public void NegativeTest()
{
const string formula = "C(-2) O(3)";
var composition = UnimodComposition.CreateFromFormula(formula, atomProvider);
var cardinalities = composition.GetAtomCardinalities();
Assert.AreEqual(2, cardinalities.Count);
Assert.AreEqual(atomProvider.GetUnimodCompositionAtom("C"), cardinalities[0].Atom);
Assert.AreEqual(-2, cardinalities[0].Count);
Assert.AreEqual(atomProvider.GetUnimodCompositionAtom("O"), cardinalities[1].Atom);
Assert.AreEqual(3, cardinalities[1].Count);
}
public void FucoseTest()
{
const string formula = "dHex";
var composition = UnimodComposition.CreateFromFormula(formula, atomProvider);
var cardinalities = composition.GetAtomCardinalities();
Assert.AreEqual(1, cardinalities.Count);
Assert.AreEqual(atomProvider.GetUnimodCompositionAtom("dHex"), cardinalities[0].Atom);
Assert.AreEqual(1, cardinalities[0].Count);
var chemicalFormula = composition.GetChemicalFormula();
Assert.AreEqual(146.057909, chemicalFormula.GetMass(MassType.Monoisotopic), 0.00001);
Assert.AreEqual(146.1412, chemicalFormula.GetMass(MassType.Average), 0.001);
}
public void WaterTest()
{
const string formula = "H(2) O";
var composition = UnimodComposition.CreateFromFormula(formula, atomProvider);
var cardinalities = composition.GetAtomCardinalities();
Assert.AreEqual(2, cardinalities.Count);
Assert.AreEqual(atomProvider.GetUnimodCompositionAtom("H"), cardinalities[0].Atom);
Assert.AreEqual(2, cardinalities[0].Count);
Assert.AreEqual(atomProvider.GetUnimodCompositionAtom("O"), cardinalities[1].Atom);
Assert.AreEqual(1, cardinalities[1].Count);
var chemicalFormula = composition.GetChemicalFormula();
Assert.AreEqual(1.007825035 * 2 + 15.99491463, chemicalFormula.GetMass(MassType.Monoisotopic), 0.00001);
Assert.AreEqual(1.00794 * 2 + 15.9994, chemicalFormula.GetMass(MassType.Average), 0.00001);
}
public void IsotopeTest()
{
const string formula = "C(-9) 13C(9)";
var composition = UnimodComposition.CreateFromFormula(formula, atomProvider);
var cardinalities = composition.GetAtomCardinalities();
Assert.AreEqual(2, cardinalities.Count);
Assert.AreEqual(atomProvider.GetUnimodCompositionAtom("C"), cardinalities[0].Atom);
Assert.AreEqual(-9, cardinalities[0].Count);
Assert.AreEqual(atomProvider.GetUnimodCompositionAtom("13C"), cardinalities[1].Atom);
Assert.AreEqual(9, cardinalities[1].Count);
IChemicalFormula chemicalFormula = composition.GetChemicalFormula();
var elements = chemicalFormula.GetElements();
Assert.AreEqual(2, elements.Count);
Assert.AreEqual(-9, elements.Single(x => x.Entity.Symbol == "C").Count);
Assert.AreEqual(9, elements.Single(x => x.Entity.Symbol == "13C").Count);
}
public void SingleAtomTest()
{
var composition = UnimodComposition.CreateFromFormula("C", atomProvider);
var cardinalities = composition.GetAtomCardinalities();
Assert.AreEqual(1, cardinalities.Count);
Assert.AreEqual(atomProvider.GetUnimodCompositionAtom("C"), cardinalities[0].Atom);
Assert.AreEqual(1, cardinalities[0].Count);
composition = UnimodComposition.CreateFromFormula("C(1)", atomProvider);
cardinalities = composition.GetAtomCardinalities();
Assert.AreEqual(1, cardinalities.Count);
Assert.AreEqual(atomProvider.GetUnimodCompositionAtom("C"), cardinalities[0].Atom);
Assert.AreEqual(1, cardinalities[0].Count);
composition = UnimodComposition.CreateFromFormula("C(100)", atomProvider);
cardinalities = composition.GetAtomCardinalities();
Assert.AreEqual(1, cardinalities.Count);
Assert.AreEqual(atomProvider.GetUnimodCompositionAtom("C"), cardinalities[0].Atom);
Assert.AreEqual(100, cardinalities[0].Count);
}
public void InvalidArgumentsStrings()
{
Assert.Throws <ArgumentNullException>(() => UnimodComposition.CreateFromFormula(null, atomProvider));
Assert.Throws <ArgumentNullException>(() => UnimodComposition.CreateFromFormula(string.Empty, atomProvider));
}
/// <summary>
/// Gets the chemical formula.
/// </summary>
/// <param name="modification">The modification.</param>
/// <returns></returns>
protected override IChemicalFormula GetChemicalFormula(UnimodModification modification)
{
var composition = UnimodComposition.CreateFromFormula(modification.DeltaComposition, _atomProvider);
return(composition.GetChemicalFormula());
}
