private static Dictionary<string, double> ParseFormula(string formula)
{
var parsedFormula = new Dictionary<string, double>();
var regexSymbols = @"\d+"; //digit at least once
var regexNumbers = @"[A-Z]{1}"; //not a digit
var pSymbols = new Regex(regexSymbols);
var pNumbers = new Regex(regexNumbers);
var symbols = pSymbols.Split(formula).Where(s => !string.IsNullOrEmpty(s)).ToArray();
var numbers = pNumbers.Split(formula);
var numberCount = 1;
for (var i = 0; i < symbols.Length; i++)
{
//create temporary atom with symbol and "configure" it
IAtom a = new Atom(symbols[i]);
var isofac = IsotopeFactory.getInstance(new ChemObject().getBuilder());
isofac.configure(a);
//fix if the digit is not written
if (string.IsNullOrEmpty(numbers[numberCount]) && numberCount > 0)
{
numbers[numberCount] = "1";
}
var mass = a.getExactMass().doubleValue();
mass = mass * double.Parse(numbers[numberCount], CultureInfo.InvariantCulture);
numberCount++;
parsedFormula[symbols[i]] = mass;
}
return parsedFormula;
}
public static Dictionary<string, double> ParseFormula(IMolecularFormula formula)
{
var parsedFormula = new Dictionary<string, double>();
var elements = MolecularFormulaManipulator.elements(formula);
foreach (var element in elements.ToWindowsEnumerable<IElement>())
{
var elementCount = MolecularFormulaManipulator.getElementCount(formula, element);
var symbol = element.getSymbol();
var a = new Atom(symbol);
var isofac = IsotopeFactory.getInstance(new ChemObject().getBuilder());
isofac.configure(a);
var mass = a.getExactMass().doubleValue();
mass = mass * elementCount;
parsedFormula[symbol] = mass;
}
return parsedFormula;
}
public static IMolecularFormula GetMolecularFormula(IAtomContainer atomContainer)
{
var formula = new MolecularFormula();
var charge = 0;
var hydrogen = new Atom("H");
foreach (var iAtom in atomContainer.atoms().ToWindowsEnumerable<IAtom>())
{
formula.addIsotope(iAtom);
charge += iAtom.getFormalCharge().intValue();
var implicitHydrogenCount = iAtom.getImplicitHydrogenCount();
var implicitHydrogenCountValue = implicitHydrogenCount != null ? implicitHydrogenCount.intValue() : (int?) null;
if (implicitHydrogenCountValue.HasValue && implicitHydrogenCountValue.Value > 0)
{
formula.addIsotope(hydrogen, implicitHydrogenCountValue.Value);
}
}
formula.setCharge(new Integer(charge));
return formula;
}