public void getIsotopicProfileTest1()
{
var utils = new PeptideUtils();
var formula = utils.GetEmpiricalFormulaForPeptideSequence("SAMPLERPAMPLERSAMPLERPAMPLERSAMPLERPAMPLERSAMPLERPAMPLER");
var iso1 = isotopicDistributionCalculator.GetIsotopePattern(formula);
PeakUtilities.TrimIsotopicProfile(iso1, 0.001);
var tomGen = new TomIsotopicPattern();
var iso2 = tomGen.GetIsotopePattern(formula);
PeakUtilities.TrimIsotopicProfile(iso2, 0.001);
for (var i = 0; i < iso1.Peaklist.Count; i++)
{
var roundedI1 = (decimal)Math.Round(iso1.Peaklist[i].Height, 2);
var roundedI2 = (decimal)Math.Round(iso2.Peaklist[i].Height, 2);
Assert.AreEqual(roundedI1, roundedI2);
}
TestUtilities.DisplayIsotopicProfileData(iso1);
}
public IsotopicProfile GetDHIsotopicProfile2(TargetBase mt, double lowpeakCutoff, double fractionLabeling, double molarMixingofH)
{
Check.Require(mt != null, "Mass tag not defined");
Check.Require(mt.IsotopicProfile != null, "Mass tag's theor isotopic profile not defined");
Check.Require(mt.ChargeState != 0, "Can't have a charge state of '0'");
//int numNitrogens = mt.GetAtomCountForElement("N");
var numDeuterium = 0;
//_isotopicDistributionCalculator.SetLabeling("H", H_ISOTOPE_NUMBER, this.HLabelingAmount, D_ISOTOPE_NUMBER, this.DLabelingAmount);
var hydrogenTheoreticalProfile = _isotopicDistributionCalculator.GetIsotopePattern(mt.EmpiricalFormula);
var deuteriumTheoreticalProfile = _isotopicDistributionCalculator.GetIsotopePattern(mt.EmpiricalFormula);
HLabelingAmount = molarMixingofH;
DLabelingAmount = 1 - molarMixingofH;
//convert to floats
var labelingAmountFraction = Convert.ToSingle(fractionLabeling);
var HLabelingAmountMix = Convert.ToSingle(HLabelingAmount);
var DLabelingAmountMix = Convert.ToSingle(DLabelingAmount);
//initialization
float maxHeightForNormalization = 0;
if (hydrogenTheoreticalProfile.Peaklist.Count > 0)
{
maxHeightForNormalization = hydrogenTheoreticalProfile.Peaklist[0].Height * HLabelingAmountMix;
}
//add deuterated peaks as an offset index
for (var i = 0; i < hydrogenTheoreticalProfile.Peaklist.Count; i++)
{
var peakH = hydrogenTheoreticalProfile.Peaklist[i];
MSPeak peakD;
if (i == 0) //initial peak where there is no D contribution
{
peakD = new MSPeak(0);
}
else
{
peakD = deuteriumTheoreticalProfile.Peaklist[i - 1];
}
var contributionH = peakH.Height * HLabelingAmountMix;
var contributionD = (1 - labelingAmountFraction) * peakD.Height * DLabelingAmountMix + labelingAmountFraction * peakD.Height * DLabelingAmountMix;
peakH.Height = contributionH + contributionD;
//peakH.Height = peakH.Height + (1-Convert.ToSingle(fractionLabeling)) * peakD.Height +Convert.ToSingle(fractionLabeling) * peakD.Height;
//find true hightes peak in combined distribusion
if (peakH.Height > maxHeightForNormalization)
{
maxHeightForNormalization = peakH.Height;
}
}
//rename for clarity
var labeledTheoreticalProfile = hydrogenTheoreticalProfile;
//normalize to 1
foreach (var peak in labeledTheoreticalProfile.Peaklist)
{
peak.Height /= maxHeightForNormalization;
}
//should be good up to here
addMZInfoToTheorProfile(mt.IsotopicProfile, labeledTheoreticalProfile, numDeuterium, mt.ChargeState);//Keep this as the H mass?
//_isotopicDistributionCalculator.ResetToUnlabeled();
PeakUtilities.TrimIsotopicProfile(labeledTheoreticalProfile, lowpeakCutoff);
labeledTheoreticalProfile.ChargeState = mt.ChargeState;
return(labeledTheoreticalProfile);
}