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 AtomicCount(AtomicCount ac)
{
Index = ac.Index;
NumCopies = ac.NumCopies;
}
public void SetMolecularFormula(string molFormula, clsElementIsotopes atomicInformation)
{
Formula = molFormula;
var formula = molFormula;
TotalAtomCount = 0;
ElementalComposition.Clear();
var formulaLength = formula.Length;
var index = 0;
//var numAtoms = atomicInformation.GetNumElements();
MonoisotopicMass = 0;
while (index < formulaLength)
{
while (index < formulaLength && (formula[index] == ' ' || formula[index] == '\t'))
{
index++;
}
var startIndex = index;
var stopIndex = startIndex;
var symbolChar = formula[stopIndex];
if (!(symbolChar >= 'A' && symbolChar <= 'Z') && !(symbolChar >= 'a' && symbolChar <= 'z'))
{
var errorStr = "Molecular Formula specified was incorrect at position: " + (stopIndex + 1) +
". Should have element symbol there";
throw new Exception(errorStr);
}
while ((symbolChar >= 'A' && symbolChar <= 'Z') || (symbolChar >= 'a' && symbolChar <= 'z'))
{
stopIndex++;
if (stopIndex == formulaLength)
{
break;
}
symbolChar = formula[stopIndex];
}
var atomicSymbol = formula.Substring(startIndex, stopIndex - startIndex);
index = stopIndex;
while (index < formulaLength && (formula[index] == ' ' || formula[index] == '\t'))
{
index++;
}
double count = 0;
if (index == formulaLength)
{
// assume that the last symbol had a 1.
count = 1;
}
startIndex = index;
stopIndex = startIndex;
symbolChar = formula[stopIndex];
var decimalFound = false;
while ((symbolChar >= '0' && symbolChar <= '9') || symbolChar == '.')
{
if (symbolChar == '.')
{
if (decimalFound)
{
// theres an error. two decimals.
var errorStr = "Molecular Formula specified was incorrect at position: " +
(stopIndex + 1) + ". Two decimal points present";
throw new Exception(errorStr);
}
decimalFound = true;
}
stopIndex++;
if (stopIndex == formulaLength)
{
break;
}
symbolChar = formula[stopIndex];
}
if (startIndex == stopIndex)
{
count = 1;
}
else
{
count = Helpers.atof(formula.Substring(index));
}
// now we should have a symbol and a count. Lets get the atomicity of the atom.
var elementIndex = atomicInformation.GetElementIndex(atomicSymbol);
if (elementIndex == -1)
{
// theres an error. two decimals.
var errorStr =
"Molecular Formula specified was incorrect. Symbol in formula was not recognize from elements provided: ";
errorStr += atomicSymbol;
throw new Exception(errorStr);
}
var currentAtom = new AtomicCount(elementIndex, count);
ElementalComposition.Add(currentAtom);
index = stopIndex;
TotalAtomCount += count;
MonoisotopicMass += atomicInformation.ElementalIsotopesList[elementIndex].Isotopes[0].Mass * count;
AverageMass += atomicInformation.ElementalIsotopesList[elementIndex].AverageMass * count;
}
}
