public IsotopicProfile GetIsotopePattern(string empiricalFormula, double[][] aafIsoLocal)
{
var elementTable = _peptideUtils.ParseEmpiricalFormulaString(empiricalFormula);
var formulaArray = new int[5];
formulaArray[0] = getAtomCount(elementTable, "C");
formulaArray[1] = getAtomCount(elementTable, "H");
formulaArray[2] = getAtomCount(elementTable, "N");
formulaArray[3] = getAtomCount(elementTable, "O");
formulaArray[4] = getAtomCount(elementTable, "S");
double EPS = 0.001f;
var afIonIntensity = new double[100]; // store structure here
var aafIons = new double[5, 100];
double fLogTotalLast = 0;
var maxIndices = new int[5];
for (var i0 = 0; i0 < 5; i0++)
{ // iterate thru elements
var fLogAmtLight = Math.Log10(aafIsoLocal[i0][0]);
var fLogAmtHeavy = Math.Log10(aafIsoLocal[i0][1]);
for (var i1 = 0; i1 <= formulaArray[i0]; i1++)
{
var fLogTotal = fLogAmtLight * (formulaArray[i0] - i1) + fLogAmtHeavy * i1;
fLogTotal += IsotopicDistributionCalculator.LogAChooseB(formulaArray[i0], i1);
aafIons[i0, i1] = System.Math.Pow(10, fLogTotal);
maxIndices[i0] = i1;
if (i1 > 1 && fLogTotalLast > fLogTotal && aafIons[i0, i1] < EPS)
{
break;
}
fLogTotalLast = fLogTotal;
}
}
var maxOffset = 1;
for (var i = 0; i <= maxIndices[0]; i++)
{
for (var j = 0; j <= maxIndices[1]; j++)
{
for (var k = 0; k <= maxIndices[2]; k++)
{
for (var l = 0; l <= maxIndices[3]; l++)
{
for (var m = 0; m <= maxIndices[4]; m++)
{
var offset = i + j + k + 2 * l + 2 * m; // O and S are +2
var fIntTmp = aafIons[0, i] * aafIons[1, j] *
aafIons[2, k] * aafIons[3, l] * aafIons[4, m];
if (offset > maxOffset)
{
maxOffset = offset;
}
afIonIntensity[offset] += fIntTmp;
}
}
}
}
}
// normalize
double max = 0;
for (var j1 = 0; j1 <= maxOffset; j1++)
{
if (afIonIntensity[j1] > max)
{
max = afIonIntensity[j1];
}
}
for (var j1 = 0; j1 <= maxOffset; j1++)
{
afIonIntensity[j1] /= max;
}
var isoCluster = new IsotopicProfile();
for (var j1 = 0; j1 < afIonIntensity.Length && j1 <= maxOffset; j1++)
{
isoCluster.Peaklist.Add(new MSPeak(0.0f, (float)afIonIntensity[j1], 0.0f, 0.0f));
}
return(isoCluster);
}
