public void ChemicalForulaMyTest()
{
ChemicalFormula formula = new ChemicalFormula();
formula.Add(ChemicalFormula.ParseFormula("C3H5NO"));
Assert.AreEqual(PeriodicTable.GetElement("C").PrincipalIsotope.AtomicMass * 3 + PeriodicTable.GetElement("H").PrincipalIsotope.AtomicMass * 5 + PeriodicTable.GetElement("N").PrincipalIsotope.AtomicMass + PeriodicTable.GetElement("O").PrincipalIsotope.AtomicMass, formula.MonoisotopicMass);
}
public void ChemicalForulaIsSubSet()
{
ChemicalFormula formulaA = ChemicalFormula.ParseFormula("C2H3NO");
ChemicalFormula formulaB = ChemicalFormula.ParseFormula("C3H3NO");
Assert.IsTrue(formulaA.IsSubsetOf(formulaB));
}
public void ChemicalForulaIsNotSuperSet()
{
ChemicalFormula formulaA = ChemicalFormula.ParseFormula("C2H3NO2");
ChemicalFormula formulaB = ChemicalFormula.ParseFormula("C3H3NO");
Assert.IsFalse(formulaB.IsSupersetOf(formulaA));
}
public void FormulaValueInequality()
{
ChemicalFormula formulaA = ChemicalFormula.ParseFormula("C2H3NO");
ChemicalFormula formulaB = ChemicalFormula.ParseFormula("NC1OH3");
Assert.AreNotEqual(formulaA, formulaB);
}
public static void ChemicalFormulaIsSuperSet()
{
ChemicalFormula formulaA = ChemicalFormula.ParseFormula("C2H3NO");
ChemicalFormula formulaB = ChemicalFormula.ParseFormula("C3H3NO");
Assert.IsTrue(formulaB.IsSupersetOf(formulaA));
}
public static void TestCompactPeptideMasses_nTerminalModifiedPeptide_NeutralLoss_DissociationTypes_CID_and_HCD()//there should be no added neutral losses in this case becuase the allowed dissociation type doesn't match the dissociation type used in the experiment
{
Protein p = new Protein("PET", "accession");
ModificationMotif.TryGetMotif("P", out ModificationMotif motif);
Modification phosphorylation = new Modification(_originalId: "phospho", _modificationType: "CommonBiological", _target: motif, _locationRestriction: "Anywhere.", _chemicalFormula: ChemicalFormula.ParseFormula("H1O3P1"), _neutralLosses: new Dictionary <DissociationType, List <double> > {
{ MassSpectrometry.DissociationType.CID, new List <double> {
0, ChemicalFormula.ParseFormula("H3O4P1").MonoisotopicMass
} }
});
DigestionParams digestionParams = new DigestionParams(minPeptideLength: 2);
var aPeptideWithSetModifications = p.Digest(digestionParams, new List <Modification> {
phosphorylation
}, new List <Modification>()).First();
var aCompactPeptide = aPeptideWithSetModifications.CompactPeptide(FragmentationTerminus.Both);
//evaluate N-terminal masses
var nTerminalMasses = aCompactPeptide.TerminalMasses.Where(v => v.Terminus == FragmentationTerminus.N);
HashSet <int> expectedNTerminalMasses = new HashSet <int> {
177, 306
};
Assert.That(expectedNTerminalMasses.SetEquals(nTerminalMasses.Select(v => (int)Math.Round(v.NeutralMass, 1))));
//evaluate C-terminal masses
var cTerminalMasses = aCompactPeptide.TerminalMasses.Where(v => v.Terminus == FragmentationTerminus.C);
HashSet <int> expectedCTerminalMasses = new HashSet <int> {
101, 230, 407
};
Assert.That(expectedCTerminalMasses.SetEquals(cTerminalMasses.Select(v => (int)Math.Round(v.NeutralMass, 1))));
}
public void TerminusModification()
{
Peptide pepA = new Peptide("DERLEK");
pepA.AddModification(new OldSchoolChemicalFormulaModification(ChemicalFormula.ParseFormula("SO")), Terminus.N);
Assert.AreEqual("[OS]-DERLEK", pepA.ToString());
}
public static void FormulaAlmostEquality()
{
ChemicalFormula formulaA = ChemicalFormula.ParseFormula("C2H3NO");
ChemicalFormula formulaB = ChemicalFormula.ParseFormula("C{12}2H3NO");
Assert.AreNotEqual(formulaA, formulaB);
}
public void Test_FragmentationModNeutralLoss()
{
// Now we'll check the mass of modified peptide with no neutral losses
ModificationMotif.TryGetMotif("T", out ModificationMotif motif);
Modification mod = new Modification(_originalId: "phospho", _modificationType: "testModType", _target: motif, _chemicalFormula: ChemicalFormula.ParseFormula("H1 O3 P1"), _neutralLosses: new Dictionary <DissociationType, List <double> > {
{ DissociationType.HCD, new List <double> {
ChemicalFormula.ParseFormula("H3 O4 P1").MonoisotopicMass
} }
}, _locationRestriction: "Anywhere.");
List <Modification> modlist = new List <Modification> {
mod
};
DigestionParams digestionParams = new DigestionParams(
protease: "trypsin",
maxMissedCleavages: 0,
minPeptideLength: 1,
initiatorMethionineBehavior: InitiatorMethionineBehavior.Retain);
var prot = new Protein("PEPTIDE", null, oneBasedModifications: new Dictionary <int, List <Modification> > {
{ 4, modlist }
});
var ye = prot.Digest(digestionParams, new List <Modification>(), new List <Modification>()).ToList();
var peptideWithNeutralMassMod = ye.Where(v => v.AllModsOneIsNterminus.Count > 0).First();
var myModFragments = peptideWithNeutralMassMod.Fragment(DissociationType.HCD, FragmentationTerminus.Both).ToList();
HashSet <int> neutralMasses = new HashSet <int>(myModFragments.Select(m => (int)m.NeutralMass.ToMz(1)).ToList());
HashSet <int> expectedMasses = new HashSet <int> {
98, 227, 324, 407, 520, 635, 505, 618, 733, //b-ions with and without neutral loss
148, 263, 376, 459, 556, 685, 557, 654, 783, //y-ions with and without neutral loss
782
}; //molecular ion with neutral loss
Assert.That(neutralMasses.SetEquals(expectedMasses));
}
public static void HashCodeEquality()
{
ChemicalFormula formulaA = ChemicalFormula.ParseFormula("C2H3NO");
ChemicalFormula formulaB = ChemicalFormula.ParseFormula("H3C2NO");
Assert.AreEqual(formulaA.GetHashCode(), formulaB.GetHashCode());
}
public static void FormulaValueEquality()
{
ChemicalFormula formulaA = ChemicalFormula.ParseFormula("C2H3NO");
ChemicalFormula formulaB = ChemicalFormula.ParseFormula("NC2OH3");
Assert.AreEqual(formulaA, formulaB);
}
public static void TestCompactPeptideMasses_internallyModifiedPeptide_NeutralLoss()
{
Protein p = new Protein("PET", "accession");
ModificationMotif.TryGetMotif("E", out ModificationMotif motif);
Modification phosphorylation = new Modification(_originalId: "phospho", _modificationType: "CommonBiological", _target: motif, _locationRestriction: "Anywhere.", _chemicalFormula: ChemicalFormula.ParseFormula("H1O3P1"), _neutralLosses: new Dictionary <DissociationType, List <double> > {
{ MassSpectrometry.DissociationType.HCD, new List <double> {
0, ChemicalFormula.ParseFormula("H3O4P1").MonoisotopicMass
} }
});
DigestionParams digestionParams = new DigestionParams(minPeptideLength: 2);
var aPeptideWithSetModifications = p.Digest(digestionParams, new List <Modification> {
phosphorylation
}, new List <Modification>()).First();
var aCompactPeptide = aPeptideWithSetModifications.CompactPeptide(FragmentationTerminus.Both);
var allFragmentNeutralMasses = aPeptideWithSetModifications.Fragment(DissociationType.HCD, FragmentationTerminus.Both);
//evaluate N-terminal masses
var n = allFragmentNeutralMasses.Where(f => f.TerminusFragment.Terminus == FragmentationTerminus.N).ToList();
HashSet <int> expectedNTerminalMasses = new HashSet <int> {
97, 306, 208
};
Assert.That(expectedNTerminalMasses.SetEquals(n.Select(v => (int)Math.Round(v.NeutralMass, 1))));
//evaluate C-terminal masses
var c = allFragmentNeutralMasses.Where(f => f.TerminusFragment.Terminus == FragmentationTerminus.C).ToList();
HashSet <int> expectedCTerminalMasses = new HashSet <int> {
119, 328, 230
};
Assert.That(expectedCTerminalMasses.SetEquals(c.Select(v => (int)Math.Round(v.NeutralMass, 1))));
}
public static void FormulaValueInequalityHeavyIsotope()
{
ChemicalFormula formulaA = ChemicalFormula.ParseFormula("C2H3NO");
ChemicalFormula formulaB = ChemicalFormula.ParseFormula("CC{13}H3NO");
Assert.AreNotEqual(formulaA, formulaB);
}
public static void CopyConstructorReferenceInequality()
{
ChemicalFormula formulaA = ChemicalFormula.ParseFormula("C2H3NO");
ChemicalFormula formulaB = new ChemicalFormula(formulaA);
Assert.AreNotSame(formulaA, formulaB);
}
public static void CopyConstructorValueEquality()
{
ChemicalFormula formulaA = ChemicalFormula.ParseFormula("C2H3NO");
ChemicalFormula formulaB = new ChemicalFormula(formulaA);
Assert.AreEqual(formulaA, formulaB);
}
public static void HashCodeCheck()
{
ChemicalFormula formulaA = ChemicalFormula.ParseFormula("Al");
ChemicalFormula formulaB = ChemicalFormula.ParseFormula("Al{27}");
Assert.AreNotEqual(formulaA.GetHashCode(), formulaB.GetHashCode());
}
public static void ParsingFormulaNoNumbers()
{
ChemicalFormula formulaA = ChemicalFormula.ParseFormula("CCHHHNO");
ChemicalFormula formulaB = ChemicalFormula.ParseFormula("C2H3NO");
Assert.AreEqual(formulaA, formulaB);
}
public static void ParsingFormulaWithSpaces()
{
ChemicalFormula formulaA = ChemicalFormula.ParseFormula(" C2 H3 N O ");
ChemicalFormula formulaB = ChemicalFormula.ParseFormula("C2H3NO");
Assert.AreEqual(formulaA, formulaB);
}
public static void TestReplaceIsotopes()
{
ChemicalFormula formulaA = ChemicalFormula.ParseFormula("CC{13}2H3NO");
formulaA.Replace(PeriodicTable.GetElement("C")[13], PeriodicTable.GetElement("C")[12]);
Assert.AreEqual("CC{12}2H3NO", formulaA.Formula);
}
public static void ChemicalFormulaIsNotSubSet()
{
ChemicalFormula formulaA = ChemicalFormula.ParseFormula("C2H3NO");
ChemicalFormula formulaB = ChemicalFormula.ParseFormula("C3H2NO");
Assert.IsFalse(formulaA.IsSubsetOf(formulaB));
}
public static void ParsingFormulaRepeatedElementsCancelEachOther()
{
ChemicalFormula formulaA = ChemicalFormula.ParseFormula("C2H3NOC-2");
ChemicalFormula formulaB = ChemicalFormula.ParseFormula("H3NO");
Assert.AreEqual(formulaA, formulaB);
}
public static void IsSuperSetOf()
{
ChemicalFormula formulaA = ChemicalFormula.ParseFormula("CH3NO{17}C");
ChemicalFormula formulaB = ChemicalFormula.ParseFormula("CHNO{16}");
Assert.IsFalse(formulaA.IsSupersetOf(formulaB));
}
public static void ParsingFormulaRepeatedElements()
{
ChemicalFormula formulaA = ChemicalFormula.ParseFormula("CH3NOC");
ChemicalFormula formulaB = ChemicalFormula.ParseFormula("C2H3NO");
Assert.AreEqual(formulaA, formulaB);
}
public static void ParsingFormulaNoNumbersRandomOrder()
{
ChemicalFormula formulaA = ChemicalFormula.ParseFormula("OCHHCHN");
ChemicalFormula formulaB = ChemicalFormula.ParseFormula("C2H3NO");
Assert.AreEqual(formulaA, formulaB);
}
public static void ClearFormula()
{
ChemicalFormula formulaA = ChemicalFormula.ParseFormula("C2H3NO");
formulaA.Clear();
Assert.AreEqual(formulaA, new ChemicalFormula());
}
public static void TestIsotopicDistribution()
{
ChemicalFormula formulaA = ChemicalFormula.ParseFormula("C2H3NO");
var a = IsotopicDistribution.GetDistribution(formulaA);
Assert.True(Math.Abs(formulaA.MonoisotopicMass - a.Masses.ToArray()[Array.IndexOf(a.Intensities.ToArray(), a.Intensities.Max())]) < 1e-9);
}
public static void ContainsIsotopesOf()
{
ChemicalFormula formulaA = ChemicalFormula.ParseFormula("O{16}");
Assert.IsTrue(formulaA.ContainsIsotopesOf("O"));
Assert.IsTrue(formulaA.ContainsSpecificIsotope("O", 16));
Assert.AreEqual(1, formulaA.CountSpecificIsotopes("O", 16));
}
public void PeptideMassTryptic()
{
ChemicalFormula formula = new ChemicalFormula(ChemicalFormula.ParseFormula("C37H66N12O21"));
ChemicalFormula formula2;
formula2 = _mockTrypticPeptide.GetChemicalFormula();
Assert.AreEqual(formula, formula2);
}
public void SetCTerminusModStringRepresentationofChemicalModification()
{
IHasChemicalFormula formula = new OldSchoolChemicalFormulaModification(ChemicalFormula.ParseFormula("Fe"), "Test");
_mockPeptideEveryAminoAcid.SetModification(formula, Terminus.C);
Assert.AreEqual("ACDEFGHIKLMNPQRSTVWY-[Test]", _mockPeptideEveryAminoAcid.ToString());
}
public static void NotEqual()
{
ChemicalFormula formulaB = ChemicalFormula.ParseFormula("C15O15H15S15N15");
ChemicalFormula formulaA = ChemicalFormula.ParseFormula("N15S15H15O15C15");
Assert.AreEqual(formulaA, formulaB);
Assert.IsTrue(Math.Abs(formulaA.MonoisotopicMass - formulaB.MonoisotopicMass) < 1e-9);
}