public IsotopicProfile GetIsotopePattern(string empiricalFormula, int chargeState)
{
_elementTable = EmpiricalFormulaUtilities.ParseEmpiricalFormulaString(empiricalFormula);
AddElementsToReferenceTable();
var frequencyData = new double[2 * _mercuryArraySize + 1];
double monoIsotopicMass = 0;
double averageMass = 0;
GetMonoAndAverageMass(_elementTable, out monoIsotopicMass, out averageMass);
CalculateFrequencies(_mercuryArraySize, chargeState, ref frequencyData);
Apodize(ApodizationType, _mercuryArraySize, averageMass, chargeState, ref frequencyData);
Realft(ref frequencyData);
var intensityVals = new List <double>();
var mzVals = new List <double>();
for (var i = _mercuryArraySize / 2 + 1; i <= _mercuryArraySize; i++)
{
var mz = (i - _mercuryArraySize - 1) / _pointsPerAtomicMassUnit + monoIsotopicMass / chargeState + Globals.PROTON_MASS;
var intensity = frequencyData[2 * i - 1];
mzVals.Add(mz);
intensityVals.Add(intensity);
}
for (var i = 1; i <= _mercuryArraySize / 2; i++)
{
var mz = (i - 1) / _pointsPerAtomicMassUnit + monoIsotopicMass / chargeState + Globals.PROTON_MASS;
var intensity = frequencyData[2 * i - 1];
mzVals.Add(mz);
intensityVals.Add(intensity);
}
//StringBuilder sb = new StringBuilder();
//for (int i = 0; i < intensityVals.Count; i++)
//{
// sb.Append(mzVals[i] + "\t" + intensityVals[i] + "\n");
//}
//Console.WriteLine(sb.ToString());
//Console.WriteLine();
//Console.WriteLine("Monomass= " + monoIsotopicMass.ToString("0.000000"));
//Console.WriteLine("monoMZ= " + (monoIsotopicMass/chargeState + Globals.PROTON_MASS));
//Console.WriteLine("Average mass= " + averageMass.ToString("0.000000"));
return(null);
}
public void parseUnimodStyleFormulaTest4()
{
var formula = @"H32C34N4O4Fe";
var formulaDictionary = EmpiricalFormulaUtilities.ParseEmpiricalFormulaString(formula);
Assert.AreEqual(34, formulaDictionary["C"]);
Assert.AreEqual(32, formulaDictionary["H"]);
Assert.AreEqual(1, formulaDictionary["Fe"]);
}
public void parseUnimodStyleFormulaTest1()
{
var formula = @"H(-3) N(-1)";
var formulaDictionary = EmpiricalFormulaUtilities.ParseEmpiricalFormulaString(formula);
Assert.AreEqual(-3, formulaDictionary["H"]);
Assert.AreEqual(-1, formulaDictionary["N"]);
var parsedFormula = EmpiricalFormulaUtilities.GetEmpiricalFormulaFromElementTable(formulaDictionary);
}
public void ParseUnimodStyleTest5()
{
var formula = "H(-3) 2H(3) C(-1) 13C O 15N(10)";
var formulaDictionary = EmpiricalFormulaUtilities.ParseEmpiricalFormulaString(formula);
Assert.AreEqual(-1, formulaDictionary["C"]);
Assert.AreEqual(-3, formulaDictionary["H"]);
Assert.AreEqual(1, formulaDictionary["13C"]);
Assert.AreEqual(10, formulaDictionary["15N"]);
}
public void parseUnimodStyleFormulaTest2A()
{
var formula = @"H26 2H(8) C20 N4 O5 S";
var formulaDictionary = EmpiricalFormulaUtilities.ParseEmpiricalFormulaString(formula);
Assert.AreEqual(8, formulaDictionary["2H"]);
Assert.AreEqual(26, formulaDictionary["H"]);
Assert.AreEqual(1, formulaDictionary["S"]);
var parsedFormula = EmpiricalFormulaUtilities.GetEmpiricalFormulaFromElementTable(formulaDictionary);
}
private void CalculateMZValuesForLabeledProfile(IsotopicProfile iso, string empiricalFormula, string elementLabelled, int chargeState, int lightIsotope, int heavyIsotope)
{
var elementTable = EmpiricalFormulaUtilities.ParseEmpiricalFormulaString(empiricalFormula);
var numLabelledAtoms = elementTable[elementLabelled];
for (var i = 0; i < iso.Peaklist.Count; i++)
{
var keyLightIsotope = elementLabelled + lightIsotope;
var keyHeavyIsotope = elementLabelled + heavyIsotope;
var lightIsotopeMass = Constants.Elements[elementLabelled].IsotopeDictionary[keyLightIsotope].Mass;
var heavyIsotopeMass = Constants.Elements[elementLabelled].IsotopeDictionary[keyHeavyIsotope].Mass;
var massDiff = heavyIsotopeMass - lightIsotopeMass;
var monoMZ = iso.MonoIsotopicMass / chargeState + Globals.PROTON_MASS;
var peakMZIfUnlabelled = monoMZ + (i * Globals.MASS_DIFF_BETWEEN_ISOTOPICPEAKS) / chargeState;
var monoPeakFullyLabelled = monoMZ + massDiff * numLabelledAtoms / chargeState;
var peakMZBasedOnLabeled = monoPeakFullyLabelled -
(numLabelledAtoms - i) * Globals.MASS_DIFF_BETWEEN_ISOTOPICPEAKS /
chargeState;
int peaksToUse;
if (i > numLabelledAtoms)
{
peaksToUse = numLabelledAtoms;
}
else
{
peaksToUse = i;
}
iso.Peaklist[i].XValue = peakMZBasedOnLabeled * peaksToUse / numLabelledAtoms +
peakMZIfUnlabelled * (numLabelledAtoms - peaksToUse) / numLabelledAtoms;
}
}
public void TempTest1()
{
var code = "FEQDGENYTGTIDGNMGAYAR";
var peptideUtils = new PeptideUtils();
var empiricalFormula = peptideUtils.GetEmpiricalFormulaForPeptideSequence(code);
var monomass = peptideUtils.GetMonoIsotopicMassForPeptideSequence(code);
var mztheo = monomass / 2 + DeconTools.Backend.Globals.PROTON_MASS;
Console.WriteLine(monomass + "\t" + mztheo);
var formula = EmpiricalFormulaUtilities.ParseEmpiricalFormulaString("H(3) C(2) N O");
var revisedFormula = EmpiricalFormulaUtilities.GetEmpiricalFormulaFromElementTable(formula);
var iodoMass = EmpiricalFormulaUtilities.GetMonoisotopicMassFromEmpiricalFormula(revisedFormula);
Console.WriteLine("iodomass= " + iodoMass);
}