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); }