public void TestSetFormula_IMolecularFormula()
{
IsotopeContainer isoC = new IsotopeContainer();
IMolecularFormula formula = builder.NewMolecularFormula();
isoC.Formula = formula;
Assert.IsNotNull(isoC);
}
public void TestGetMonoIsotope()
{
var isoP = new IsotopePattern();
var isoC = new IsotopeContainer();
isoP.MonoIsotope = isoC;
Assert.AreEqual(isoC, isoP.MonoIsotope);
}
public void TestGetFormula()
{
IsotopeContainer isoC = new IsotopeContainer();
IMolecularFormula formula = builder.NewMolecularFormula();
isoC.Formula = formula;
Assert.AreEqual(formula, isoC.Formula);
}
public void TestGetMass()
{
IsotopeContainer isoC = new IsotopeContainer();
double mass = 130.00;
isoC.Mass = mass;
Assert.AreEqual(mass, isoC.Mass, 0.001);
}
public void TestGetIntensity()
{
IsotopeContainer isoC = new IsotopeContainer();
double intensity = 130.00;
isoC.Intensity = intensity;
Assert.AreEqual(intensity, isoC.Intensity, 0.001);
}
public void TestSetIntensity_Double()
{
IsotopeContainer isoC = new IsotopeContainer {
Intensity = 5000000.0
};
Assert.IsNotNull(isoC);
}
public void TestSetMass_Double()
{
IsotopeContainer isoC = new IsotopeContainer {
Mass = 130.00
};
Assert.IsNotNull(isoC);
}
/// <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 TestIsotopeContainer_Double_double()
{
double mass = 130.00;
double intensity = 500000.00;
IsotopeContainer isoC = new IsotopeContainer(mass, intensity);
Assert.IsNotNull(isoC);
Assert.AreEqual(mass, isoC.Mass, 0.001);
Assert.AreEqual(intensity, isoC.Intensity, 0.001);
}
public void TestIsotopeContainer_IMolecularFormula_Double()
{
IMolecularFormula formula = builder.NewMolecularFormula();
double intensity = 130.00;
IsotopeContainer isoC = new IsotopeContainer(formula, intensity);
Assert.IsNotNull(isoC);
Assert.AreEqual(formula, isoC.Formula);
Assert.AreEqual(intensity, isoC.Intensity, 0.001);
}
public void TestGetNumberOfIsotopes()
{
var iso1 = new IsotopeContainer();
var iso2 = new IsotopeContainer();
var isoP = new IsotopePattern(new[] { iso1, iso2 })
{
MonoIsotope = iso1
};
Assert.AreEqual(2, isoP.Isotopes.Count);
}
private void AddDistinctFormula(IsotopeContainer container, IMolecularFormula mf)
{
foreach (var curr in container.Formulas)
{
if (MolecularFormulaManipulator.Compare(curr, mf))
{
return;
}
}
container.AddFormula(mf);
}
public void TestGetIsotopes()
{
var iso1 = new IsotopeContainer();
var iso2 = new IsotopeContainer();
var isoP = new IsotopePattern(new[] { iso1, iso2 })
{
MonoIsotope = iso1
};
Assert.AreEqual(iso1, isoP.Isotopes[0]);
Assert.AreEqual(iso2, isoP.Isotopes[1]);
}
/// <summary>
/// Search and find the closest difference in an array in terms of mass and
/// intensity. Always return the position in this List.
/// </summary>
/// <param name="isoContainer"></param>
/// <param name="pattern"></param>
/// <returns></returns>
private int GetClosestDataDiff(IsotopeContainer isoContainer, IsotopePattern pattern)
{
double diff = 100;
int posi = -1;
for (int i = 0; i < pattern.Isotopes.Count; i++)
{
double tempDiff = Math.Abs((isoContainer.Mass) - pattern.Isotopes[i].Mass);
if (tempDiff <= (Tolerance / isoContainer.Mass) && tempDiff < diff)
{
diff = tempDiff;
posi = i;
}
}
return(posi);
}
/// <summary>
/// Return the isotope pattern normalized to the highest abundance.
/// </summary>
/// <param name="isotopeP">The IsotopePattern object to normalize</param>
/// <returns>The IsotopePattern normalized</returns>
public static IsotopePattern Normalize(IsotopePattern isotopeP)
{
IsotopeContainer isoHighest = null;
double biggestAbundance = 0;
/* Extraction of the isoContainer with the highest abundance */
foreach (var isoContainer in isotopeP.Isotopes)
{
double abundance = isoContainer.Intensity;
if (biggestAbundance < abundance)
{
biggestAbundance = abundance;
isoHighest = isoContainer;
}
}
IsotopePattern isoNormalized;
{
/* Normalize */
var newIsotopes = new List <IsotopeContainer>();
IsotopeContainer monoIsotope = null;
foreach (var isoContainer in isotopeP.Isotopes)
{
var inten = isoContainer.Intensity / isoHighest.Intensity;
var icClone = (IsotopeContainer)isoContainer.Clone();
icClone.Intensity = inten;
if (isoHighest.Equals(isoContainer))
{
monoIsotope = icClone;
}
newIsotopes.Add(icClone);
}
isoNormalized = new IsotopePattern(newIsotopes);
if (monoIsotope != null)
{
isoNormalized.MonoIsotope = monoIsotope;
}
isoNormalized.Charge = isotopeP.Charge;
}
return(isoNormalized);
}
public void TestClone()
{
IsotopeContainer isoC = new IsotopeContainer();
IMolecularFormula formula = builder.NewMolecularFormula();
isoC.Formula = formula;
double mass = 130.00;
isoC.Mass = mass;
double intensity = 130.00;
isoC.Intensity = intensity;
IsotopeContainer clone = (IsotopeContainer)isoC.Clone();
Assert.AreEqual(mass, clone.Mass, 0.001);
Assert.AreEqual(intensity, clone.Intensity, 0.001);
Assert.AreEqual(formula, clone.Formula);
}
/// <summary>
/// Normalize the intensity (relative abundance) of all isotopes in relation
/// of the most abundant isotope.
/// </summary>
/// <param name="isopattern">The IsotopePattern object</param>
/// <param name="minIntensity">The minimum abundance</param>
/// <returns>The IsotopePattern cleaned</returns>
private static IsotopePattern CleanAbundance(IsotopePattern isopattern, double minIntensity)
{
double intensity;
double biggestIntensity = 0;
foreach (var sc in isopattern.Isotopes)
{
intensity = sc.Intensity;
if (intensity > biggestIntensity)
{
biggestIntensity = intensity;
}
}
foreach (var sc in isopattern.Isotopes)
{
intensity = sc.Intensity;
intensity /= biggestIntensity;
if (intensity < 0)
{
intensity = 0;
}
sc.Intensity = intensity;
}
var sortedIsoPattern = new IsotopePattern
{
MonoIsotope = new IsotopeContainer(isopattern.Isotopes[0])
};
for (int i = 1; i < isopattern.Isotopes.Count; i++)
{
if (isopattern.Isotopes[i].Intensity >= (minIntensity))
{
var container = new IsotopeContainer(isopattern.Isotopes[i]);
sortedIsoPattern.isotopes.Add(container);
}
}
return(sortedIsoPattern);
}
/// <summary>
/// Calculates the mass and abundance of all isotopes generated by adding one
/// atom. Receives the periodic table element and calculate the isotopes, if
/// there exist a previous calculation, add these new isotopes. In the
/// process of adding the new isotopes, remove those that has an abundance
/// less than setup parameter minIntensity, and remove duplicated masses.
/// </summary>
/// <param name="additional">additional isotopes to 'multiple' the current pattern by</param>
/// <returns>the calculation was successful</returns>
private IsotopePattern CalculateAbundanceAndMass(IsotopePattern current, List <IsotopeContainer> additional)
{
if (additional == null || additional.Count == 0)
{
return(current);
}
var containers = new List <IsotopeContainer>();
// Verify if there is a previous calculation. If it exists, add the new
// isotopes
if (current == null)
{
current = new IsotopePattern();
foreach (var container in additional)
{
current.isotopes.Add(container);
}
}
else
{
foreach (var container in current.Isotopes)
{
foreach (IsotopeContainer other in additional)
{
var abundance = container.Intensity * other.Intensity * 0.01;
var mass = container.Mass + other.Mass;
// merge duplicates with some resolution
var existing = FindExisting(containers, mass, resolution);
if (existing != null)
{
var newIntensity = existing.Intensity + abundance;
// moving weighted avg
existing.Mass = (existing.Mass * existing.Intensity +
mass * abundance) / newIntensity;
existing.Intensity = newIntensity;
if (storeFormula)
{
foreach (var mf in container.Formulas)
{
AddDistinctFormula(existing, Union(mf, other.Formula));
}
}
continue;
}
// Filter isotopes too small
if (abundance > minAbundance)
{
var newcontainer = new IsotopeContainer(mass, abundance);
if (storeFormula)
{
foreach (var mf in container.Formulas)
{
newcontainer.AddFormula(Union(mf, other.Formula));
}
}
containers.Add(newcontainer);
}
}
}
current = new IsotopePattern();
foreach (var container in containers)
{
current.isotopes.Add(container);
}
}
return(current);
}
public IsotopeContainer(IsotopeContainer container)
{
mass = container.mass;
intensity = container.intensity;
forms = new List <IMolecularFormula>(container.forms);
}
public void TestIsotopeContainer()
{
IsotopeContainer isoC = new IsotopeContainer();
Assert.IsNotNull(isoC);
}