private IsotopicDistribution GetDistribution(IChemicalFormula formula, double fineResolution, double minProbability, double molecularWeightResolution)
{
var a = GetNewFineAndMergeResolutions(fineResolution);
fineResolution = a.Item1;
double _mergeFineResolution = a.Item2;
var elementalComposition = new List <List <Composition> >();
// Get all the unique elements that might have isotopes
foreach (var elementAndCount in formula.GetElements())
{
int count = elementAndCount.Count;
var isotopeComposition = new List <Composition>();
foreach (Isotope isotope in elementAndCount.Entity.Isotopes.OrderBy(iso => iso.AtomicMass))
{
var 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 / molecularWeightResolution + 0.5);
}
}
IsotopicDistribution dist = CalculateFineGrain(elementalComposition, molecularWeightResolution, _mergeFineResolution, fineResolution, minProbability);
// RTF: Not handling isotopes right now
//double additionalMass = 0;
//foreach (var isotopeAndCount in formula.Isotopes)
// additionalMass += isotopeAndCount.Key.AtomicMass * isotopeAndCount.Value;
//for (int i = 0; i < dist.masses.Length; i++)
// dist.masses[i] += additionalMass;
return(dist);
}
/// <summary>Gets the chemical formula as a string in Hill notation.</summary>
/// <param name="chemicalFormula">The chemical formula.</param>
/// <returns></returns>
public static string GetChemicalFormulaString(IChemicalFormula chemicalFormula)
{
// Local function for converting a single element to a string.
string GetElementString(IEntityCardinality <IElement> element)
{
if (element.Count == 0) // Don't write zero.
{
return(string.Empty);
}
if (element.Count == 1) // If the count is 1, just use the symbol.
{
return(element.Entity.Symbol);
}
// In all other cases need to write out count too.
return($"{element.Entity.Symbol}{element.Count}");
}
// Main function.
ICollection <IEntityCardinality <IElement> > elements = chemicalFormula.GetElements().ToList();
IList <string> elementStrings = new List <string>();
// Look for carbon first. If it exists, write it and then hydrogen.
IEntityCardinality <IElement> carbon = elements.SingleOrDefault(e => e.Entity.AtomicNumber == 6);
if (carbon != null && carbon.Count > 0)
{
elementStrings.Add(GetElementString(carbon));
elements.Remove(carbon);
IEntityCardinality <IElement> hydrogen = elements.SingleOrDefault(e => e.Entity.AtomicNumber == 1);
if (hydrogen != null && hydrogen.Count > 0)
{
elementStrings.Add(GetElementString(hydrogen));
elements.Remove(hydrogen);
}
}
// Write out the rest in alphabetical order.
foreach (IEntityCardinality <IElement> element in elements.OrderBy(e => e.Entity.Symbol))
{
if (element.Count > 0)
{
elementStrings.Add(GetElementString(element));
}
}
return(string.Join("", elementStrings));
}
/// <summary>
/// Indicates whether the current object is equal to another object of the same type.
/// </summary>
/// <param name="other">An object to compare with this object.</param>
/// <returns>
/// true if the current object is equal to the <paramref name="other">other</paramref> parameter; otherwise, false.
/// </returns>
public bool Equals(IChemicalFormula other)
{
if (other == null)
{
return(false);
}
if (this == other)
{
return(true);
}
IReadOnlyCollection <IEntityCardinality <IElement> > otherElements = other.GetElements();
if (_elements.Count != otherElements.Count)
{
return(false);
}
if (_elements.Sum(x => x.Count) != otherElements.Sum(x => x.Count))
{
return(false);
}
foreach (IEntityCardinality <IElement> element in _elements)
{
var otherElement = otherElements.SingleOrDefault(x => x.Entity.Equals(element.Entity));
// Check that the other chemical formula has this element.
if (otherElement == null)
{
return(false);
}
// Check the counts.
if (element.Count != otherElement.Count)
{
return(false);
}
}
return(true);
}
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);
}
/// <summary>
/// Adds the specified formula.
/// </summary>
/// <param name="otherFormula">The formula.</param>
/// <returns></returns>
public IChemicalFormula Add(IChemicalFormula otherFormula)
{
if (otherFormula == null)
{
return(this);
}
var otherElements = otherFormula.GetElements().ToList();
if (otherElements.Count == 0)
{
return(this);
}
var formula = new ChemicalFormula();
// Add everything from this formula
foreach (var element in _elements)
{
var otherElement = otherElements.SingleOrDefault(x => x.Entity.Equals(element.Entity));
if (otherElement == null)
{
formula._elements.Add(element);
}
else
{
formula._elements.Add(new EntityCardinality <IElement>(element.Entity, element.Count + otherElement.Count));
otherElements.Remove(otherElement);
}
}
// Add unique things from other formula
foreach (var otherElement in otherElements)
{
formula._elements.Add(otherElement);
}
return(formula);
}
private IIsotopicDistribution Mercury(IChemicalFormula cf, double limit)
{
// Build up the molecular super atom (MSA) until it is the entire molecule
// A "molecular super atom" refers to a fictitious chemical compound whose
// formula is a partial composition of the target compound.
double[]? msaMz = null;
double[]? msaAbundance = null;
double[]? tmpMz = null;
double[]? tmpAbundance = null;
bool msaInitialized = false;
foreach (IEntityCardinality <IElement> kvp in cf.GetElements())
{
uint n = (uint)kvp.Count;
if (n == 0)
{
continue;
}
int isotopeCount = kvp.Entity.Isotopes.Count;
double[] esaMz = new double[isotopeCount];
double[] esaAbundance = new double[isotopeCount];
int i = 0;
foreach (var iso in kvp.Entity.Isotopes.OrderBy(x => x.AtomicMass)) // Algorithm requires it to be sorted.
{
esaMz[i] = iso.AtomicMass;
esaAbundance[i] = iso.RelativeAbundance;
i++;
}
while (true)
{
// This is an implicit FFT that decomposes the number of a particular element
// into the sum of its powers of 2.
// Check if we need to do the MSA update - only if n is odd
if ((n & 1) == 1)
{
// MSA update
if (msaInitialized)
{
// normal update
Convolve(ref tmpMz, ref tmpAbundance, msaMz, msaAbundance, esaMz, esaAbundance);
msaMz = this.CopyArray(tmpMz);
msaAbundance = this.CopyArray(tmpAbundance);
}
else
{
// for first assignment, MSA = ESA
msaMz = this.CopyArray(esaMz);
msaAbundance = this.CopyArray(esaAbundance);
msaInitialized = true;
}
Prune(ref msaMz, ref msaAbundance, limit);
}
// The ESA update is always carried out (with the exception of the last time, i.e., when n == 1)
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;
}
}
if (msaMz != null && msaAbundance != null)
{
return(new IsotopicDistribution(msaMz, msaAbundance));
}
throw new Exception("Couldn't create masses or abundances.");
}