private void SetupUnimod() { var atomProvider = new UnimodHardCodedAtomProvider(_elementProvider); var parser = new UnimodOboParser(); UnimodModification[] modifications = parser.Parse(UnimodTest.GetUnimodFilePath()).ToArray(); _unimod37 = modifications.Single(x => x.Id == "UNIMOD:37"); //_unimodLookup = UnimodModificationLookup.CreateFromModifications(new[] { _unimod37 }, // atomProvider); _unimodLookup = UnimodModificationLookup.CreateFromModifications(modifications, atomProvider); }
public void BasicTest() { var parser = new UnimodOboParser(); var mods = parser.Parse(GetUnimodFilePath()).ToList(); Assert.AreEqual(2017, mods.Max(x => Convert.ToInt32(x.Id.Substring(7)))); UnimodModification unimod1 = mods.Single(x => x.Id == "UNIMOD:1"); Assert.IsNotNull(unimod1); Assert.AreEqual("Acetyl", unimod1.Name); Assert.AreEqual(@"""Acetylation."" [RESID:AA0048, RESID:AA0049, RESID:AA0041, RESID:AA0052, RESID:AA0364, RESID:AA0056, RESID:AA0046, RESID:AA0051, RESID:AA0045, RESID:AA0354, RESID:AA0044, RESID:AA0043, PMID:11999733, URL:http://www.ionsource.com/Card/acetylation/acetylation.htm, RESID:AA0055, PMID:14730666, PMID:15350136, RESID:AA0047, PMID:12175151, PMID:11857757, RESID:AA0042, RESID:AA0050, RESID:AA0053, RESID:AA0054, FindMod:ACET, UNIMODURL:http://www.unimod.org/modifications_view.php?editid1=1]", unimod1.Definition); Assert.AreEqual("H(2) C(2) O", unimod1.DeltaComposition); Assert.AreEqual(42.0367, unimod1.DeltaAverageMass); Assert.AreEqual(42.010565, unimod1.DeltaMonoisotopicMass); }
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); }