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|
// ./tests/catch2-tests [section] -s
/////////////////////// Stdlib includes
/////////////////////// 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 "TestUtils.hpp"
#include <libXpertMass/PolChemDefSpec.hpp>
#include <libXpertMass/PolChemDef.hpp>
#include <libXpertMass/globals.hpp>
#include <libXpertMass/IsotopicData.hpp>
#include <libXpertMass/Monomer.hpp>
#include <libXpertMass/Modif.hpp>
#include <libXpertMass/CrossLinker.hpp>
#include <libXpertMass/CleavageAgent.hpp>
#include <libXpertMass/FragmentationPathway.hpp>
namespace MsXpS
{
namespace libXpertMassCore
{
ErrorList error_list_pol_chem_def;
// In the tests below, we do not use TestUtils because we want
// more granularity that what is -by design- offered by TestUtils.
SCENARIO(
"PolChemDef instantiated using the specification in a PolChemDefSpec "
"instance",
"[PolChemdef]")
{
PolChemDefSpec pol_chem_def_spec;
PolChemDef pol_chem_def;
// We use polymer chemistry definitions copied to the
// tests/data/polymer-chemistry-definitions directory.
QString test_pol_chem_defs_dir =
QString("%1/polymer-chemistry-definitions").arg(TESTS_INPUT_DIR);
QString pol_chem_def_name = "protein-1-letter";
QString pol_chem_def_file_base_name =
QString("%1.xml").arg(pol_chem_def_name);
// Relative is to one of the polChemDefs directory (in system or user
// directory)
QString pol_chem_def_relative_dir_path = "protein-1-letter";
QString pol_chem_def_relative_file_path =
QString("%1/%2")
.arg(pol_chem_def_relative_dir_path)
.arg(pol_chem_def_file_base_name);
QString pol_chem_def_absolute_dir_path =
QString("%1/%2")
.arg(test_pol_chem_defs_dir)
.arg(pol_chem_def_relative_dir_path);
QString pol_chem_def_absolute_file_path =
QString("%1/%2")
.arg(pol_chem_def_absolute_dir_path)
.arg(pol_chem_def_file_base_name);
GIVEN("Constructing an empty PolChemDefSpec")
{
THEN("The member data are empty")
{
REQUIRE(pol_chem_def_spec.getName() == "");
REQUIRE(pol_chem_def_spec.getFilePath() == "");
}
}
AND_GIVEN("Set name and file path")
{
pol_chem_def_spec.setName(pol_chem_def_file_base_name);
pol_chem_def_spec.setFilePath(pol_chem_def_relative_file_path);
THEN("The name and file path are set to the member data")
{
REQUIRE(pol_chem_def_spec.getName().toStdString() ==
pol_chem_def_file_base_name.toStdString());
REQUIRE(pol_chem_def_spec.getFilePath().toStdString() ==
pol_chem_def_relative_file_path.toStdString());
}
AND_GIVEN("That PolChemDefSpec, allocate a PolChemDef")
{
PolChemDef pol_chem_def(pol_chem_def_spec);
THEN("The PolChemDef name is set to the PolChemDefSpec name")
{
REQUIRE(pol_chem_def.getName().toStdString() ==
pol_chem_def_spec.getName().toStdString());
}
AND_THEN("The file path is set also")
{
REQUIRE(pol_chem_def.getXmlDataFilePath().toStdString() ==
pol_chem_def_spec.getFilePath().toStdString());
}
AND_THEN("Code length value is 1")
{
REQUIRE(pol_chem_def.getCodeLength() == -1);
}
}
}
}
SCENARIO(
"PolChemDef version 1 instantiated empty and then got to load the file",
"[PolChemDef]")
{
int version = 1;
PolChemDef pol_chem_def;
PolChemDefSPtr pol_chem_def_sp = nullptr;
// We use polymer chemistry definitions copied to the
// tests/data/polymer-chemistry-definitions directory.
QString test_pol_chem_defs_dir =
QString("%1/polymer-chemistry-definitions").arg(TESTS_INPUT_DIR);
QString test_pol_chem_defs_versioned_dir =
QString("%1/version-%2").arg(test_pol_chem_defs_dir).arg(version);
QString pol_chem_def_name = "protein-1-letter";
QString pol_chem_def_file_base_name =
QString("%1.xml").arg(pol_chem_def_name);
// Relative is to one of the polChemDefs directory (in system or user
// directory)
QString pol_chem_def_relative_dir_path = "protein-1-letter";
QString pol_chem_def_relative_file_path =
QString("%1/%2")
.arg(pol_chem_def_relative_dir_path)
.arg(pol_chem_def_file_base_name);
QString pol_chem_def_isotopic_data_relative_file_path =
QString("%1/%2/%3")
.arg(pol_chem_def_relative_dir_path)
.arg(pol_chem_def_file_base_name)
.arg("isotopic-data.dat");
QString pol_chem_def_absolute_dir_path =
QString("%1/%2")
.arg(test_pol_chem_defs_versioned_dir)
.arg(pol_chem_def_relative_dir_path);
// qDebug() << "The dir: " << pol_chem_def_absolute_dir_path.toStdString()
// << std::endl;
QString pol_chem_def_absolute_file_path =
QString("%1/%2")
.arg(pol_chem_def_absolute_dir_path)
.arg(pol_chem_def_file_base_name);
QString pol_chem_def_isotopic_data_absolute_file_path =
QString("%1/%2")
.arg(pol_chem_def_absolute_dir_path)
.arg("isotopic-data.dat");
GIVEN("Constructing an empty PolChemDef")
{
THEN("The member data are empty")
{
REQUIRE(pol_chem_def.getName() == "");
REQUIRE(pol_chem_def.getXmlDataFilePath() == "");
}
}
WHEN("Setting name and XML file path")
{
pol_chem_def.setName(pol_chem_def_file_base_name);
pol_chem_def.setXmlDataFilePath(pol_chem_def_absolute_file_path);
THEN("The name and file path are set to the member data")
{
REQUIRE(pol_chem_def.getName().toStdString() ==
pol_chem_def_file_base_name.toStdString());
REQUIRE(pol_chem_def.getXmlDataFilePath().toStdString() ==
pol_chem_def_absolute_file_path.toStdString());
REQUIRE(pol_chem_def.getXmlDataDirPath().toStdString() ==
pol_chem_def_absolute_dir_path.toStdString());
}
AND_THEN("The path to the isotopic data can be deduced")
{
QString isotopic_data_file_path =
pol_chem_def.deduceIsotopicDataFilePath();
REQUIRE(isotopic_data_file_path.toStdString() ==
pol_chem_def_isotopic_data_absolute_file_path.toStdString());
}
AND_WHEN("Loading isotopic data from disk file using static function")
{
// REQUIRE(pol_chem_def.getName().toStdString() ==
// pol_chem_def_file_base_name.toStdString());
// REQUIRE(pol_chem_def.getXmlDataFilePath().toStdString() ==
// pol_chem_def_absolute_file_path.toStdString());
// REQUIRE(pol_chem_def.getXmlDataDirPath().toStdString() ==
// pol_chem_def_absolute_dir_path.toStdString());
pol_chem_def_sp = std::make_shared<PolChemDef>(pol_chem_def);
REQUIRE(pol_chem_def_sp != nullptr);
REQUIRE(pol_chem_def_sp.use_count() == 1);
std::size_t isotope_count = PolChemDef::loadIsotopicData(pol_chem_def_sp);
THEN("Count the isotopes that have been loaded")
{
REQUIRE(isotope_count > 0);
// qDebug() << "Loaded " << isotope_count << " isotopes" << std::endl;
}
WHEN("Loading the polymer chemistry definition using static function")
{
REQUIRE(pol_chem_def_sp != nullptr);
bool result = PolChemDef::renderXmlPolChemDefFile(pol_chem_def_sp);
THEN("That should not fail")
{
REQUIRE(result == true);
}
}
}
}
}
SCENARIO("Loading a PolChemDef version 1", "[PolChemDef]")
{
int version = 1;
PolChemDef pol_chem_def;
PolChemDefSPtr pol_chem_def_sp = nullptr;
// We use polymer chemistry definitions copied to the
// tests/data/polymer-chemistry-definitions directory.
QString test_pol_chem_defs_dir =
QString("%1/polymer-chemistry-definitions").arg(TESTS_INPUT_DIR);
QString test_pol_chem_defs_versioned_dir =
QString("%1/version-%2").arg(test_pol_chem_defs_dir).arg(version);
QString pol_chem_def_name = "protein-1-letter";
QString pol_chem_def_file_base_name =
QString("%1.xml").arg(pol_chem_def_name);
// Relative is to one of the polChemDefs directory (in system or user
// directory)
QString pol_chem_def_relative_dir_path = "protein-1-letter";
QString pol_chem_def_relative_file_path =
QString("%1/%2")
.arg(pol_chem_def_relative_dir_path)
.arg(pol_chem_def_file_base_name);
QString pol_chem_def_isotopic_data_relative_file_path =
QString("%1/%2/%3")
.arg(pol_chem_def_relative_dir_path)
.arg(pol_chem_def_file_base_name)
.arg("isotopic-data.dat");
QString pol_chem_def_absolute_dir_path =
QString("%1/%2")
.arg(test_pol_chem_defs_versioned_dir)
.arg(pol_chem_def_relative_dir_path);
// qDebug() << "The dir: " << pol_chem_def_absolute_dir_path.toStdString()
// << std::endl;
QString pol_chem_def_absolute_file_path =
QString("%1/%2")
.arg(pol_chem_def_absolute_dir_path)
.arg(pol_chem_def_file_base_name);
QString pol_chem_def_isotopic_data_absolute_file_path =
QString("%1/%2")
.arg(pol_chem_def_absolute_dir_path)
.arg("isotopic-data.dat");
pol_chem_def_sp = std::make_shared<PolChemDef>(pol_chem_def);
pol_chem_def_sp->setName(pol_chem_def_file_base_name);
pol_chem_def_sp->setXmlDataFilePath(pol_chem_def_absolute_file_path);
GIVEN("Loading isotopic data and polymer chemistry definition")
{
std::size_t isotope_count = PolChemDef::loadIsotopicData(pol_chem_def_sp);
bool result = PolChemDef::renderXmlPolChemDefFile(pol_chem_def_sp);
THEN(
"Count the isotopes that have been loaded and check PolChemDef load was "
"successful")
{
REQUIRE(isotope_count > 0);
// qDebug() << "Loaded " << isotope_count << " isotopes" << std::endl;
REQUIRE(result == true);
}
AND_THEN("The singular chemical entities are checked (end cap chemistry")
{
REQUIRE(pol_chem_def_sp->getName().toStdString() ==
pol_chem_def_name.toStdString());
REQUIRE(pol_chem_def_sp->getLeftCap()
.getActionFormula(/*with_title*/ true)
.toStdString() == "\"N-term amine\"+H");
REQUIRE(pol_chem_def_sp->getRightCap()
.getActionFormula(/*with_title*/ true)
.toStdString() == "\"C-term carboxylic acid\"+OH");
}
AND_THEN("And the ionization rule is checked")
{
Ionizer ionizer = pol_chem_def_sp->getIonizerCstRef();
REQUIRE(ionizer.getFormulaCstRef().getActionFormula().toStdString() ==
"+H");
REQUIRE(ionizer.getNominalCharge() == 1);
REQUIRE(ionizer.getLevel() == 1);
}
AND_THEN("And the code length is checked")
{
REQUIRE(pol_chem_def_sp->getCodeLength() == 1);
}
AND_THEN("The Monomer_s are checked")
{
MonomerSPtr monomer_csp = nullptr;
// Because of diaminopimelic acid, not 20, but 21.
REQUIRE(pol_chem_def_sp->getMonomersCstRef().size() == 21);
monomer_csp = pol_chem_def_sp->getMonomerCstSPtrByCode("G");
REQUIRE(monomer_csp->getName().toStdString() == "Glycine");
REQUIRE(monomer_csp->getCode().toStdString() == "G");
REQUIRE(monomer_csp->getFormula().toStdString() == "C2H3N1O1");
REQUIRE(monomer_csp->validate(error_list_pol_chem_def));
double mono;
double avg;
REQUIRE(monomer_csp->calculateMasses(
pol_chem_def_sp->getIsotopicDataCstSPtr(), mono, avg));
monomer_csp = pol_chem_def_sp->getMonomerCstSPtrByCode("O");
REQUIRE(monomer_csp->getName().toStdString() == "DiaminoPimelic");
REQUIRE(monomer_csp->getCode().toStdString() == "O");
REQUIRE(monomer_csp->getFormula().toStdString() == "C7H12N2O3");
REQUIRE(monomer_csp->validate(error_list_pol_chem_def) == true);
REQUIRE(monomer_csp->calculateMasses(
pol_chem_def_sp->getIsotopicDataCstSPtr(), mono, avg));
monomer_csp = pol_chem_def_sp->getMonomerCstSPtrByCode("D");
REQUIRE(monomer_csp->getName().toStdString() == "Aspartate");
REQUIRE(monomer_csp->getCode().toStdString() == "D");
REQUIRE(monomer_csp->getFormula().toStdString() == "C4H5N1O3");
REQUIRE(monomer_csp->validate(error_list_pol_chem_def) == true);
REQUIRE(monomer_csp->calculateMasses(
pol_chem_def_sp->getIsotopicDataCstSPtr(), mono, avg));
monomer_csp = pol_chem_def_sp->getMonomerCstSPtrByCode("P");
REQUIRE(monomer_csp->getName().toStdString() == "Proline");
REQUIRE(monomer_csp->getCode().toStdString() == "P");
REQUIRE(monomer_csp->getFormula().toStdString() == "C5H7N1O1");
REQUIRE(monomer_csp->validate(error_list_pol_chem_def) == true);
REQUIRE(monomer_csp->calculateMasses(
pol_chem_def_sp->getIsotopicDataCstSPtr(), mono, avg));
}
AND_THEN("The Modif_s are checked")
{
ModifCstSPtr modif_cspp = nullptr;
REQUIRE(pol_chem_def_sp->getModifsCstRef().size() == 26);
modif_cspp = pol_chem_def_sp-> getModifCstSPtrByName("Acetylation");
REQUIRE(modif_cspp->getName().toStdString() == "Acetylation");
REQUIRE(modif_cspp->getFormula().toStdString() == "C2H2O1");
REQUIRE(modif_cspp->getTargets().toStdString() == ";K;");
REQUIRE(modif_cspp->getMaxCount() == 1);
REQUIRE(modif_cspp->validate(error_list_pol_chem_def) == true);
double mono;
double avg;
REQUIRE(modif_cspp->calculateMasses(
pol_chem_def_sp->getIsotopicDataCstSPtr(), mono, avg) == true);
modif_cspp = pol_chem_def_sp-> getModifCstSPtrByName("CarboxyMethylation");
REQUIRE(modif_cspp->getName().toStdString() == "CarboxyMethylation");
REQUIRE(modif_cspp->getFormula().toStdString() == "C2H2O2");
REQUIRE(modif_cspp->getTargets().toStdString() == ";C;");
REQUIRE(modif_cspp->getMaxCount() == 1);
REQUIRE(modif_cspp->validate(error_list_pol_chem_def) == true);
REQUIRE(modif_cspp->calculateMasses(
pol_chem_def_sp->getIsotopicDataCstSPtr(), mono, avg) == true);
modif_cspp = pol_chem_def_sp-> getModifCstSPtrByName("Chromo-H3");
REQUIRE(modif_cspp->getName().toStdString() == "Chromo-H3");
REQUIRE(modif_cspp->getFormula().toStdString() == "-H3");
REQUIRE(modif_cspp->getTargets().toStdString() == ";Y;F;W;");
REQUIRE(modif_cspp->getMaxCount() == 1);
REQUIRE(modif_cspp->validate(error_list_pol_chem_def) == true);
REQUIRE(modif_cspp->calculateMasses(
pol_chem_def_sp->getIsotopicDataCstSPtr(), mono, avg) == true);
modif_cspp = pol_chem_def_sp-> getModifCstSPtrByName("Formylation");
REQUIRE(modif_cspp->getName().toStdString() == "Formylation");
REQUIRE(modif_cspp->getFormula().toStdString() == "C1O1");
REQUIRE(modif_cspp->getTargets().toStdString() == "*");
REQUIRE(modif_cspp->getMaxCount() == 1);
REQUIRE(modif_cspp->validate(error_list_pol_chem_def) == true);
REQUIRE(modif_cspp->calculateMasses(
pol_chem_def_sp->getIsotopicDataCstSPtr(), mono, avg) == true);
modif_cspp = pol_chem_def_sp-> getModifCstSPtrByName("Glycylation");
REQUIRE(modif_cspp->getName().toStdString() == "Glycylation");
REQUIRE(modif_cspp->getFormula().toStdString() == "C2H3N1O1");
REQUIRE(modif_cspp->getTargets().toStdString() == ";E;");
REQUIRE(modif_cspp->getMaxCount() == 34);
REQUIRE(modif_cspp->validate(error_list_pol_chem_def) == true);
REQUIRE(modif_cspp->calculateMasses(
pol_chem_def_sp->getIsotopicDataCstSPtr(), mono, avg) == true);
modif_cspp = pol_chem_def_sp-> getModifCstSPtrByName("Phosphorylation");
REQUIRE(modif_cspp->getName().toStdString() == "Phosphorylation");
REQUIRE(modif_cspp->getFormula().toStdString() == "H1O3P1");
REQUIRE(modif_cspp->getTargets().toStdString() == ";S;T;Y;");
REQUIRE(modif_cspp->getMaxCount() == 1);
REQUIRE(modif_cspp->validate(error_list_pol_chem_def) == true);
REQUIRE(modif_cspp->calculateMasses(
pol_chem_def_sp->getIsotopicDataCstSPtr(), mono, avg) == true);
}
AND_THEN("The CrossLinker_s are checked")
{
CrossLinkerCstSPtr crossLinker_csp = nullptr;
ModifCstSPtr modif_csp = nullptr;
REQUIRE(pol_chem_def_sp->getCrossLinkersCstRef().size() == 2);
crossLinker_csp =
pol_chem_def_sp-> getCrossLinkerCstSPtrByName("CFP-chromophore");
REQUIRE(crossLinker_csp->getName().toStdString() == "CFP-chromophore");
REQUIRE(crossLinker_csp->getFormula().toStdString() == "");
REQUIRE(crossLinker_csp->getModifsCstRef().size() == 3);
modif_csp = crossLinker_csp->getModifsCstRef().at(0);
REQUIRE(modif_csp->getName().toStdString() == "Chromo-O");
modif_csp = crossLinker_csp->getModifsCstRef().at(1);
REQUIRE(modif_csp->getName().toStdString() == "Chromo-H3");
modif_csp = crossLinker_csp->getModifsCstRef().at(2);
REQUIRE(modif_csp->getName().toStdString() == "Chromo-H");
crossLinker_csp =
pol_chem_def_sp-> getCrossLinkerCstSPtrByName("DisulfideBond");
REQUIRE(crossLinker_csp->getName().toStdString() == "DisulfideBond");
REQUIRE(crossLinker_csp->getFormula().toStdString() == "");
REQUIRE(crossLinker_csp->getModifsCstRef().size() == 2);
modif_csp = crossLinker_csp->getModifsCstRef().at(0);
REQUIRE(modif_csp->getName().toStdString() == "ProtonLoss");
modif_csp = crossLinker_csp->getModifsCstRef().at(1);
REQUIRE(modif_csp->getName().toStdString() == "ProtonLoss");
}
AND_THEN("The CleavageAgent_s are checked (and the CleavageRules_ if any)")
{
CleavageAgentCstSPtr cleavage_agent_csp = nullptr;
REQUIRE(pol_chem_def_sp->getCleavageAgentsCstRef().size() == 8);
cleavage_agent_csp =
pol_chem_def_sp-> getCleavageAgentCstSPtrByName("EndoAspN+GluN");
REQUIRE(cleavage_agent_csp->getName().toStdString() == "EndoAspN+GluN");
REQUIRE(cleavage_agent_csp->getPattern().toStdString() == "/D;/E");
cleavage_agent_csp =
pol_chem_def_sp-> getCleavageAgentCstSPtrByName("EndoLysC");
REQUIRE(cleavage_agent_csp->getName().toStdString() == "EndoLysC");
REQUIRE(cleavage_agent_csp->getPattern().toStdString() == "K/");
cleavage_agent_csp =
pol_chem_def_sp-> getCleavageAgentCstSPtrByName("CyanogenBromide");
REQUIRE(cleavage_agent_csp->getName().toStdString() == "CyanogenBromide");
REQUIRE(cleavage_agent_csp->getPattern().toStdString() == "M/");
CleavageRuleSPtr cleavage_rule_sp =
cleavage_agent_csp->getCleavageRuleSPtrByName("Homoseryl");
REQUIRE(cleavage_rule_sp->getName().toStdString() == "Homoseryl");
REQUIRE(cleavage_rule_sp->getRightCode().toStdString() == "M");
REQUIRE(
cleavage_rule_sp->getRightFormula().getActionFormula().toStdString() ==
"-CH2S+O");
}
AND_THEN("The FragmentationPathway_s are checked")
{
FragmentationPathwayCstSPtr fragmentation_pathway_csp = nullptr;
REQUIRE(pol_chem_def_sp->getFragmentationPathwaysCstRef().size() == 7);
fragmentation_pathway_csp =
pol_chem_def_sp-> getFragmentationPathwayCstSPtrByName("a");
REQUIRE(fragmentation_pathway_csp->getName().toStdString() == "a");
REQUIRE(fragmentation_pathway_csp->getFragEnd() == Enums::FragEnd::LE);
REQUIRE(fragmentation_pathway_csp->getFormulaCstRef()
.getActionFormula()
.toStdString() == "-C1O1H1");
REQUIRE(fragmentation_pathway_csp->getMonomerContribution() == 0);
REQUIRE(fragmentation_pathway_csp->getComment().toStdString() == "");
fragmentation_pathway_csp =
pol_chem_def_sp-> getFragmentationPathwayCstSPtrByName("z");
REQUIRE(fragmentation_pathway_csp->getName().toStdString() == "z");
REQUIRE(fragmentation_pathway_csp->getFragEnd() == Enums::FragEnd::RE);
REQUIRE(fragmentation_pathway_csp->getFormulaCstRef()
.getActionFormula()
.toStdString() == "-N1H1");
REQUIRE(fragmentation_pathway_csp->getMonomerContribution() == 0);
REQUIRE(fragmentation_pathway_csp->getComment().toStdString() ==
"Typically in ECD of protonated ions");
}
}
}
SCENARIO(
"Loading the same PolChemDef version 1, writing it as version 2 and checking "
"the chemical identity of the two versions",
"[PolChemDef]")
{
int input_version_1 = 1;
PolChemDefSPtr pol_chem_def_sp = nullptr;
// We use polymer chemistry definitions copied to the
// tests/data/polymer-chemistry-definitions directory.
QString test_pol_chem_defs_dir =
QString("%1/polymer-chemistry-definitions").arg(TESTS_INPUT_DIR);
QString test_pol_chem_defs_versioned_dir =
QString("%1/version-%2").arg(test_pol_chem_defs_dir).arg(input_version_1);
QString pol_chem_def_name = "protein-1-letter";
QString pol_chem_def_file_base_name =
QString("%1.xml").arg(pol_chem_def_name);
// Relative is to one of the polChemDefs directory (in system or user
// directory)
QString pol_chem_def_relative_dir_path = "protein-1-letter";
QString pol_chem_def_relative_file_path =
QString("%1/%2")
.arg(pol_chem_def_relative_dir_path)
.arg(pol_chem_def_file_base_name);
QString pol_chem_def_isotopic_data_relative_file_path =
QString("%1/%2/%3")
.arg(pol_chem_def_relative_dir_path)
.arg(pol_chem_def_file_base_name)
.arg("isotopic-data.dat");
QString pol_chem_def_absolute_dir_path =
QString("%1/%2")
.arg(test_pol_chem_defs_versioned_dir)
.arg(pol_chem_def_relative_dir_path);
// qDebug() << "The dir: " << pol_chem_def_absolute_dir_path.toStdString()
// << std::endl;
QString pol_chem_def_absolute_file_path =
QString("%1/%2")
.arg(pol_chem_def_absolute_dir_path)
.arg(pol_chem_def_file_base_name);
QString pol_chem_def_isotopic_data_absolute_file_path =
QString("%1/%2")
.arg(pol_chem_def_absolute_dir_path)
.arg("isotopic-data.dat");
pol_chem_def_sp = std::make_shared<PolChemDef>();
pol_chem_def_sp->setName(pol_chem_def_file_base_name);
pol_chem_def_sp->setXmlDataFilePath(pol_chem_def_absolute_file_path);
std::size_t isotope_count = PolChemDef::loadIsotopicData(pol_chem_def_sp);
REQUIRE(isotope_count == 288);
REQUIRE(PolChemDef::renderXmlPolChemDefFile(pol_chem_def_sp));
GIVEN("A fully loaded PolChemDef version 1 along with its IsotopicData")
{
QString pol_chem_def_output_dir = QString("%1/%2/%3")
.arg(TESTS_OUTPUT_DIR)
.arg("polymer-chemistry-definitions")
.arg(pol_chem_def_name);
// qDebug() << "The output directory:" << pol_chem_def_output_dir;
QString pol_chem_def_output_file_name = QString("%1/%2")
.arg(pol_chem_def_output_dir)
.arg(pol_chem_def_file_base_name);
// qDebug() << "The output file:" << pol_chem_def_output_file_name;
QDir dir;
REQUIRE(dir.mkpath(pol_chem_def_output_dir));
WHEN("Writing that PolChemDef back to file")
{
pol_chem_def_sp->setXmlDataFilePath(pol_chem_def_output_file_name);
THEN("The writing should be succesful")
{
REQUIRE(pol_chem_def_sp->writeXmlFile());
}
}
AND_WHEN("Loading the written PolChemDef")
{
PolChemDefSPtr new_pol_chem_def_sp = nullptr;
// We use polymer chemistry definitions copied to the
// tests/data/polymer-chemistry-definitions directory.
QString test_pol_chem_defs_dir =
QString("%1/polymer-chemistry-definitions").arg(TESTS_OUTPUT_DIR);
QString pol_chem_def_name = "protein-1-letter";
QString pol_chem_def_file_base_name =
QString("%1.xml").arg(pol_chem_def_name);
// Relative is to one of the polChemDefs directory (in system or user
// directory)
QString pol_chem_def_relative_dir_path = "protein-1-letter";
QString pol_chem_def_relative_file_path =
QString("%1/%2")
.arg(pol_chem_def_relative_dir_path)
.arg(pol_chem_def_file_base_name);
QString pol_chem_def_isotopic_data_relative_file_path =
QString("%1/%2/%3")
.arg(pol_chem_def_relative_dir_path)
.arg(pol_chem_def_file_base_name)
.arg("isotopic-data.dat");
QString pol_chem_def_absolute_dir_path =
QString("%1/%2")
.arg(test_pol_chem_defs_dir)
.arg(pol_chem_def_relative_dir_path);
qDebug() << "The dir: " << pol_chem_def_absolute_dir_path;
QString pol_chem_def_absolute_file_path =
QString("%1/%2")
.arg(pol_chem_def_absolute_dir_path)
.arg(pol_chem_def_file_base_name);
QString pol_chem_def_isotopic_data_absolute_file_path =
QString("%1/%2")
.arg(pol_chem_def_absolute_dir_path)
.arg("isotopic-data.dat");
new_pol_chem_def_sp = std::make_shared<PolChemDef>();
new_pol_chem_def_sp->setName(pol_chem_def_file_base_name);
new_pol_chem_def_sp->setXmlDataFilePath(pol_chem_def_absolute_file_path);
qDebug() << "Now loading PolChemDef:" << pol_chem_def_absolute_file_path;
std::size_t isotope_count =
PolChemDef::loadIsotopicData(new_pol_chem_def_sp);
REQUIRE(isotope_count == 288);
REQUIRE(PolChemDef::renderXmlPolChemDefFile(new_pol_chem_def_sp));
// qDebug() << "Loaded pol chem def:" <<
// new_pol_chem_def_sp->getXmlDataFilePath();
REQUIRE(new_pol_chem_def_sp->getIsotopicDataCstSPtr()->size() == 288);
THEN(
"The first and the second PolChemDef need to be identical in a deep "
"comparison way")
{
REQUIRE(
pol_chem_def_sp->isChemicallyEquivalent(*new_pol_chem_def_sp.get()));
}
}
}
}
} // namespace libXpertMassCore
} // namespace MsXpS
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