internal static void ConvertElementTableToFormula(
ref clsElementIsotopes elemental_isotope_composition,
Hashtable elementCounts, out DeconToolsV2.MolecularFormula formula)
{
var elements = elementCounts.Keys.GetEnumerator();
formula = new DeconToolsV2.MolecularFormula();
while (elements.MoveNext())
{
// Get the next element symbol in the table
var element = (string)elements.Current;
// Put it in a character array
var count = (int)elementCounts[element];
// find the index of the element in the AtomicInformation
var index = elemental_isotope_composition.GetElementIndex(element);
if (index == -1)
{
throw new ApplicationException(string.Concat("Unknown element ", element));
}
var atomic_count = new DeconToolsV2.AtomicCount(index, count);
var mono_mass =
elemental_isotope_composition.ElementalIsotopesList[index].Isotopes[0].Mass * count;
var avg_mass = elemental_isotope_composition.ElementalIsotopesList[index].AverageMass *
count;
formula.AddAtomicCount(atomic_count, mono_mass, avg_mass);
}
}
public MolecularFormula(MolecularFormula formula)
{
Formula = formula.Formula;
TotalAtomCount = formula.TotalAtomCount;
MonoisotopicMass = formula.MonoisotopicMass;
ElementalComposition.Clear();
ElementalComposition.AddRange(formula.ElementalComposition);
}
public void CalculateMasses(DeconToolsV2.MolecularFormula formula)
{
MonoMw = 0;
AverageMw = 0;
var numElementsFound = formula.NumElements;
for (var j = 0; j < numElementsFound; j++)
{
var elementIndex = formula.ElementalComposition[j].Index;
var atomicity = (int)formula.ElementalComposition[j].NumCopies;
if (atomicity == 0)
{
continue;
}
//int numIsotopes = ElementalIsotopeComposition.ElementalIsotopesList[elementIndex].NumberOfIsotopes;
var monoMw = ElementalIsotopeComposition.ElementalIsotopesList[elementIndex].Isotopes[0].Mass;
var avgMw = ElementalIsotopeComposition.ElementalIsotopesList[elementIndex].AverageMass;
MonoMw += atomicity * monoMw;
AverageMw += atomicity * avgMw;
}
}
private void CalcVariancesAndMassRange(int charge, DeconToolsV2.MolecularFormula formula)
{
MassVariance = 0;
var numElementsFound = formula.NumElements;
for (var elementNum = 0; elementNum < numElementsFound; elementNum++)
{
var elementIndex = formula.ElementalComposition[elementNum].Index;
var atomicity = (int)formula.ElementalComposition[elementNum].NumCopies;
var elementalVariance = ElementalIsotopeComposition.ElementalIsotopesList[elementIndex].MassVariance;
MassVariance += elementalVariance * atomicity;
}
if (charge == 0)
{
_massRange = (int)(Math.Sqrt(1 + MassVariance) * 10);
}
else
{
_massRange = (int)(Math.Sqrt(1 + MassVariance) * 10.0 / charge);
}
/* +/- 5 sd's : Multiply charged */
/* Set to nearest (upper) power of 2 */
for (var i = 1024; i > 0; i /= 2)
{
if (i < _massRange)
{
_massRange = i * 2;
i = 0;
}
}
if (_massRange <= 0)
{
_massRange = 1;
}
}
private void CalcFrequencies(int charge, int numPoints, DeconToolsV2.MolecularFormula formula)
{
int i;
int j, k;
double real, imag, freq, x, theta, r, tempr;
var numElementsInEntity = formula.NumElements;
/* Calculate first half of Frequency Domain (+)masses */
for (i = 1; i <= numPoints / 2; i++)
{
freq = (double)(i - 1) / _massRange;
r = 1;
theta = 0;
for (j = 0; j < numElementsInEntity; j++)
{
var elementIndex = formula.ElementalComposition[j].Index;
var atomicity = (int)formula.ElementalComposition[j].NumCopies;
var numIsotopes = ElementalIsotopeComposition.ElementalIsotopesList[elementIndex].NumberOfIsotopes;
var averageMass = ElementalIsotopeComposition.ElementalIsotopesList[elementIndex].AverageMass;
real = imag = 0.0;
for (k = 0; k < numIsotopes; k++)
{
double wrapFreq = 0;
var isotopeAbundance =
ElementalIsotopeComposition.ElementalIsotopesList[elementIndex].Isotopes[k].Probability;
if (numIsotopes > 1)
{
wrapFreq =
ElementalIsotopeComposition.ElementalIsotopesList[elementIndex].Isotopes[k].Mass /
charge - averageMass / charge;
if (wrapFreq < 0)
{
wrapFreq += _massRange;
}
}
x = 2 * Pi * wrapFreq * freq;
real += isotopeAbundance * Math.Cos(x);
imag += isotopeAbundance * Math.Sin(x);
}
/* Convert to polar coordinates, r then theta */
tempr = Math.Sqrt(real * real + imag * imag);
r *= Math.Pow(tempr, atomicity);
if (real > 0)
{
theta += atomicity * Math.Atan(imag / real);
}
else if (real < 0)
{
theta += atomicity * (Math.Atan(imag / real) + Pi);
}
else if (imag > 0)
{
theta += atomicity * Pi / 2;
}
else
{
theta += atomicity * -Pi / 2;
}
}
/* Convert back to real:imag coordinates and store */
_frequencyData[i - 1] = new Complex(r * Math.Cos(theta), r * Math.Sin(theta));
} /* end for(i) */
/* Calculate second half of Frequency Domain (-)masses */
for (i = numPoints / 2 + 1; i <= numPoints; i++)
{
freq = (double)(i - numPoints - 1) / _massRange;
r = 1;
theta = 0;
for (j = 0; j < numElementsInEntity; j++)
{
var elementIndex = formula.ElementalComposition[j].Index;
var atomicity = (int)formula.ElementalComposition[j].NumCopies;
var numIsotopes = ElementalIsotopeComposition.ElementalIsotopesList[elementIndex].NumberOfIsotopes;
var averageMass = ElementalIsotopeComposition.ElementalIsotopesList[elementIndex].AverageMass;
real = imag = 0;
for (k = 0; k < numIsotopes; k++)
{
double wrapFreq = 0;
var isotopeAbundance =
ElementalIsotopeComposition.ElementalIsotopesList[elementIndex].Isotopes[k].Probability;
if (numIsotopes > 1)
{
wrapFreq =
ElementalIsotopeComposition.ElementalIsotopesList[elementIndex].Isotopes[k].Mass /
charge - averageMass / charge;
if (wrapFreq < 0)
{
wrapFreq += _massRange;
}
}
x = 2 * Pi * wrapFreq * freq;
real += isotopeAbundance * Math.Cos(x);
imag += isotopeAbundance * Math.Sin(x);
}
/* Convert to polar coordinates, r then theta */
tempr = Math.Sqrt(real * real + imag * imag);
r *= Math.Pow(tempr, atomicity);
if (real > 0)
{
theta += atomicity * Math.Atan(imag / real);
}
else if (real < 0)
{
theta += atomicity * (Math.Atan(imag / real) + Pi);
}
else if (imag > 0)
{
theta += atomicity * Pi / 2;
}
else
{
theta -= atomicity * Pi / 2;
}
} /* end for(j) */
/* Convert back to real:imag coordinates and store */
_frequencyData[i - 1] = new Complex(r * Math.Cos(theta), r * Math.Sin(theta));
} /* end of for(i) */
}
/// <summary>
/// Calculate the isotope distribution
/// </summary>
/// <param name="charge"></param>
/// <param name="resolution"></param>
/// <param name="formula"></param>
/// <param name="x">mz values of isotopic profile that are above the threshold</param>
/// <param name="y">intensity values of isotopic profile that are above the threshold</param>
/// <param name="threshold"></param>
/// <param name="isotopeMzs">peak top mz's for the peaks of the isotopic profile</param>
/// <param name="isotopeIntensities">peak top intensities's for the peaks of the isotopic profile</param>
/// <param name="debug"></param>
public void CalculateDistribution(int charge, double resolution, DeconToolsV2.MolecularFormula formula, out List <double> x,
out List <double> y, double threshold, out List <double> isotopeMzs, out List <double> isotopeIntensities,
bool debug = false)
{
/* Calculate mono and average mass */
CalculateMasses(formula);
if (debug)
{
Console.Error.WriteLine("MonoMW =" + MonoMw + " AverageMW =" + AverageMw);
}
/* Calculate mass range to use based on molecular variance */
CalcVariancesAndMassRange(charge, formula);
if (debug)
{
Console.Error.WriteLine("Variance =" + MassVariance + " Mass Range =" + _massRange);
}
_minMz = AverageMw / charge + (ChargeCarrierMass - MercuryCache.ElectronMass) - _massRange * 1.0 / 2;
_maxMz = _minMz + _massRange;
PointsPerAmu = MercurySize / _massRange; /* Use maximum of 2048 real, 2048 imag points */
// calculate Ap_subscript to from requested Res
double aPSubscript;
if (charge == 0)
{
aPSubscript = AverageMw / resolution * MercurySize * 2.0 / _massRange;
}
else
{
aPSubscript = AverageMw / (resolution * Math.Abs(charge)) * MercurySize * 2.0 / _massRange;
}
/* Allocate memory for Axis arrays */
var numPoints = _massRange * PointsPerAmu;
_frequencyData = new Complex[numPoints];
if (charge == 0)
{
charge = 1;
}
if (debug)
{
Console.Error.WriteLine("MINMZ = " + _minMz + " MAXMZ = " + _maxMz);
Console.Error.WriteLine("Num Points per AMU = " + PointsPerAmu);
}
CalcFrequencies(charge, numPoints, formula);
/* Apodize data */
double apResolution = 1; /* Resolution used in apodization. Not used yet */
Apodize(numPoints, apResolution, aPSubscript);
Fourier.Inverse(_frequencyData, FourierOptions.NumericalRecipes);
// myers changes this line to Realft(FreqData,NumPoints,-1);
/*
* [gord] 'OutputData' fills 'x', 'y'
* [gord] x = mz values of isotopic profile that are above the threshold
* [gord] y = intensity values of isotopic profile that are above the threshold
* [gord] isotopeMzs = peak top mz's for the peaks of the isotopic profile
* [gord] isotopeIntensities = peak top intensities's for the peaks of the isotopic profile
*/
OutputData(numPoints, charge, out x, out y, threshold, out isotopeMzs, out isotopeIntensities);
//NormalizeToPercentIons(vect_y);
}