libpappsomspp
Library for mass spectrometry
pappso::PeptideInterface Class Referenceabstract

#include <peptideinterface.h>

Inheritance diagram for pappso::PeptideInterface:
pappso::Ion pappso::AtomNumberInterface pappso::Peptide pappso::PeptideFragment pappso::PeptideFragmentIon pappso::PeptideNaturalIsotope

Public Member Functions

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

Detailed Description

Definition at line 63 of file peptideinterface.h.

Member Function Documentation

◆ getFormula()

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

Definition at line 57 of file peptideinterface.cpp.

59  {
60  oxygen.append(
61  QString(" (17)O %1").arg(this->getNumberOfIsotope(Isotope::O17)));
62  }
63  if(this->getNumberOfIsotope(Isotope::O18) > 0)
64  {
65  oxygen.append(
66  QString(" (18)O %1").arg(this->getNumberOfIsotope(Isotope::O18)));
67  }
68  QString nitrogen(
69  QString("N %1").arg(this->getNumberOfAtom(AtomIsotopeSurvey::N) -
71  if(this->getNumberOfIsotope(Isotope::N15) > 0)
72  {
73  nitrogen.append(
74  QString(" (15)N %1").arg(this->getNumberOfIsotope(Isotope::N15)));
75  }
76 
77  QString sulfur(
78  QString("S %1").arg(this->getNumberOfAtom(AtomIsotopeSurvey::S) -
82  if(this->getNumberOfIsotope(Isotope::S33) > 0)
83  {
84  sulfur.append(
85  QString(" (33)S %1").arg(this->getNumberOfIsotope(Isotope::S33)));
86  }
87  if(this->getNumberOfIsotope(Isotope::S34) > 0)
88  {
89  sulfur.append(
90  QString(" (34)S %1").arg(this->getNumberOfIsotope(Isotope::S34)));
91  }
92  if(this->getNumberOfIsotope(Isotope::S36) > 0)
93  {
94  sulfur.append(
95  QString(" (36)S %1").arg(this->getNumberOfIsotope(Isotope::S36)));
96  }
97  return QString("%1 %2 %3 %4 %5")
98  .arg(carbon)
99  .arg(hydrogen)
100  .arg(oxygen)
101  .arg(nitrogen)
102  .arg(sulfur);
103 }
104 } // namespace pappso

◆ getName()

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

Reimplemented in pappso::PeptideFragmentIon.

Definition at line 81 of file peptideinterface.h.

◆ getSequence()

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

amino acid sequence without modification

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

◆ getSequenceLi()

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

amino acid sequence without modification where L are replaced by I

Definition at line 52 of file peptideinterface.cpp.

◆ isPalindrome()

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

tells if the peptide sequence is a palindrome

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

◆ matchPeak()

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

Definition at line 89 of file peptideinterface.h.

◆ size()

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

The documentation for this class was generated from the following files:
pappso::AtomIsotopeSurvey::S
@ S
pappso::Isotope::S36
@ S36
pappso::Isotope::N15
@ N15
pappso::Isotope::O17
@ O17
pappso::AtomNumberInterface::getNumberOfIsotope
virtual int getNumberOfIsotope(Isotope isotope) const =0
get the number of isotopes C13, H2, O17, O18, N15, S33, S34, S36 in the molecule
pappso::Isotope::S34
@ S34
pappso::AtomIsotopeSurvey::N
@ N
pappso::Isotope::O18
@ O18
pappso::AtomNumberInterface::getNumberOfAtom
virtual int getNumberOfAtom(AtomIsotopeSurvey atom) const =0
get the number of atom C, O, N, H in the molecule
pappso::Isotope::S33
@ S33