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());
}