public void HandleTerminalModificationNameTag()
{
const string sequence = "SEQVENCE";
var modificationLookup = new BrnoModificationLookup(_elementProvider);
ProFormaDescriptor descriptor = this.CreateBrnoDescriptor("ac");
var term = new ProFormaTerm(sequence, null, new[] { descriptor }, null, null);
var proteoform = _factory.CreateProteoformGroup(term, modificationLookup);
Assert.IsNull(proteoform.LocalizedModifications);
Assert.IsNotNull(proteoform.NTerminalModification);
Assert.IsNull(proteoform.CTerminalModification);
// Residue masses plus modification plus water (approx)
Assert.AreEqual(978.36, proteoform.GetMass(MassType.Monoisotopic), 0.01);
Assert.AreEqual(978.98, proteoform.GetMass(MassType.Average), 0.01);
// C terminal case
term = new ProFormaTerm(sequence, null, null, new[] { descriptor }, null);
proteoform = _factory.CreateProteoformGroup(term, modificationLookup);
Assert.IsNull(proteoform.LocalizedModifications);
Assert.IsNull(proteoform.NTerminalModification);
Assert.IsNotNull(proteoform.CTerminalModification);
// Residue masses plus modification plus water (approx)
Assert.AreEqual(978.36, proteoform.GetMass(MassType.Monoisotopic), 0.01);
Assert.AreEqual(978.98, proteoform.GetMass(MassType.Average), 0.01);
}
public void InvalidIntegerHandling()
{
var descriptor = new ProFormaDescriptor(ProFormaKey.Name, ProFormaEvidenceType.Unimod, "abc");
// I want this to return true and then throw an exception later.
// This gives me an opportunity to give a meaningful error (and not just return false)
// In this case, it is also obvious that the Unimod handler was intended, so an attempt to create
// a modification should be made.
Assert.True(_unimodLookup.CanHandleDescriptor(descriptor));
Assert.Throws <ProteoformModificationLookupException>(() => _unimodLookup.GetModification(descriptor));
}
public void FormulaLookup()
{
string formulaString = "C2H2O";
ProFormaDescriptor proFormaDescriptor = new ProFormaDescriptor(ProFormaKey.Formula, formulaString);
ChemicalFormula chemicalFormula = new ChemicalFormula(new IEntityCardinality <IElement>[]
{
new EntityCardinality <IElement>(_elementProvider.GetElement("C"), 2),
new EntityCardinality <IElement>(_elementProvider.GetElement("H"), 2),
new EntityCardinality <IElement>(_elementProvider.GetElement("O"), 1),
});
var proteoformModification = _formulaLookup.GetModification(proFormaDescriptor);
Assert.IsInstanceOf(typeof(IHasChemicalFormula), proteoformModification);
var formulaMod = (IHasChemicalFormula)proteoformModification;
Assert.AreEqual(chemicalFormula, formulaMod.GetChemicalFormula());
}
