pappso::PeptideInterface Class Reference

#include <peptideinterface.h>

Inheritance diagram for pappso::PeptideInterface:

Public Member Functions
virtual const QString	getSequence () const =0
	amino acid sequence without modification
virtual bool	isPalindrome () const =0
	tells if the peptide sequence is a palindrome
virtual const QString	getSequenceLi () const
	amino acid sequence without modification where L are replaced by I
virtual unsigned int	size () const =0
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	getMass () const =0
virtual pappso_double	getMz (unsigned int charge) const final
Public Member Functions inherited from pappso::AtomNumberInterface
virtual int	getNumberOfAtom (Enums::AtomIsotopeSurvey atom) const =0
	get the number of atom C, O, N, H in the molecule
virtual int	getNumberOfIsotope (Enums::Isotope isotope) const =0
	get the number of isotopes C13, H2, O17, O18, N15, S33, S34, S36 in the molecule
virtual const ChemicalFormula	getChemicalFormula () const

Detailed Description

Definition at line 43 of file peptideinterface.h.

Member Function Documentation

getChemicalFormulaCharge()

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

virtual

Reimplemented in pappso::Peptide.

Definition at line 89 of file peptideinterface.cpp.

{
  pappso::ChemicalFormula formula(*this);
 
  formula.addIsotopeCount({Enums::Isotope::H, (std::int16_t)charge});
 
  return formula;
}

References pappso::ChemicalFormula::addIsotopeCount(), and pappso::Enums::H.

Referenced by pappso::Peptide::getChemicalFormulaCharge().

getFormula()

const QString pappso::PeptideInterface::getFormula ( unsigned int charge ) const

finalvirtual

Definition at line 37 of file peptideinterface.cpp.

{
  QString carbon(QString("C %1").arg(this->getNumberOfAtom(Enums::AtomIsotopeSurvey::C) -
                                     this->getNumberOfIsotope(Enums::Isotope::C13)));
  if(this->getNumberOfIsotope(Enums::Isotope::C13) > 0)
    {
      carbon.append(QString(" (13)C %1").arg(this->getNumberOfIsotope(Enums::Isotope::C13)));
    }
  QString hydrogen(QString("H %1").arg(this->getNumberOfAtom(Enums::AtomIsotopeSurvey::H) + charge -
                                       this->getNumberOfIsotope(Enums::Isotope::H2)));
  if(this->getNumberOfIsotope(Enums::Isotope::H2) > 0)
    {
      hydrogen.append(QString(" (2)H %1").arg(this->getNumberOfIsotope(Enums::Isotope::H2)));
    }
  QString oxygen(QString("O %1").arg(this->getNumberOfAtom(Enums::AtomIsotopeSurvey::O) -
                                     this->getNumberOfIsotope(Enums::Isotope::O17) -
                                     this->getNumberOfIsotope(Enums::Isotope::O18)));
  if(this->getNumberOfIsotope(Enums::Isotope::O17) > 0)
    {
      oxygen.append(QString(" (17)O %1").arg(this->getNumberOfIsotope(Enums::Isotope::O17)));
    }
  if(this->getNumberOfIsotope(Enums::Isotope::O18) > 0)
    {
      oxygen.append(QString(" (18)O %1").arg(this->getNumberOfIsotope(Enums::Isotope::O18)));
    }
  QString nitrogen(QString("N %1").arg(this->getNumberOfAtom(Enums::AtomIsotopeSurvey::N) -
                                       this->getNumberOfIsotope(Enums::Isotope::N15)));
  if(this->getNumberOfIsotope(Enums::Isotope::N15) > 0)
    {
      nitrogen.append(QString(" (15)N %1").arg(this->getNumberOfIsotope(Enums::Isotope::N15)));
    }
 
  QString sulfur(QString("S %1").arg(
    this->getNumberOfAtom(Enums::AtomIsotopeSurvey::S) - this->getNumberOfIsotope(Enums::Isotope::S33) -
    this->getNumberOfIsotope(Enums::Isotope::S34) - this->getNumberOfIsotope(Enums::Isotope::S36)));
  if(this->getNumberOfIsotope(Enums::Isotope::S33) > 0)
    {
      sulfur.append(QString(" (33)S %1").arg(this->getNumberOfIsotope(Enums::Isotope::S33)));
    }
  if(this->getNumberOfIsotope(Enums::Isotope::S34) > 0)
    {
      sulfur.append(QString(" (34)S %1").arg(this->getNumberOfIsotope(Enums::Isotope::S34)));
    }
  if(this->getNumberOfIsotope(Enums::Isotope::S36) > 0)
    {
      sulfur.append(QString(" (36)S %1").arg(this->getNumberOfIsotope(Enums::Isotope::S36)));
    }
  return QString("%1 %2 %3 %4 %5").arg(carbon).arg(hydrogen).arg(oxygen).arg(nitrogen).arg(sulfur);
}

References pappso::Enums::C, pappso::Enums::C13, pappso::AtomNumberInterface::getNumberOfAtom(), pappso::AtomNumberInterface::getNumberOfIsotope(), pappso::Enums::H, pappso::Enums::H2, 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.

getName()

virtual const QString pappso::PeptideInterface::getName ( ) const

inlinevirtual

Reimplemented in pappso::PeptideFragmentIon.

Definition at line 61 of file peptideinterface.h.

  {
    return QString("unknown");
  };

getSequence()

virtual const QString pappso::PeptideInterface::getSequence ( ) const

pure virtual

amino acid sequence without modification

Implemented in pappso::Peptide, pappso::PeptideFragment, pappso::PeptideFragmentIon, and pappso::PeptideNaturalIsotope.

Referenced by getSequenceLi().

getSequenceLi()

const QString pappso::PeptideInterface::getSequenceLi ( ) const

virtual

amino acid sequence without modification where L are replaced by I

Definition at line 31 of file peptideinterface.cpp.

{
  return QString(this->getSequence()).replace("L", "I");
}

References getSequence().

Referenced by isPalindrome().

isPalindrome()

virtual bool pappso::PeptideInterface::isPalindrome ( ) const

pure virtual

tells if the peptide sequence is a palindrome

Implemented in pappso::Peptide, pappso::PeptideFragment, pappso::PeptideFragmentIon, and pappso::PeptideNaturalIsotope.

References getSequenceLi().

matchPeak()

virtual bool pappso::PeptideInterface::matchPeak ( PrecisionPtr precision, pappso_double peak_mz, unsigned int charge ) const

inlinefinalvirtual

tells if the peptide m/z matches a given experimental mass

Definition at line 73 of file peptideinterface.h.

  {
    return (MzRange((getMass() + (MHPLUS * charge)) / charge, precision).contains(peak_mz));
  };

References pappso::Ion::getMass(), and pappso::MHPLUS().

size()

virtual unsigned int pappso::PeptideInterface::size ( ) const

pure virtual

Implemented in pappso::Peptide, pappso::PeptideFragment, pappso::PeptideFragmentIon, and pappso::PeptideNaturalIsotope.

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

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