pappso::AaModification Class Reference

#include <aamodification.h>

Inheritance diagram for pappso::AaModification:

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 (Enums::AtomIsotopeSurvey atom) const override final
	get the number of atom C, O, N, H in the molecule
int	getNumberOfIsotope (Enums::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
Public Member Functions inherited from pappso::AtomNumberInterface
virtual const ChemicalFormula	getChemicalFormula () const

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 pappso::ChemicalFormula &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< Enums::AtomIsotopeSurvey, int >	m_atomCount
std::map< Enums::Isotope, int >	m_mapIsotope

Static Private Attributes
static MapAccessionModifications	m_mapAccessionModifications
static QMutex	m_mutex

Detailed Description

Definition at line 56 of file aamodification.h.

Member Typedef Documentation

MapAccessionModifications

using pappso::AaModification::MapAccessionModifications = std::map<QString, AaModificationP>

private

Definition at line 147 of file aamodification.h.

Constructor & Destructor Documentation

AaModification() [1/2]

pappso::AaModification::AaModification

(

AaModification &&

toCopy

)

Definition at line 79 of file aamodification.cpp.

  : m_accession(toCopy.m_accession),
    m_name(toCopy.m_name),
    m_mass(toCopy.m_mass),
    m_atomCount(std::move(toCopy.m_atomCount)),
    m_mapIsotope(toCopy.m_mapIsotope)
{
  m_origin = toCopy.m_origin;
}

References AaModification(), m_accession, m_atomCount, m_mapIsotope, m_mass, m_name, and m_origin.

Referenced by AaModification(), createInstance(), createInstanceMutation(), and getInstanceCustomizedMod().

~AaModification()

pappso::AaModification::~AaModification

(

)

Definition at line 89 of file aamodification.cpp.

{
}

AaModification() [2/2]

pappso::AaModification::AaModification ( const QString & accession, pappso_double mass )

private

Definition at line 58 of file aamodification.cpp.

  : m_accession(accession), m_mass(mass)
{
  m_atomCount = {{Enums::AtomIsotopeSurvey::C, 0},
                 {Enums::AtomIsotopeSurvey::H, 0},
                 {Enums::AtomIsotopeSurvey::N, 0},
                 {Enums::AtomIsotopeSurvey::O, 0},
                 {Enums::AtomIsotopeSurvey::S, 0},
                 {Enums::AtomIsotopeSurvey::P, 0}};
 
  m_mapIsotope = {{Enums::Isotope::C13, 0},
                  {Enums::Isotope::H2, 0},
                  {Enums::Isotope::N15, 0},
                  {Enums::Isotope::O17, 0},
                  {Enums::Isotope::O18, 0},
                  {Enums::Isotope::S33, 0},
                  {Enums::Isotope::S34, 0},
                  {Enums::Isotope::S36, 0}};
}

References pappso::Enums::C, pappso::Enums::C13, pappso::Enums::H, pappso::Enums::H2, m_accession, m_atomCount, m_mapIsotope, m_mass, pappso::Enums::N, pappso::Enums::N15, pappso::Enums::O, pappso::Enums::O17, pappso::Enums::O18, pappso::Enums::P, pappso::Enums::S, pappso::Enums::S33, pappso::Enums::S34, and pappso::Enums::S36.

Member Function Documentation

calculateMassFromChemicalComponents()

void pappso::AaModification::calculateMassFromChemicalComponents ( )

private

Definition at line 269 of file aamodification.cpp.

{
  pappso_double theoreticalm_mass                          = 0;
  std::map<Enums::AtomIsotopeSurvey, int>::const_iterator it_atom = m_atomCount.find(Enums::AtomIsotopeSurvey::C);
  if(it_atom != m_atomCount.end())
    {
      theoreticalm_mass += MASSCARBON * (it_atom->second);
    }
  it_atom = m_atomCount.find(Enums::AtomIsotopeSurvey::H);
  if(it_atom != m_atomCount.end())
    {
      theoreticalm_mass += MPROTIUM * (it_atom->second);
    }
 
  it_atom = m_atomCount.find(Enums::AtomIsotopeSurvey::O);
  if(it_atom != m_atomCount.end())
    {
      theoreticalm_mass += MASSOXYGEN * (it_atom->second);
    }
 
  it_atom = m_atomCount.find(Enums::AtomIsotopeSurvey::N);
  if(it_atom != m_atomCount.end())
    {
      theoreticalm_mass += MASSNITROGEN * (it_atom->second);
    }
  it_atom = m_atomCount.find(Enums::AtomIsotopeSurvey::S);
  if(it_atom != m_atomCount.end())
    {
      theoreticalm_mass += MASSSULFUR * (it_atom->second);
    }
 
  qDebug() << theoreticalm_mass;
 
  theoreticalm_mass += DIFFC12C13 * m_mapIsotope.at(Enums::Isotope::C13);
  theoreticalm_mass += DIFFH1H2 * m_mapIsotope.at(Enums::Isotope::H2);
  theoreticalm_mass += DIFFN14N15 * m_mapIsotope.at(Enums::Isotope::N15);
  theoreticalm_mass += DIFFO16O17 * m_mapIsotope.at(Enums::Isotope::O17);
  theoreticalm_mass += DIFFO16O18 * m_mapIsotope.at(Enums::Isotope::O18);
  theoreticalm_mass += DIFFS32S33 * m_mapIsotope.at(Enums::Isotope::S33);
  theoreticalm_mass += DIFFS32S34 * m_mapIsotope.at(Enums::Isotope::S34);
  theoreticalm_mass += DIFFS32S36 * m_mapIsotope.at(Enums::Isotope::S36);
 
 
  if(m_mass == 0.0)
    {
      m_mass = theoreticalm_mass;
    }
  else
    {
      pappso_double diff = std::fabs((pappso_double)m_mass - theoreticalm_mass);
      if(diff < 0.001)
        {
          m_mass = theoreticalm_mass;
          qDebug() << diff;
        }
      else
        {
          qDebug() << "ERROR in AaModification::calculateMassFromChemicalComponents "
                      "theo="
                   << theoreticalm_mass << " m=" << m_mass << " diff=" << diff
                   << " accession=" << m_accession;
        }
    }
}

References pappso::Enums::C, pappso::Enums::C13, pappso::DIFFC12C13(), pappso::DIFFH1H2(), pappso::DIFFN14N15(), pappso::DIFFO16O17(), pappso::DIFFO16O18(), pappso::DIFFS32S33(), pappso::DIFFS32S34(), pappso::DIFFS32S36(), pappso::Enums::H, pappso::Enums::H2, m_accession, m_atomCount, m_mapIsotope, m_mass, pappso::MASSCARBON(), pappso::MASSNITROGEN(), pappso::MASSOXYGEN(), pappso::MASSSULFUR(), pappso::MPROTIUM(), 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.

Referenced by setDiffFormula().

createInstance() [1/2]

AaModificationP pappso::AaModification::createInstance ( const OboPsiModTerm & term )

staticprivate

Definition at line 155 of file aamodification.cpp.

{
  AaModification *new_mod;
  // qDebug() << " AaModification::createInstance begin";
  new_mod = new AaModification(term.getAccession(), term.m_diffMono);
  // xref: DiffFormula: "C 0 H 0 N 0 O 1 S 0"
  pappso::ChemicalFormula formula;
  formula.setOboPsiModTerm(term);
  new_mod->setDiffFormula(formula);
  new_mod->setXrefOrigin(term.m_origin);
  new_mod->m_name = term.m_name;
 
  qDebug() << new_mod->m_mass;
  return new_mod;
}

References AaModification(), pappso::OboPsiModTerm::getAccession(), pappso::OboPsiModTerm::m_diffMono, m_mass, m_name, pappso::OboPsiModTerm::m_name, pappso::OboPsiModTerm::m_origin, setDiffFormula(), pappso::ChemicalFormula::setOboPsiModTerm(), and setXrefOrigin().

createInstance() [2/2]

AaModificationP pappso::AaModification::createInstance ( const QString & saccession )

staticprivate

Definition at line 172 of file aamodification.cpp.

{
  if(accession == "internal:Nter_hydrolytic_cleavage_H")
    {
      OboPsiModTerm term;
      term.setAccession(accession);
      term.m_diffFormula = "H 1";
      term.m_diffMono    = MPROTIUM;
      term.m_name        = "Nter hydrolytic cleavage H+";
      return (AaModification::createInstance(term));
    }
  if(accession == "internal:Cter_hydrolytic_cleavage_HO")
    {
      OboPsiModTerm term;
      term.setAccession(accession);
      term.m_diffFormula = "H 1 O 1";
      term.m_diffMono    = MPROTIUM + MASSOXYGEN;
      term.m_name        = "Cter hydrolytic cleavage HO";
      return (AaModification::createInstance(term));
    }
  if(accession.startsWith("MUTATION:"))
    {
      QRegularExpression regexp_mutation("^MUTATION:([A-Z])=>([A-Z])$");
      QRegularExpressionMatch match = regexp_mutation.match(accession);
      if(match.hasMatch())
        {
          qDebug() << match.capturedTexts()[1].at(0) << " " << match.capturedTexts()[2].at(0);
 
          Aa aa_from(match.capturedTexts()[1].toStdString().c_str()[0]);
          Aa aa_to(match.capturedTexts()[2].toStdString().c_str()[0]);
          AaModificationP instance_mutation = createInstanceMutation(aa_from, aa_to);
          return instance_mutation;
          // m_psiModLabel<<"|";
        }
    }
  if(accession.startsWith("C13N15:"))
    {
      QRegularExpression regexp_label("^C13N15:([A-Z])$");
      QRegularExpressionMatch match = regexp_label.match(accession);
      if(match.hasMatch())
        {
          char labelled_aa(match.capturedTexts()[1].toStdString().c_str()[0]);
 
          AaModificationP instance_labelled_aa_p =
            createInstanceC13N15LabelledAminoAcid(QChar(labelled_aa));
 
 
          return instance_labelled_aa_p;
          // m_psiModLabel<<"|";
        }
    }
  // initMyResource();
  FilterOboPsiModSink term_list;
  FilterOboPsiModTermAccession filterm_accession(term_list, accession);
 
  OboPsiMod psimod(filterm_accession);
 
  try
    {
      return (AaModification::createInstance(term_list.getOne()));
    }
  catch(ExceptionNotFound &e)
    {
      pappso::FilterOboPsiModMap obo_unimod_map;
      pappso::OboUnimod unimod_parser(obo_unimod_map);
      // OboUnimod unimod(filterm_accession);
 
      try
        {
          return (AaModification::createInstance(
            obo_unimod_map.getOboPsiModTermWithAccession(accession)));
        }
      catch(ExceptionNotFound &e)
        {
          try
            {
              return (
                AaModification::createInstance(obo_unimod_map.getOboPsiModTermWithName(accession)));
            }
          catch(ExceptionNotFound &e)
            {
              throw ExceptionNotFound(
                QObject::tr("modification not found : [%1]\n%2").arg(accession).arg(e.qwhat()));
            }
        }
    }
}

References createInstance(), createInstanceC13N15LabelledAminoAcid(), createInstanceMutation(), pappso::FilterOboPsiModMap::getOboPsiModTermWithAccession(), pappso::FilterOboPsiModMap::getOboPsiModTermWithName(), pappso::FilterOboPsiModSink::getOne(), pappso::OboPsiModTerm::m_diffFormula, pappso::OboPsiModTerm::m_diffMono, pappso::OboPsiModTerm::m_name, pappso::MASSOXYGEN(), pappso::MPROTIUM(), pappso::PappsoException::qwhat(), and pappso::OboPsiModTerm::setAccession().

Referenced by createInstance(), createInstanceC13N15LabelledAminoAcid(), getInstance(), and getInstance().

createInstanceC13N15LabelledAminoAcid()

AaModificationP pappso::AaModification::createInstanceC13N15LabelledAminoAcid ( const QChar & aa_from )

staticprivate

get heavy amino acid modification C13 N15

Parameters

aa_from

orginal amino acid

Definition at line 853 of file aamodification.cpp.

{
  switch(from_aa.toLatin1())
    {
      case 'R':
        return createInstance("MOD:00587");
        break;
      case 'K':
        return createInstance("MOD:00582");
        break;
      case 'F':
        return createInstance("MOD:00589");
        break;
    }
 
  // At this point we have no MOD ontology term for all the other amino-acid
  // residue, we need to craft the stuff ourselves.
 
  QString accession(QString("C13N15:%1").arg(from_aa));
 
  // Define the diff formula for each amino acid code not handled above.
 
  QString diff_formula;
 
  switch(from_aa.toLatin1())
    {
      case 'G':
        diff_formula = "(12)C -2 (13)C 2 (14)N -1 (15)N 1";
        break;
      case 'A':
        diff_formula = "(12)C -3 (13)C 3 (14)N -1 (15)N 1";
        break;
      case 'V':
        diff_formula = "(12)C -5 (13)C 5 (14)N -1 (15)N 1";
        break;
      case 'I':
        diff_formula = "(12)C -6 (13)C 6 (14)N -1 (15)N 1";
        break;
      case 'L':
        diff_formula = "(12)C -6 (13)C 6 (14)N -1 (15)N 1";
        break;
      case 'S':
        diff_formula = "(12)C -3 (13)C 3 (14)N -1 (15)N 1";
        break;
      case 'T':
        diff_formula = "(12)C -4 (13)C 4 (14)N -1 (15)N 1";
        break;
      case 'C':
        diff_formula = "(12)C -3 (13)C 3 (14)N -1 (15)N 1";
        break;
      case 'M':
        diff_formula = "(12)C -5 (13)C 5 (14)N -1 (15)N 1";
        break;
      case 'D':
        diff_formula = "(12)C -4 (13)C 4 (14)N -1 (15)N 1";
        break;
      case 'E':
        diff_formula = "(12)C -5 (13)C 5 (14)N -1 (15)N 1";
        break;
      case 'N':
        diff_formula = "(12)C -4 (13)C 4 (14)N -2 (15)N 2";
        break;
      case 'Q':
        diff_formula = "(12)C -5 (13)C 5 (14)N -2 (15)N 2";
        break;
      case 'W':
        diff_formula = "(12)C -11 (13)C 11 (14)N -2 (15)N 2";
        break;
      case 'Y':
        diff_formula = "(12)C -9 (13)C 9 (14)N -1 (15)N 1";
        break;
      case 'H':
        diff_formula = "(12)C -6 (13)C 6 (14)N -3 (15)N 3";
        break;
      case 'P':
        diff_formula = "(12)C -5 (13)C 5 (14)N -1 (15)N 1";
        break;
      default:
        throw PappsoException(
          QObject::tr("ERROR creating C13N15-labelled amino acid residue %1\n").arg(from_aa));
    }
 
  OboPsiModTerm obo_psi_term;
  obo_psi_term.setAccession(accession);
  obo_psi_term.m_diffFormula = diff_formula;
  obo_psi_term.m_name        = QString("Fully C13N15-labelled %1").arg(from_aa);
  obo_psi_term.m_diffMono    = 0;
 
  qDebug() << "obo_psi_term.m_diffFormula: " << obo_psi_term.m_diffFormula;
  return AaModification::createInstance(obo_psi_term);
}

References createInstance(), pappso::OboPsiModTerm::m_diffFormula, pappso::OboPsiModTerm::m_diffMono, pappso::OboPsiModTerm::m_name, and pappso::OboPsiModTerm::setAccession().

Referenced by createInstance().

createInstanceMutation()

AaModificationP pappso::AaModification::createInstanceMutation ( const Aa & aa_from, const Aa & aa_to )

staticprivate

Definition at line 786 of file aamodification.cpp.

{
  QString accession(QString("MUTATION:%1=>%2").arg(aa_from.getLetter()).arg(aa_to.getLetter()));
  double diffMono = aa_to.getMass() - aa_from.getMass();
  // not found
  AaModification *instance_mutation;
  // qDebug() << " AaModification::createInstance begin";
  instance_mutation = new AaModification(accession, diffMono);
  // xref: DiffFormula: "C 0 H 0 N 0 O 1 S 0"
 
  for(std::int8_t atomInt = (std::int8_t)Enums::AtomIsotopeSurvey::C;
      atomInt != (std::int8_t)Enums::AtomIsotopeSurvey::last;
      atomInt++)
    {
      Enums::AtomIsotopeSurvey atom = static_cast<Enums::AtomIsotopeSurvey>(atomInt);
      instance_mutation->m_atomCount[atom] =
        aa_to.getNumberOfAtom(atom) - aa_from.getNumberOfAtom(atom);
    }
  instance_mutation->m_name =
    QString("mutation from %1 to %2").arg(aa_from.getLetter()).arg(aa_to.getLetter());
  return instance_mutation;
}

References AaModification(), pappso::Enums::C, pappso::AaBase::getLetter(), pappso::Aa::getMass(), pappso::Aa::getNumberOfAtom(), pappso::Enums::last, m_atomCount, and m_name.

Referenced by createInstance(), and getInstanceMutation().

getAccession()

const QString & pappso::AaModification::getAccession

(

)

const

Definition at line 94 of file aamodification.cpp.

{
 
  // qDebug();
  return m_accession;
}

References m_accession.

Referenced by pappso::Aa::addAaModification(), pappso::PeptideProFormaParser::parseStringToPeptide(), pappso::Peptide::setCleavageCterModification(), pappso::Peptide::setCleavageNterModification(), pappso::Peptide::setCterModification(), pappso::Peptide::setNterModification(), toProForma(), and pappso::MzIdentMlWriter::writeCvParam().

getInstance() [1/2]

AaModificationP pappso::AaModification::getInstance ( const OboPsiModTerm & oboterm )

static

Definition at line 617 of file aamodification.cpp.

{
 
  QMutexLocker locker(&m_mutex);
 
  std::pair<MapAccessionModifications::iterator, bool> insert_res =
    m_mapAccessionModifications.insert(
      std::pair<QString, AaModificationP>(oboterm.getAccession(), nullptr));
 
  if(!insert_res.second)
    {
      // Failed to insert, was there already by same key.
    }
  else
    {
      // Could insert (albeit with nullptr), was not there already by same key.
      // Just assign to the *correct* pair member the pointer to an
      // extemporaneously allocated AaModification.
      insert_res.first->second = AaModification::createInstance(oboterm);
    }
 
  return insert_res.first->second;
}

References createInstance(), pappso::OboPsiModTerm::getAccession(), m_mapAccessionModifications, and m_mutex.

getInstance() [2/2]

AaModificationP pappso::AaModification::getInstance ( const QString & accession )

static

Definition at line 354 of file aamodification.cpp.

{
  try
    {
      QMutexLocker locker(&m_mutex);
      MapAccessionModifications::iterator it = m_mapAccessionModifications.find(accession);
      if(it == m_mapAccessionModifications.end())
        {
 
          // not found
          std::pair<MapAccessionModifications::iterator, bool> insert_res =
            m_mapAccessionModifications.insert(std::pair<QString, AaModificationP>(
              accession, AaModification::createInstance(accession)));
          it = insert_res.first;
        }
      else
        {
          // found
        }
      return it->second;
    }
  catch(ExceptionNotFound &e)
    {
      throw ExceptionNotFound(
        QObject::tr("ERROR getting instance of : %1 NOT FOUND\n%2").arg(accession).arg(e.qwhat()));
    }
  catch(PappsoException &e)
    {
      throw PappsoException(
        QObject::tr("ERROR getting instance of %1\n%2").arg(accession).arg(e.qwhat()));
    }
  catch(std::exception &e)
    {
      throw PappsoException(
        QObject::tr("ERROR getting instance of %1\n%2").arg(accession).arg(e.what()));
    }
}

References createInstance(), m_mapAccessionModifications, m_mutex, pappso::PappsoException::qwhat(), and pappso::PappsoException::what().

Referenced by pappso::Peptide::Peptide(), pappso::PeptideFragmentIonListBase::PeptideFragmentIonListBase(), pappso::cbor::psm::PsmSpecPeptidOms::PsmSpecPeptidOms(), pappso::specglob::PostTreatment::findReplaceMutations(), getInstanceInsertionAccessionByAaLetter(), getInstanceRemovalAccessionByAaLetter(), getInstanceXtandemMod(), pappso::Utils::guessAaModificationPbyMonoisotopicMassDelta(), pappso::PeptideModificatorPipeline::parseFixedModification(), pappso::PeptideModificatorPipeline::parseLabeledModification(), pappso::PeptideModificatorPipeline::parsePotentialModification(), pappso::PeptideProFormaParser::parseStringToPeptide(), pappso::PeptideStrParser::parseStringToPeptide(), and pappso::Utils::translateAaModificationFromUnimod().

getInstanceCustomizedMod()

AaModificationP pappso::AaModification::getInstanceCustomizedMod ( pappso_double modificationMass )

static

Definition at line 335 of file aamodification.cpp.

{
  QString accession = QString("%1").arg(modificationMass);
  qDebug() << accession;
  QMutexLocker locker(&m_mutex);
  if(m_mapAccessionModifications.find(accession) == m_mapAccessionModifications.end())
    {
      // not found
      m_mapAccessionModifications.insert(std::pair<QString, AaModification *>(
        accession, new AaModification(accession, modificationMass)));
    }
  else
    {
      // found
    }
  return m_mapAccessionModifications.at(accession);
}

References AaModification(), m_mapAccessionModifications, and m_mutex.

Referenced by pappso::Utils::guessAaModificationPbyMonoisotopicMassDelta(), and pappso::PeptideStrParser::parseStringToPeptide().

getInstanceInsertionAccessionByAaLetter()

AaModificationP pappso::AaModification::getInstanceInsertionAccessionByAaLetter ( const QChar & amino_acid )

static

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

Parameters

amino_acid

orginal amino acid letter

Returns

AaModificationP

Definition at line 499 of file aamodification.cpp.

{
  pappso::AaModificationP aa_insert = nullptr;
  switch(amino_acid.toLatin1())
    {
      //    Enums::AminoAcidChar::alanine
      case 'A':
        aa_insert = getInstance("MOD:00010");
        break;
 
        // Enums::AminoAcidChar::arginine,
      case 'R':
        aa_insert = getInstance("MOD:00011");
        break;
 
        // Enums::AminoAcidChar::cysteine,
      case 'C':
        aa_insert = getInstance("MOD:00014");
        break;
 
        // Enums::AminoAcidChar::aspartic_acid,
      case 'D':
        aa_insert = getInstance("MOD:00013");
        break;
 
        // Enums::AminoAcidChar::glutamic_acid,
      case 'E':
        aa_insert = getInstance("MOD:00015");
        break;
 
        // Enums::AminoAcidChar::phenylalanine,
      case 'F':
        aa_insert = getInstance("MOD:00023");
        break;
 
        // Enums::AminoAcidChar::glycine,
      case 'G':
        aa_insert = getInstance("MOD:00017");
        break;
 
        // Enums::AminoAcidChar::histidine,
      case 'H':
        aa_insert = getInstance("MOD:00018");
        break;
 
        // Enums::AminoAcidChar::isoleucine,
      case 'I':
        aa_insert = getInstance("MOD:00019");
        break;
 
        // Enums::AminoAcidChar::lysine,
      case 'K':
        aa_insert = getInstance("MOD:00021");
        break;
        // Enums::AminoAcidChar::leucine,
      case 'L':
        aa_insert = getInstance("MOD:00020");
        break;
 
        // Enums::AminoAcidChar::methionine,
      case 'M':
        aa_insert = getInstance("MOD:00022");
        break;
 
        // Enums::AminoAcidChar::asparagine,
      case 'N':
        aa_insert = getInstance("MOD:00012");
        break;
 
        // Enums::AminoAcidChar::proline,
      case 'P':
        aa_insert = getInstance("MOD:00024");
        break;
 
        // Enums::AminoAcidChar::glutamine,
      case 'Q':
        aa_insert = getInstance("MOD:00016");
        break;
        // Enums::AminoAcidChar::serine,
      case 'S':
        aa_insert = getInstance("MOD:00025");
        break;
 
        // Enums::AminoAcidChar::threonine,
      case 'T':
        aa_insert = getInstance("MOD:00026");
        break;
 
 
        // Enums::AminoAcidChar::valine,
      case 'V':
        aa_insert = getInstance("MOD:00029");
        break;
 
        // Enums::AminoAcidChar::tryptophan,
      case 'W':
        aa_insert = getInstance("MOD:00027");
        break;
 
        // Enums::AminoAcidChar::tyrosine,
      case 'Y':
        aa_insert = getInstance("MOD:00028");
        break;
        // Enums::AminoAcidChar::selenocysteine,
      case 'U':
        aa_insert = getInstance("MOD:00031");
        break;
      default:
        throw ExceptionNotFound(
          QObject::tr("ERROR getting removal accession instance of amino acid: "
                      "%1 NOT FOUND")
            .arg(amino_acid));
    }
 
  return aa_insert;
}

References getInstance().

Referenced by pappso::specglob::PeptideModel::checkForMutation(), pappso::specglob::PeptideModel::checkForMutations(), and toProForma().

getInstanceMutation()

AaModificationP pappso::AaModification::getInstanceMutation ( const QChar & mut_from, const QChar & mut_to )

static

get a fake modification coding a mutation from an amino acid to an other

Parameters

mut_from	orginal amino acid
mut_to	targeted amino acid

Definition at line 811 of file aamodification.cpp.

{
  QString accession(QString("MUTATION:%1=>%2").arg(mut_from).arg(mut_to));
  try
    {
      QMutexLocker locker(&m_mutex);
      MapAccessionModifications::iterator it = m_mapAccessionModifications.find(accession);
      if(it == m_mapAccessionModifications.end())
        {
          Aa aa_from(mut_from.toLatin1());
          Aa aa_to(mut_to.toLatin1());
          AaModificationP instance_mutation = createInstanceMutation(aa_from, aa_to);
 
          std::pair<MapAccessionModifications::iterator, bool> insert_res =
            m_mapAccessionModifications.insert(
              std::pair<QString, AaModificationP>(accession, instance_mutation));
          it = insert_res.first;
        }
      else
        {
          // found
        }
      return it->second;
    }
  catch(ExceptionNotFound &e)
    {
      throw ExceptionNotFound(
        QObject::tr("ERROR getting instance of : %1 NOT FOUND\n%2").arg(accession).arg(e.qwhat()));
    }
  catch(PappsoException &e)
    {
      throw PappsoException(
        QObject::tr("ERROR getting instance of %1\n%2").arg(accession).arg(e.qwhat()));
    }
  catch(std::exception &e)
    {
      throw PappsoException(
        QObject::tr("ERROR getting instance of %1\n%2").arg(accession).arg(e.what()));
    }
}

References createInstanceMutation(), m_mapAccessionModifications, m_mutex, pappso::PappsoException::qwhat(), and pappso::PappsoException::what().

getInstanceRemovalAccessionByAaLetter()

AaModificationP pappso::AaModification::getInstanceRemovalAccessionByAaLetter ( const QChar & amino_acid )

static

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

Parameters

amino_acid

orginal amino acid letter

Returns

AaModificationP

Definition at line 393 of file aamodification.cpp.

{
  switch(amino_acid.toLatin1())
    {
      //    Enums::AminoAcidChar::alanine
      case 'A':
        return getInstance("MOD:01631");
        break;
        // Enums::AminoAcidChar::arginine,
      case 'R':
        return getInstance("MOD:01632");
        break;
        // Enums::AminoAcidChar::cysteine,
      case 'C':
        return getInstance("MOD:01635");
        break;
        // Enums::AminoAcidChar::aspartic_acid,
      case 'D':
        return getInstance("MOD:01634");
        break;
        // Enums::AminoAcidChar::glutamic_acid,
      case 'E':
        return getInstance("MOD:01636");
        break;
 
        // Enums::AminoAcidChar::phenylalanine,
      case 'F':
        return getInstance("MOD:01644");
        break;
        // Enums::AminoAcidChar::glycine,
      case 'G':
        return getInstance("MOD:01638");
        break;
        // Enums::AminoAcidChar::histidine,
      case 'H':
        return getInstance("MOD:01639");
        break;
 
        // Enums::AminoAcidChar::isoleucine,
      case 'I':
        return getInstance("MOD:01640");
        break;
 
        // Enums::AminoAcidChar::lysine,
      case 'K':
        return getInstance("MOD:01642");
        break;
        // Enums::AminoAcidChar::leucine,
      case 'L':
        return getInstance("MOD:01641");
        break;
 
        // Enums::AminoAcidChar::methionine,
      case 'M':
        return getInstance("MOD:01643");
        break;
 
        // Enums::AminoAcidChar::asparagine,
      case 'N':
        return getInstance("MOD:01633");
        break;
 
        // Enums::AminoAcidChar::proline,
      case 'P':
        return getInstance("MOD:01645");
        break;
 
        // Enums::AminoAcidChar::glutamine,
      case 'Q':
        return getInstance("MOD:01637");
        break;
        // Enums::AminoAcidChar::serine,
      case 'S':
        return getInstance("MOD:01646");
        break;
 
        // Enums::AminoAcidChar::threonine,
      case 'T':
        return getInstance("MOD:01647");
        break;
 
 
        // Enums::AminoAcidChar::valine,
      case 'V':
        return getInstance("MOD:01650");
        break;
 
        // Enums::AminoAcidChar::tryptophan,
      case 'W':
        return getInstance("MOD:01648");
        break;
 
        // Enums::AminoAcidChar::tyrosine,
      case 'Y':
        return getInstance("MOD:01649");
        break;
 
      default:
        throw ExceptionNotFound(
          QObject::tr("ERROR getting removal accession instance of amino acid: "
                      "%1 NOT FOUND")
            .arg(amino_acid));
    }
}

References getInstance().

Referenced by pappso::specglob::PeptideModel::checkForMutation(), pappso::specglob::PeptideModel::checkForMutations(), toProForma(), and pappso::specglob::PeptideModel::toProForma().

getInstanceXtandemMod()

AaModificationP pappso::AaModification::getInstanceXtandemMod ( const QString & type, pappso_double mass, const PeptideSp & peptide_sp, unsigned int position )

static

Definition at line 643 of file aamodification.cpp.

{
  PrecisionPtr precision = PrecisionFactory::getDaltonInstance(0.001);
  if(MzRange(mass, precision).contains(getInstance("MOD:00719")->getMass()))
    {
      if(type == "M")
        {
          return getInstance("MOD:00719");
        }
      if(type == "K")
        {
          return getInstance("MOD:01047");
        }
    }
  // accession== "MOD:00057"
  if(MzRange(mass, precision).contains(getInstance("MOD:00408")->getMass()))
    {
      // id: MOD:00394
      // name: acetylated residue
      // potential N-terminus modifications
      if(position == 0)
        {
          return getInstance("MOD:00408");
        }
    }
  if(MzRange(mass, precision).contains(getInstance("MOD:01160")->getMass()))
    {
      //-17.02655
      // loss of ammonia [MOD:01160] -17.026549
      return getInstance("MOD:01160");
    }
 
  if(MzRange(mass, precision).contains(getInstance("MOD:01060")->getMass()))
    {
      //// iodoacetamide [MOD:00397] 57.021464
      if(type == "C")
        {
          return getInstance("MOD:01060");
        }
      else
        {
          return getInstance("MOD:00397");
        }
    }
  if(MzRange(mass, precision).contains(getInstance("MOD:00704")->getMass()))
    {
      // loss of water
      /*
        if (position == 0) {
            if (peptide_sp.get()->getSequence().startsWith("EG")) {
                return getInstance("MOD:00365");
            }
            if (peptide_sp.get()->getSequence().startsWith("ES")) {
                return getInstance("MOD:00953");
            }
            if (type == "E") {
                return getInstance("MOD:00420");
            }
        }
      */
      // dehydrated residue [MOD:00704] -18.010565
      return getInstance("MOD:00704");
    }
  if(MzRange(mass, precision).contains(getInstance("MOD:00696")->getMass()))
    {
      // phosphorylated residue [MOD:00696] 79.966330
      return getInstance("MOD:00696");
    }
  bool isCter = false;
  if(peptide_sp.get()->size() == (position + 1))
    {
      isCter = true;
    }
  if((position == 0) || isCter)
    {
      if(MzRange(mass, precision).contains(getInstance("MOD:00429")->getMass()))
        {
          // dimethyl
          return getInstance("MOD:00429");
        }
      if(MzRange(mass, precision).contains(getInstance("MOD:00552")->getMass()))
        {
          // 4x(2)H labeled dimethyl residue
          return getInstance("MOD:00552");
        }
      if(MzRange(mass, precision).contains(getInstance("MOD:00638")->getMass()))
        {
          // 2x(13)C,6x(2)H-dimethylated arginine
          return getInstance("MOD:00638");
        }
    }
  throw PappsoException(QObject::tr("tandem modification not found : %1 %2 %3 %4")
                          .arg(type)
                          .arg(mass)
                          .arg(peptide_sp.get()->getSequence())
                          .arg(position));
}

References pappso::PrecisionFactory::getDaltonInstance(), getInstance(), and getMass().

getMass()

pappso_double pappso::AaModification::getMass

(

)

const

Definition at line 745 of file aamodification.cpp.

{
  return m_mass;
}

References m_mass.

Referenced by pappso::PeptideRawFragmentMasses::PeptideRawFragmentMasses(), pappso::specglob::PeptideModel::checkForAaModificationP(), pappso::specglob::PeptideModel::checkForMutation(), pappso::specglob::PeptideModel::checkForMutations(), getInstanceXtandemMod(), pappso::cbor::psm::SageReader::getStaticModificationList(), pappso::cbor::psm::SageReader::getVariableModificationList(), and pappso::Utils::guessAaModificationPbyMonoisotopicMassDelta().

getName()

const QString & pappso::AaModification::getName

(

)

const

Definition at line 137 of file aamodification.cpp.

{
  return m_name;
}

References m_name.

Referenced by pappso::MzIdentMlWriter::writeCvParam().

getNumberOfAtom()

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

finaloverridevirtual

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

Implements pappso::AtomNumberInterface.

Definition at line 752 of file aamodification.cpp.

{
  // qDebug() << "AaModification::getNumberOfAtom(Enums::AtomIsotopeSurvey atom) NOT
  // IMPLEMENTED";
  return m_atomCount.at(atom);
}

References m_atomCount.

getNumberOfIsotope()

int pappso::AaModification::getNumberOfIsotope ( Enums::Isotope isotope ) const

finaloverridevirtual

get the number of isotopes C13, H2, O17, O18, N15, S33, S34, S36 in the molecule

Implements pappso::AtomNumberInterface.

Definition at line 761 of file aamodification.cpp.

{
  try
    {
      return m_mapIsotope.at(isotope);
    }
  catch(std::exception &e)
    {
      throw PappsoException(
        QObject::tr("ERROR in AaModification::getNumberOfIsotope %2").arg(e.what()));
    }
}

References m_mapIsotope.

getXrefOrigin()

const QString & pappso::AaModification::getXrefOrigin

(

)

const

get list of amino acid on which this modification takes place

Returns

origin string of the form "S T" for Serine or Threonine, "X" for any amino acid (see OBO PSI format)

Definition at line 143 of file aamodification.cpp.

{
  return m_origin;
}

References m_origin.

isInternal()

bool pappso::AaModification::isInternal

(

)

const

Definition at line 776 of file aamodification.cpp.

{
  if(m_accession.startsWith("internal:"))
    {
      return true;
    }
  return false;
}

References m_accession.

setDiffFormula()

void pappso::AaModification::setDiffFormula ( const pappso::ChemicalFormula & diff_formula )

protected

Definition at line 948 of file aamodification.cpp.

{
  m_atomCount[Enums::AtomIsotopeSurvey::C] = diff_formula.getNumberOfAtom(Enums::AtomIsotopeSurvey::C);
  m_atomCount[Enums::AtomIsotopeSurvey::H] = diff_formula.getNumberOfAtom(Enums::AtomIsotopeSurvey::H);
  m_atomCount[Enums::AtomIsotopeSurvey::N] = diff_formula.getNumberOfAtom(Enums::AtomIsotopeSurvey::N);
  m_atomCount[Enums::AtomIsotopeSurvey::O] = diff_formula.getNumberOfAtom(Enums::AtomIsotopeSurvey::O);
  m_atomCount[Enums::AtomIsotopeSurvey::S] = diff_formula.getNumberOfAtom(Enums::AtomIsotopeSurvey::S);
  m_atomCount[Enums::AtomIsotopeSurvey::P] = diff_formula.getNumberOfAtom(Enums::AtomIsotopeSurvey::P);
 
  for(Enums::Isotope isotope : {Enums::Isotope::C13,
                                 Enums::Isotope::H2,
                                 Enums::Isotope::N15,
                                 Enums::Isotope::O17,
                                 Enums::Isotope::O18,
                                 Enums::Isotope::S33,
                                 Enums::Isotope::S34,
                                 Enums::Isotope::S36})
    {
      m_mapIsotope.at(isotope) = diff_formula.getNumberOfIsotope(isotope);
    }
 
  calculateMassFromChemicalComponents();
}

References pappso::Enums::C, pappso::Enums::C13, calculateMassFromChemicalComponents(), pappso::ChemicalFormula::getNumberOfAtom(), pappso::ChemicalFormula::getNumberOfIsotope(), pappso::Enums::H, pappso::Enums::H2, m_atomCount, m_mapIsotope, pappso::Enums::N, pappso::Enums::N15, pappso::Enums::O, pappso::Enums::O17, pappso::Enums::O18, pappso::Enums::P, pappso::Enums::S, pappso::Enums::S33, pappso::Enums::S34, and pappso::Enums::S36.

Referenced by createInstance().

setXrefOrigin()

void pappso::AaModification::setXrefOrigin ( const QString & origin )

protected

set list of amino acid on which this modification takes place

• origin string of the form "S T" for Serine or Threonine, "X" for any amino acid (see OBO PSI format)

Definition at line 261 of file aamodification.cpp.

{
  // xref: Origin: "N"
  // xref: Origin: "X"
  m_origin = origin;
}

References m_origin.

Referenced by createInstance().

toProForma()

const QString pappso::AaModification::toProForma

(

)

const

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

Returns

QString as described in ProForma

Definition at line 103 of file aamodification.cpp.

{
  QString str_return;
  // qDebug();
  if(m_accession.startsWith("MOD:"))
    return m_accession;
  if(m_accession.startsWith("UNIMOD:"))
    return m_accession;
 
  if(m_accession.startsWith("internal:"))
    return str_return;
 
  if(m_accession.startsWith("MUTATION:"))
    {
      // MUTATION:%1=>%2
      QStringList aa_list = m_accession.mid(9).split("=>");
      // first, find removal accession
      return QString("%1][%2")
        .arg(getInstanceRemovalAccessionByAaLetter(aa_list[0].at(0))->getAccession())
        .arg(getInstanceInsertionAccessionByAaLetter(aa_list[1].at(0))->getAccession());
    }
 
  if(m_mass > 0)
    {
      return QString("+%1").arg(QString::number(m_mass, 'f', 4));
    }
  else
    {
      return QString("%1").arg(QString::number(m_mass, 'f', 4));
    }
  return str_return;
}

References getAccession(), getInstanceInsertionAccessionByAaLetter(), getInstanceRemovalAccessionByAaLetter(), m_accession, and m_mass.

Member Data Documentation

m_accession

const QString pappso::AaModification::m_accession

protected

Definition at line 122 of file aamodification.h.

Referenced by AaModification(), AaModification(), calculateMassFromChemicalComponents(), getAccession(), isInternal(), and toProForma().

m_atomCount

std::map<Enums::AtomIsotopeSurvey, int> pappso::AaModification::m_atomCount

private

Definition at line 153 of file aamodification.h.

Referenced by AaModification(), AaModification(), calculateMassFromChemicalComponents(), createInstanceMutation(), getNumberOfAtom(), and setDiffFormula().

m_mapAccessionModifications

AaModification::MapAccessionModifications pappso::AaModification::m_mapAccessionModifications

staticprivate

Initial value:

= [] {
  MapAccessionModifications ret;
 
  return ret;
}()

Definition at line 157 of file aamodification.h.

Referenced by getInstance(), getInstance(), getInstanceCustomizedMod(), and getInstanceMutation().

m_mapIsotope

std::map<Enums::Isotope, int> pappso::AaModification::m_mapIsotope

private

Definition at line 154 of file aamodification.h.

Referenced by AaModification(), AaModification(), calculateMassFromChemicalComponents(), getNumberOfIsotope(), and setDiffFormula().

m_mass

pappso_double pappso::AaModification::m_mass

private

Definition at line 151 of file aamodification.h.

Referenced by AaModification(), AaModification(), calculateMassFromChemicalComponents(), createInstance(), getMass(), and toProForma().

m_mutex

QMutex pappso::AaModification::m_mutex

staticprivate

Definition at line 159 of file aamodification.h.

Referenced by getInstance(), getInstance(), getInstanceCustomizedMod(), and getInstanceMutation().

m_name

QString pappso::AaModification::m_name

protected

Definition at line 123 of file aamodification.h.

Referenced by AaModification(), createInstance(), createInstanceMutation(), and getName().

m_origin

QString pappso::AaModification::m_origin

private

Definition at line 152 of file aamodification.h.

Referenced by AaModification(), getXrefOrigin(), and setXrefOrigin().

---

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

• pappsomspp/core/amino_acid/aamodification.h
• pappsomspp/core/amino_acid/aamodification.cpp