public void TestSortAndNormalizedByIntensityIsotopePattern()
{
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.SortAndNormalizedByIntensity(spExp);
var listISO = isoNorma.Isotopes;
Assert.AreEqual(156.07770, isoNorma.MonoIsotope.Mass, 0.00001);
Assert.AreEqual(156.07770, listISO[0].Mass, 0.00001);
Assert.AreEqual(158.08135, listISO[1].Mass, 0.00001);
Assert.AreEqual(157.08059, listISO[2].Mass, 0.00001);
Assert.AreEqual(157.07503, listISO[3].Mass, 0.00001);
Assert.AreEqual(1, isoNorma.MonoIsotope.Intensity, 0.00001);
Assert.AreEqual(1, listISO[0].Intensity, 0.00001);
Assert.AreEqual(0.002, listISO[1].Intensity, 0.00001);
Assert.AreEqual(0.0003, listISO[2].Intensity, 0.00001);
Assert.AreEqual(0.0001, 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);
}
public void TestCompareIsotopePatternIsotopePattern()
{
var is_ = new IsotopePatternSimilarity();
IsotopePattern spExp = new IsotopePattern(new[]
{
new IsotopeContainer(156.07770, 1),
new IsotopeContainer(157.07503, 0.0004),
new IsotopeContainer(157.08059, 0.0003),
new IsotopeContainer(158.08135, 0.002),
});
spExp.MonoIsotope = spExp.Isotopes[0];
var formula = MolecularFormulaManipulator.GetMajorIsotopeMolecularFormula("C6H10N3O2", builder);
var isotopeGe = new IsotopePatternGenerator(0.1);
var patternIsoPredicted = isotopeGe.GetIsotopes(formula);
var patternIsoNormalize = IsotopePatternManipulator.Normalize(patternIsoPredicted);
var score = is_.Compare(spExp, patternIsoNormalize);
Assert.AreNotSame(0.0, score);
}
public void TestSelectingMF()
{
var is_ = new IsotopePatternSimilarity();
IsotopePattern spExp = new IsotopePattern(new[]
{
new IsotopeContainer(156.07770, 1),
new IsotopeContainer(157.07503, 0.0101),
new IsotopeContainer(157.08059, 0.074),
new IsotopeContainer(158.08135, 0.0024),
});
spExp.MonoIsotope = spExp.Isotopes[0];
spExp.Charge = 1;
double score = 0;
string mfString = "";
string[] listMF = { "C4H8N6O", "C2H12N4O4", "C3H12N2O5", "C6H10N3O2", "CH10N5O4", "C4H14NO5" };
for (int i = 0; i < listMF.Length; i++)
{
IMolecularFormula formula = MolecularFormulaManipulator.GetMajorIsotopeMolecularFormula(listMF[i], builder);
IsotopePatternGenerator isotopeGe = new IsotopePatternGenerator(0.01);
IsotopePattern patternIsoPredicted = isotopeGe.GetIsotopes(formula);
IsotopePattern patternIsoNormalize = IsotopePatternManipulator.Normalize(patternIsoPredicted);
double tempScore = is_.Compare(spExp, patternIsoNormalize);
if (score < tempScore)
{
mfString = MolecularFormulaManipulator.GetString(formula);
score = tempScore;
}
}
Assert.AreEqual("C6H10N3O2", mfString);
}
/// <summary>
/// Compare the IMolecularFormula with a isotope
/// abundance pattern.
/// </summary>
/// <param name="isoto1">The Isotope pattern reference (predicted)</param>
/// <param name="isoto2">The Isotope pattern reference (detected)</param>
/// <returns>The hit score of similarity</returns>
public double Compare(IsotopePattern isoto1, IsotopePattern isoto2)
{
IsotopePattern iso1 = IsotopePatternManipulator.SortAndNormalizedByIntensity(isoto1);
IsotopePattern iso2 = IsotopePatternManipulator.SortAndNormalizedByIntensity(isoto2);
/* charge to add */
if (isoto1.Charge == 1)
{
chargeToAdd = massE;
}
else if (isoto1.Charge == -1)
{
chargeToAdd = -massE;
}
else
{
chargeToAdd = 0;
}
foreach (var isoC in iso1.Isotopes)
{
double mass = isoC.Mass;
isoC.Mass = mass + chargeToAdd;
}
double diffMass, diffAbun, factor, totalFactor = 0d;
double score = 0d, tempScore;
// Maximum number of isotopes to be compared according predicted isotope
// pattern. It is assumed that this will have always more isotopeContainers
int length = iso1.Isotopes.Count;
for (int i = 0; i < length; i++)
{
var isoContainer = iso1.Isotopes[i];
factor = isoContainer.Intensity;
totalFactor += factor;
// Search for the closest isotope in the second pattern (detected) to the
// current isotope (predicted pattern)
int closestDp = GetClosestDataDiff(isoContainer, iso2);
if (closestDp == -1)
{
continue;
}
diffMass = isoContainer.Mass - iso2.Isotopes[closestDp].Mass;
diffMass = Math.Abs(diffMass);
diffAbun = 1.0d - (isoContainer.Intensity / iso2.Isotopes[closestDp].Intensity);
diffAbun = Math.Abs(diffAbun);
tempScore = 1 - (diffMass + diffAbun);
if (tempScore < 0)
{
tempScore = 0;
}
score += (tempScore * factor);
}
return(score / totalFactor);
}
