public void FragmentNTermModTest()
{
_mockPeptideEveryAminoAcid.AddModification(new OldSchoolChemicalFormulaModification(ChemicalFormula.ParseFormula("O"), "lala", ModificationSites.NTerminus));
Fragment fragment = _mockPeptideEveryAminoAcid.Fragment(FragmentTypes.b, 1).First();
Assert.IsTrue(fragment.Modifications.SequenceEqual(new List <OldSchoolModification> {
new OldSchoolChemicalFormulaModification(ChemicalFormula.ParseFormula("O"), "lala", ModificationSites.NTerminus)
}));
}
public void TestMultipleModificationsAtSingleResidue()
{
Peptide a = new Peptide("ACDEFGHIKLMNPQRSTVWY");
a.AddModification(new OldSchoolChemicalFormulaModification(ChemicalFormula.ParseFormula("O"), ModificationSites.D));
a.AddModification(new OldSchoolChemicalFormulaModification(ChemicalFormula.ParseFormula("H"), ModificationSites.D));
var products = a.Fragment(FragmentTypes.b | FragmentTypes.y, true);
foreach (Fragment fragment in products)
{
}
foreach (IHasChemicalFormula fragment in products)
{
}
}
public void WriteMzmlTest()
{
var peptide = new Peptide("GPEAPPPALPAGAPPPCTAVTSDHLNSLLGNILR");
ChemicalFormulaModification carbamidomethylationOfCMod = new ChemicalFormulaModification("H3C2NO", "carbamidomethylation of C", ModificationSites.C);
peptide.AddModification(carbamidomethylationOfCMod);
DefaultMzSpectrum MS1 = createSpectrum(peptide.GetChemicalFormula(), 300, 2000, 1);
DefaultMzSpectrum MS2 = createMS2spectrum(peptide.Fragment(FragmentTypes.b | FragmentTypes.y, true), 100, 1500);
MsDataScan <IMzSpectrum <MzPeak> >[] Scans = new MsDataScan <IMzSpectrum <MzPeak> > [2];
Scans[0] = new MsDataScan <IMzSpectrum <MzPeak> >(1, MS1.newSpectrumApplyFunctionToX(b => b + 0.000001 * b + 0.000001), "spectrum 1", 1, false, Polarity.Positive, 1.0, new MzRange(300, 2000), "FTMS first spectrum", MZAnalyzerType.Unknown, 1, MS1.SumOfAllY);
Scans[1] = new MsDataScan <IMzSpectrum <MzPeak> >(2, MS2.newSpectrumApplyFunctionToX(b => b + 0.00001 * b + 0.00001), "spectrum 2", 2, false, Polarity.Positive, 2.0, new MzRange(100, 1500), "FTMS second spectrum", MZAnalyzerType.Unknown, 1, MS2.SumOfAllY, "spectrum 1", 1134.26091302033, 3, 0.141146966879759, 1134.3, 1, DissociationType.Unknown, 1, 0.141146966879759, 1134.26091302033);
var myMsDataFile = new FakeMsDataFile(@"myFakeFile.mzML", Scans);
MzmlMethods.CreateAndWriteMyIndexedMZmlwithCalibratedSpectra(myMsDataFile, Path.Combine(Path.GetDirectoryName(myMsDataFile.FilePath), Path.GetFileNameWithoutExtension(myMsDataFile.FilePath)) + ".mzML");
Mzml okay = new Mzml(@"myFakeFile.mzML");
okay.Open();
okay.GetScan(2);
Assert.AreEqual(1, okay.GetSpectrumNumber(1));
Assert.AreEqual(2, okay.GetSpectrumNumber(2));
}
public void TerminusModification()
{
Peptide pepA = new Peptide("DERLEK");
pepA.AddModification(new OldSchoolChemicalFormulaModification(ChemicalFormula.ParseFormula("SO")), Terminus.N);
Assert.AreEqual("[OS]-DERLEK", pepA.ToString());
}
public void PeptideCountElements()
{
Peptide pep = new Peptide("G");
pep.AddModification(new OldSchoolModification(1));
Assert.AreEqual(5, pep.ElementCountWithIsotopes("H"));
pep.AddModification(new OldSchoolChemicalFormulaModification(ChemicalFormula.ParseFormula("H{1}")));
Assert.AreEqual(5, pep.ElementCountWithIsotopes("H")); // NOTHING HAS BEEN ADDED!
pep.AddModification(new OldSchoolChemicalFormulaModification(ChemicalFormula.ParseFormula("H{1}"), ModificationSites.G));
Assert.AreEqual(6, pep.ElementCountWithIsotopes("H"));
Isotope isotope = PeriodicTable.GetElement("H").PrincipalIsotope;
Assert.AreEqual(1, pep.SpecificIsotopeCount(isotope));
}
public void TestChemicalFormula2()
{
Peptide A = new Peptide("A");
OldSchoolModification a = new OldSchoolModification(1, "Modification without chemical formula", ModificationSites.A);
A.AddModification(a);
Assert.Throws <MzLibException>(() => { A.GetChemicalFormula(); }, "Modification Modification without chemical formula does not have a chemical formula!");
}
public void TestClearModifications()
{
Peptide a = new Peptide("ACDEFGHIKLMNPQRSTVWY");
a.AddModification(new OldSchoolChemicalFormulaModification(ChemicalFormula.ParseFormula("O"), ModificationSites.D));
a.AddModification(new OldSchoolChemicalFormulaModification(ChemicalFormula.ParseFormula("H"), ModificationSites.E));
Assert.AreEqual(2, a.ModificationCount());
a.ClearModifications();
Assert.AreEqual(0, a.ModificationCount());
a.AddModification(new OldSchoolChemicalFormulaModification(ChemicalFormula.ParseFormula("O"), ModificationSites.NTerminus));
a.AddModification(new OldSchoolModification(1), ModificationSites.TerminusC);
Assert.AreEqual(2, a.ModificationCount());
a.Fragment(FragmentTypes.y);
Peptide peptide = new Peptide("[C2H3NO]-LLL-[C2H3NO]");
ModificationSites ff = ModificationSites.NPep | ModificationSites.PepC;
peptide.ClearModifications(ff);
Assert.AreEqual("LLL", peptide.GetSequenceWithModifications());
}
public void ParseCTerminalChemicalFormulaWithLastResidueModStringRepresentation()
{
Peptide peptide = new Peptide("TTGSSSSSSSK[H2O]-[C2H3NO]");
Assert.AreEqual("TTGSSSSSSSK[H2O]-[C2H3NO]", peptide.GetSequenceWithModifications());
peptide.NTerminus = new ChemicalFormulaTerminus(ChemicalFormula.ParseFormula("N"));
Assert.AreEqual("TTGSSSSSSSK[H2O]-[C2H3NO]", peptide.GetSequenceWithModifications());
ChemicalFormula formulaA = new ChemicalFormula(ChemicalFormula.ParseFormula("C39H70N14O23"));
var formulaB = peptide.GetChemicalFormula();
Assert.AreEqual(formulaA, formulaB);
peptide.AddModification(new ObjectWithMass100(), 0);
Assert.AreEqual("[mass: 100]-TTGSSSSSSSK[H2O]-[C2H3NO]", peptide.GetSequenceWithModifications());
Assert.AreEqual(1, peptide.AddModification(new ObjectWithMass100(), Terminus.C));
Assert.AreEqual(3, peptide.ModificationCount());
Assert.AreEqual(0, peptide.ReplaceModification(new ObjectWithMass100(), new ObjectWithMass100()));
Assert.That(() => peptide.ReplaceModification(null, new ObjectWithMass100()),
Throws.TypeOf <MzLibException>()
.With.Property("Message")
.EqualTo("Cannot replace a null modification"));
peptide.SetModification(new ObjectWithMass100(), new int[] { 1, 11 });
Assert.AreEqual(4, peptide.ModificationCount());
OldSchoolModification mod1 = new OldSchoolModification(5, "mass 5 on T", ModificationSites.T);
peptide.SetModifications(new List <OldSchoolModification> {
mod1
});
Assert.AreEqual(5, peptide.ModificationCount());
}
public void WriteMzmlTest()
{
var peptide = new Peptide("GPEAPPPALPAGAPPPCTAVTSDHLNSLLGNILR");
OldSchoolChemicalFormulaModification carbamidomethylationOfCMod = new OldSchoolChemicalFormulaModification(ChemicalFormula.ParseFormula("H3C2NO"), "carbamidomethylation of C", ModificationSites.C);
peptide.AddModification(carbamidomethylationOfCMod);
MzmlMzSpectrum MS1 = CreateSpectrum(peptide.GetChemicalFormula(), 300, 2000, 1);
MzmlMzSpectrum MS2 = CreateMS2spectrum(peptide.Fragment(FragmentTypes.b | FragmentTypes.y, true), 100, 1500);
IMzmlScan[] Scans = new IMzmlScan[2];
Scans[0] = new MzmlScan(1, MS1, 1, true, Polarity.Positive, 1.0, new MzRange(300, 2000), " first spectrum", MZAnalyzerType.Unknown, MS1.SumOfAllY, 1, "scan=1");
Scans[1] = new MzmlScanWithPrecursor(2, MS2, 2, true, Polarity.Positive, 2.0, new MzRange(100, 1500), " second spectrum", MZAnalyzerType.Unknown, MS2.SumOfAllY, 1134.26091302033, 3, 0.141146966879759, 1134.3, 1, DissociationType.Unknown, 1, 1134.26091302033, 1, "scan=2");
var myMsDataFile = new FakeMsDataFile(Scans);
var oldFirstValue = myMsDataFile.GetOneBasedScan(1).MassSpectrum.FirstX;
var secondScan = myMsDataFile.GetOneBasedScan(2) as IMsDataScanWithPrecursor <MzmlMzSpectrum>;
Assert.AreEqual(1, secondScan.IsolationRange.Maximum - secondScan.IsolationRange.Minimum);
MzmlMethods.CreateAndWriteMyMzmlWithCalibratedSpectra(myMsDataFile, "argh.mzML", false);
Mzml okay = Mzml.LoadAllStaticData(@"argh.mzML");
okay.GetOneBasedScan(2);
Assert.AreEqual(1, okay.GetClosestOneBasedSpectrumNumber(1));
Assert.AreEqual(2, okay.GetClosestOneBasedSpectrumNumber(2));
var newFirstValue = okay.GetOneBasedScan(1).MassSpectrum.FirstX;
Assert.AreEqual(oldFirstValue.Value, newFirstValue.Value, 1e-9);
var secondScan2 = okay.GetOneBasedScan(2) as IMsDataScanWithPrecursor <MzmlMzSpectrum>;
Assert.AreEqual(1, secondScan2.IsolationRange.Maximum - secondScan2.IsolationRange.Minimum);
secondScan2.MassSpectrum.ReplaceXbyApplyingFunction((a) => 44);
Assert.AreEqual(44, secondScan2.MassSpectrum.LastX);
}
public void TestFormulaTerminusMods()
{
var pep1 = new Peptide("ACDEFG");
pep1.AddModification(new OldSchoolChemicalFormulaModification(ChemicalFormula.ParseFormula("H"), ModificationSites.NTerminus));
Assert.IsTrue(pep1.Fragment(FragmentTypes.b, true).First() is IHasChemicalFormula);
var pep2 = new Peptide("ACDEFG");
pep2.AddModification(new OldSchoolModification(2, "haha", ModificationSites.NTerminus));
Assert.IsFalse(pep2.Fragment(FragmentTypes.b, true).First() is IHasChemicalFormula);
var pep3 = new Peptide("ACDEFG");
pep3.AddModification(new OldSchoolModification(3, "haha", ModificationSites.D));
var list = pep3.Fragment(FragmentTypes.b, true).ToList();
Assert.IsTrue(list[0] is IHasChemicalFormula);
Assert.IsFalse(list[2] is IHasChemicalFormula);
}
