public void TestSortByMassIsotopePattern()
{
var spExp = new IsotopePattern(new[]
{
new IsotopeContainer(157.07503, 0.0002),
new IsotopeContainer(156.07770, 2),
new IsotopeContainer(158.08135, 0.004),
new IsotopeContainer(157.08059, 0.0006),
});
spExp.MonoIsotope = spExp.Isotopes[1];
spExp.Charge = 1;
var isoNorma = IsotopePatternManipulator.SortByMass(spExp);
var listISO = isoNorma.Isotopes;
Assert.AreEqual(156.07770, isoNorma.MonoIsotope.Mass, 0.001);
Assert.AreEqual(156.07770, listISO[0].Mass, 0.00001);
Assert.AreEqual(157.07503, listISO[1].Mass, 0.00001);
Assert.AreEqual(157.08059, listISO[2].Mass, 0.00001);
Assert.AreEqual(158.08135, listISO[3].Mass, 0.00001);
Assert.AreEqual(2, isoNorma.MonoIsotope.Intensity, 0.001);
Assert.AreEqual(2, listISO[0].Intensity, 0.001);
Assert.AreEqual(0.0002, listISO[1].Intensity, 0.00001);
Assert.AreEqual(0.0006, listISO[2].Intensity, 0.00001);
Assert.AreEqual(0.004, listISO[3].Intensity, 0.00001);
Assert.AreEqual(1, isoNorma.Charge, 0.001);
}
/// <summary>
/// Get all combinatorial chemical isotopes given a structure.
/// </summary>
/// <param name="molFor">The IMolecularFormula to start</param>
/// <returns>A IsotopePattern object containing the different combinations</returns>
public IsotopePattern GetIsotopes(IMolecularFormula molFor)
{
if (builder == null)
{
try
{
isoFactory = CDK.IsotopeFactory;
builder = molFor.Builder;
}
catch (Exception e)
{
Console.WriteLine(e.StackTrace);
}
}
var mf = MolecularFormulaManipulator.GetString(molFor, true);
var molecularFormula = MolecularFormulaManipulator.GetMajorIsotopeMolecularFormula(mf, builder);
IsotopePattern abundance_Mass = null;
foreach (var isos in molecularFormula.Isotopes)
{
var elementSymbol = isos.Symbol;
var atomCount = molecularFormula.GetCount(isos);
// Generate possible isotope containers for the current atom's
// these will then me 'multiplied' with the existing patten
var additional = new List <IsotopeContainer>();
foreach (var isotope in isoFactory.GetIsotopes(elementSymbol))
{
double mass = isotope.ExactMass.Value;
double abundance = isotope.Abundance.Value;
if (abundance <= 0.000000001)
{
continue;
}
IsotopeContainer container = new IsotopeContainer(mass, abundance);
if (storeFormula)
{
container.Formula = AsFormula(isotope);
}
additional.Add(container);
}
for (int i = 0; i < atomCount; i++)
{
abundance_Mass = CalculateAbundanceAndMass(abundance_Mass, additional);
}
}
var isoP = IsotopePatternManipulator.SortAndNormalizedByIntensity(abundance_Mass);
isoP = CleanAbundance(isoP, minIntensity);
var isoPattern = IsotopePatternManipulator.SortByMass(isoP);
return(isoPattern);
}