コード例 #1
0
		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;
		}
コード例 #2
0
		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;
		}
コード例 #3
0
		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;
		}