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//
// File: test_peptide.cpp
// Created by: Olivier Langella
// Created on: 7/3/2015
//
/*******************************************************************************
* 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
******************************************************************************/
// make test ARGS="-V -I 6,6"
// ./tests/catch2-only-tests [Peptide] -s
#include <catch2/catch_test_macros.hpp>
#include <catch2/catch_approx.hpp>
#include <pappsomspp/core/mzrange.h>
#include <pappsomspp/core/amino_acid/aa.h>
#include <pappsomspp/core/peptide/peptide.h>
#include <pappsomspp/core/peptide/peptidestrparser.h>
#include <pappsomspp/core/peptide/peptideproformaparser.h>
#include <iostream>
#include <QDebug>
#include <QString>
#include <pappsomspp/core/exception/exceptionnotpossible.h>
using namespace pappso;
using namespace std;
TEST_CASE("Test Peptide", "[Peptide]")
{
// Set the debugging message formatting pattern.
qSetMessagePattern(QString("%{file}@%{line}, %{function}(): %{message}"));
SECTION("..:: Test Peptide ::..", "[Peptide]")
{
std::cout << std::endl << "..:: peptide init ::.." << std::endl;
Peptide peptide("LA");
std::cout << std::endl << "..:: peptide LI ::.." << std::endl;
std::cout << peptide.getSequence().toStdString() << " " << peptide.getSequenceLi().toStdString()
<< std::endl;
MzRange mz_range(peptide.getMass(), PrecisionFactory::getPpmInstance(10));
REQUIRE(mz_range.contains(Aa('L').getMass() + Aa('A').getMass() + MASSH2O));
// 202.13179
// http://db.systemsbiology.net:8080/proteomicsToolkit/FragIonServlet?sequence=LA&massType=monoRB&charge=1&bCB=1&yCB=1&nterm=0.0&cterm=0.0&addModifType=&addModifVal=
MzRange mz_range_very_precise(peptide.getMass(), PrecisionFactory::getPpmInstance(0.5));
REQUIRE(mz_range_very_precise.contains(202.13179));
Peptide peptide2("CCAADDKEACFAVEGPK");
// 1756.73395
MzRange mz_range_very_preciseb(peptide2.getMz(1), PrecisionFactory::getPpmInstance(0.5));
REQUIRE(mz_range_very_preciseb.contains(1756.73395));
/*
<psimod position="1" accession="MOD:00397"/>
<psimod position="2" accession="MOD:00397"/>
<psimod position="10" accession="MOD:00397"/>
<psimod position="1" accession="MOD:01160"/>
*/
pappso::AaModificationP aaModcarba = AaModification::getInstance("MOD:00397");
/*
pappso::AaModificationP aaModcarbab =
AaModification::getInstance("MOD:00397");
AaModificationP met_oxy = AaModification::getInstance("MOD:00719");*/
peptide2.addAaModification(aaModcarba, 0);
peptide2.addAaModification(aaModcarba, 1);
peptide2.addAaModification(aaModcarba, 9);
peptide2.addAaModification(AaModification::getInstance("MOD:01160"), 0);
std::cerr << peptide2.getFormula(1).toStdString().c_str() << std::endl;
MzRange mz_range2(peptide2.getMz(1), PrecisionFactory::getPpmInstance(10));
REQUIRE(mz_range2.contains(1910.7722));
PeptideSp peptide_from_str =
PeptideStrParser::parseString("C(MOD:00397+MOD:01160)C(MOD:00397)AADDKEAC(MOD:00397)FAVEGPK");
REQUIRE(peptide_from_str.get()->getMass() == peptide2.getMass());
PeptideSp peptide_from_str2 = PeptideStrParser::parseString(
"C(Carbamidomethyl+MOD:01160)C(MOD:00397)AADDKEAC(57.021464)FAVEGPK");
PeptideSp peptide_from_str3 =
PeptideStrParser::parseString("C(Carbamidomethyl+MOD:01160)C(397)AADDKEAC(57.021464)FAVEGPK");
REQUIRE(peptide_from_str2.get()->getMass() == peptide_from_str3.get()->getMass());
qDebug();
// SUCCESS
Peptide copy_str2(*peptide_from_str2.get());
qDebug();
copy_str2.rotate();
std::cerr << copy_str2.toAbsoluteString().toStdString() << std::endl;
REQUIRE(peptide_from_str2.get()->getMass() == copy_str2.getMass());
// testing isotope labels
//[Term]
// id: MOD:00582
// name: 6x(13)C,2x(15)N labeled L-lysine
std::cout << std::endl << "..:: Test peptide isotope labels::.." << std::endl;
PeptideSp peptide_normal = PeptideStrParser::parseString("CCAALDDKEACFAVEGPK");
PeptideSp peptide_lys_label = PeptideStrParser::parseString("CCAAL(MOD:00582)DDKEACFAVEGPK");
REQUIRE(peptide_normal.get()->getNumberOfAtom(Enums::AtomIsotopeSurvey::C) ==
peptide_lys_label.get()->getNumberOfAtom(Enums::AtomIsotopeSurvey::C));
REQUIRE(peptide_normal.get()->getNumberOfIsotope(Enums::Isotope::C13) == 0);
REQUIRE(peptide_lys_label.get()->getNumberOfIsotope(Enums::Isotope::C13) == 6);
// xref: DiffMono: "8.014199"
MzRange mz_range_lys(8.014199, PrecisionFactory::getPpmInstance(10));
REQUIRE(
mz_range_lys.contains(peptide_lys_label.get()->getMz(1) - peptide_normal.get()->getMz(1)));
REQUIRE_FALSE(peptide_normal.get()->toString().toStdString() ==
peptide_lys_label.get()->toString().toStdString());
REQUIRE_FALSE(peptide_normal.get()->toString().toStdString() <
peptide_lys_label.get()->toString().toStdString());
PeptideSp peptide_lys_label_bis =
PeptideStrParser::parseString("CCAAL(MOD:00582)DDKEACFAVEGPK");
REQUIRE(peptide_lys_label_bis.get()->toString().toStdString() ==
peptide_lys_label.get()->toString().toStdString());
std::cout << std::endl << "..:: peptide palindrome ::.." << std::endl;
Peptide peptide_pal_a("ALA");
REQUIRE(peptide_pal_a.isPalindrome());
REQUIRE_FALSE(peptide_normal.get()->isPalindrome());
std::cout << std::endl << "..:: peptide dimethyl ::.." << std::endl;
//"Q(internal:Nter_hydrolytic_cleavage_H,MOD:00429)SLPSLSS(MOD:00696)FLNR(internal:Cter_hydrolytic_cleavage_HO)"
Peptide peptide_dimethyl("QSLPSLSSFLNR");
pappso::AaModificationP aaModDimethyl = AaModification::getInstance("MOD:00429");
pappso::AaModificationP aaModDimethyl2 = AaModification::getInstance("MOD:00696");
peptide_dimethyl.addAaModification(aaModDimethyl, 0);
peptide_dimethyl.addAaModification(aaModDimethyl2, 7);
std::cout << "Before " << peptide_dimethyl.toAbsoluteString().toStdString();
std::cout << std::endl << "remove AaModif" << std::endl;
peptide_dimethyl.removeAaModification(aaModDimethyl);
REQUIRE(peptide_dimethyl.toAbsoluteString().toStdString() ==
"Q(internal:Nter_hydrolytic_cleavage_H)SLPSLSS(MOD:00696)FLNR(internal:"
"Cter_hydrolytic_cleavage_HO)");
std::cout << "Finish " << peptide_dimethyl.toAbsoluteString().toStdString();
}
SECTION("..:: Test Peptide modification replacement ::..", "[Peptide]")
{
pappso::AaModificationP aaModcarba = AaModification::getInstance("MOD:00397");
pappso::AaModificationP aaModdeaminated = AaModification::getInstance("MOD:01160");
REQUIRE(aaModdeaminated->getName().toStdString() == "deaminated residue");
PeptideSp peptide_from_str = PeptideStrParser::parseString(
"C(MOD:00397+MOD:01160)C(MOD:00397)AADDKEAC(MOD:00397)FAV(MOD:00397)EGPK");
pappso::Peptide peptide_mut(*(peptide_from_str.get()));
REQUIRE(Catch::Approx(peptide_mut.getMass()) == 1966.7859341481);
REQUIRE(peptide_mut.toProForma().toStdString() ==
"C[MOD:00397][MOD:01160]C[MOD:00397]AADDKEAC[MOD:00397]FAV[MOD:00397]EGPK");
peptide_mut.replaceAaModificationOnAminoAcid(
Enums::AminoAcidChar::alanine, aaModcarba, aaModdeaminated);
REQUIRE(Catch::Approx(peptide_mut.getMass()) == 1966.7859341481);
REQUIRE(peptide_mut.toProForma().toStdString() ==
"C[MOD:00397][MOD:01160]C[MOD:00397]AADDKEAC[MOD:00397]FAV[MOD:00397]EGPK");
peptide_mut.replaceAaModificationOnAminoAcid(
Enums::AminoAcidChar::valine, aaModcarba, aaModdeaminated);
REQUIRE(Catch::Approx(peptide_mut.getMass()) == 1892.7379213255);
REQUIRE(peptide_mut.toProForma().toStdString() ==
"C[MOD:00397][MOD:01160]C[MOD:00397]AADDKEAC[MOD:00397]FAV[MOD:01160]EGPK");
}
}
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