libpappsomspp
Library for mass spectrometry
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#include <aamodification.h>
Public Member Functions | |
AaModification (AaModification &&toCopy) | |
const QString & | getAccession () const |
const QString & | getName () const |
const QString | toProForma () const |
get the amino acid in ProForma notation https://github.com/HUPO-PSI/ProForma/blob/master/README.md | |
~AaModification () | |
pappso_double | getMass () const |
int | getNumberOfAtom (AtomIsotopeSurvey atom) const override final |
get the number of atom C, O, N, H in the molecule | |
int | getNumberOfIsotope (Isotope isotope) const override final |
get the number of isotopes C13, H2, O17, O18, N15, S33, S34, S36 in the molecule | |
bool | isInternal () const |
const QString & | getXrefOrigin () const |
get list of amino acid on which this modification takes place | |
Static Public Member Functions | |
static AaModificationP | getInstance (const QString &accession) |
static AaModificationP | getInstance (const OboPsiModTerm &oboterm) |
static AaModificationP | getInstanceMutation (const QChar &mut_from, const QChar &mut_to) |
get a fake modification coding a mutation from an amino acid to an other | |
static AaModificationP | getInstanceRemovalAccessionByAaLetter (const QChar &amino_acid) |
get a PSI MOD instance corresponding to the removal of the given amino acid find the modifications that corresponds to the removal of a residue id: MOD:01651 name: natural, standard, encoded residue removal | |
static AaModificationP | getInstanceInsertionAccessionByAaLetter (const QChar &amino_acid) |
get a PSI MOD instance corresponding to the insertion of the given amino acid find the modifications. | |
static AaModificationP | getInstanceXtandemMod (const QString &type, pappso_double mass, const PeptideSp &peptide_sp, unsigned int position) |
static AaModificationP | getInstanceCustomizedMod (pappso_double modificationMass) |
Protected Member Functions | |
void | setDiffFormula (const QString &diff_formula) |
void | setXrefOrigin (const QString &origin) |
set list of amino acid on which this modification takes place | |
Protected Attributes | |
const QString | m_accession |
QString | m_name |
Private Types | |
using | MapAccessionModifications = std::map< QString, AaModificationP > |
Private Member Functions | |
AaModification (const QString &accession, pappso_double mass) | |
void | calculateMassFromChemicalComponents () |
Static Private Member Functions | |
static AaModificationP | createInstance (const QString &saccession) |
static AaModificationP | createInstance (const OboPsiModTerm &term) |
static AaModificationP | createInstanceMutation (const Aa &aa_from, const Aa &aa_to) |
static AaModificationP | createInstanceC13N15LabelledAminoAcid (const QChar &aa_from) |
get heavy amino acid modification C13 N15 | |
Private Attributes | |
pappso_double | m_mass |
QString | m_origin |
std::map< AtomIsotopeSurvey, int > | m_atomCount |
std::map< Isotope, int > | m_mapIsotope |
Static Private Attributes | |
static MapAccessionModifications | m_mapAccessionModifications |
static QMutex | m_mutex |
Definition at line 56 of file aamodification.h.
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Definition at line 153 of file aamodification.h.
pappso::AaModification::AaModification | ( | AaModification && | toCopy | ) |
Definition at line 76 of file aamodification.cpp.
References m_origin.
pappso::AaModification::~AaModification | ( | ) |
Definition at line 86 of file aamodification.cpp.
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Definition at line 56 of file aamodification.cpp.
References pappso::C, pappso::C13, pappso::H, pappso::H2, m_atomCount, m_mapIsotope, pappso::N, pappso::N15, pappso::O, pappso::O17, pappso::O18, pappso::S, pappso::S33, pappso::S34, and pappso::S36.
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Definition at line 368 of file aamodification.cpp.
References pappso::C, pappso::C13, pappso::DIFFC12C13(), pappso::DIFFH1H2(), pappso::DIFFN14N15(), pappso::DIFFO16O17(), pappso::DIFFO16O18(), pappso::DIFFS32S33(), pappso::DIFFS32S34(), pappso::DIFFS32S36(), pappso::H, pappso::H2, m_accession, m_atomCount, m_mapIsotope, m_mass, pappso::MASSCARBON(), pappso::MASSNITROGEN(), pappso::MASSOXYGEN(), pappso::MASSSULFUR(), pappso::MPROTIUM(), pappso::N, pappso::N15, pappso::O, pappso::O17, pappso::O18, pappso::S, pappso::S33, pappso::S34, and pappso::S36.
Referenced by setDiffFormula().
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Definition at line 153 of file aamodification.cpp.
References pappso::OboPsiModTerm::isA(), pappso::OboPsiModTerm::m_accession, pappso::OboPsiModTerm::m_diffFormula, pappso::OboPsiModTerm::m_diffMono, pappso::OboPsiModTerm::m_formula, pappso::OboPsiModTerm::m_isA, m_mass, m_name, pappso::OboPsiModTerm::m_name, pappso::OboPsiModTerm::m_origin, setDiffFormula(), and setXrefOrigin().
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Definition at line 182 of file aamodification.cpp.
References createInstance(), createInstanceC13N15LabelledAminoAcid(), createInstanceMutation(), pappso::FilterOboPsiModSink::getOne(), pappso::OboPsiModTerm::m_accession, pappso::OboPsiModTerm::m_diffFormula, pappso::OboPsiModTerm::m_diffMono, pappso::OboPsiModTerm::m_name, pappso::MASSOXYGEN(), pappso::MPROTIUM(), and pappso::PappsoException::qwhat().
Referenced by createInstance(), createInstanceC13N15LabelledAminoAcid(), getInstance(), and getInstance().
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get heavy amino acid modification C13 N15
aa_from | orginal amino acid |
Definition at line 972 of file aamodification.cpp.
References createInstance(), pappso::OboPsiModTerm::m_accession, pappso::OboPsiModTerm::m_diffFormula, pappso::OboPsiModTerm::m_diffMono, and pappso::OboPsiModTerm::m_name.
Referenced by createInstance().
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Definition at line 896 of file aamodification.cpp.
References pappso::C, pappso::AaBase::getLetter(), pappso::Aa::getMass(), pappso::Aa::getNumberOfAtom(), pappso::last, m_atomCount, and m_name.
Referenced by createInstance(), and getInstanceMutation().
const QString & pappso::AaModification::getAccession | ( | ) | const |
Definition at line 91 of file aamodification.cpp.
References m_accession.
Referenced by pappso::Aa::addAaModification(), pappso::Peptide::setInternalCterModification(), pappso::Peptide::setInternalNterModification(), toProForma(), and pappso::specglob::PeptideModel::toProForma().
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Definition at line 725 of file aamodification.cpp.
References createInstance(), pappso::OboPsiModTerm::m_accession, m_mapAccessionModifications, and m_mutex.
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Definition at line 456 of file aamodification.cpp.
References createInstance(), m_mapAccessionModifications, m_mutex, pappso::PappsoException::qwhat(), and pappso::PappsoException::what().
Referenced by pappso::Peptide::Peptide(), pappso::PeptideFragment::PeptideFragment(), pappso::PeptideFragmentIonListBase::PeptideFragmentIonListBase(), pappso::specglob::PostTreatment::findReplaceMutations(), getInstanceInsertionAccessionByAaLetter(), getInstanceRemovalAccessionByAaLetter(), getInstanceXtandemMod(), pappso::PeptideModificatorPipeline::parseFixedModification(), pappso::PeptideModificatorPipeline::parseLabeledModification(), pappso::PeptideModificatorPipeline::parsePotentialModification(), pappso::PeptideProFormaParser::parseStringToPeptide(), and pappso::PeptideStrParser::parseStringToPeptide().
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Definition at line 436 of file aamodification.cpp.
References m_mapAccessionModifications, and m_mutex.
Referenced by pappso::PeptideProFormaParser::parseStringToPeptide(), and pappso::PeptideStrParser::parseStringToPeptide().
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get a PSI MOD instance corresponding to the insertion of the given amino acid find the modifications.
insertion of residue id: MOD:01441 name: natural, standard, encoded residue
amino_acid | orginal amino acid letter |
Definition at line 607 of file aamodification.cpp.
References getInstance().
Referenced by pappso::specglob::PeptideModel::checkForMutation(), pappso::specglob::PeptideModel::checkForMutations(), and toProForma().
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get a fake modification coding a mutation from an amino acid to an other
mut_from | orginal amino acid |
mut_to | targeted amino acid |
Definition at line 923 of file aamodification.cpp.
References createInstanceMutation(), m_mapAccessionModifications, m_mutex, pappso::PappsoException::qwhat(), and pappso::PappsoException::what().
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get a PSI MOD instance corresponding to the removal of the given amino acid find the modifications that corresponds to the removal of a residue id: MOD:01651 name: natural, standard, encoded residue removal
amino_acid | orginal amino acid letter |
Definition at line 501 of file aamodification.cpp.
References getInstance().
Referenced by pappso::specglob::PeptideModel::checkForMutation(), pappso::specglob::PeptideModel::checkForMutations(), toProForma(), and pappso::specglob::PeptideModel::toProForma().
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Definition at line 751 of file aamodification.cpp.
References pappso::PrecisionFactory::getDaltonInstance(), getInstance(), and getMass().
pappso_double pappso::AaModification::getMass | ( | ) | const |
Definition at line 854 of file aamodification.cpp.
References m_mass.
Referenced by pappso::PeptideFragment::PeptideFragment(), pappso::PeptideRawFragmentMasses::PeptideRawFragmentMasses(), pappso::specglob::PeptideModel::checkForAaModificationP(), pappso::specglob::PeptideModel::checkForMutation(), pappso::specglob::PeptideModel::checkForMutations(), pappso::specglob::PeptideModel::generateTheoreticalPeaks(), getInstanceXtandemMod(), and pappso::specglob::PeptideModel::getMass().
const QString & pappso::AaModification::getName | ( | ) | const |
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finaloverridevirtual |
get the number of atom C, O, N, H in the molecule
Implements pappso::AtomNumberInterface.
Definition at line 861 of file aamodification.cpp.
References m_atomCount.
Referenced by pappso::PeptideFragment::getNumberOfAtom().
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finaloverridevirtual |
get the number of isotopes C13, H2, O17, O18, N15, S33, S34, S36 in the molecule
Implements pappso::AtomNumberInterface.
Definition at line 870 of file aamodification.cpp.
References m_mapIsotope.
const QString & pappso::AaModification::getXrefOrigin | ( | ) | const |
get list of amino acid on which this modification takes place
Definition at line 140 of file aamodification.cpp.
References m_origin.
bool pappso::AaModification::isInternal | ( | ) | const |
Definition at line 886 of file aamodification.cpp.
References m_accession.
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Definition at line 261 of file aamodification.cpp.
References pappso::C, pappso::C13, calculateMassFromChemicalComponents(), pappso::H, pappso::H2, m_atomCount, m_mapIsotope, pappso::N, pappso::N15, pappso::O, pappso::O17, pappso::O18, pappso::S, pappso::S33, pappso::S34, and pappso::S36.
Referenced by createInstance().
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set list of amino acid on which this modification takes place
Definition at line 254 of file aamodification.cpp.
References m_origin.
Referenced by createInstance().
const QString pappso::AaModification::toProForma | ( | ) | const |
get the amino acid in ProForma notation https://github.com/HUPO-PSI/ProForma/blob/master/README.md
Definition at line 100 of file aamodification.cpp.
References getAccession(), getInstanceInsertionAccessionByAaLetter(), getInstanceRemovalAccessionByAaLetter(), m_accession, and m_mass.
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Definition at line 126 of file aamodification.h.
Referenced by calculateMassFromChemicalComponents(), getAccession(), isInternal(), and toProForma().
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Definition at line 159 of file aamodification.h.
Referenced by AaModification(), calculateMassFromChemicalComponents(), createInstanceMutation(), getNumberOfAtom(), and setDiffFormula().
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Definition at line 163 of file aamodification.h.
Referenced by getInstance(), getInstance(), getInstanceCustomizedMod(), and getInstanceMutation().
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Definition at line 160 of file aamodification.h.
Referenced by AaModification(), calculateMassFromChemicalComponents(), getNumberOfIsotope(), and setDiffFormula().
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Definition at line 157 of file aamodification.h.
Referenced by calculateMassFromChemicalComponents(), createInstance(), getMass(), and toProForma().
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Definition at line 165 of file aamodification.h.
Referenced by getInstance(), getInstance(), getInstanceCustomizedMod(), and getInstanceMutation().
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Definition at line 127 of file aamodification.h.
Referenced by createInstance(), createInstanceMutation(), and getName().
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Definition at line 158 of file aamodification.h.
Referenced by AaModification(), getXrefOrigin(), and setXrefOrigin().