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);
}
