pappso::PeptideNaturalIsotope Class Reference

#include <peptidenaturalisotope.h>

Inheritance diagram for pappso::PeptideNaturalIsotope:

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

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

Detailed Description

Definition at line 64 of file peptidenaturalisotope.h.

Constructor & Destructor Documentation

PeptideNaturalIsotope() [1/2]

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

Definition at line 200 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(Isotope::O18) +
    m_peptide.get()->getNumberOfIsotope(Isotope::O17);
  int number_of_fixed_sulfur =
    m_peptide.get()->getNumberOfIsotope(Isotope::S33) +
    m_peptide.get()->getNumberOfIsotope(Isotope::S34) +
    m_peptide.get()->getNumberOfIsotope(Isotope::S36);
 
  m_ratio = isotopem_ratio_cache(
    Isotope::C13,
    m_peptide.get()->getNumberOfAtom(AtomIsotopeSurvey::C) -
      m_peptide.get()->getNumberOfIsotope(Isotope::C13),
    m_mapIsotope.at(Isotope::C13));
  m_ratio *= isotopem_ratio_cache(
    Isotope::N15,
    m_peptide.get()->getNumberOfAtom(AtomIsotopeSurvey::N) -
      m_peptide.get()->getNumberOfIsotope(Isotope::N15),
    m_mapIsotope.at(Isotope::N15));
  m_ratio *= isotopem_ratio_cache(
    Isotope::O18,
    m_peptide.get()->getNumberOfAtom(AtomIsotopeSurvey::O) -
      number_of_fixed_oxygen,
    m_mapIsotope.at(Isotope::O18));
  m_ratio *= isotopem_ratio_cache(
    Isotope::O17,
    m_peptide.get()->getNumberOfAtom(AtomIsotopeSurvey::O) -
      number_of_fixed_oxygen,
    m_mapIsotope.at(Isotope::O17));
  m_ratio *= isotopem_ratio_cache(
    Isotope::S33,
    m_peptide.get()->getNumberOfAtom(AtomIsotopeSurvey::S) -
      number_of_fixed_sulfur,
    m_mapIsotope.at(Isotope::S33));
  m_ratio *= isotopem_ratio_cache(
    Isotope::S34,
    m_peptide.get()->getNumberOfAtom(AtomIsotopeSurvey::S) -
      number_of_fixed_sulfur,
    m_mapIsotope.at(Isotope::S34));
  m_ratio *= isotopem_ratio_cache(
    Isotope::S36,
    m_peptide.get()->getNumberOfAtom(AtomIsotopeSurvey::S) -
      number_of_fixed_sulfur,
    m_mapIsotope.at(Isotope::S36));
 
 
  // qDebug() << "Aa::getMass() begin";
  m_mass = m_peptide.get()->getMass();
  m_mass += (DIFFC12C13 * m_mapIsotope.at(Isotope::C13));
  m_mass += (DIFFS32S33 * m_mapIsotope.at(Isotope::S33));
  m_mass += (DIFFS32S34 * m_mapIsotope.at(Isotope::S34));
  m_mass += (DIFFS32S36 * m_mapIsotope.at(Isotope::S36));
  m_mass += (DIFFH1H2 * m_mapIsotope.at(Isotope::H2));
  m_mass += (DIFFO16O18 * m_mapIsotope.at(Isotope::O18));
  m_mass += (DIFFN14N15 * m_mapIsotope.at(Isotope::N15));
  m_mass += (DIFFO16O17 * m_mapIsotope.at(Isotope::O17));
 
 
  // qDebug() << "Aa::getMass() end " << mass;

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

PeptideNaturalIsotope() [2/2]

pappso::PeptideNaturalIsotope::PeptideNaturalIsotope

(

const PeptideNaturalIsotope &

other

)

Definition at line 277 of file peptidenaturalisotope.cpp.

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

References m_ratio.

~PeptideNaturalIsotope()

pappso::PeptideNaturalIsotope::~PeptideNaturalIsotope

(

)

Definition at line 283 of file peptidenaturalisotope.cpp.

{

Member Function Documentation

getIntensityRatio()

pappso_double pappso::PeptideNaturalIsotope::getIntensityRatio

(

unsigned int

charge

)

const

Definition at line 297 of file peptidenaturalisotope.cpp.

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

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

getIsotopeMap()

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

(

)

const

Definition at line 323 of file peptidenaturalisotope.cpp.

{
  return m_mapIsotope;

References m_mapIsotope.

getIsotopeNumber()

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

virtual

Definition at line 349 of file peptidenaturalisotope.cpp.

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

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

getMass()

pappso_double pappso::PeptideNaturalIsotope::getMass ( ) const

overridevirtual

Implements pappso::Ion.

Definition at line 289 of file peptidenaturalisotope.cpp.

{
 
  return m_mass;

References m_mass.

getNumberOfAtom()

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

overridevirtual

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

Implements pappso::AtomNumberInterface.

Definition at line 310 of file peptidenaturalisotope.cpp.

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

References m_peptide.

getNumberOfIsotope()

int pappso::PeptideNaturalIsotope::getNumberOfIsotope ( 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 316 of file peptidenaturalisotope.cpp.

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

References m_mapIsotope, and m_peptide.

getSequence()

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

overridevirtual

amino acid sequence without modification

Implements pappso::PeptideInterface.

Definition at line 343 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 330 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 337 of file peptidenaturalisotope.cpp.

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

References m_peptide.

Member Data Documentation

m_mapIsotope

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

private

Definition at line 90 of file peptidenaturalisotope.h.

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

m_mass

pappso_double pappso::PeptideNaturalIsotope::m_mass

private

Definition at line 92 of file peptidenaturalisotope.h.

Referenced by getMass(), and PeptideNaturalIsotope().

m_peptide

const PeptideInterfaceSp pappso::PeptideNaturalIsotope::m_peptide

private

Definition at line 88 of file peptidenaturalisotope.h.

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

m_ratio

pappso_double pappso::PeptideNaturalIsotope::m_ratio

private

Definition at line 91 of file peptidenaturalisotope.h.

Referenced by getIntensityRatio(), and PeptideNaturalIsotope().

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

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