public double GetTracerPercent(TracerPercentFormula tracerPercentFormula)
{
if (_traceeSymbols.Count == 0)
{
return(0);
}
return(tracerPercentFormula.Dictionary.Values.Sum() / _traceeSymbols.Count);
}
public TracerPercentFormula ComputePrecursorEnrichmentAndTurnover(IDictionary <TracerFormula, double> peptideDistribution, out double turnover, out double turnoverScore, out IDictionary <TracerFormula, double> bestMatch)
{
if (peptideDistribution.Count < 3)
{
turnover = 0;
turnoverScore = 0;
bestMatch = null;
return(null);
}
var tracerFormulaIndexes = new Dictionary <TracerFormula, int>();
var observedPercentages = new DenseVector(peptideDistribution.Count);
foreach (var entry in peptideDistribution)
{
var tracerFormula = entry.Key;
observedPercentages[tracerFormulaIndexes.Count] = entry.Value;
tracerFormulaIndexes.Add(tracerFormula, tracerFormulaIndexes.Count);
}
var initialVector = DistributionToVector(GetDistribution(GetInitialTracerPercents()), tracerFormulaIndexes);
bestMatch = null;
TracerPercentFormula bestFormula = null;
double bestScore = 0;
double bestTurnover = 0;
var tracerPercentEnumerator = new TracerPercentEnumerator(_tracerDefs.Values);
while (tracerPercentEnumerator.MoveNext())
{
var tracerPercents = tracerPercentEnumerator.Current;
var distribution = GetDistribution(tracerPercents);
var newlySynthesizedVector = DistributionToVector(distribution, tracerFormulaIndexes);
var combination = FindBestCombination(observedPercentages, initialVector, newlySynthesizedVector);
if (combination == null)
{
continue;
}
if (combination[0] < 0 || combination[1] < 0 || combination.Sum() <= 0)
{
continue;
}
if (combination.Sum() <= 0)
{
continue;
}
var resultVector = initialVector.Multiply(combination[0]).Add(newlySynthesizedVector.Multiply(combination[1]));
var score = Score(observedPercentages, resultVector);
if (bestFormula == null || score > bestScore)
{
bestFormula = tracerPercents;
bestScore = score;
bestTurnover = combination[1] / (combination[0] + combination[1]);
bestMatch = tracerFormulaIndexes.ToDictionary(kv => kv.Key, kv => resultVector[kv.Value]);
}
}
turnover = bestTurnover;
turnoverScore = bestScore;
return(bestFormula);
}
public Dictionary <TracerFormula, double> GetDistribution(TracerPercentFormula tracerPercents)
{
var tracerFormulaEnumerator = new TracerFormulaEnumerator(Sequence, _tracerDefs.Values);
var result = new Dictionary <TracerFormula, double>();
while (tracerFormulaEnumerator.MoveNext())
{
result.Add(tracerFormulaEnumerator.Current, ComputeProbability(tracerFormulaEnumerator, tracerPercents));
}
return(result);
}
public AminoAcidFormulas GetAminoAcidFormulas(TracerPercentFormula tracerPercents)
{
var result = _aminoAcidFormulas;
foreach (var entry in tracerPercents)
{
var tracerDef = _tracerDefs[entry.Key];
var isotopeAbundances = result.IsotopeAbundances;
var massDistribution = isotopeAbundances[tracerDef.TraceeSymbol];
massDistribution = massDistribution.Average(tracerDef.TracerMasses, entry.Value / 100.0);
isotopeAbundances = isotopeAbundances.SetAbundances(tracerDef.TraceeSymbol, massDistribution);
result = result.SetIsotopeAbundances(isotopeAbundances);
}
return(result);
}
private double ComputeProbability(TracerFormulaEnumerator tracerFormulaEnumerator, TracerPercentFormula tracerPercents)
{
var tracerFormula = tracerFormulaEnumerator.Current;
var tracerSymbolCounts = tracerFormulaEnumerator.GetTracerSymbolCounts();
var traceePercents = tracerSymbolCounts.Keys.ToDictionary(s => s, s => 1.0);
var result = 1.0;
foreach (var tracerDef in _tracerDefs.Values)
{
int tracerTraceeCount = tracerSymbolCounts[tracerDef.TraceeSymbol];
int tracerCount = tracerFormula.GetElementCount(tracerDef.Name);
double probability = Math.Pow(tracerPercents.GetElementCount(tracerDef.Name) / 100, tracerCount)
* Choose(tracerTraceeCount, tracerCount);
result *= probability;
tracerSymbolCounts[tracerDef.TraceeSymbol] = tracerTraceeCount - tracerCount;
traceePercents[tracerDef.TraceeSymbol] = traceePercents[tracerDef.TraceeSymbol] -
tracerPercents.GetElementCount(tracerDef.Name) / 100;
}
foreach (var entry in tracerSymbolCounts)
{
result *= Math.Pow(traceePercents[entry.Key], entry.Value);
}
return(result);
}
