pappso::Peptide Class Reference

#include <peptide.h>

Inheritance diagram for pappso::Peptide:

Public Member Functions
	Peptide (const QString &pepstr)
virtual	~Peptide ()
	Peptide (const Peptide &peptide)
	Peptide (Peptide &&toCopy)
PeptideSp	makePeptideSp () const
NoConstPeptideSp	makeNoConstPeptideSp () const
void	addAaModification (AaModificationP aaModification, unsigned int position)
	adds a modification to amino acid sequence
void	addAaModificationOnAllAminoAcid (AaModificationP aaModification, Enums::AminoAcidChar amino_acid)
	adds a modification to all amino acid of the sequence
std::vector< Aa >::iterator	begin ()
std::vector< Aa >::iterator	end ()
std::vector< Aa >::const_iterator	begin () const
std::vector< Aa >::const_iterator	end () const
std::vector< Aa >::const_reverse_iterator	rbegin () const
std::vector< Aa >::const_reverse_iterator	rend () const
Aa &	getAa (unsigned int position)
const Aa &	getConstAa (unsigned int position) const
std::vector< double >	getRawMassArray () const
	get raw mass array of the amino acid sequence
std::vector< double >	getMassIonSerie (unsigned int charge, pappso::Enums::PeptideIon ion_type) const
	get complete serie of product masses for a given charge and ion type
pappso_double	getMass ()
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
const QString	getSequence () const override
	print amino acid sequence without modifications
unsigned int	size () const override
unsigned int	getNumberOfModification (AaModificationP mod) const
	count modification occurence
unsigned int	countModificationOnAa (AaModificationP mod, const std::vector< char > &aa_list) const
	count modification occurence
void	replaceAaModification (AaModificationP oldmod, AaModificationP newmod)
	replaces all occurences of a modification by a new one
void	replaceAaModificationOnAminoAcid (Enums::AminoAcidChar aa, pappso::AaModificationP oldmod, pappso::AaModificationP newmod)
	replaces all occurences of a modification by a new one on a specific amino acid
void	removeAaModification (AaModificationP mod)
	removes all occurences of a modification
std::vector< unsigned int >	getModificationPositionList (AaModificationP mod) const
	get modification positions
std::vector< unsigned int >	getModificationPositionList (AaModificationP mod, const std::vector< char > &aa_list) const
	get modification positions
std::vector< unsigned int >	getAaPositionList (char aa) const
	get positions of one amino acid in peptide
std::vector< unsigned int >	getAaPositionList (std::list< char > list_aa) const
const QString	toString () const
	print modification except internal modifications
const QString	toAbsoluteString () const
	print all modifications
const QString	getLiAbsoluteString () const
	get all sequence string with modifications and converting Leucine to Isoleucine
void	setCleavageNterModification (AaModificationP mod)
void	setCleavageCterModification (AaModificationP mod)
AaModificationP	getCleavageNterModification () const
AaModificationP	getCleavageCterModification () const
void	setNterModification (AaModificationP mod)
void	setCterModification (AaModificationP mod)
AaModificationP	getNterModification () const
AaModificationP	getCterModification () const
void	setGlobalModification (Enums::Isotope isotope_kind)
	apply 100% isotope replacement
void	rotate ()
void	reverse ()
virtual bool	isPalindrome () const override
	tells if the peptide sequence is a palindrome
void	replaceLeucineIsoleucine ()
void	removeNterAminoAcid ()
void	removeCterAminoAcid ()
QString	toProForma () const
	get the peptide model in ProForma notation https://github.com/HUPO-PSI/ProForma/blob/master/README.md
virtual const ChemicalFormula	getChemicalFormula () const override
virtual const ChemicalFormula	getChemicalFormulaCharge (unsigned int charge) const override
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 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

Protected Attributes
std::vector< Aa >	m_aaVec
bool	m_fullC13 = false
bool	m_fullN15 = false
bool	m_fullH2 = false
double	m_proxyMass = -1
AaModificationP	m_cleavageNterMod = nullptr
AaModificationP	m_cleavageCterMod = nullptr
AaModificationP	m_NterMod = nullptr
AaModificationP	m_CterMod = nullptr

Friends
class	PeptideProFormaParser
bool	operator< (const Peptide &l, const Peptide &r)
bool	operator== (const Peptide &l, const Peptide &r)

Detailed Description

Definition at line 101 of file peptide.h.

Constructor & Destructor Documentation

Peptide() [1/3]

pappso::Peptide::Peptide

(

const QString &

pepstr

)

Definition at line 106 of file peptide.cpp.

{
  qDebug();
  m_cleavageNterMod = AaModification::getInstance("internal:Nter_hydrolytic_cleavage_H");
  m_cleavageCterMod = AaModification::getInstance("internal:Cter_hydrolytic_cleavage_HO");
 
  m_NterMod = nullptr;
  m_CterMod = nullptr;
  QString::const_iterator it(pepstr.begin());
 
  while(it != pepstr.end())
    {
      qDebug() << it->toLatin1();
      m_aaVec.push_back(Aa(it->toLatin1()));
      it++;
    }
  qDebug();
  getMass();
}

References pappso::AaModification::getInstance(), getMass(), m_aaVec, m_cleavageCterMod, m_cleavageNterMod, m_CterMod, and m_NterMod.

Referenced by Peptide(), Peptide(), and PeptideProFormaParser.

~Peptide()

pappso::Peptide::~Peptide ( )

virtual

Definition at line 126 of file peptide.cpp.

{
}

Peptide() [2/3]

pappso::Peptide::Peptide

(

const Peptide &

peptide

)

Definition at line 130 of file peptide.cpp.

  : m_aaVec(peptide.m_aaVec),
    m_fullC13(peptide.m_fullC13),
    m_fullN15(peptide.m_fullN15),
    m_fullH2(peptide.m_fullH2),
    m_proxyMass(peptide.m_proxyMass),
    m_cleavageNterMod(peptide.m_cleavageNterMod),
    m_cleavageCterMod(peptide.m_cleavageCterMod),
    m_NterMod(peptide.m_NterMod),
    m_CterMod(peptide.m_CterMod)
{
  qDebug();
}

References Peptide(), m_aaVec, m_cleavageCterMod, m_cleavageNterMod, m_CterMod, m_fullC13, m_fullH2, m_fullN15, m_NterMod, and m_proxyMass.

Peptide() [3/3]

pappso::Peptide::Peptide

(

Peptide &&

toCopy

)

Definition at line 145 of file peptide.cpp.

  : m_aaVec(std::move(toCopy.m_aaVec)),
    m_fullC13(toCopy.m_fullC13),
    m_fullN15(toCopy.m_fullN15),
    m_fullH2(toCopy.m_fullH2),
    m_proxyMass(toCopy.m_proxyMass),
    m_cleavageNterMod(toCopy.m_cleavageNterMod),
    m_cleavageCterMod(toCopy.m_cleavageCterMod),
    m_NterMod(toCopy.m_NterMod),
    m_CterMod(toCopy.m_CterMod)
{
}

References Peptide(), m_aaVec, m_cleavageCterMod, m_cleavageNterMod, m_CterMod, m_fullC13, m_fullH2, m_fullN15, m_NterMod, and m_proxyMass.

Member Function Documentation

addAaModification()

void pappso::Peptide::addAaModification	(	AaModificationP	aaModification,
		unsigned int	position )

adds a modification to amino acid sequence

Parameters

aaModification	pointer on modification to add
position	position in the amino acid sequence (starts at 0)

Definition at line 222 of file peptide.cpp.

{
  if(position >= size())
    {
      throw ExceptionOutOfRange(QObject::tr("position (%1) > size (%2)").arg(position).arg(size()));
    }
  m_proxyMass = -1;
  qDebug() << "Peptide::addAaModification begin " << position;
  std::vector<Aa>::iterator it = m_aaVec.begin() + position;
  it->addAaModification(aaModification);
  getMass();
  qDebug() << "Peptide::addAaModification end";
}

References getMass(), m_aaVec, m_proxyMass, and size().

Referenced by pappso::PeptideStrParser::parseStringToPeptide(), PeptideProFormaParser, pappso::PeptideBuilder::setPeptide(), pappso::PeptideFixedModificationBuilder::setPeptideSp(), and pappso::PeptideVariableModificationBuilder::setPeptideSp().

addAaModificationOnAllAminoAcid()

void pappso::Peptide::addAaModificationOnAllAminoAcid	(	AaModificationP	aaModification,
		Enums::AminoAcidChar	amino_acid )

adds a modification to all amino acid of the sequence

Parameters

aaModification	pointer on modification to add
Enums::AminoAcidChar	amino_acid to apply the modification

Definition at line 237 of file peptide.cpp.

{
 
  for(auto &aa : *this)
    {
      if(aa.getAminoAcidChar() == amino_acid)
        {
          aa.addAaModification(aaModification);
        }
    }
 
 
  m_proxyMass = -1;
  getMass();
}

References getMass(), and m_proxyMass.

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

begin() [1/2]

std::vector< Aa >::iterator pappso::Peptide::begin

(

)

Definition at line 173 of file peptide.cpp.

{
  return m_aaVec.begin();
}

References m_aaVec.

Referenced by pappso::PeptideRawFragmentMasses::PeptideRawFragmentMasses(), and PeptideProFormaParser.

begin() [2/2]

std::vector< Aa >::const_iterator pappso::Peptide::begin

(

)

const

Definition at line 185 of file peptide.cpp.

{
  return m_aaVec.begin();
}

References m_aaVec.

countModificationOnAa()

unsigned int pappso::Peptide::countModificationOnAa	(	AaModificationP	mod,
		const std::vector< char > &	aa_list ) const

count modification occurence

Parameters

mod	modification to look for
aa_list	amino acid list targets (one letter code)

Returns

number of occurences

Definition at line 457 of file peptide.cpp.

{
  unsigned int number = 0;
  std::vector<Aa>::const_iterator it(m_aaVec.begin());
  while(it != m_aaVec.end())
    {
      if(std::find(aa_list.begin(), aa_list.end(), it->getLetter()) != aa_list.end())
        {
          number += it->getNumberOfModification(mod);
        }
      it++;
    }
  // qDebug() << "Aa::getMass() end " << mass;
  return number;
}

References m_aaVec.

Referenced by PeptideProFormaParser.

end() [1/2]

std::vector< Aa >::iterator pappso::Peptide::end

(

)

Definition at line 179 of file peptide.cpp.

{
  return m_aaVec.end();
}

References m_aaVec.

Referenced by pappso::PeptideRawFragmentMasses::PeptideRawFragmentMasses(), and PeptideProFormaParser.

end() [2/2]

std::vector< Aa >::const_iterator pappso::Peptide::end

(

)

const

Definition at line 191 of file peptide.cpp.

{
  return m_aaVec.end();
}

References m_aaVec.

getAa()

Aa & pappso::Peptide::getAa

(

unsigned int

position

)

Definition at line 720 of file peptide.cpp.

{
  if(position >= m_aaVec.size())
    {
      throw ExceptionOutOfRange(QObject::tr("no AA at position %1").arg(position));
    }
  return m_aaVec.at(position);
}

References m_aaVec.

Referenced by PeptideProFormaParser, and pappso::PeptideVariableModificationReplacement::replaceModificationsAtPosition().

getAaPositionList() [1/2]

std::vector< unsigned int > pappso::Peptide::getAaPositionList

(

char

aa

)

const

get positions of one amino acid in peptide

Parameters

aa	the one letter code of the amino acid

Returns

vector containing positions (from 0 to size-1)

Definition at line 567 of file peptide.cpp.

{
  std::vector<unsigned int> position_list;
  unsigned int number = 0;
  std::vector<Aa>::const_iterator it(m_aaVec.begin());
  while(it != m_aaVec.end())
    {
      if(it->getLetter() == aa)
        position_list.push_back(number);
      number++;
      it++;
    }
  // qDebug() << "Aa::getMass() end " << mass;
  return position_list;
}

References m_aaVec.

Referenced by PeptideProFormaParser, and pappso::PeptideBuilder::setPeptide().

getAaPositionList() [2/2]

std::vector< unsigned int > pappso::Peptide::getAaPositionList

(

std::list< char >

list_aa

)

const

Definition at line 584 of file peptide.cpp.

{
  std::vector<unsigned int> position_list;
  unsigned int number = 0;
  std::vector<Aa>::const_iterator it(m_aaVec.begin());
  while(it != m_aaVec.end())
    {
 
      bool found = (std::find(list_aa.begin(), list_aa.end(), it->getLetter()) != list_aa.end());
      if(found)
        {
          position_list.push_back(number);
        }
      number++;
      it++;
    }
  // qDebug() << "Aa::getMass() end " << mass;
  return position_list;
}

References m_aaVec.

getChemicalFormula()

const pappso::ChemicalFormula pappso::Peptide::getChemicalFormula ( ) const

overridevirtual

Reimplemented from pappso::AtomNumberInterface.

Definition at line 838 of file peptide.cpp.

{
  return getChemicalFormulaCharge(0);
}

References getChemicalFormulaCharge().

Referenced by getMass(), and PeptideProFormaParser.

getChemicalFormulaCharge()

const pappso::ChemicalFormula pappso::Peptide::getChemicalFormulaCharge ( unsigned int charge ) const

overridevirtual

Reimplemented from pappso::PeptideInterface.

Definition at line 845 of file peptide.cpp.

{
  ChemicalFormula formula = PeptideInterface::getChemicalFormulaCharge(charge);
 
  qDebug() << formula.toString();
  if(m_fullC13)
    {
      formula.setFullIsotope(Enums::Isotope::C13);
      qDebug() << formula.toString();
    }
  if(m_fullN15)
    {
      formula.setFullIsotope(Enums::Isotope::N15);
      qDebug() << formula.toString();
    }
  if(m_fullH2)
    {
      formula.setFullIsotope(Enums::Isotope::H2);
      qDebug() << formula.toString();
    }
  return formula;
}

References pappso::Enums::C13, pappso::PeptideInterface::getChemicalFormulaCharge(), pappso::Enums::H2, m_fullC13, m_fullH2, m_fullN15, pappso::Enums::N15, pappso::ChemicalFormula::setFullIsotope(), and pappso::ChemicalFormula::toString().

Referenced by getChemicalFormula(), and PeptideProFormaParser.

getCleavageCterModification()

AaModificationP pappso::Peptide::getCleavageCterModification

(

)

const

Definition at line 643 of file peptide.cpp.

{
  return m_cleavageCterMod;
}

References m_cleavageCterMod.

Referenced by pappso::specglob::PeptideModel::PeptideModel(), operator==, and PeptideProFormaParser.

getCleavageNterModification()

AaModificationP pappso::Peptide::getCleavageNterModification

(

)

const

Definition at line 638 of file peptide.cpp.

{
  return m_cleavageNterMod;
}

References m_cleavageNterMod.

Referenced by pappso::specglob::PeptideModel::PeptideModel(), operator==, and PeptideProFormaParser.

getConstAa()

const Aa & pappso::Peptide::getConstAa

(

unsigned int

position

)

const

Definition at line 729 of file peptide.cpp.

{
  if(position >= m_aaVec.size())
    {
      throw ExceptionOutOfRange(QObject::tr("no AA at position %1").arg(position));
    }
  return m_aaVec.at(position);
}

References m_aaVec.

Referenced by pappso::PeptideModificatorBase::getModificationPositionList(), and PeptideProFormaParser.

getCterModification()

AaModificationP pappso::Peptide::getCterModification

(

)

const

Definition at line 680 of file peptide.cpp.

{
  return m_CterMod;
}

References m_CterMod.

Referenced by pappso::PeptideRawFragmentMasses::PeptideRawFragmentMasses(), operator==, and PeptideProFormaParser.

getLiAbsoluteString()

const QString pappso::Peptide::getLiAbsoluteString

(

)

const

get all sequence string with modifications and converting Leucine to Isoleucine

Definition at line 298 of file peptide.cpp.

{
  QString seq = "";
  std::vector<Aa>::const_iterator it(m_aaVec.begin());
  while(it != m_aaVec.end())
    {
      seq += it->toAbsoluteString();
      it++;
    }
  return seq.replace("L", "I");
}

References m_aaVec.

Referenced by PeptideProFormaParser.

getMass() [1/2]

pappso_double pappso::Peptide::getMass

(

)

Definition at line 375 of file peptide.cpp.

{
  qDebug() << "begin";
  if(m_proxyMass < 0)
    {
      if(m_fullC13 || m_fullH2 || m_fullN15)
        {
          ChemicalFormula formula = getChemicalFormula();
          m_proxyMass             = formula.getMass();
        }
      else
        {
          m_proxyMass = m_cleavageNterMod->getMass() + m_cleavageCterMod->getMass();
          if(m_NterMod != nullptr)
            m_proxyMass += m_NterMod->getMass();
          if(m_CterMod != nullptr)
            m_proxyMass += m_CterMod->getMass();
          for(auto aa : m_aaVec)
            {
              m_proxyMass += aa.getMass();
            }
        }
    }
  qDebug() << "end " << m_proxyMass;
  return m_proxyMass;
}

References getChemicalFormula(), pappso::ChemicalFormula::getMass(), m_aaVec, m_cleavageCterMod, m_cleavageNterMod, m_CterMod, m_fullC13, m_fullH2, m_fullN15, m_NterMod, and m_proxyMass.

Referenced by Peptide(), addAaModification(), addAaModificationOnAllAminoAcid(), pappso::Protein::getMass(), pappso::PeptideProFormaParser::parseStringToPeptide(), PeptideProFormaParser, removeAaModification(), removeCterAminoAcid(), removeNterAminoAcid(), replaceAaModification(), replaceAaModificationOnAminoAcid(), setCleavageCterModification(), setCleavageNterModification(), setCterModification(), setNterModification(), and pappso::PsmFeatures::setPeptideSpectrumCharge().

getMass() [2/2]

pappso_double pappso::Peptide::getMass ( ) const

overridevirtual

Implements pappso::Ion.

Definition at line 210 of file peptide.cpp.

{
  return m_proxyMass;
}

References m_proxyMass.

getMassIonSerie()

std::vector< double > pappso::Peptide::getMassIonSerie	(	unsigned int	charge,
		pappso::Enums::PeptideIon	ion_type ) const

get complete serie of product masses for a given charge and ion type

Definition at line 336 of file peptide.cpp.

{
  std::vector<double> mz_arr;
  double mass_accumulator = 0;
  double mass_shift       = 0;
  if(ion_type == pappso::Enums::PeptideIon::b)
    {
      for(const Aa &aa : m_aaVec)
        {
          mass_accumulator += aa.getMass();
          mz_arr.push_back(mass_accumulator);
        }
    }
  else if(ion_type == pappso::Enums::PeptideIon::y)
    {
      std::vector<Aa>::const_reverse_iterator it(m_aaVec.rbegin());
      while(it != m_aaVec.rend())
        {
          mass_accumulator += it->getMass();
          mz_arr.push_back(mass_accumulator);
          it++;
        }
      mass_shift = MASSH2O;
    }
  else
    {
      throw pappso::ExceptionNotImplemented(
        QObject::tr("Peptide::getMassIonSerie not implemented for ion type %1")
          .arg(Utils::toString(ion_type)));
    }
  for(double &mass : mz_arr)
    {
      mass = (mass + mass_shift + (MHPLUS * (double)charge)) / (double)charge;
    }
 
  return mz_arr;
}

References pappso::Enums::b, m_aaVec, pappso::MASSH2O(), pappso::MHPLUS(), pappso::Utils::toString(), and pappso::Enums::y.

Referenced by PeptideProFormaParser.

getModificationPositionList() [1/2]

std::vector< unsigned int > pappso::Peptide::getModificationPositionList

(

AaModificationP

mod

)

const

get modification positions

Parameters

mod	modification to look for

Returns

vector containing positions (from 0 to size-1)

Definition at line 522 of file peptide.cpp.

{
  std::vector<unsigned int> position_list;
  unsigned int position = 0;
  std::vector<Aa>::const_iterator it(m_aaVec.begin());
  while(it != m_aaVec.end())
    {
      unsigned int number = 0;
      number += it->getNumberOfModification(mod);
      for(unsigned int j = 0; j < number; j++)
        {
          position_list.push_back(position);
        }
      it++;
      position++;
    }
  // qDebug() << "Aa::getMass() end " << mass;
  return position_list;
}

References m_aaVec.

Referenced by PeptideProFormaParser.

getModificationPositionList() [2/2]

std::vector< unsigned int > pappso::Peptide::getModificationPositionList	(	AaModificationP	mod,
		const std::vector< char > &	aa_list ) const

get modification positions

Parameters

mod	modification to look for
aa_list	amino acid list targets (one letter code)

Returns

vector containing positions (from 0 to size-1)

Definition at line 543 of file peptide.cpp.

{
  std::vector<unsigned int> position_list;
  unsigned int position = 0;
  std::vector<Aa>::const_iterator it(m_aaVec.begin());
  while(it != m_aaVec.end())
    {
      if(std::find(aa_list.begin(), aa_list.end(), it->getLetter()) != aa_list.end())
        {
          unsigned int number = 0;
          number += it->getNumberOfModification(mod);
          for(unsigned int j = 0; j < number; j++)
            {
              position_list.push_back(position);
            }
        }
      it++;
      position++;
    }
  // qDebug() << "Aa::getMass() end " << mass;
  return position_list;
}

References m_aaVec.

getNterModification()

AaModificationP pappso::Peptide::getNterModification

(

)

const

Definition at line 686 of file peptide.cpp.

{
  return m_NterMod;
}

References m_NterMod.

Referenced by pappso::PeptideRawFragmentMasses::PeptideRawFragmentMasses(), operator==, and PeptideProFormaParser.

getNumberOfAtom()

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

overridevirtual

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

Implements pappso::AtomNumberInterface.

Definition at line 403 of file peptide.cpp.

{
  int number = m_cleavageNterMod->getNumberOfAtom(atom);
  number += m_cleavageCterMod->getNumberOfAtom(atom);
 
  if(m_NterMod != nullptr)
    number += m_NterMod->getNumberOfAtom(atom);
  if(m_CterMod != nullptr)
    number += m_CterMod->getNumberOfAtom(atom);
  std::vector<Aa>::const_iterator it(m_aaVec.begin());
  while(it != m_aaVec.end())
    {
      number += it->getNumberOfAtom(atom);
      it++;
    }
  // qDebug() << "Aa::getMass() end " << mass;
  return number;
}

References m_aaVec, m_cleavageCterMod, m_cleavageNterMod, m_CterMod, and m_NterMod.

Referenced by PeptideProFormaParser.

getNumberOfIsotope()

int pappso::Peptide::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 423 of file peptide.cpp.

{
  int number = m_cleavageNterMod->getNumberOfIsotope(isotope);
  number += m_cleavageCterMod->getNumberOfIsotope(isotope);
  if(m_NterMod != nullptr)
    number += m_NterMod->getNumberOfIsotope(isotope);
  if(m_CterMod != nullptr)
    number += m_CterMod->getNumberOfIsotope(isotope);
  std::vector<Aa>::const_iterator it(m_aaVec.begin());
  while(it != m_aaVec.end())
    {
      number += it->getNumberOfIsotope(isotope);
      it++;
    }
  // qDebug() << "Aa::getMass() end " << mass;
  return number;
}

References m_aaVec, m_cleavageCterMod, m_cleavageNterMod, m_CterMod, and m_NterMod.

Referenced by PeptideProFormaParser.

getNumberOfModification()

unsigned int pappso::Peptide::getNumberOfModification

(

AaModificationP

mod

)

const

count modification occurence

Parameters

mod	modification to look for

Returns

number of occurences

Definition at line 443 of file peptide.cpp.

{
  unsigned int number = 0;
  std::vector<Aa>::const_iterator it(m_aaVec.begin());
  while(it != m_aaVec.end())
    {
      number += it->getNumberOfModification(mod);
      it++;
    }
  // qDebug() << "Aa::getMass() end " << mass;
  return number;
}

References m_aaVec.

Referenced by PeptideProFormaParser.

getRawMassArray()

std::vector< double > pappso::Peptide::getRawMassArray

(

)

const

get raw mass array of the amino acid sequence

Definition at line 325 of file peptide.cpp.

{
  std::vector<double> raw_mass_arr;
  for(const Aa &aa : m_aaVec)
    {
      raw_mass_arr.push_back(aa.getMass());
    }
  return raw_mass_arr;
}

References m_aaVec.

Referenced by PeptideProFormaParser.

getSequence()

const QString pappso::Peptide::getSequence ( ) const

overridevirtual

print amino acid sequence without modifications

Implements pappso::PeptideInterface.

Definition at line 255 of file peptide.cpp.

{
  QString seq = "";
  std::vector<Aa>::const_iterator it(m_aaVec.begin());
  while(it != m_aaVec.end())
    {
      seq += it->getLetter();
      it++;
    }
  return seq;
}

References m_aaVec.

Referenced by pappso::XtandemHyperscoreBis::computeXtandemHyperscore(), pappso::PeptideModificatorBase::getModificationPositionList(), PeptideProFormaParser, and pappso::PeptideFixedModificationBuilder::setPeptideSp().

isPalindrome()

bool pappso::Peptide::isPalindrome ( ) const

overridevirtual

tells if the peptide sequence is a palindrome

Implements pappso::PeptideInterface.

Definition at line 705 of file peptide.cpp.

{
  std::size_t size = m_aaVec.size();
  std::size_t k    = (size - 1);
  for(std::size_t i = 0; i < (size / 2); i++, k--)
    {
      if(m_aaVec[i].getLetter() != m_aaVec[k].getLetter())
        {
          return false;
        }
    }
  return true;
}

References m_aaVec, and size().

Referenced by PeptideProFormaParser.

makeNoConstPeptideSp()

NoConstPeptideSp pappso::Peptide::makeNoConstPeptideSp

(

)

const

Definition at line 166 of file peptide.cpp.

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

Referenced by pappso::PeptideProFormaParser::parseNoConstString(), pappso::PeptideStrParser::parseNoConstString(), and PeptideProFormaParser.

makePeptideSp()

PeptideSp pappso::Peptide::makePeptideSp

(

)

const

Definition at line 160 of file peptide.cpp.

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

Referenced by pappso::PeptideProFormaParser::parseString(), pappso::PeptideStrParser::parseString(), PeptideProFormaParser, pappso::PeptideBuilder::setPeptide(), pappso::PeptideModificatorPipeline::setPeptide(), pappso::PeptideFixedModificationBuilder::setPeptideSp(), pappso::PeptideVariableModificationBuilder::setPeptideSp(), and pappso::PeptideVariableModificationReplacement::setPeptideSp().

rbegin()

std::vector< Aa >::const_reverse_iterator pappso::Peptide::rbegin

(

)

const

Definition at line 197 of file peptide.cpp.

{
  return m_aaVec.rbegin();
}

References m_aaVec.

Referenced by pappso::PeptideRawFragmentMasses::PeptideRawFragmentMasses(), and PeptideProFormaParser.

removeAaModification()

void pappso::Peptide::removeAaModification

(

AaModificationP

mod

)

removes all occurences of a modification

Parameters

mod	modification to remove

Definition at line 508 of file peptide.cpp.

{
  std::vector<Aa>::iterator it(m_aaVec.begin());
  while(it != m_aaVec.end())
    {
      it->removeAaModification(mod);
      qDebug() << it->toString() << " " << toAbsoluteString();
      it++;
    }
  m_proxyMass = -1;
  getMass();
  // qDebug() << "Aa::getMass() end " << mass;
}

References getMass(), m_aaVec, m_proxyMass, and toAbsoluteString().

Referenced by PeptideProFormaParser.

removeCterAminoAcid()

void pappso::Peptide::removeCterAminoAcid

(

)

Definition at line 770 of file peptide.cpp.

{
  std::vector<Aa>::iterator it(m_aaVec.end());
  it--;
  if(it != m_aaVec.end())
    {
      m_aaVec.erase(it);
      m_proxyMass = -1;
      getMass();
    }
  else
    {
      throw ExceptionOutOfRange(QObject::tr("peptide is empty"));
    }
}

References getMass(), m_aaVec, and m_proxyMass.

Referenced by PeptideProFormaParser.

removeNterAminoAcid()

void pappso::Peptide::removeNterAminoAcid

(

)

Definition at line 753 of file peptide.cpp.

{
  std::vector<Aa>::iterator it(m_aaVec.begin());
  if(it != m_aaVec.end())
    {
      m_aaVec.erase(it);
      m_proxyMass = -1;
      getMass();
    }
  else
    {
      throw ExceptionOutOfRange(QObject::tr("peptide is empty"));
    }
}

References getMass(), m_aaVec, and m_proxyMass.

Referenced by PeptideProFormaParser.

rend()

std::vector< Aa >::const_reverse_iterator pappso::Peptide::rend

(

)

const

Definition at line 203 of file peptide.cpp.

{
  return m_aaVec.rend();
}

References m_aaVec.

Referenced by pappso::PeptideRawFragmentMasses::PeptideRawFragmentMasses(), and PeptideProFormaParser.

replaceAaModification()

void pappso::Peptide::replaceAaModification	(	AaModificationP	oldmod,
		AaModificationP	newmod )

replaces all occurences of a modification by a new one

Parameters

oldmod	modification to change
newmod	new modification

Definition at line 474 of file peptide.cpp.

{
  if(oldmod == newmod)
    return;
  std::vector<Aa>::iterator it(m_aaVec.begin());
  while(it != m_aaVec.end())
    {
      it->replaceAaModification(oldmod, newmod);
      it++;
    }
  m_proxyMass = -1;
  getMass();
}

References getMass(), m_aaVec, and m_proxyMass.

Referenced by PeptideProFormaParser.

replaceAaModificationOnAminoAcid()

void pappso::Peptide::replaceAaModificationOnAminoAcid	(	Enums::AminoAcidChar	aa,
		pappso::AaModificationP	oldmod,
		pappso::AaModificationP	newmod )

replaces all occurences of a modification by a new one on a specific amino acid

Parameters

aa	the amino acid to modify
oldmod	modification to change
newmod	new modification

Definition at line 489 of file peptide.cpp.

{
  if(oldmod == newmod)
    return;
  std::vector<Aa>::iterator it(m_aaVec.begin());
  while(it != m_aaVec.end())
    {
      if(it->getAminoAcidChar() == aa)
        {
          it->replaceAaModification(oldmod, newmod);
        }
      it++;
    }
  m_proxyMass = -1;
  getMass();
}

References getMass(), m_aaVec, and m_proxyMass.

Referenced by PeptideProFormaParser.

replaceLeucineIsoleucine()

void pappso::Peptide::replaceLeucineIsoleucine

(

)

Definition at line 740 of file peptide.cpp.

{
 
  std::vector<Aa>::iterator it(m_aaVec.begin());
  std::vector<Aa>::iterator itend(m_aaVec.end());
  for(; it != itend; it++)
    {
      it->replaceLeucineIsoleucine();
    }
}

References m_aaVec.

Referenced by PeptideProFormaParser.

reverse()

void pappso::Peptide::reverse

(

)

Definition at line 698 of file peptide.cpp.

{
  std::reverse(m_aaVec.begin(), m_aaVec.end());
}

References m_aaVec.

Referenced by PeptideProFormaParser.

rotate()

void pappso::Peptide::rotate

(

)

Definition at line 692 of file peptide.cpp.

{
  std::rotate(m_aaVec.begin(), m_aaVec.begin() + 1, m_aaVec.end());
}

References m_aaVec.

Referenced by PeptideProFormaParser.

setCleavageCterModification()

void pappso::Peptide::setCleavageCterModification

(

AaModificationP

mod

)

Definition at line 621 of file peptide.cpp.

{
  if(mod->getAccession().startsWith("internal:Cter_"))
    {
      m_proxyMass       = -1;
      m_cleavageNterMod = mod;
      getMass();
    }
  else
    {
      throw ExceptionNotPossible(
        QObject::tr("modification is not a cleavage Cter modification : %1")
          .arg(mod->getAccession()));
    }
}

References pappso::AaModification::getAccession(), getMass(), m_cleavageNterMod, and m_proxyMass.

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

setCleavageNterModification()

void pappso::Peptide::setCleavageNterModification

(

AaModificationP

mod

)

Definition at line 605 of file peptide.cpp.

{
  if(mod->getAccession().startsWith("internal:Nter_"))
    {
      m_proxyMass       = -1;
      m_cleavageNterMod = mod;
      getMass();
    }
  else
    {
      throw ExceptionNotPossible(
        QObject::tr("modification is not a cleavage Nter modification : %1")
          .arg(mod->getAccession()));
    }
}

References pappso::AaModification::getAccession(), getMass(), m_cleavageNterMod, and m_proxyMass.

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

setCterModification()

void pappso::Peptide::setCterModification

(

AaModificationP

mod

)

Definition at line 664 of file peptide.cpp.

{
  if(mod != nullptr)
    {
      m_proxyMass = -1;
      m_CterMod   = mod;
      getMass();
    }
  else
    {
      throw ExceptionNotPossible(
        QObject::tr("modification is not a peptide Cter modification : mod == nulptr"));
    }
}

References getMass(), m_CterMod, and m_proxyMass.

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

setGlobalModification()

void pappso::Peptide::setGlobalModification

(

Enums::Isotope

isotope_kind

)

apply 100% isotope replacement

Todo

Definition at line 826 of file peptide.cpp.

{
  if(isotope_kind == Enums::Isotope::C13)
    m_fullC13 = true;
  else if(isotope_kind == Enums::Isotope::N15)
    m_fullN15 = true;
  else if(isotope_kind == Enums::Isotope::H2)
    m_fullH2 = true;
}

References pappso::Enums::C13, pappso::Enums::H2, m_fullC13, m_fullH2, m_fullN15, and pappso::Enums::N15.

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

setNterModification()

void pappso::Peptide::setNterModification

(

AaModificationP

mod

)

Definition at line 649 of file peptide.cpp.

{
  if(mod != nullptr)
    {
      m_proxyMass = -1;
      m_NterMod   = mod;
      getMass();
    }
  else
    {
      throw ExceptionNotPossible(
        QObject::tr("modification is not a peptide Nter modification : mod == nulptr"));
    }
}

References getMass(), m_NterMod, and m_proxyMass.

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

size()

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

overridevirtual

Implements pappso::PeptideInterface.

Definition at line 217 of file peptide.cpp.

{
  return m_aaVec.size();
}

References m_aaVec.

Referenced by pappso::IonIsotopeRatioScore::IonIsotopeRatioScore(), addAaModification(), pappso::PsmFeatures::findComplementIonPairs(), isPalindrome(), PeptideProFormaParser, and pappso::PeptideFixedModificationBuilder::setPeptideSp().

toAbsoluteString()

const QString pappso::Peptide::toAbsoluteString

(

)

const

print all modifications

Definition at line 267 of file peptide.cpp.

{
  QString seq = "";
  std::vector<Aa>::const_iterator it(m_aaVec.begin());
 
  QStringList modification_str_list;
  modification_str_list << m_cleavageNterMod->getAccession();
  if(m_NterMod != nullptr)
    modification_str_list << m_NterMod->getAccession();
  while(it != m_aaVec.end())
    {
      seq += it->getLetter();
      if(it == m_aaVec.end() - 1)
        {
          modification_str_list << m_cleavageCterMod->getAccession();
          if(m_CterMod != nullptr)
            modification_str_list << m_CterMod->getAccession();
        }
      for(auto &pmod : it->getModificationList())
        {
          modification_str_list << pmod->getAccession();
        }
      if(modification_str_list.size() > 0)
        seq += QString("(%1)").arg(modification_str_list.join(","));
      modification_str_list.clear();
      it++;
    }
  return seq;
}

References m_aaVec, m_cleavageCterMod, m_cleavageNterMod, m_CterMod, and m_NterMod.

Referenced by PeptideProFormaParser, and removeAaModification().

toProForma()

QString pappso::Peptide::toProForma

(

)

const

get the peptide model in ProForma notation https://github.com/HUPO-PSI/ProForma/blob/master/README.md

Returns

QString as described in ProForma

Definition at line 787 of file peptide.cpp.

{
 
  QString seq = "";
  if(m_fullC13)
    {
      seq += "<13C>";
    }
  if(m_fullN15)
    {
      seq += "<15N>";
    }
  if(m_fullH2)
    {
      seq += "<D>";
    }
 
  if(m_NterMod != nullptr)
    {
      QString nter_accession = m_NterMod->getAccession();
      seq                    = QString("[%1]-").arg(nter_accession);
    }
  std::vector<Aa>::const_iterator it(m_aaVec.begin());
  while(it != m_aaVec.end())
    {
      seq += it->toProForma();
      it++;
    }
 
  if(m_CterMod != nullptr)
    {
      QString cter_accession = m_CterMod->getAccession();
      seq += QString("-[%1]").arg(cter_accession);
    }
  return seq;
}

References m_aaVec, m_CterMod, m_fullC13, m_fullH2, m_fullN15, and m_NterMod.

Referenced by PeptideProFormaParser.

toString()

const QString pappso::Peptide::toString

(

)

const

print modification except internal modifications

Definition at line 312 of file peptide.cpp.

{
  QString seq = "";
  std::vector<Aa>::const_iterator it(m_aaVec.begin());
  while(it != m_aaVec.end())
    {
      seq += it->toString();
      it++;
    }
  return seq;
}

References m_aaVec.

Referenced by PeptideProFormaParser.

Friends And Related Symbol Documentation

operator<

bool operator< ( const Peptide & l, const Peptide & r )

friend

Definition at line 46 of file peptide.cpp.

{
  return (l.m_aaVec < r.m_aaVec);
}

References m_aaVec.

Referenced by PeptideProFormaParser.

operator==

bool operator== ( const Peptide & l, const Peptide & r )

friend

Definition at line 53 of file peptide.cpp.

{
  if(l.getCleavageNterModification() != r.getCleavageNterModification())
    return false;
  if(l.getCleavageCterModification() != r.getCleavageCterModification())
    return false;
  if(l.getNterModification() && r.getNterModification() &&
     (l.getNterModification() != r.getNterModification()))
    return false;
  if(l.getCterModification() && r.getCterModification() &&
     (l.getCterModification() != r.getCterModification()))
    return false;
 
  return (l.m_aaVec == r.m_aaVec);
}

References getCleavageCterModification(), getCleavageNterModification(), getCterModification(), getNterModification(), and m_aaVec.

Referenced by PeptideProFormaParser.

PeptideProFormaParser

friend class PeptideProFormaParser

friend

Definition at line 103 of file peptide.h.

References Peptide(), addAaModification(), addAaModificationOnAllAminoAcid(), begin(), countModificationOnAa(), end(), getAa(), getAaPositionList(), getChemicalFormula(), getChemicalFormulaCharge(), getCleavageCterModification(), getCleavageNterModification(), getConstAa(), getCterModification(), getLiAbsoluteString(), getMass(), getMassIonSerie(), getModificationPositionList(), getNterModification(), getNumberOfAtom(), getNumberOfIsotope(), getNumberOfModification(), getRawMassArray(), getSequence(), isPalindrome(), makeNoConstPeptideSp(), makePeptideSp(), operator<, operator==, PeptideProFormaParser, rbegin(), removeAaModification(), removeCterAminoAcid(), removeNterAminoAcid(), rend(), replaceAaModification(), replaceAaModificationOnAminoAcid(), replaceLeucineIsoleucine(), reverse(), rotate(), setCleavageCterModification(), setCleavageNterModification(), setCterModification(), setGlobalModification(), setNterModification(), size(), toAbsoluteString(), toProForma(), and toString().

Referenced by PeptideProFormaParser.

Member Data Documentation

m_aaVec

std::vector<Aa> pappso::Peptide::m_aaVec

protected

Definition at line 266 of file peptide.h.

Referenced by Peptide(), Peptide(), Peptide(), addAaModification(), begin(), begin(), countModificationOnAa(), end(), end(), getAa(), getAaPositionList(), getAaPositionList(), getConstAa(), getLiAbsoluteString(), getMass(), getMassIonSerie(), getModificationPositionList(), getModificationPositionList(), getNumberOfAtom(), getNumberOfIsotope(), getNumberOfModification(), getRawMassArray(), getSequence(), isPalindrome(), operator<, operator==, pappso::PeptideProFormaParser::parseStringToPeptide(), rbegin(), removeAaModification(), removeCterAminoAcid(), removeNterAminoAcid(), rend(), replaceAaModification(), replaceAaModificationOnAminoAcid(), replaceLeucineIsoleucine(), reverse(), rotate(), size(), toAbsoluteString(), toProForma(), and toString().

m_cleavageCterMod

AaModificationP pappso::Peptide::m_cleavageCterMod = nullptr

protected

Definition at line 274 of file peptide.h.

Referenced by Peptide(), Peptide(), Peptide(), getCleavageCterModification(), getMass(), getNumberOfAtom(), getNumberOfIsotope(), and toAbsoluteString().

m_cleavageNterMod

AaModificationP pappso::Peptide::m_cleavageNterMod = nullptr

protected

Definition at line 272 of file peptide.h.

Referenced by Peptide(), Peptide(), Peptide(), getCleavageNterModification(), getMass(), getNumberOfAtom(), getNumberOfIsotope(), setCleavageCterModification(), setCleavageNterModification(), and toAbsoluteString().

m_CterMod

AaModificationP pappso::Peptide::m_CterMod = nullptr

protected

Definition at line 276 of file peptide.h.

Referenced by Peptide(), Peptide(), Peptide(), getCterModification(), getMass(), getNumberOfAtom(), getNumberOfIsotope(), setCterModification(), toAbsoluteString(), and toProForma().

m_fullC13

bool pappso::Peptide::m_fullC13 = false

protected

Definition at line 267 of file peptide.h.

Referenced by Peptide(), Peptide(), getChemicalFormulaCharge(), getMass(), setGlobalModification(), and toProForma().

m_fullH2

bool pappso::Peptide::m_fullH2 = false

protected

Definition at line 269 of file peptide.h.

Referenced by Peptide(), Peptide(), getChemicalFormulaCharge(), getMass(), setGlobalModification(), and toProForma().

m_fullN15

bool pappso::Peptide::m_fullN15 = false

protected

Definition at line 268 of file peptide.h.

Referenced by Peptide(), Peptide(), getChemicalFormulaCharge(), getMass(), setGlobalModification(), and toProForma().

m_NterMod

AaModificationP pappso::Peptide::m_NterMod = nullptr

protected

Definition at line 275 of file peptide.h.

Referenced by Peptide(), Peptide(), Peptide(), getMass(), getNterModification(), getNumberOfAtom(), getNumberOfIsotope(), setNterModification(), toAbsoluteString(), and toProForma().

m_proxyMass

double pappso::Peptide::m_proxyMass = -1

protected

Definition at line 270 of file peptide.h.

Referenced by Peptide(), Peptide(), addAaModification(), addAaModificationOnAllAminoAcid(), getMass(), getMass(), pappso::PeptideProFormaParser::parseStringToPeptide(), removeAaModification(), removeCterAminoAcid(), removeNterAminoAcid(), replaceAaModification(), replaceAaModificationOnAminoAcid(), setCleavageCterModification(), setCleavageNterModification(), setCterModification(), and setNterModification().

---

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

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