private void SetupPsiMod()
{
var parser = new PsiModOboParser();
PsiModTerm[] modifications = parser.Parse(PsiModOboParserTest.GetFilePath()).ToArray();
_psiMod38 = modifications.Single(x => x.Id == "MOD:00038");
//_psiModLookup = PsiModModificationLookup.CreateFromModifications(new[] { _psiMod38 },
// _elementProvider);
_psiModLookup = PsiModModificationLookup.CreateFromModifications(modifications,
_elementProvider);
}
public void PsiModIsotope()
{
var parser = new PsiModOboParser();
PsiModTerm[] modifications = parser.Parse(PsiModOboParserTest.GetFilePath()).ToArray();
PsiModTerm psiMod402 = modifications.Single(x => x.Id == "MOD:00402");
IProteoformModificationLookup psiModLookup = PsiModModificationLookup.CreateFromModifications(new[] { psiMod402 },
_elementProvider);
this.FindById(psiModLookup, ProFormaKey.Identifier, ProFormaEvidenceType.PsiMod, 402, "MOD:");
var mod = psiModLookup.GetModification(new ProFormaDescriptor(ProFormaKey.Identifier,
ProFormaEvidenceType.PsiMod, "MOD:00402"));
ChemicalFormula chemicalFormula = new ChemicalFormula(
new IEntityCardinality <IElement>[]
{
new EntityCardinality <IElement>(_elementProvider.GetElement("C"), 22),
new EntityCardinality <IElement>(_elementProvider.GetElement("H", 1), 30),
new EntityCardinality <IElement>(_elementProvider.GetElement("H", 2), 8),
new EntityCardinality <IElement>(_elementProvider.GetElement("N"), 4),
new EntityCardinality <IElement>(_elementProvider.GetElement("O"), 6),
new EntityCardinality <IElement>(_elementProvider.GetElement("S"), 1),
});
Assert.IsInstanceOf(typeof(IHasChemicalFormula), mod);
var formulaMod = (IHasChemicalFormula)mod;
Assert.IsTrue(chemicalFormula.Equals(formulaMod.GetChemicalFormula()));
Assert.IsInstanceOf(typeof(IIdentifiable), mod);
var idMod = (IIdentifiable)mod;
Assert.AreEqual("MOD:00402", idMod.Id);
Assert.AreEqual("Gygi ICAT(TM) d8 modified cysteine", idMod.Name);
}
