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// ./tests/catch2-tests [section] -s
/////////////////////// Qt includes
#include <QDebug>
#include <QString>
#include <QDir>
/////////////////////// IsoSpec
#include <IsoSpec++/isoSpec++.h>
#include <IsoSpec++/element_tables.h>
/////////////////////// Catch2 includes
#include <catch2/catch_test_macros.hpp>
#include <catch2/matchers/catch_matchers_floating_point.hpp>
/////////////////////// Local includes
// #include "tests-config.h"
#include "TestUtils.hpp"
#include <libXpertMass/globals.hpp>
#include <libXpertMass/Polymer.hpp>
namespace MsXpS
{
namespace libXpertMassCore
{
TestUtils test_utils_1_letter_polymer("protein-1-letter", 1);
ErrorList error_list_polymer;
SCENARIO(
"Polymer instances can be constructed empty and initialized piecemeal until "
"they are valid",
"[Polymer]")
{
test_utils_1_letter_polymer.initializeXpertmassLibrary();
PolChemDefCstSPtr pol_chem_def_csp =
test_utils_1_letter_polymer.msp_polChemDef;
QDateTime now_date_time = QDateTime::currentDateTime();
GIVEN("An allocated polymer chemistry definition")
{
WHEN("A Polymer is allocated as a SPtr and totally unconfigured")
{
PolymerSPtr polymer_sp = Polymer::createSPtr();
THEN("The Polymer is not valid and does not validate successfully")
{
REQUIRE_FALSE(polymer_sp->isValid());
REQUIRE(polymer_sp->getName().toStdString() == "");
REQUIRE(polymer_sp->getCode().toStdString() == "");
REQUIRE(polymer_sp->getAuthor().toStdString() == "");
REQUIRE(polymer_sp->getFilePath().toStdString() == "");
REQUIRE(polymer_sp->getDateTime().toStdString() == "");
REQUIRE(polymer_sp->getSequenceCstRef().getSequence().toStdString() ==
"");
REQUIRE(polymer_sp->getSequenceCstRef().size() == 0);
REQUIRE_FALSE(polymer_sp->getLeftEndModifCstRef().isValid());
REQUIRE_FALSE(polymer_sp->getRightEndModifCstRef().isValid());
REQUIRE_FALSE(polymer_sp->getIonizerCstRef().isValid());
REQUIRE(polymer_sp->getCrossLinksCstRef().size() == 0);
}
AND_WHEN("Setting PolChemDef and other member data but not sequence")
{
polymer_sp->setPolChemDefCstSPtr(pol_chem_def_csp);
polymer_sp->setName("Test name");
polymer_sp->setCode("Test code");
polymer_sp->setAuthor("Rusconi");
polymer_sp->setFilePath(
QString("%1/polymer-sequences/chicken-telokin.mxp")
.arg(test_utils_1_letter_polymer.m_testsInputDataDir));
QFileInfo file_info(polymer_sp->getFilePath());
REQUIRE(file_info.exists());
polymer_sp->setDateTime(now_date_time.toString("yyyy-MM-dd:mm:ss"));
THEN(
"The Polymer still is invalid because the sequence needs to be "
"valid.")
{
REQUIRE_FALSE(polymer_sp->isValid());
}
AND_WHEN("Setting the sequence as a string")
{
polymer_sp->setSequence(
test_utils_1_letter_polymer.m_telokinAsMonomerText1Letter);
THEN(
"The Polymer valid because the sequence at last is there and "
"is valid.")
{
REQUIRE(polymer_sp->isValid());
}
}
AND_WHEN("Setting the sequence as a Sequence object")
{
polymer_sp->getSequenceRef().clear();
Sequence sequence(
pol_chem_def_csp,
test_utils_1_letter_polymer.m_telokinAsMonomerText1Letter);
polymer_sp->setSequence(sequence);
THEN(
"The Polymer valid because the sequence at last is there and "
"is valid.")
{
REQUIRE(polymer_sp->isValid());
}
AND_THEN("All the members are set correctly")
{
REQUIRE(polymer_sp->getPolChemDefCstSPtr() == pol_chem_def_csp);
REQUIRE(polymer_sp->getName().toStdString() == "Test name");
REQUIRE(polymer_sp->getCode().toStdString() == "Test code");
REQUIRE(polymer_sp->getAuthor().toStdString() == "Rusconi");
REQUIRE(polymer_sp->getFilePath().toStdString() ==
QString("%1/polymer-sequences/chicken-telokin.mxp")
.arg(test_utils_1_letter_polymer.m_testsInputDataDir)
.toStdString());
QFileInfo file_info(polymer_sp->getFilePath());
REQUIRE(polymer_sp->getDateTime().toStdString() ==
now_date_time.toString("yyyy-MM-dd:mm:ss").toStdString());
REQUIRE(polymer_sp->size() ==
(std::size_t)test_utils_1_letter_polymer
.m_telokinAsMonomerText1Letter.size());
}
}
}
}
}
}
SCENARIO("Polymer instances can be constructed and initialized in one go",
"[Polymer]")
{
test_utils_1_letter_polymer.initializeXpertmassLibrary();
PolChemDefCstSPtr pol_chem_def_csp =
test_utils_1_letter_polymer.msp_polChemDef;
QDateTime now_date_time = QDateTime::currentDateTime();
GIVEN("An allocated polymer chemistry definition")
{
WHEN("A Polymer is allocated as a SPtr with valid parameters")
{
PolymerSPtr polymer_sp = Polymer::createSPtr(
pol_chem_def_csp, "Test name", "Test code", "Rusconi");
polymer_sp->setFilePath(
QString("%1/polymer-sequences/chicken-telokin.mxp")
.arg(test_utils_1_letter_polymer.m_testsInputDataDir));
QFileInfo file_info(polymer_sp->getFilePath());
REQUIRE(file_info.exists());
polymer_sp->setDateTime(now_date_time.toString("yyyy-MM-dd:mm:ss"));
polymer_sp->setSequence(
test_utils_1_letter_polymer.m_telokinAsMonomerText1Letter);
THEN("The Polymer is valid and all the members are set correctly")
{
REQUIRE(polymer_sp->getPolChemDefCstSPtr() == pol_chem_def_csp);
REQUIRE(polymer_sp->getName().toStdString() == "Test name");
REQUIRE(polymer_sp->getCode().toStdString() == "Test code");
REQUIRE(polymer_sp->getAuthor().toStdString() == "Rusconi");
REQUIRE(polymer_sp->getFilePath().toStdString() ==
QString("%1/polymer-sequences/chicken-telokin.mxp")
.arg(test_utils_1_letter_polymer.m_testsInputDataDir)
.toStdString());
QFileInfo file_info(polymer_sp->getFilePath());
REQUIRE(polymer_sp->getDateTime().toStdString() ==
now_date_time.toString("yyyy-MM-dd:mm:ss").toStdString());
REQUIRE(polymer_sp->size() == (std::size_t)test_utils_1_letter_polymer
.m_telokinAsMonomerText1Letter.size());
}
THEN("The end modifications are invalid because not defined")
{
REQUIRE_FALSE(polymer_sp->getLeftEndModifCstRef().isValid());
REQUIRE_FALSE(
polymer_sp->getLeftEndModifCstRef().validate(error_list_polymer));
REQUIRE_FALSE(polymer_sp->getRightEndModifCstRef().isValid());
REQUIRE_FALSE(
polymer_sp->getRightEndModifCstRef().validate(error_list_polymer));
}
AND_WHEN("Setting the left end modification by name")
{
REQUIRE(polymer_sp->setLeftEndModifByName("Acetylation"));
THEN("The left end modif becomes valid")
{
REQUIRE(polymer_sp->getLeftEndModifCstRef().isValid());
REQUIRE(
polymer_sp->getLeftEndModifCstRef().validate(error_list_polymer));
REQUIRE(polymer_sp->getLeftEndModifCstRef().getName().toStdString() ==
"Acetylation");
}
AND_WHEN("Setting the right end modification by name")
{
REQUIRE(polymer_sp->setRightEndModifByName("AmidationGlu"));
THEN("The right end modif becomes valid")
{
REQUIRE(polymer_sp->getRightEndModifCstRef().isValid());
REQUIRE(polymer_sp->getRightEndModifCstRef().validate(
error_list_polymer));
REQUIRE(
polymer_sp->getRightEndModifCstRef().getName().toStdString() ==
"AmidationGlu");
}
}
}
WHEN("Setting the Ionizer (monoprotonation)")
{
Ionizer ionizer(pol_chem_def_csp->getIsotopicDataCstSPtr(),
"\"protonation\"+H",
/*charge*/ 1,
/*level*/ 1);
polymer_sp->setIonizer(ionizer);
THEN("The Ionizer must be set correctly as a member datum")
{
REQUIRE(polymer_sp->getIonizerCstRef()
.getFormulaCstRef()
.getActionFormula(/*with_title*/ false)
.toStdString() == "+H");
REQUIRE(polymer_sp->getIonizerCstRef().getLevel() == 1);
REQUIRE(polymer_sp->getIonizerCstRef().getNominalCharge() == 1);
REQUIRE(polymer_sp->getIonizerCstRef().charge() == 1);
}
}
}
}
}
SCENARIO("Polymer instances can be modified on their left and/or right ends",
"[Polymer]")
{
test_utils_1_letter_polymer.initializeXpertmassLibrary();
PolChemDefCstSPtr pol_chem_def_csp =
test_utils_1_letter_polymer.msp_polChemDef;
QDateTime now_date_time = QDateTime::currentDateTime();
GIVEN("An allocated polymer chemistry definition")
{
WHEN(
"A Polymer is allocated as a SPtr with valid parameters and a sequence "
"is set")
{
PolymerSPtr polymer_sp = Polymer::createSPtr(
pol_chem_def_csp,
"Test name",
"Test code",
"Rusconi",
test_utils_1_letter_polymer.m_telokinAsMonomerText1Letter);
THEN("The left end modifs are not yet initialized and are invalid")
{
REQUIRE_FALSE(polymer_sp->getLeftEndModifCstRef().isValid());
REQUIRE_FALSE(polymer_sp->getRightEndModifCstRef().isValid());
}
AND_WHEN("That polymer is modified on its left end using Modif name")
{
polymer_sp->setLeftEndModifByName("Acetylation");
THEN("The Modif is properly set and valid")
{
REQUIRE(polymer_sp->getLeftEndModifCstRef().isValid());
ModifCstSPtr modif_csp =
pol_chem_def_csp->getModifCstSPtrByName("Acetylation");
REQUIRE(modif_csp != nullptr);
REQUIRE(*modif_csp.get() == polymer_sp->getLeftEndModifCstRef());
}
AND_WHEN("That polymer is modified on its right end using Modif name")
{
polymer_sp->setRightEndModifByName("AmidationGlu");
THEN("The Modif is properly set and valid")
{
REQUIRE(polymer_sp->getRightEndModifCstRef().isValid());
ModifCstSPtr modif_csp =
pol_chem_def_csp->getModifCstSPtrByName("AmidationGlu");
REQUIRE(modif_csp != nullptr);
REQUIRE(*modif_csp.get() == polymer_sp->getRightEndModifCstRef());
}
}
}
}
}
}
SCENARIO("Polymer instances can be initialized from files on disk", "[Polymer]")
{
test_utils_1_letter_polymer.initializeXpertmassLibrary();
PolChemDefCstSPtr pol_chem_def_csp =
test_utils_1_letter_polymer.msp_polChemDef;
QString polymer_file_path = QString("%1/polymer-sequences/%2")
.arg(TESTS_INPUT_DIR)
.arg("chicken-telokin.mxp");
GIVEN("A polymer sequence file loaded from disk")
{
PolymerSPtr polymer_sp = Polymer::createSPtr(pol_chem_def_csp);
REQUIRE(polymer_sp->renderXmlPolymerFile(polymer_file_path));
REQUIRE(polymer_sp->isLeftEndModified());
REQUIRE(polymer_sp->getLeftEndModifCstRef().getName().toStdString() ==
"Acetylation");
REQUIRE(polymer_sp->getRightEndModifCstRef().getName().toStdString() ==
"AmidationGlu");
REQUIRE(polymer_sp->isRightEndModified());
REQUIRE(polymer_sp->size() == 157);
REQUIRE(polymer_sp->getSequenceCstRef().hasModifiedMonomer(0, 156));
std::vector<std::size_t> indices =
polymer_sp->getSequenceCstRef().modifiedMonomerIndices(0, 156);
REQUIRE(indices.size() == 1);
REQUIRE(polymer_sp->getSequenceCstRef()
.getMonomerCstRPtrAt(indices.front())
->getModifsCstRef()
.front()
->getName()
.toStdString() == "Phosphorylation");
AND_GIVEN("Calculation options with default parameters")
{
CalcOptions calc_options(/*deep_calculation*/ false,
/*mass_type*/ Enums::MassType::BOTH,
/*capping*/ Enums::CapType::BOTH,
/*monomer_entities*/ Enums::ChemicalEntity::NONE,
/*polymer_entities*/ Enums::ChemicalEntity::NONE);
calc_options.setIndexRange(IndexRange(0, 156));
WHEN("The Polymer is asked to compute its masses")
{
REQUIRE(polymer_sp->calculateMasses(calc_options, /*reset*/ true));
THEN("The masses are checked and are as expected")
{
REQUIRE_THAT(
polymer_sp->getMass(Enums::MassType::MONO),
Catch::Matchers::WithinAbs(17325.7923591224, 0.0000000001));
REQUIRE_THAT(
polymer_sp->getMass(Enums::MassType::AVG),
Catch::Matchers::WithinAbs(17336.8283764289, 0.0000000001));
}
AND_WHEN(
"An Ionizer is setup, set to the Polymer and then the latter is "
"ionized")
{
Ionizer ionizer(pol_chem_def_csp->getIsotopicDataCstSPtr(),
"\"protonation\"+H",
/*charge*/ 1,
/*level*/ 1);
polymer_sp->setIonizer(ionizer);
polymer_sp->ionize();
THEN("The masses are updated as expected and the Polymer is ionized")
{
REQUIRE_THAT(
polymer_sp->getMass(Enums::MassType::MONO),
Catch::Matchers::WithinAbs(17326.8001841546, 0.0000000001));
REQUIRE_THAT(
polymer_sp->getMass(Enums::MassType::AVG),
Catch::Matchers::WithinAbs(17337.8363178973, 0.0000000001));
REQUIRE(polymer_sp->getIonizerCstRef().isIonized());
}
AND_WHEN("The Polymer is deionized")
{
polymer_sp->deionize();
THEN(
"The masses are updated as expected and the Polymer is no more "
"ionized")
{
// qDebug() << "HERE mono" <<
// polymer_sp->getMassRef(Enums::MassType::MONO); qDebug() << "HERE avg"
// << polymer_sp->getMassRef(Enums::MassType::AVG);
REQUIRE_THAT(
polymer_sp->getMass(Enums::MassType::MONO),
Catch::Matchers::WithinAbs(17325.7923591224, 0.0000000001));
REQUIRE_THAT(
polymer_sp->getMass(Enums::MassType::AVG),
Catch::Matchers::WithinAbs(17336.8283764289, 0.0000000001));
REQUIRE_FALSE(polymer_sp->getIonizerCstRef().isIonized());
}
AND_WHEN(
"A complex Mg2+-based ionizer is set up to ionize the Polymer")
{
Ionizer ionizer(pol_chem_def_csp->getIsotopicDataCstSPtr(),
"\"magnesiumylation\"+Mg",
/*charge*/ 2,
/*level*/ 2);
polymer_sp->setIonizer(ionizer);
polymer_sp->ionize();
THEN(
"The masses are updated as expected and the Polymer is "
"ionized")
{
REQUIRE_THAT(
polymer_sp->getMass(Enums::MassType::MONO),
Catch::Matchers::WithinAbs(4343.4406106311, 0.0000000001));
REQUIRE_THAT(
polymer_sp->getMass(Enums::MassType::AVG),
Catch::Matchers::WithinAbs(4346.3596420894, 0.0000000001));
REQUIRE(polymer_sp->getIonizerCstRef().isIonized());
REQUIRE(polymer_sp->getIonizerCstRef().charge() == 4);
}
AND_WHEN(
"Molecular masses are asked for, the polymer is deionized")
{
Ionizer ionizer(pol_chem_def_csp->getIsotopicDataCstSPtr(),
"\"magnesiumylation\"+Mg",
/*charge*/ 2,
/*level*/ 2);
polymer_sp->setIonizer(ionizer);
polymer_sp->ionize();
THEN(
"The masses are updated as expected and the Polymer is "
"ionized")
{
REQUIRE_THAT(
polymer_sp->getMass(Enums::MassType::MONO),
Catch::Matchers::WithinAbs(4343.4406106311, 0.0000000001));
REQUIRE_THAT(
polymer_sp->getMass(Enums::MassType::AVG),
Catch::Matchers::WithinAbs(4346.3596420894, 0.0000000001));
REQUIRE(polymer_sp->getIonizerCstRef().isIonized());
REQUIRE(polymer_sp->getIonizerCstRef().charge() == 4);
AND_THEN("Asking for molecular masses returns proper values")
{
double mol_mass_mono;
double mol_mass_avg;
polymer_sp->molecularMasses(mol_mass_mono, mol_mass_avg);
// The masses *IN* the polymer do not change.
REQUIRE_THAT(polymer_sp->getMass(Enums::MassType::MONO),
Catch::Matchers::WithinAbs(4343.4406106311,
0.0000000001));
REQUIRE_THAT(polymer_sp->getMass(Enums::MassType::AVG),
Catch::Matchers::WithinAbs(4346.3596420894,
0.0000000001));
// The masses returned are correct.
REQUIRE_THAT(mol_mass_mono,
Catch::Matchers::WithinAbs(17325.7923591224,
0.0000000001));
REQUIRE_THAT(mol_mass_avg,
Catch::Matchers::WithinAbs(17336.8283764289,
0.0000000001));
}
}
}
}
}
}
}
}
}
}
SCENARIO("Construction of a Polymer with 7 CrossLink instances right from file",
"[Polymer]")
{
test_utils_1_letter_polymer.initializeXpertmassLibrary();
PolChemDefCstSPtr pol_chem_def_csp =
test_utils_1_letter_polymer.msp_polChemDef;
QString polymer_file_path = QString("%1/polymer-sequences/%2")
.arg(TESTS_INPUT_DIR)
.arg("kunitz-inhibitor-human-cross-links.mxp");
GIVEN("A Polymer instance created by loading an XML file")
{
PolymerSPtr polymer_sp = Polymer::createSPtr(pol_chem_def_csp);
REQUIRE(polymer_sp->renderXmlPolymerFile(polymer_file_path));
REQUIRE(polymer_sp->size() == 352);
WHEN("Configuring calculation options NOT to account for cross-links")
{
CalcOptions calc_options(/*deep_calculation*/ false,
/*mass_type*/ Enums::MassType::BOTH,
/*capping*/ Enums::CapType::BOTH,
/*monomer_entities*/ Enums::ChemicalEntity::NONE,
/*polymer_entities*/ Enums::ChemicalEntity::NONE);
calc_options.setIndexRange(IndexRange(0, polymer_sp->size() - 1));
AND_WHEN("The Polymer is asked to compute its masses")
{
REQUIRE(polymer_sp->calculateMasses(calc_options, /*reset*/ true));
THEN("The masses are checked and are as expected")
{
REQUIRE_THAT(
polymer_sp->getMass(Enums::MassType::MONO),
Catch::Matchers::WithinAbs(38973.9813242497, 0.0000000001));
REQUIRE_THAT(
polymer_sp->getMass(Enums::MassType::AVG),
Catch::Matchers::WithinAbs(38999.3128988044, 0.0000000001));
}
AND_WHEN("Configuring calculation options to account for cross-links")
{
CalcOptions calc_options(
/*deep_calculation*/ false,
/*mass_type*/ Enums::MassType::BOTH,
/*capping*/ Enums::CapType::BOTH,
/*monomer_entities*/ Enums::ChemicalEntity::CROSS_LINKER,
/*polymer_entities*/ Enums::ChemicalEntity::NONE);
calc_options.setIndexRange(IndexRange(0, polymer_sp->size() - 1));
AND_WHEN("The Polymer is asked to compute its masses")
{
REQUIRE(polymer_sp->calculateMasses(calc_options, /*reset*/ true));
THEN("The masses are checked and are as expected")
{
REQUIRE_THAT(
polymer_sp->getMass(Enums::MassType::MONO),
Catch::Matchers::WithinAbs(38959.8717737979, 0.0000000001));
REQUIRE_THAT(
polymer_sp->getMass(Enums::MassType::AVG),
Catch::Matchers::WithinAbs(38985.2017182470, 0.0000000001));
}
}
}
}
}
}
}
} // namespace libXpertMassCore
} // namespace MsXpS
|
