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 TestLeucineSequence() { Assert.AreEqual("ACDEFGHLKLMNPQRSTVWY", _mockPeptideEveryAminoAcid.GetSequenceWithModifications(true)); Assert.AreEqual(20, _mockPeptideEveryAminoAcid.ResidueCount()); Assert.AreEqual(7, _mockTrypticPeptide.ResidueCount('S')); Assert.AreEqual(7, _mockTrypticPeptide.ResidueCount(Residue.GetResidue('S'))); Assert.AreEqual(2, _mockTrypticPeptide.ResidueCount(Residue.GetResidue('S'), 2, 3)); Assert.AreEqual(3, _mockTrypticPeptide.ResidueCount('S', 2, 4)); Peptide peptide = new Peptide("III-[C2H3NO]"); Assert.AreEqual("LLL-[C2H3NO]", peptide.GetSequenceWithModifications(true)); }
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()); }