public void AddAtomicCount(AtomicCount cnt, double monoMass, double avgMass)
{
var numElements = ElementalComposition.Count;
for (var elemNum = 0; elemNum < numElements; elemNum++)
{
if (ElementalComposition[elemNum].Index == cnt.Index)
{
ElementalComposition[elemNum].NumCopies += cnt.NumCopies;
MonoisotopicMass += monoMass;
AverageMass += avgMass;
TotalAtomCount += cnt.NumCopies;
return;
}
}
ElementalComposition.Add(cnt);
MonoisotopicMass += monoMass;
AverageMass += avgMass;
TotalAtomCount += cnt.NumCopies;
}
public MolecularFormula GetAverageFormulaForMass(double mw)
{
// still need to add tag mass.
if (_useTag && mw > _tagMass)
{
mw -= _tagMass;
}
var empiricalFormula = new MolecularFormula();
var numElements = _averagineFormula.NumElements;
//var totalElementCount = _averagineFormula.TotalAtomCount;
empiricalFormula.ElementalComposition.Clear();
double averageMass = 0;
double monoMass = 0;
var hydrogenIndex = -1;
double totalAtomCount = 0;
for (var elementNum = 0; elementNum < numElements; elementNum++)
{
var elementCount = new AtomicCount(_averagineFormula.ElementalComposition[elementNum]);
var numAtoms = (int)(mw / _averagineFormula.MonoisotopicMass * elementCount.NumCopies + 0.5);
if (
string.Compare(_elementIsotopeAbundance.ElementalIsotopesList[elementCount.Index].Symbol, "H",
StringComparison.InvariantCulture) == 0)
{
// Hydrogen is used as the remainder mass, so we skip it in the formula calculation by assigning it to 0
// for now and later below assigning the remainder to it.
hydrogenIndex = elementNum;
numAtoms = 0;
}
else
{
var elementAvgMass = _elementIsotopeAbundance.ElementalIsotopesList[elementCount.Index].AverageMass;
var elementMonoMass =
_elementIsotopeAbundance.ElementalIsotopesList[elementCount.Index].Isotopes[0].Mass;
averageMass += elementAvgMass * numAtoms;
monoMass += elementMonoMass * numAtoms;
}
totalAtomCount += numAtoms;
elementCount.NumCopies = numAtoms;
empiricalFormula.ElementalComposition.Add(elementCount);
}
// if tag mass is enabled, add it to the formula.
if (_useTag)
{
var numElementsTag = _tagFormula.NumElements;
//var totalElementCountTag = _tagFormula.TotalAtomCount;
for (var elementNum = 0; elementNum < numElementsTag; elementNum++)
{
var elementCount = _tagFormula.ElementalComposition[elementNum];
var numAtoms = (int)elementCount.NumCopies;
var elementAvgMass = _elementIsotopeAbundance.ElementalIsotopesList[elementCount.Index].AverageMass;
var elementMonoMass =
_elementIsotopeAbundance.ElementalIsotopesList[elementCount.Index].Isotopes[0].Mass;
averageMass += elementAvgMass * numAtoms;
monoMass += elementMonoMass * numAtoms;
totalAtomCount += numAtoms;
elementCount.NumCopies = numAtoms;
// now go through each elementCount. If already added, then just add to its count.
// otherwise, create new.
var elementNumAlreadyPushed = -1;
for (var elementNumPushed = 0;
elementNumPushed < empiricalFormula.ElementalComposition.Count;
elementNumPushed++)
{
if (empiricalFormula.ElementalComposition[elementNumPushed].Index == elementCount.Index)
{
elementNumAlreadyPushed = elementNumPushed;
break;
}
}
if (elementNumAlreadyPushed == -1)
{
empiricalFormula.ElementalComposition.Add(elementCount);
}
else
{
empiricalFormula.ElementalComposition[elementNumAlreadyPushed].NumCopies +=
elementCount.NumCopies;
}
}
}
// now whatever's left over in mass, is assigned to hydrogen because it is not expected to cause
// much of a distortion in the isotope profile.
var remainderMass = mw - averageMass;
if (_useTag)
{
remainderMass += _tagMass;
}
var numHydrogens =
(int)
(remainderMass / _elementIsotopeAbundance.ElementalIsotopesList[_hydrogenElementIndex].AverageMass +
0.5);
averageMass += numHydrogens *
_elementIsotopeAbundance.ElementalIsotopesList[_hydrogenElementIndex].AverageMass;
monoMass += numHydrogens *
_elementIsotopeAbundance.ElementalIsotopesList[_hydrogenElementIndex].Isotopes[0].Mass;
totalAtomCount += numHydrogens;
if (numHydrogens > 0)
{
if (hydrogenIndex != -1)
{
empiricalFormula.ElementalComposition[hydrogenIndex].NumCopies += numHydrogens;
}
else
{
empiricalFormula.ElementalComposition.Add(new AtomicCount(_hydrogenElementIndex, numHydrogens));
}
}
empiricalFormula.MonoisotopicMass = monoMass;
empiricalFormula.AverageMass = averageMass;
empiricalFormula.TotalAtomCount = totalAtomCount;
return(empiricalFormula);
}
