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/**
* \file test/test_unimod.cpp
* \date 06/04/2025
* \author Olivier Langella
* \brief test UNIMOD OBO terms
*/
/*******************************************************************************
* Copyright (c) 2025 Olivier Langella
*<Olivier.Langella@universite-paris-saclay.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/>.
*
******************************************************************************/
// ./tests/catch2-only-tests [unimod] -s
#include <catch2/catch_test_macros.hpp>
#include <catch2/catch_approx.hpp>
#include <pappsomspp/core/obo/filterobopsimodmap.h>
#include <pappsomspp/core/obo/obounimod.h>
#include <pappsomspp/core/obo/obopsimod.h>
#include <pappsomspp/core/exception/exceptionnotpossible.h>
#include "common.h"
#include "tests/tests-config.h"
/// home/langella/developpement/git/i2masschroq/src/input/sage/sagetsvhandler.cpp@457,
/// SageTsvHandler::parsePeptide(): "[+42.0106]-M[MOD:00719]QNDAGEFVDLYVPR"
TEST_CASE("Test OBO UNIMOD", "[unimod]")
{
// Set the debugging message formatting pattern.
qSetMessagePattern(QString("%{file}@%{line}, %{function}(): %{message}"));
SECTION("..:: Test OBO UNIMOD ::..", "[unimod]")
{
pappso::FilterOboPsiModMap obo_unimod_map;
pappso::OboUnimod unimod_parser(obo_unimod_map);
pappso::FilterOboPsiModMap obo_psimod_map;
pappso::OboPsiMod psimod_parser(obo_psimod_map);
// MOD:00394 == UNIMOD:1
pappso::OboPsiModTerm uterm = obo_unimod_map.getOboPsiModTermWithAccession("UNIMOD:1");
REQUIRE(uterm.getAccession().toStdString() == "UNIMOD:1");
REQUIRE(uterm.m_name.toStdString() == "Acetyl");
REQUIRE(uterm.m_diffMono == Catch::Approx(42.010565));
REQUIRE(uterm.m_diffFormula.toStdString() == "H(2) C(2) O");
REQUIRE(uterm.m_definition.toStdString() == "Acetylation.");
pappso::OboPsiModTerm pterm = obo_psimod_map.getOboPsiModTermWithAccession("MOD:00394");
REQUIRE(pterm.getAccession().toStdString() == "MOD:00394");
REQUIRE(pterm.m_name.toStdString() == "monoacetylated residue");
REQUIRE(pterm.m_diffMono == Catch::Approx(uterm.m_diffMono));
REQUIRE(pterm.m_diffFormula.toStdString() == "C 2 H 2 O 1");
REQUIRE(
pterm.m_definition.toStdString() ==
"A protein modification that effectively replaces one hydrogen atom with one acetyl group.");
// Unimod:188 MOD:00544
uterm = obo_unimod_map.getOboPsiModTermWithAccession("UNIMOD:188");
REQUIRE(uterm.getAccession().toStdString() == "UNIMOD:188");
REQUIRE(uterm.m_name.toStdString() == "Label:13C(6)");
REQUIRE(uterm.m_diffMono == Catch::Approx(6.020129));
REQUIRE(uterm.m_diffFormula.toStdString() == "C(-6) 13C(6)");
REQUIRE(uterm.m_definition.toStdString() == "13C(6) Silac label.");
pterm = obo_psimod_map.getOboPsiModTermWithAccession("MOD:00544");
REQUIRE(pterm.getAccession().toStdString() == "MOD:00544");
REQUIRE(pterm.m_name.toStdString() == "6x(13)C labeled residue");
REQUIRE(pterm.m_diffFormula.toStdString() == "(12)C -6 (13)C 6");
REQUIRE(pterm.m_diffMono == Catch::Approx(uterm.m_diffMono));
REQUIRE(pterm.m_definition.toStdString() ==
"A protein modification that effectively converts a residue containing common isotopes "
"to a 6x(13)C labeled residue.");
}
}
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