public void SetElementalIsotopeComposition(ElementIsotopes elementIsotopes)
{
_elementIsotopeAbundance = elementIsotopes;
_hydrogenElementIndex = _elementIsotopeAbundance.GetElementIndex("H");
if (!_averagineFormula.IsAssigned())
{
AveragineFormula = DefaultProteinAveragineFormula;
}
}
public void SetMolecularFormula(string molFormula, ElementIsotopes atomicInformation)
{
Formula = molFormula;
var formula = molFormula;
TotalAtomCount = 0;
MonoisotopicMass = 0;
ElementalComposition.Clear();
var validator = new Regex(@"^(\s*[A-Z][a-z]?\s*\d*\.?\d*)*\s*$", RegexOptions.CultureInvariant);
if (!validator.IsMatch(molFormula))
{
throw new Exception("Molecular formula specified was invalid. Format required is one or more " +
"groups similar to \"[atomic symbol][count]\", where atomic symbol is an " +
"uppercase letter that may be followed by a lowercase letter, and count " +
"is a number that consists of numeric digits and maybe one decimal point.");
}
var grouper = new Regex(@"([A-Z][a-z]?)\s*(\d*\.?\d*)", RegexOptions.CultureInvariant);
var groups = grouper.Matches(molFormula);
foreach (Match group in groups)
{
var match = group.Groups;
// match[0] returns the entire match, match[1] and match[2] will have the individual groups
var atomicSymbol = match[1].Value;
var countStr = match[2].Value;
double count = 1;
if (!string.IsNullOrWhiteSpace(countStr))
{
count = Convert.ToDouble(countStr.Trim());
}
// 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);
}
ElementalComposition.Add(new AtomicCount(elementIndex, count));
TotalAtomCount += count;
MonoisotopicMass += atomicInformation.ElementalIsotopesList[elementIndex].Isotopes[0].Mass * count;
AverageMass += atomicInformation.ElementalIsotopesList[elementIndex].AverageMass * count;
}
/*
* // Regular expressions simplify this code so much. See above.
* var formulaLength = formula.Length;
* var index = 0;
* //var numAtoms = atomicInformation.GetNumElements();
* 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;
* }
* count = Convert.ToDouble(formula.Substring(startIndex, stopIndex - startIndex));
* //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);
* }
* ElementalComposition.Add(new AtomicCount(elementIndex, count));
* index = stopIndex;
* TotalAtomCount += count;
* MonoisotopicMass += atomicInformation.ElementalIsotopesList[elementIndex].Isotopes[0].Mass * count;
* AverageMass += atomicInformation.ElementalIsotopesList[elementIndex].AverageMass * count;
* }*/
}
