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/*******************************************************************************
* Copyright (c) 2015 Olivier Langella <Olivier.Langella@moulon.inra.fr>.
*
* This file is part of the PAPPSOms++ library.
*
* PAPPSOms++ is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* PAPPSOms++ is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with PAPPSOms++. If not, see <http://www.gnu.org/licenses/>.
*
* Contributors:
* Olivier Langella <Olivier.Langella@moulon.inra.fr> - initial API and
*implementation
******************************************************************************/
// ./tests/catch2-only-tests [peptidenaturalisotopeaverage] -s
#include <catch2/catch_test_macros.hpp>
#include <catch2/catch_approx.hpp>
#include <iostream>
#include <pappsomspp/core/peptide/peptidenaturalisotopeaverage.h>
#include <pappsomspp/core/peptide/peptidenaturalisotopelist.h>
#include <pappsomspp/core/peptide/peptidestrparser.h>
// #include "common.h"
#include "config.h"
using namespace pappso;
using namespace std;
// using namespace pwiz::msdata;
// make test ARGS="-V -I 8,8"
TEST_CASE("Test peptidenaturalisotopeaverage", "[peptidenaturalisotopeaverage]")
{
// Set the debugging message formatting pattern.
qSetMessagePattern(QString("%{file}@%{line}, %{function}(): %{message}"));
SECTION("..:: Test peptidenaturalisotopeaverage ::..",
"[peptidenaturalisotopeaverage]")
{
std::cout << std::endl
<< "..:: Test natural isotope average ::.." << std::endl;
Peptide peptide("ALLDEMAVVATEEYR");
peptide.addAaModification(AaModification::getInstance("MOD:00397"), 0);
pappso_double check_mass = 1747.84;
MzRange test_mass(check_mass, PrecisionFactory::getDaltonInstance(0.01));
REQUIRE(test_mass.contains(peptide.getMass() - MASSH2O));
unsigned int askedIsotopeRank = 1;
unsigned int isotopeLevel = 2;
unsigned int charge = 1;
PrecisionPtr precision = PrecisionFactory::getPpmInstance(5);
PeptideNaturalIsotopeAverage isotopeAverageMono(
peptide.makePeptideSp(), askedIsotopeRank, 0, 1, precision);
REQUIRE(MzRange(peptide.getMz(1), PrecisionFactory::getDaltonInstance(0.01))
.contains(isotopeAverageMono.getMz()));
PeptideNaturalIsotopeAverage isotopeAverage(peptide.makePeptideSp(),
askedIsotopeRank,
isotopeLevel,
charge,
precision);
std::cout << "monosiotope mz=" << peptide.getMz(charge)
<< "average mz=" << isotopeAverage.getMz() << std::endl;
std::cout << "intensity ratio =" << isotopeAverage.getIntensityRatio()
<< std::endl;
std::cout << "z=" << isotopeAverage.getCharge() << std::endl;
std::cout << "sum of :" << std::endl;
unsigned int rank = 1;
for(auto &&peptideNaturalIsotope : isotopeAverage.getComponents())
{
std::cout
<< "number=" << isotopeAverage.getIsotopeNumber() << " rank=" << rank
<< " mz=" << peptideNaturalIsotope.get()->getMz(charge)
<< " ratio=" << peptideNaturalIsotope.get()->getIntensityRatio(charge)
<< " formula="
<< peptideNaturalIsotope.get()->getFormula(charge).toStdString()
<< std::endl;
rank++;
}
REQUIRE(isotopeAverage.getComponents().size() == 8);
PrecisionPtr precision2 = PrecisionFactory::getDaltonInstance(0.2);
PeptideNaturalIsotopeAverage isotopeAverage2(
peptide.makePeptideSp(), 1, isotopeLevel, charge, precision2);
std::cout << "monosiotope mz=" << peptide.getMz(charge)
<< "average mz=" << isotopeAverage2.getMz() << std::endl;
std::cout << "intensity ratio =" << isotopeAverage2.getIntensityRatio()
<< std::endl;
std::cout << "z=" << isotopeAverage2.getCharge() << std::endl;
std::cout << "sum of :" << std::endl;
rank = 1;
for(auto &&peptideNaturalIsotope : isotopeAverage2.getComponents())
{
std::cout
<< "number=" << isotopeAverage2.getIsotopeNumber() << " rank=" << rank
<< " mz=" << peptideNaturalIsotope.get()->getMz(charge)
<< " ratio=" << peptideNaturalIsotope.get()->getIntensityRatio(charge)
<< " formula="
<< peptideNaturalIsotope.get()->getFormula(charge).toStdString()
<< std::endl;
rank++;
}
REQUIRE(isotopeAverage2.getComponents().size() == 11);
/*
Spectrum spectrum_low_masses(spectrum_parent.applyCutOff(150));
if (! spectrum_low_masses.equals(sremove_low_masses, precision)) {
std::cerr << "spectrum_low_masses() != tandem"<< std::endl;
return 1;
}*/
std::cout << std::endl
<< "..:: Test natural isotope average on labelled peptide ::.."
<< std::endl;
peptide.addAaModification(AaModification::getInstance("MOD:00587"), 14);
std::cout << std::endl
<< "labelled formula " << peptide.getFormula(1).toStdString()
<< std::endl;
PeptideNaturalIsotopeAverage isotopeAverage_labeled(peptide.makePeptideSp(),
askedIsotopeRank,
isotopeLevel,
charge,
precision);
std::cout << "labeled monosiotope mz=" << peptide.getMz(charge)
<< "average mz=" << isotopeAverage_labeled.getMz() << std::endl;
std::cout << "intensity ratio ="
<< isotopeAverage_labeled.getIntensityRatio() << std::endl;
std::cout << "z=" << isotopeAverage_labeled.getCharge() << std::endl;
std::cout << "sum of :" << std::endl;
rank = 1;
for(auto &&peptideNaturalIsotope : isotopeAverage_labeled.getComponents())
{
std::cout
<< "labeled number=" << isotopeAverage_labeled.getIsotopeNumber()
<< " rank=" << rank
<< " mz=" << peptideNaturalIsotope.get()->getMz(charge)
<< " ratio=" << peptideNaturalIsotope.get()->getIntensityRatio(charge)
<< " formula="
<< peptideNaturalIsotope.get()->getFormula(charge).toStdString()
<< std::endl;
rank++;
}
// peptideSp.get()->getSequence()= "AGYEVRDVHYSHYGR" max_isotope_number= 3
// spectrum.size= 307 parent_charge= 3
////ion_type_list.size= 9 max_isotope_rank= 2
PeptideNaturalIsotopeList isotope_list(peptide.makePeptideSp());
PeptideNaturalIsotopeAverage isotopeAverage_labeled2(
isotope_list, askedIsotopeRank, isotopeLevel, charge, precision);
REQUIRE(isotopeAverage_labeled.getMz() ==
Catch::Approx(isotopeAverage_labeled2.getMz()));
}
}
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