public void Setup() { //_elementProvider = new MockElementProvider(); NistElementParser parser = new NistElementParser(); IElement[] elements = parser.ParseFile(Path.Combine(TestContext.CurrentContext.TestDirectory, "TestData", "elements.dat")).ToArray(); _elementProvider = new InMemoryElementProvider(elements); this.SetupUnimod(); this.SetupResid(); this.SetupPsiMod(); this.SetupUniProt(); this.SetupFormula(); }
public void LoadEntireFile() { var parser = new NistElementParser(); var elements = parser.ParseFile(Path.Combine(TestContext.CurrentContext.TestDirectory, "TestData", "elements.dat")); Assert.IsNotNull(elements); Assert.AreEqual(84, elements.Count); // Only count elements with isotope abundances var h = elements.Single(x => x.AtomicNumber == 1); Assert.AreEqual("H", h.Symbol); Assert.AreEqual(2, h.Isotopes.Count); var h1 = h.Isotopes.Single(x => x.AtomicMass < 2); Assert.AreEqual(1.00782503223, h1.AtomicMass); Assert.AreEqual(0.999885, h1.RelativeAbundance); var h2 = h.Isotopes.Single(x => x.AtomicMass > 2); Assert.AreEqual(2.01410177812, h2.AtomicMass); Assert.AreEqual(0.000115, h2.RelativeAbundance); var c = elements.Single(x => x.AtomicNumber == 6); var c12 = c.Isotopes.Single(x => Math.Round(x.AtomicMass) == 12); Assert.AreEqual(6, c12.NeutronCount); var c13 = c.Isotopes.Single(x => Math.Round(x.AtomicMass) == 13); Assert.AreEqual(7, c13.NeutronCount); var ru = elements.Single(x => x.AtomicNumber == 44); Assert.AreEqual("Ru", ru.Symbol); Assert.AreEqual(7, ru.Isotopes.Count); var xe = elements.Single(x => x.AtomicNumber == 54); Assert.AreEqual("Xe", xe.Symbol); Assert.AreEqual(9, xe.Isotopes.Count); var u = elements.Single(x => x.AtomicNumber == 92); Assert.AreEqual("U", u.Symbol); Assert.AreEqual(3, u.Isotopes.Count); }
public void Setup() { var unimodOboParser = new UnimodOboParser(); UnimodModification[] modifications = unimodOboParser.Parse(UnimodTest.GetUnimodFilePath()).ToArray(); NistElementParser nistParser = new NistElementParser(); IElement[] elements = nistParser.ParseFile(Path.Combine(TestContext.CurrentContext.TestDirectory, "TestData", "elements.dat")).ToArray(); _elementProvider = new InMemoryElementProvider(elements); _residueProvider = new IupacAminoAcidProvider(_elementProvider); var atomProvider = new UnimodHardCodedAtomProvider(_elementProvider); _lookup = new CompositeModificationLookup(new IProteoformModificationLookup[] { UnimodModificationLookup.CreateFromModifications(modifications, atomProvider), new FormulaLookup(_elementProvider), new MassLookup(), new BrnoModificationLookup(_elementProvider), new IgnoreKeyModificationLookup(ProFormaKey.Info), }); ProFormaParser proFormaParser = new ProFormaParser(); ProteoformGroupFactory proteoformGroupFactory = new ProteoformGroupFactory(_elementProvider, _residueProvider); var mapper = new RelayAccessionMapper(d => { if (d == "B:ac") { return(Tuple.Create(ProFormaEvidenceType.PsiMod, "MOD:00394")); // acetylated residue } return(Tuple.Create(ProFormaEvidenceType.None, d)); }); var parser = new UniProtPtmListParser(); var entries = parser.Parse(File.ReadAllText(UniProtTests.GetPtmListPath())).ToList(); _chemicalProteoformHashGenerator = new ChemicalProteoformHashGenerator(proFormaParser, proteoformGroupFactory, _lookup, mapper); }