33 #include "../pappsoexception.h"
48 unsigned int number_of_neutral_phospho_loss)
49 : msp_fragment(sp_fragment), m_ionType(ion_type)
56 QString(
"PeptideIon %1 is not an %2 fragment")
83 : msp_fragment(other.msp_fragment), m_ionType(other.m_ionType)
91 : msp_fragment(std::move(toCopy.msp_fragment)),
92 m_ionType(toCopy.m_ionType),
114 QString plusstr =
"+";
115 plusstr = plusstr.repeated(charge);
118 return QString(
"y%1(-P%2)%3")
125 return QString(
"b%1(-P%2)%3")
131 return QString(
"%1%2%3")
142 return QString(
"%1(%2)")
209 return QColor(
"red");
212 return QColor(
"red");
215 return QColor(
"red");
218 return QColor(
"orange");
221 return QColor(
"orange");
224 return QColor(
"blue");
227 return QColor(
"#ff00ff");
230 return QColor(
"green");
233 return QColor(
"green");
236 return QColor(
"green");
239 return QColor(
"blue");
243 return QColor(
"red");
246 return QColor(
"blue");
249 return QColor(
"blue");
528 QObject::tr(
"PeptideIon name not implemented"));
535 qDebug() <<
"PeptideFragmentIon::getNumberOfAtom(AtomIsotopeSurvey "
536 "atom) NOT IMPLEMENTED";
538 return number + diff;
545 int number =
msp_fragment.get()->getNumberOfIsotope(isotope);
552 return std::make_shared<PeptideFragmentIon>(*
this);
PeptideFragmentIonSp makePeptideFragmentIonSp() const
unsigned int m_neutralPhosphoLossNumber
const QString getPeptideIonName() const
virtual const PeptideFragmentSp & getPeptideFragmentSp() const
PeptideIon getPeptideIonType() const
const PeptideFragmentSp msp_fragment
const QString getCompletePeptideIonName(unsigned int charge) const
get a complete ion name string
unsigned int getNumberOfNeutralPhosphoLoss() const
virtual const QString getSequence() const override
amino acid sequence without modification
virtual ~PeptideFragmentIon()
virtual unsigned int size() const override
PeptideFragmentIon(const PeptideFragmentSp &sp_fragment, PeptideIon ion_type, unsigned int number_of_neutral_phospho_loss)
const PeptideIon m_ionType
static const QColor getPeptideIonColor(PeptideIon ion_type)
virtual int getNumberOfAtom(AtomIsotopeSurvey atom) const override
get the number of atom C, O, N, H in the molecule
pappso_double getMass() const override
PeptideDirection getPeptideIonDirection() const
virtual bool isPalindrome() const override
tells if the peptide sequence is a palindrome
virtual const QString getName() const override
virtual int getNumberOfIsotope(Isotope isotope) const override
get the number of isotopes C13, H2, O17, O18, N15, S33, S34, S36 in the molecule
static const QString getPeptideIonDirectionName(PeptideDirection direction)
static pappso_double getDeltaMass(PeptideIon ion_type)
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
PeptideIon
PeptideIon enum defines all types of ions (Nter or Cter)
@ astar
Nter aldimine ions + NH3 loss.
@ ystar
Cter amino ions + NH3 loss.
@ yo
Cter amino ions + H2O loss.
@ bstar
Nter acylium ions + NH3 loss.
@ bo
Nter acylium ions + H2O loss.
@ ao
Nter aldimine ions + H2O loss.
PeptideDirection getPeptideIonDirection(PeptideIon ion_type)
get the direction of a peptide ion
std::shared_ptr< const PeptideFragmentIon > PeptideFragmentIonSp
double pappso_double
A type definition for doubles.
const pappso_double MASSH2O((MPROTIUM *2)+MASSOXYGEN)
const pappso_double MASSPHOSPHORYLATEDR(MPROTIUM+(MASSOXYGEN *3)+MASSPHOSPHORUS)
std::shared_ptr< const PeptideFragment > PeptideFragmentSp
peptide natural isotope model
class dedicated to raw mass computations of peptide products (fragments)