#include <peptidenaturalisotopelist.h>

Public Types
typedef std::list< PeptideNaturalIsotopeSp >::const_iterator	const_iterator

Public Member Functions
	PeptideNaturalIsotopeList (const PeptideInterfaceSp &peptide, pappso_double minimum_ratio_to_compute=0.001)
	compute the list of possible isotopes for a peptide

	PeptideNaturalIsotopeList (const PeptideNaturalIsotopeList &other)

	~PeptideNaturalIsotopeList ()

PeptideNaturalIsotopeListSp	makePeptideNaturalIsotopeListSp () const

const_iterator	begin () const

const_iterator	end () const

const std::map< unsigned int, pappso_double >	getIntensityRatioPerIsotopeNumber () const

std::vector< PeptideNaturalIsotopeSp >	getByIsotopeNumber (unsigned int isotopeLevel, unsigned int charge) const

std::vector< PeptideNaturalIsotopeAverageSp >	getByIntensityRatio (unsigned int charge, PrecisionPtr precision, pappso_double minimum_isotope_pattern_ratio) const
	get the list of natural isotopes representing at least a minimum ratio of the whole isotope pattern

unsigned int	size () const

const PeptideInterfaceSp &	getPeptideInterfaceSp () const

Private Attributes
const PeptideInterfaceSp	msp_peptide

std::list< PeptideNaturalIsotopeSp >	msp_peptide_natural_isotope_list

Detailed Description

Definition at line 48 of file peptidenaturalisotopelist.h.

Member Typedef Documentation

◆ const_iterator

typedef std::list<PeptideNaturalIsotopeSp>::const_iterator pappso::PeptideNaturalIsotopeList::const_iterator

Definition at line 67 of file peptidenaturalisotopelist.h.

Constructor & Destructor Documentation

◆ PeptideNaturalIsotopeList() [1/2]

pappso::PeptideNaturalIsotopeList::PeptideNaturalIsotopeList	(	const PeptideInterfaceSp &	peptide,
		pappso_double	minimum_ratio_to_compute = 0.001 )

compute the list of possible isotopes for a peptide

Parameters

peptide	the peptide
minimu_ratio_to_compute	the limit under which we stop to compute because the ratio is too thin and not informative (default is 0.001). This limit is the same for each atom to survey : CHNOS

Definition at line 38 of file peptidenaturalisotopelist.cpp.

  : msp_peptide(peptide)
{
  // qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " "
  //          << minimum_ratio_to_compute;
  int number_of_fixed_oxygen =
    msp_peptide.get()->getNumberOfIsotope(Enums::Isotope::O18) +
    msp_peptide.get()->getNumberOfIsotope(Enums::Isotope::O17);
  int number_of_fixed_sulfur =
    msp_peptide.get()->getNumberOfIsotope(Enums::Isotope::S33) +
    msp_peptide.get()->getNumberOfIsotope(Enums::Isotope::S34) +
    msp_peptide.get()->getNumberOfIsotope(Enums::Isotope::S36);
  int number_of_fixed_nitrogen =
    msp_peptide.get()->getNumberOfIsotope(Enums::Isotope::N15);
  int number_of_fixed_hydrogen =
    msp_peptide.get()->getNumberOfIsotope(Enums::Isotope::H2);
 
  int total_carbon(msp_peptide.get()->getNumberOfAtom(Enums::AtomIsotopeSurvey::C) -
                   msp_peptide.get()->getNumberOfIsotope(Enums::Isotope::C13));
 
  // qDebug() << "total_carbon " << total_carbon;
  // qDebug() << "total_sulfur " << total_sulfur;
  std::map<Enums::Isotope, int> map_isotope;
  map_isotope.insert(std::pair<Enums::Isotope, int>(Enums::Isotope::C13, 0));
  map_isotope.insert(std::pair<Enums::Isotope, int>(Enums::Isotope::H2, 0));
  map_isotope.insert(std::pair<Enums::Isotope, int>(Enums::Isotope::N15, 0));
  map_isotope.insert(std::pair<Enums::Isotope, int>(Enums::Isotope::O17, 0));
  map_isotope.insert(std::pair<Enums::Isotope, int>(Enums::Isotope::O18, 0));
  map_isotope.insert(std::pair<Enums::Isotope, int>(Enums::Isotope::S33, 0));
  map_isotope.insert(std::pair<Enums::Isotope, int>(Enums::Isotope::S34, 0));
  map_isotope.insert(std::pair<Enums::Isotope, int>(Enums::Isotope::S36, 0));
 
  for(int nbc13 = 0; nbc13 <= total_carbon; nbc13++)
    {
      map_isotope[Enums::Isotope::C13] = nbc13;
      PeptideNaturalIsotopeSp pepIsotope =
        std::make_shared<PeptideNaturalIsotope>(msp_peptide, map_isotope);
      this->msp_peptide_natural_isotope_list.push_back(pepIsotope);
      if(pepIsotope.get()->getIntensityRatio(1) < minimum_ratio_to_compute)
        {
          break;
        }
    }
  std::list<PeptideNaturalIsotopeSp> temp_list;
 
  // ******************************************************************
  // Sulfur isotope list
  int total_sulfur(msp_peptide.get()->getNumberOfAtom(Enums::AtomIsotopeSurvey::S) -
                   number_of_fixed_sulfur);
  std::list<PeptideNaturalIsotopeSp>::iterator it =
    msp_peptide_natural_isotope_list.begin();
  while(it != msp_peptide_natural_isotope_list.end())
    {
      map_isotope = it->get()->getIsotopeMap();
      for(int nbS34 = 1; nbS34 <= total_sulfur; nbS34++)
        {
          map_isotope[Enums::Isotope::S34] = nbS34;
          PeptideNaturalIsotopeSp pepIsotope =
            std::make_shared<PeptideNaturalIsotope>(msp_peptide, map_isotope);
          temp_list.push_back(pepIsotope);
          if(pepIsotope.get()->getIntensityRatio(1) < minimum_ratio_to_compute)
            {
              // qDebug() << "peptide " << pepIsotope.get()->getFormula(1) << "
              // " << pepIsotope.get()->getIntensityRatio(1); it++;
              break;
            }
        }
      it++;
    }
  msp_peptide_natural_isotope_list.insert(
    it, temp_list.begin(), temp_list.end());
 
  // compute S33 abundance
  temp_list.resize(0);
  it = msp_peptide_natural_isotope_list.begin();
  while(it != msp_peptide_natural_isotope_list.end())
    {
      // qDebug() << "peptide S33 " << it->get()->getFormula(1) << " "
      // <<it->get()->getIntensityRatio(1);
      map_isotope = it->get()->getIsotopeMap();
      for(int nbS33 = 1; nbS33 <= (total_sulfur - map_isotope[Enums::Isotope::S34]);
          nbS33++)
        {
          map_isotope[Enums::Isotope::S33] = nbS33;
          PeptideNaturalIsotopeSp pepIsotopeS33 =
            std::make_shared<PeptideNaturalIsotope>(msp_peptide, map_isotope);
          temp_list.push_back(pepIsotopeS33);
          if(pepIsotopeS33.get()->getIntensityRatio(1) <
             minimum_ratio_to_compute)
            {
              // it++;
              break;
            }
        }
      it++;
    }
  msp_peptide_natural_isotope_list.insert(
    it, temp_list.begin(), temp_list.end());
 
  // compute S36 abundance
  temp_list.resize(0);
  it = msp_peptide_natural_isotope_list.begin();
  while(it != msp_peptide_natural_isotope_list.end())
    {
      map_isotope = it->get()->getIsotopeMap();
      for(int nbS36 = 1; nbS36 <= (total_sulfur - map_isotope[Enums::Isotope::S34] -
                                   map_isotope[Enums::Isotope::S33]);
          nbS36++)
        {
          map_isotope[Enums::Isotope::S36] = nbS36;
          PeptideNaturalIsotopeSp pepIsotopeS36 =
            std::make_shared<PeptideNaturalIsotope>(msp_peptide, map_isotope);
          temp_list.push_back(pepIsotopeS36);
          if(pepIsotopeS36.get()->getIntensityRatio(1) <
             minimum_ratio_to_compute)
            {
              // it++;
              break;
            }
        }
      it++;
    }
  msp_peptide_natural_isotope_list.insert(
    it, temp_list.begin(), temp_list.end());
 
  // ******************************************************************
 
 
  // ******************************************************************
  // Hydrogen isotope list
  temp_list.resize(0);
  // qDebug() << "PeptideNaturalIsotopeList::PeptideNaturalIsotopeList
  // total_hydrogen";
  int total_hydrogen(msp_peptide.get()->getNumberOfAtom(Enums::AtomIsotopeSurvey::H) -
                     number_of_fixed_hydrogen);
  it = msp_peptide_natural_isotope_list.begin();
  while(it != msp_peptide_natural_isotope_list.end())
    {
      // qDebug() << "PeptideNaturalIsotopeList::PeptideNaturalIsotopeList
      // getIsotopeMap " << it->getFormula(1) << " " <<
      // msp_peptide_natural_isotope_list.size();
      map_isotope = it->get()->getIsotopeMap();
      for(int nbH2 = 1; nbH2 <= total_hydrogen; nbH2++)
        {
          map_isotope[Enums::Isotope::H2] = nbH2;
          PeptideNaturalIsotopeSp pepIsotope =
            std::make_shared<PeptideNaturalIsotope>(msp_peptide, map_isotope);
          temp_list.push_back(pepIsotope);
          if(pepIsotope.get()->getIntensityRatio(1) < minimum_ratio_to_compute)
            {
              // it++;
              break;
            }
        }
      it++;
    }
  msp_peptide_natural_isotope_list.insert(
    it, temp_list.begin(), temp_list.end());
  // ******************************************************************
 
 
  // ******************************************************************
  // Oxygen isotope list
  temp_list.resize(0);
  // qDebug() << "PeptideNaturalIsotopeList::PeptideNaturalIsotopeList
  // total_oxygen";
  unsigned int total_oxygen(
    msp_peptide.get()->getNumberOfAtom(Enums::AtomIsotopeSurvey::O) -
    number_of_fixed_oxygen);
  it = msp_peptide_natural_isotope_list.begin();
  while(it != msp_peptide_natural_isotope_list.end())
    {
      // qDebug() << "PeptideNaturalIsotopeList::PeptideNaturalIsotopeList
      // getIsotopeMap " << it->getFormula(1) << " " <<
      // msp_peptide_natural_isotope_list.size();
      map_isotope = it->get()->getIsotopeMap();
      for(unsigned int nbO18 = 1; nbO18 <= total_oxygen; nbO18++)
        {
          // qDebug() << "PeptideNaturalIsotopeList::PeptideNaturalIsotopeList
          // nbO18 " << nbO18;
          map_isotope[Enums::Isotope::O18] = nbO18;
          PeptideNaturalIsotopeSp pepIsotope =
            std::make_shared<PeptideNaturalIsotope>(msp_peptide, map_isotope);
          temp_list.push_back(pepIsotope);
          if(pepIsotope.get()->getIntensityRatio(1) < minimum_ratio_to_compute)
            {
              // it++;
              break;
            }
        }
      it++;
    }
  msp_peptide_natural_isotope_list.insert(
    it, temp_list.begin(), temp_list.end());
  // ******************************************************************
 
 
  // ******************************************************************
  // Nitrogen isotope list
  temp_list.resize(0);
  // qDebug() << "PeptideNaturalIsotopeList::PeptideNaturalIsotopeList
  // total_nitrogen";
  unsigned int total_nitrogen(
    msp_peptide.get()->getNumberOfAtom(Enums::AtomIsotopeSurvey::N) -
    number_of_fixed_nitrogen);
  it = msp_peptide_natural_isotope_list.begin();
  while(it != msp_peptide_natural_isotope_list.end())
    {
      // qDebug() << "PeptideNaturalIsotopeList::PeptideNaturalIsotopeList
      // getIsotopeMap " << it->getFormula(1) << " " <<
      // msp_peptide_natural_isotope_list.size();
      map_isotope = it->get()->getIsotopeMap();
      for(unsigned int nbN15 = 1; nbN15 <= total_nitrogen; nbN15++)
        {
          // qDebug() << "PeptideNaturalIsotopeList::PeptideNaturalIsotopeList
          // nbN15 " << nbN15;
          map_isotope[Enums::Isotope::N15] = nbN15;
          PeptideNaturalIsotopeSp pepIsotope =
            std::make_shared<PeptideNaturalIsotope>(msp_peptide, map_isotope);
          temp_list.push_back(pepIsotope);
          if(pepIsotope.get()->getIntensityRatio(1) < minimum_ratio_to_compute)
            {
              // it++;
              break;
            }
        }
      it++;
    }
  msp_peptide_natural_isotope_list.insert(
    it, temp_list.begin(), temp_list.end());
  // ******************************************************************
 
  // qDebug() << "PeptideNaturalIsotopeList::PeptideNaturalIsotopeList end
  // size="<<msp_peptide_natural_isotope_list.size();
}

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

Referenced by PeptideNaturalIsotopeList().

◆ PeptideNaturalIsotopeList() [2/2]

pappso::PeptideNaturalIsotopeList::PeptideNaturalIsotopeList ( const PeptideNaturalIsotopeList & other )

Definition at line 281 of file peptidenaturalisotopelist.cpp.

  : msp_peptide(other.msp_peptide),
    msp_peptide_natural_isotope_list(other.msp_peptide_natural_isotope_list)
{
}

References PeptideNaturalIsotopeList(), msp_peptide, and msp_peptide_natural_isotope_list.

◆ ~PeptideNaturalIsotopeList()

pappso::PeptideNaturalIsotopeList::~PeptideNaturalIsotopeList ( )

Definition at line 288 of file peptidenaturalisotopelist.cpp.

289{

290}

Member Function Documentation

◆ begin()

PeptideNaturalIsotopeList::const_iterator pappso::PeptideNaturalIsotopeList::begin ( ) const

Definition at line 513 of file peptidenaturalisotopelist.cpp.

{
  return msp_peptide_natural_isotope_list.begin();
}

References msp_peptide_natural_isotope_list.

◆ end()

PeptideNaturalIsotopeList::const_iterator pappso::PeptideNaturalIsotopeList::end ( ) const

Definition at line 519 of file peptidenaturalisotopelist.cpp.

{
  return msp_peptide_natural_isotope_list.end();
}

References msp_peptide_natural_isotope_list.

◆ getByIntensityRatio()

std::vector< PeptideNaturalIsotopeAverageSp > pappso::PeptideNaturalIsotopeList::getByIntensityRatio	(	unsigned int	charge,
		PrecisionPtr	precision,
		pappso_double	minimumIntensityRatio ) const

get the list of natural isotopes representing at least a minimum ratio of the whole isotope pattern

Parameters

charge	gives the number of H+, important to take into account for isotope ratio
precision	the mass accuracy to take into acount each isotope (C13 != H2)
minimum_isotope_pattern_ratio	the minimum ratio of the isotope pattern to represent

/brief get a sorted (by expected intensity) vector of natural isotope average

Definition at line 425 of file peptidenaturalisotopelist.cpp.

{
 
  // qDebug() << "PeptideNaturalIsotopeList::getByIntensityRatio begin";
  std::vector<PeptideNaturalIsotopeAverageSp>
    peptide_natural_isotope_average_list;
 
  std::map<unsigned int, pappso::pappso_double> map_isotope_number =
    getIntensityRatioPerIsotopeNumber();
  std::vector<std::pair<unsigned int, pappso::pappso_double>>
    sorted_number_ratio;
 
  for(unsigned int i = 0; i < map_isotope_number.size(); i++)
    {
      sorted_number_ratio.push_back(
        std::pair<unsigned int, pappso::pappso_double>(i,
                                                       map_isotope_number[i]));
      unsigned int asked_rank = 0;
      unsigned int given_rank = 0;
      bool more_rank          = true;
      while(more_rank)
        {
          asked_rank++;
          pappso::PeptideNaturalIsotopeAverage isotopeAverageMono(
            *this, asked_rank, i, charge, precision);
          given_rank = isotopeAverageMono.getIsotopeRank();
          if(given_rank < asked_rank)
            {
              more_rank = false;
            }
          else if(isotopeAverageMono.getIntensityRatio() == 0)
            {
              more_rank = false;
            }
          else
            {
              // isotopeAverageMono.makePeptideNaturalIsotopeAverageSp();
              peptide_natural_isotope_average_list.push_back(
                isotopeAverageMono.makePeptideNaturalIsotopeAverageSp());
            }
        }
    }
 
 
  // sort by intensity ratio
  std::sort(sorted_number_ratio.begin(),
            sorted_number_ratio.end(),
            [](const std::pair<unsigned int, pappso::pappso_double> &m,
               const std::pair<unsigned int, pappso::pappso_double> &n) {
              return (m.second > n.second);
            });
 
 
  double cumulativeRatio = 0;
  std::vector<unsigned int> selected_isotope_number_list;
  for(auto &pair_isotope_number : sorted_number_ratio)
    {
      if(cumulativeRatio <= minimumIntensityRatio)
        {
          selected_isotope_number_list.push_back(pair_isotope_number.first);
        }
      else
        {
          break;
        }
      cumulativeRatio += pair_isotope_number.second;
    }
 
  auto it_remove =
    std::remove_if(peptide_natural_isotope_average_list.begin(),
                   peptide_natural_isotope_average_list.end(),
                   [selected_isotope_number_list](
                     const PeptideNaturalIsotopeAverageSp &average) {
                     auto it = std::find(selected_isotope_number_list.begin(),
                                         selected_isotope_number_list.end(),
                                         average.get()->getIsotopeNumber());
                     return (it == selected_isotope_number_list.end());
                   });
  peptide_natural_isotope_average_list.erase(
    it_remove, peptide_natural_isotope_average_list.end());
  return peptide_natural_isotope_average_list;
}

References pappso::PeptideNaturalIsotopeAverage::getIntensityRatio(), getIntensityRatioPerIsotopeNumber(), pappso::PeptideNaturalIsotopeAverage::getIsotopeRank(), and pappso::PeptideNaturalIsotopeAverage::makePeptideNaturalIsotopeAverageSp().

◆ getByIsotopeNumber()

std::vector< PeptideNaturalIsotopeSp > pappso::PeptideNaturalIsotopeList::getByIsotopeNumber	(	unsigned int	isotope_number,
		unsigned int	charge ) const

/brief get a sorted (by expected intensity) vector of isotopes of the same level

Definition at line 323 of file peptidenaturalisotopelist.cpp.

{
  std::vector<PeptideNaturalIsotopeSp> v_isotope_list;
 
  for(auto &&isotopeSp : msp_peptide_natural_isotope_list)
    {
      if(isotopeSp.get()->getIsotopeNumber() == isotope_number)
        {
          v_isotope_list.push_back(isotopeSp);
        }
    }
  std::sort(v_isotope_list.begin(),
            v_isotope_list.end(),
            [charge](const PeptideNaturalIsotopeSp &m,
                     const PeptideNaturalIsotopeSp &n) {
              return (m.get()->getIntensityRatio(charge) >
                      n.get()->getIntensityRatio(charge));
            });
  return v_isotope_list;
}

References msp_peptide_natural_isotope_list.

Referenced by pappso::PeptideNaturalIsotopeAverage::PeptideNaturalIsotopeAverage().

◆ getIntensityRatioPerIsotopeNumber()

const std::map< unsigned int, pappso_double > pappso::PeptideNaturalIsotopeList::getIntensityRatioPerIsotopeNumber ( ) const

Definition at line 293 of file peptidenaturalisotopelist.cpp.

{
  std::list<PeptideNaturalIsotopeSp>::const_iterator it =
    msp_peptide_natural_isotope_list.begin();
  std::map<unsigned int, pappso_double> map_isotope_number;
 
  while(it != msp_peptide_natural_isotope_list.end())
    {
      unsigned int number = it->get()->getIsotopeNumber();
      std::pair<std::map<unsigned int, pappso_double>::iterator, bool> mapnew =
        map_isotope_number.insert(
          std::pair<unsigned int, pappso_double>(number, 0));
      if(mapnew.second == false)
        {
          // mapit = map_isotope_number.insert(std::pair<unsigned
          // int,pappso_double>(number, 0));
        }
      mapnew.first->second += it->get()->getIntensityRatio(1);
      it++;
    }
  return map_isotope_number;
}

References msp_peptide_natural_isotope_list.

Referenced by pappso::MassSpectrumWidget::computeIsotopeMassList(), and getByIntensityRatio().

◆ getPeptideInterfaceSp()

const PeptideInterfaceSp & pappso::PeptideNaturalIsotopeList::getPeptideInterfaceSp ( ) const

Definition at line 531 of file peptidenaturalisotopelist.cpp.

{
  return msp_peptide;
}

References msp_peptide.

◆ makePeptideNaturalIsotopeListSp()

PeptideNaturalIsotopeListSp pappso::PeptideNaturalIsotopeList::makePeptideNaturalIsotopeListSp ( ) const

Definition at line 276 of file peptidenaturalisotopelist.cpp.

{
  return std::make_shared<PeptideNaturalIsotopeList>(*this);
}

References makePeptideNaturalIsotopeListSp().

Referenced by makePeptideNaturalIsotopeListSp().

◆ size()

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

Definition at line 525 of file peptidenaturalisotopelist.cpp.

{
  return msp_peptide_natural_isotope_list.size();
}

References msp_peptide_natural_isotope_list.

Member Data Documentation

◆ msp_peptide

const PeptideInterfaceSp pappso::PeptideNaturalIsotopeList::msp_peptide

private

Definition at line 51 of file peptidenaturalisotopelist.h.

Referenced by PeptideNaturalIsotopeList(), PeptideNaturalIsotopeList(), and getPeptideInterfaceSp().

◆ msp_peptide_natural_isotope_list

std::list<PeptideNaturalIsotopeSp> pappso::PeptideNaturalIsotopeList::msp_peptide_natural_isotope_list

private

Definition at line 52 of file peptidenaturalisotopelist.h.

Referenced by PeptideNaturalIsotopeList(), begin(), end(), getByIsotopeNumber(), getIntensityRatioPerIsotopeNumber(), and size().

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

pappsomspp/core/peptide/peptidenaturalisotopelist.h
pappsomspp/core/peptide/peptidenaturalisotopelist.cpp

Public Types

Public Member Functions

Private Attributes

Detailed Description

Member Typedef Documentation

◆ const_iterator

Constructor & Destructor Documentation

◆ PeptideNaturalIsotopeList() [1/2]

◆ PeptideNaturalIsotopeList() [2/2]

◆ ~PeptideNaturalIsotopeList()

Member Function Documentation

◆ begin()

◆ end()

◆ getByIntensityRatio()

◆ getByIsotopeNumber()

◆ getIntensityRatioPerIsotopeNumber()

◆ getPeptideInterfaceSp()

◆ makePeptideNaturalIsotopeListSp()

◆ size()

Member Data Documentation

◆ msp_peptide

◆ msp_peptide_natural_isotope_list