public void Carbon13Test()
{
IElementProvider provider = new MockElementProvider();
IElement c = provider.GetElement("C");
IElement c13 = provider.GetElement("C", 13);
var formula = new ChemicalFormula(new[]
{
new EntityCardinality <IElement>(c, 1),
new EntityCardinality <IElement>(c13, 1),
});
var elements = formula.GetElements();
Assert.AreEqual(2, elements.Count);
// Check masses
Assert.AreEqual(c.Isotopes.FirstWithMax(x => x.RelativeAbundance).AtomicMass
+ c13.Isotopes.FirstWithMax(x => x.RelativeAbundance).AtomicMass,
formula.GetMass(MassType.Monoisotopic));
Assert.AreEqual(c.Isotopes.Sum(x => x.AtomicMass * x.RelativeAbundance)
+ c13.Isotopes.Sum(x => x.AtomicMass * x.RelativeAbundance),
formula.GetMass(MassType.Average));
Assert.AreEqual(c13.GetMass(MassType.Monoisotopic), c13.GetMass(MassType.Average));
}
public MZSpectrum CalculateDistribuition(ChemicalFormula formula, int topNPeaks = int.MaxValue, Normalization normalization = Normalization.Sum)
{
double monoisotopicMass = formula.MonoisotopicMass;
SetResolution(monoisotopicMass);
List<List<Composition>> elementalComposition = new List<List<Composition>>();
// Get all the unique elements of the formula
foreach (Element element in formula.GetElements())
{
int count = formula.Count(element);
List<Composition> isotopeComposition = new List<Composition>();
foreach (Isotope isotope in element.Isotopes.Values.OrderBy(iso => iso.AtomicMass))
{
double probability = isotope.RelativeAbundance;
if (probability <= 0)
continue;
Composition c = new Composition
{
Atoms = count,
MolecularWeight = isotope.AtomicMass,
Power = isotope.AtomicMass,
Probability = isotope.RelativeAbundance
};
isotopeComposition.Add(c);
}
elementalComposition.Add(isotopeComposition);
}
foreach (List<Composition> compositions in elementalComposition)
{
double sumProb = compositions.Sum(t => t.Probability);
foreach (Composition composition in compositions)
{
composition.Probability /= sumProb;
composition.LogProbability = Math.Log(composition.Probability);
composition.Power = Math.Floor(composition.MolecularWeight/_mwResolution + 0.5);
}
}
return CalculateFineGrain(elementalComposition, normalization);
}
private IsotopicDistribution Mercury(ChemicalFormula formula, double limit)
{
double[] msaMz = null;
double[] msaAbundance = null;
double[] tmpMz = null;
double[] tmpAbundance = null;
bool msaInitialized = false;
foreach (KeyValuePair <Element, int> kvp in formula.GetElements())
{
int n = kvp.Value;
if (n == 0)
{
continue;
}
int isotopeCount = kvp.Key.IsotopeDistribution.Count;
double[] esaMz = new double[isotopeCount];
double[] esaAbundance = new double[isotopeCount];
int i = 0;
foreach (var isotope in kvp.Key.IsotopeDistribution)
{
esaMz[i] = isotope.RelativeAtomicMass;
esaAbundance[i] = isotope.Abundance;
i++;
}
while (true)
{
if ((n & 1) == 1)
{
if (msaInitialized)
{
Convolve(ref tmpMz, ref tmpAbundance, msaMz, msaAbundance, esaMz, esaAbundance);
msaMz = this.CopyArray(tmpMz);
msaAbundance = this.CopyArray(tmpAbundance);
}
else
{
msaMz = this.CopyArray(esaMz);
msaAbundance = this.CopyArray(esaAbundance);
msaInitialized = true;
}
Prune(ref msaMz, ref msaAbundance, limit);
}
if (n == 1)
{
break;
}
Convolve(ref tmpMz, ref tmpAbundance, esaMz, esaAbundance, esaMz, esaAbundance);
esaMz = this.CopyArray(tmpMz);
esaAbundance = this.CopyArray(tmpAbundance);
Prune(ref esaMz, ref esaAbundance, limit);
n = n >> 1;
}
}
return(new IsotopicDistribution(msaMz, msaAbundance));
}