O17) + m_mapIsotope.at(Enums::Isotope::O18) * 2 +
         m_mapIsotope.at(Enums::Isotope::N15) + m_mapIsotope.at(Enums::Isotope::S33) +
         (m_mapIsotope.at(Enums::Isotope::S34) * 2) + (m_mapIsotope.at(Enums::Isotope::S36) * 4);
}

References pappso::Enums::C13, pappso::Enums::H2, m_mapIsotope, pappso::Enums::N15, pappso::Enums::O17, pappso::Enums::O18, pappso::Enums::S33, pappso::Enums::S34, and pappso::Enums::S36.

getMass()

pappso_double pappso::PeptideNaturalIsotope::getMass ( ) const

overridevirtual

Implements pappso::Ion.

Definition at line 275 of file peptidenaturalisotope.cpp.

{
 
  return m_mass;
}

References m_mass.

getNumberOfAtom()

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

overridevirtual

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

Implements pappso::AtomNumberInterface.

Definition at line 295 of file peptidenaturalisotope.cpp.

{
  return m_peptide.get()->getNumberOfAtom(atom);
}

References m_peptide.

getNumberOfIsotope()

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

overridevirtual

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

Implements pappso::AtomNumberInterface.

Definition at line 301 of file peptidenaturalisotope.cpp.

{
  return m_mapIsotope.at(isotope) + m_peptide.get()->getNumberOfIsotope(isotope);
}

References m_mapIsotope, and m_peptide.

Referenced by PeptideNaturalIsotope().

getSequence()

const QString pappso::PeptideNaturalIsotope::getSequence ( ) const

overridevirtual

amino acid sequence without modification

Implements pappso::PeptideInterface.

Definition at line 327 of file peptidenaturalisotope.cpp.

{
  return m_peptide.get()->getSequence();
}

References m_peptide.

isPalindrome()

bool pappso::PeptideNaturalIsotope::isPalindrome ( ) const

overridevirtual

tells if the peptide sequence is a palindrome

Implements pappso::PeptideInterface.

Definition at line 314 of file peptidenaturalisotope.cpp.

{
  return m_peptide.get()->isPalindrome();
}

References m_peptide.

size()

unsigned int pappso::PeptideNaturalIsotope::size ( ) const

overridevirtual

Implements pappso::PeptideInterface.

Definition at line 321 of file peptidenaturalisotope.cpp.

{
  return m_peptide.get()->size();
}

References m_peptide.

Member Data Documentation

m_mapIsotope

const std::map<Enums::Isotope, int> pappso::PeptideNaturalIsotope::m_mapIsotope

private

Definition at line 71 of file peptidenaturalisotope.h.

Referenced by PeptideNaturalIsotope(), PeptideNaturalIsotope(), getIntensityRatio(), getIsotopeMap(), getIsotopeNumber(), and getNumberOfIsotope().

m_mass

pappso_double pappso::PeptideNaturalIsotope::m_mass

private

Definition at line 73 of file peptidenaturalisotope.h.

Referenced by PeptideNaturalIsotope(), and getMass().

m_peptide

const PeptideInterfaceSp pappso::PeptideNaturalIsotope::m_peptide

private

Definition at line 69 of file peptidenaturalisotope.h.

Referenced by PeptideNaturalIsotope(), PeptideNaturalIsotope(), getIntensityRatio(), getNumberOfAtom(), getNumberOfIsotope(), getSequence(), isPalindrome(), and size().

m_ratio

pappso_double pappso::PeptideNaturalIsotope::m_ratio

private

Definition at line 72 of file peptidenaturalisotope.h.

Referenced by PeptideNaturalIsotope(), PeptideNaturalIsotope(), and getIntensityRatio().

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

• pappsomspp/core/peptide/peptidenaturalisotope.h
• pappsomspp/core/peptide/peptidenaturalisotope.cpp