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);
}
public void BasicTest()
{
var parser = new PsiModOboParser();
List <PsiModTerm> result = new List <PsiModTerm>(parser.Parse(GetFilePath()));
Assert.IsNotNull(result);
Assert.AreEqual(2077, result.Count);
Assert.AreEqual("MOD:00812", result[812].Id);
Assert.AreEqual("alkylated residue", result[1].Name);
Assert.AreEqual("A protein modification that effectively converts an L-serine residue to O3-glycosylserine.", result[2].Definition);
Assert.AreEqual("This term is for organizational use only and should not be assigned. [JSG]", result[3].Comment);
Assert.AreEqual(146.14, result[813].DiffAvg.Value, 0.001);
Assert.IsNull(result[434].DiffAvg); // Handle 'none'
Assert.AreEqual("C 6 H 10 N 0 O 4", result[813].DiffFormula);
Assert.AreEqual(146.057909, result[813].DiffMono.Value, 0.001);
Assert.AreEqual(247.25, result[813].MassAvg.Value, 0.001);
Assert.AreEqual("C 10 H 17 N 1 O 6", result[813].Formula);
Assert.AreEqual(247.105587, result[813].MassMono.Value, 0.001);
Assert.AreEqual(true, result[4].IsObsolete);
Assert.AreEqual(false, result[813].IsObsolete);
// Should be just one character unless cross link
Assert.AreEqual('T', result[813].Origin.Single());
CollectionAssert.AreEquivalent(new[] { 'C', 'C' }, result[34].Origin); // Cross-link, origin is C, C
CollectionAssert.AreEquivalent(new[] { 'K', 'K', 'K', 'K' }, result[1934].Origin); // Cross-link, 4 AA origin
Assert.AreEqual(null, result[1038].Origin); // says 'none'
Assert.AreEqual(null, result[458].Origin); // Special case for 'X'
Assert.AreEqual(null, result[0].Source);
Assert.AreEqual(null, result[1].Source);
Assert.AreEqual(PsiModModificationSource.Natural, result[812].Source);
Assert.AreEqual(PsiModModificationSource.Artifact, result[54].Source);
Assert.AreEqual(PsiModModificationSource.Hypothetical, result[231].Source);
Assert.AreEqual(null, result[813].Terminus); // says 'none'
Assert.AreEqual(null, result[9].Terminus); // doesn't exist
Assert.AreEqual(Terminus.N, result[30].Terminus);
Assert.AreEqual(Terminus.C, result[90].Terminus);
Assert.IsNull(result[4].IsA);
Assert.AreEqual(2, result[5].IsA.Count);
CollectionAssert.Contains(result[5].IsA.ToList(), "MOD:00396");
CollectionAssert.Contains(result[5].IsA.ToList(), "MOD:00917");
PsiModTerm formylMethionine = result[30];
Assert.AreEqual(9, formylMethionine.ExternalReferences.Count);
CollectionAssert.Contains(formylMethionine.ExternalReferences.Select(x => x.Id).ToList(), "AA0021#FMET");
CollectionAssert.Contains(formylMethionine.ExternalReferences.Select(x => x.Name).ToList(), "RESID");
Assert.AreEqual(11, formylMethionine.Synonyms.Count);
CollectionAssert.Contains(formylMethionine.Synonyms.Select(x => x.Scope).ToList(), "EXACT");
CollectionAssert.Contains(formylMethionine.Synonyms.Select(x => x.Text).ToList(), "2-formylamino-4-(methylthio)butanoic acid");
CollectionAssert.Contains(formylMethionine.Synonyms.Select(x => x.Type).ToList(), "PSI-MOD-alternate");
// Check formal charge
Assert.AreEqual("MOD:00083", result[83].Id);
PsiModTerm trimethylLysine = result[83];
Assert.AreEqual(1, trimethylLysine.FormalCharge);
PsiModTerm dimethylLysine = result[84];
Assert.AreEqual(0, dimethylLysine.FormalCharge);
PsiModTerm hexakis = result[147];
Assert.AreEqual(-3, hexakis.FormalCharge);
PsiModTerm stearoylated = result[2001];
Assert.AreEqual("MOD:02001", stearoylated.Id);
Assert.IsNull(stearoylated.ExternalReferences);
Assert.IsNull(stearoylated.Remap);
// Check for Obsolete and Remap
PsiModTerm residueMethylEster = result[407];
Assert.IsTrue(residueMethylEster.IsObsolete);
Assert.AreEqual("MOD:00599", residueMethylEster.Remap);
}
