public static void TestModFits()
{
ModificationMotif.TryGetMotif("X", out ModificationMotif motif);
ModificationWithMass attemptToLocalize = new ModificationWithMass(null, null, motif, TerminusLocalization.Any, double.NaN);
Protein protein = new Protein("M", null);
int peptideOneBasedIndex = 1;
int peptideLength = 1;
int proteinOneBasedIndex = 1;
Assert.IsTrue(GptmdEngine.ModFits(attemptToLocalize, protein, peptideOneBasedIndex, peptideLength, proteinOneBasedIndex));
ModificationMotif.TryGetMotif("M", out motif);
attemptToLocalize = new ModificationWithMass(null, null, motif, TerminusLocalization.Any, double.NaN);
Assert.IsTrue(GptmdEngine.ModFits(attemptToLocalize, protein, peptideOneBasedIndex, peptideLength, proteinOneBasedIndex));
ModificationMotif.TryGetMotif("N", out motif);
attemptToLocalize = new ModificationWithMass(null, null, motif, TerminusLocalization.Any, double.NaN);
Assert.IsFalse(GptmdEngine.ModFits(attemptToLocalize, protein, peptideOneBasedIndex, peptideLength, proteinOneBasedIndex));
ModificationMotif.TryGetMotif("Mx", out motif);
attemptToLocalize = new ModificationWithMass(null, null, motif, TerminusLocalization.Any, double.NaN);
Assert.IsFalse(GptmdEngine.ModFits(attemptToLocalize, protein, peptideOneBasedIndex, peptideLength, proteinOneBasedIndex));
ModificationMotif.TryGetMotif("Mr", out motif);
attemptToLocalize = new ModificationWithMass(null, null, motif, TerminusLocalization.Any, double.NaN);
Assert.IsFalse(GptmdEngine.ModFits(attemptToLocalize, protein, peptideOneBasedIndex, peptideLength, proteinOneBasedIndex));
ModificationMotif.TryGetMotif("xM", out motif);
attemptToLocalize = new ModificationWithMass(null, null, motif, TerminusLocalization.Any, double.NaN);
Assert.IsFalse(GptmdEngine.ModFits(attemptToLocalize, protein, peptideOneBasedIndex, peptideLength, proteinOneBasedIndex));
ModificationMotif.TryGetMotif("Nxs", out motif);
attemptToLocalize = new ModificationWithMass(null, null, motif, TerminusLocalization.Any, double.NaN);
protein = new Protein("MNRS", null);
peptideOneBasedIndex = 1;
peptideLength = 1;
proteinOneBasedIndex = 1;
Assert.IsFalse(GptmdEngine.ModFits(attemptToLocalize, protein, peptideOneBasedIndex, peptideLength, proteinOneBasedIndex));
ModificationMotif.TryGetMotif("Nxs", out motif);
attemptToLocalize = new ModificationWithMass(null, null, motif, TerminusLocalization.Any, double.NaN);
protein = new Protein("MNRS", null);
peptideOneBasedIndex = 1;
peptideLength = 1;
proteinOneBasedIndex = 1;
Assert.IsFalse(GptmdEngine.ModFits(attemptToLocalize, protein, peptideOneBasedIndex, peptideLength, proteinOneBasedIndex));
peptideOneBasedIndex = 2;
peptideLength = 1;
proteinOneBasedIndex = 2;
Assert.IsTrue(GptmdEngine.ModFits(attemptToLocalize, protein, peptideOneBasedIndex, peptideLength, proteinOneBasedIndex));
protein = new Protein("MNRN", null);
Assert.IsFalse(GptmdEngine.ModFits(attemptToLocalize, protein, peptideOneBasedIndex, peptideLength, proteinOneBasedIndex));
}
public static void TestUniProtGptmdConflict()
{
// this unit test checks to make sure GPTMD does not annotate mods at residues on
// proteins where the equivalent uniprot mod already exists
Modification uniProtPhospho = GlobalVariables.AllModsKnown.First(p => p.ModificationType == "UniProt" && p.IdWithMotif.Contains("Phosphoserine"));
Modification mmPhospho = GlobalVariables.AllModsKnown.First(p => p.ModificationType == "Common Biological" && p.IdWithMotif.Contains("Phosphorylation on S"));
Protein protein = new Protein("PEPTIDESK", "test",
oneBasedModifications: new Dictionary <int, List <Modification> >()
{
{ 8, new List <Modification> {
uniProtPhospho
} }
});
PeptideWithSetModifications pep = protein.Digest(new DigestionParams(), new List <Modification>(), new List <Modification>()).First(p => p.AllModsOneIsNterminus.Count == 0);
// mod should not fit anywhere on the protein
for (int i = 0; i < pep.Length; i++)
{
bool modFits = GptmdEngine.ModFits(mmPhospho, protein, i + 1, pep.Length, pep.OneBasedStartResidueInProtein + i);
Assert.That(!modFits);
}
// the following code is just a control to make sure the phosphorylation actually does fit
// at the given residue if the UniProt phosphorylation is not already present
var someOtherSMod = GlobalVariables.AllModsKnown.Where(p => p.ModificationType == "Common Biological" && p.IdWithMotif.Contains("HexNAc on S")).First();
protein = new Protein("PEPTIDESK", "test",
oneBasedModifications: new Dictionary <int, List <Modification> >()
{
{ 8, new List <Modification> {
someOtherSMod
} }
});
pep = protein.Digest(new DigestionParams(), new List <Modification>(), new List <Modification>()).First(p => p.AllModsOneIsNterminus.Count == 0);
// mod should fit at position 8
for (int i = 0; i < pep.Length; i++)
{
bool modFits = GptmdEngine.ModFits(mmPhospho, protein, i + 1, pep.Length, pep.OneBasedStartResidueInProtein + i);
if (i + 1 == 8)
{
Assert.That(modFits);
}
else
{
Assert.That(!modFits);
}
}
}
public static void Test_GptmdEngineModFits(string targetAminoAcid, string proteinSequence, string locationRestriction, int peptideOneBasedIndex, int peptideLength, int proteinOneBasedIndex, bool result)
{
ModificationMotif.TryGetMotif(targetAminoAcid, out ModificationMotif motif);
Modification attemptToLocalize = new Modification(null, null, null, null, _target: motif, _locationRestriction: locationRestriction, _chemicalFormula: null, _monoisotopicMass: 1, _databaseReference: null, _taxonomicRange: null, _keywords: null, _neutralLosses: null, _diagnosticIons: null, _fileOrigin: null);
Dictionary <int, List <Modification> > oneBasedModifications = new Dictionary <int, List <Modification> >();
oneBasedModifications.Add(proteinOneBasedIndex, new List <Modification>()
{
attemptToLocalize
});
Protein protein = new Protein(proteinSequence, null, null, null, oneBasedModifications, null, null, null, false, false, null, null, null, null, null, null, "");
Assert.AreEqual(result, GptmdEngine.ModFits(attemptToLocalize, protein, peptideOneBasedIndex, peptideLength, proteinOneBasedIndex));
}
