public ChemicalFormulaModification(ChemicalFormulaModification other)
: this(new ChemicalFormula(other.ChemicalFormula), other.Name, other.Sites)
{
}
/// <summary>
/// Basic overview of how peptides can be used and modified
/// </summary>
private static void PeptideExamples()
{
Console.WriteLine("**Peptide Examples**");
// Simple Peptide creation
Peptide peptide1 = new Peptide("ACDEFGHIKLMNPQRSTVWY");
WritePeptideToConsole(peptide1);
// Fragmenting a peptide is simple, you can include as many fragment types as you want
Console.WriteLine("{0,-4} {1,-20} {2,-10} {3,-10} {4,-5}", "Type", "Formula", "Mass", "m/z +1", "Sequence");
foreach (Fragment fragment in peptide1.Fragment(FragmentTypes.b | FragmentTypes.y))
{
WriteFragmentToConsole(fragment);
}
// Modifications can be applied to any residue or termini
Console.WriteLine("Lets add some Iron to our peptide...");
peptide1.SetModification(new ChemicalFormula("Fe"), Terminus.C | Terminus.N);
WritePeptideToConsole(peptide1);
// A chemicalmodification is a simple wrapper for a chemical formula. You can name your mods if you want
Console.WriteLine("Add a modification of Oxygen with the name \"Oxidation\" to all Methionines");
ChemicalFormulaModification oxMod = new ChemicalFormulaModification("O", "Oxidation");
peptide1.SetModification(oxMod, 'M');
WritePeptideToConsole(peptide1);
// If you fragment a modified peptide, the modifications stay part of the fragments
Console.WriteLine("{0,-4} {1,-20} {2,-20} {3,-5}", "Type", "Formula", "Mass", "m/z +1");
foreach (Fragment fragment in peptide1.Fragment(FragmentTypes.b | FragmentTypes.y, 2))
{
WriteFragmentToConsole(fragment);
}
}
public void SetCTerminusModStringRepresentationofChemicalModification()
{
IChemicalFormula formula = new ChemicalFormulaModification("Fe", "Test");
_mockPeptideEveryAminoAcid.SetModification(formula, Terminus.C);
Assert.AreEqual("ACDEFGHIKLMNPQRSTVWY-[Test]", _mockPeptideEveryAminoAcid.ToString());
}
public ChemicalFormulaModification(ChemicalFormulaModification other)
: this(new ChemicalFormula(other.ChemicalFormula), other.Name, other.Sites)
{
}