public void EmptyPeptideFormulaIsH2O()
        {
            Peptide pepA = new Peptide();
            ChemicalFormula h2O = new ChemicalFormula("H2O");
            ChemicalFormula formulaB;
            pepA.TryGetChemicalFormula(out formulaB);

            Assert.AreEqual(h2O, formulaB);
        }

        public void ClearNTerminusMod()
        {
            ChemicalFormula formula = new ChemicalFormula("Fe");
            _mockPeptideEveryAminoAcid.SetModification(formula, Terminus.N);

            _mockPeptideEveryAminoAcid.ClearModifications(Terminus.N);

            Assert.IsNull(_mockPeptideEveryAminoAcid.NTerminusModification);
        }

        public void ChemicalFormulaGeneratorContainsFormula()
        {
            ChemicalFormulaGenerator generator = new ChemicalFormulaGenerator(new ChemicalFormula("H2O"));

            List<ChemicalFormula> formulas = generator.AllFormulas().ToList();
            ChemicalFormula ho = new ChemicalFormula("HO");

            Assert.Contains(ho, formulas);
        }

        public void AddFormulaToItself()
        {
            ChemicalFormula formulaA = new ChemicalFormula("C2H3NO");
            ChemicalFormula formulaB = new ChemicalFormula("C4H6N2O2");

            formulaA.Add(formulaA);

            Assert.AreEqual(formulaA, formulaB);
        }

 internal AminoAcid(string name, char oneLetterAbbreviation, string threeLetterAbbreviation, ChemicalFormula chemicalFormula, ModificationSites site)
 {
     Name = name;
     Letter = oneLetterAbbreviation;
     Symbol = threeLetterAbbreviation;
     ChemicalFormula = chemicalFormula;
     MonoisotopicMass = ChemicalFormula.MonoisotopicMass;
     Site = site;
 }

        public void ClearAllMods()
        {
            ChemicalFormula formula = new ChemicalFormula("Fe");
            _mockPeptideEveryAminoAcid.SetModification(formula, ModificationSites.All);

            _mockPeptideEveryAminoAcid.ClearModifications();

            Assert.AreEqual("ACDEFGHIKLMNPQRSTVWY", _mockPeptideEveryAminoAcid.ToString());
        }

        public void AddIChemicalFormulaToFormula()
        {
            ChemicalFormula formulaA = new ChemicalFormula("C2H3NO");
            IChemicalFormula formulaB = new ChemicalFormula("H2O");
            ChemicalFormula formulaC = new ChemicalFormula("C2H5NO2");

            formulaA.Add(formulaB);

            Assert.AreEqual(formulaA, formulaC);
        }

        public void AddElementToFormula()
        {
            ChemicalFormula formulaA = new ChemicalFormula("C2H3NO");
            ChemicalFormula formulaB = new ChemicalFormula("C2H3N2O");

            Element n = Element.PeriodicTable["N"];

            formulaA.Add(n, 1);

            Assert.AreEqual(formulaA, formulaB);
        }

        public void AddIsotopeToFormula()
        {
            ChemicalFormula formulaA = new ChemicalFormula("C2H3NO");
            ChemicalFormula formulaB = new ChemicalFormula("C2H4NO");

            Isotope h1 = Element.PeriodicTable["H"][1];

            formulaA.Add(h1, 1);

            Assert.AreEqual(formulaA, formulaB);
        }

        /// <summary>
        /// Basic overview of how chemical formulas can be used and modified
        /// </summary>
        private static void ChemicalFormulaExamples()
        {
            Console.WriteLine("**Chemical Formula Examples**");

            // Simple chemical formula creation
            ChemicalFormula formula1 = new ChemicalFormula("C2H3NO");
            WriteFormulaToConsole(formula1);

            // Input order does not matter
            ChemicalFormula formula2 = new ChemicalFormula("NH3C2O");
            WriteFormulaToConsole(formula2);

            // Formulas are identicial if they have the exact same type of elements and count
            Console.WriteLine("Are {0} and {1} equivalent? {2}", formula1, formula2, formula1.Equals(formula2));

            // You can modify exisiting chemical formulas in many ways.
            // You can add a chemical formula to a chemical formula
            formula1.Add(formula2);
            WriteFormulaToConsole(formula1);
            Console.WriteLine("Are {0} and {1} equivalent? {2}", formula1, formula2, formula1.Equals(formula2));

            // You can completely remove an element from a chemical formula
            formula1.Remove("C");
            WriteFormulaToConsole(formula1);

            // Even negative values are possible if not physically possible
            formula1.Remove(formula2);
            WriteFormulaToConsole(formula1);

            // Implicit arithmetic is also possible (supports +, -, and *)
            ChemicalFormula formula3 = formula2 - formula1;
            WriteFormulaToConsole(formula3);
            ChemicalFormula formula4 = formula3 + formula1;
            WriteFormulaToConsole(formula4);
            ChemicalFormula formula5 = formula2*5;
            WriteFormulaToConsole(formula5);

            // Formulas consist of a dictionary of isotopes and count, and by default, the most common (abundant) isotope of an element
            // is included (i.e. Carbon 12 instead of Carbon 13). You can explicitly state that you want another isotope in a chemical formula
            // by this notation: <Element Symbol>{<Mass Number>} (e.g. C{13}, N{15}, etc..)

            formula1 = new ChemicalFormula("C2C{13}2H3NO");
            formula2 = new ChemicalFormula("C4H3NO");

            WriteFormulaToConsole(formula1);
            WriteFormulaToConsole(formula2);

            Console.WriteLine("Are {0} and {1} equivalent? {2}", formula1, formula2, formula1.Equals(formula2));

            // No need to specify the mass number of the most abundant isotope for an element
            formula3 = new ChemicalFormula("C{12}2C2H3NO");
            formula4 = new ChemicalFormula("C4H3NO");
            Console.WriteLine("Are {0} and {1} equivalent? {2}", formula3, formula4, formula3.Equals(formula4));
        }

        /// <summary>
        /// 
        /// </summary>
        /// <param name="argCompond"></param>
        /// <param name="argTheoreticalMonoIdx"></param>
        /// <param name="argIntensities"></param>
        /// <returns></returns>
        public static double IntensityNormalizationFactorByIsotope(COL.GlycoLib.GlycanCompound argCompond, int argNumOfLabelingSite, double[] argIntensities, float argPurity)
        {
            ChemicalFormula MonoChemFormula = new ChemicalFormula();
            MonoChemFormula.Add("C", argCompond.Carbon+argCompond.Carbon13);
            MonoChemFormula.Add("H", argCompond.Hydrogen+argCompond.Deuterium);
            MonoChemFormula.Add("O", argCompond.Oxygen);
            //if (argCompond.Carbon13 != 0)
            //{
            //    MonoChemFormula.Add("C{13}", argCompond.Carbon13);
            //}
            //if (argCompond.Deuterium != 0)
            //{
            //    MonoChemFormula.Add("D", argCompond.Deuterium);
            //}
            if (argCompond.Sodium != 0)
            {
                MonoChemFormula.Add("Na", argCompond.Sodium);
            }
            if (argCompond.Nitrogen != 0)
            {
                MonoChemFormula.Add("N", argCompond.Nitrogen);
            }
            IsotopicDistribution ID = new IsotopicDistribution();
            MZPeak[] Peaks=  ID.CalculateDistribuition(MonoChemFormula,7, IsotopicDistribution.Normalization.BasePeak).GetPeaks().ToArray();
            double[] isotopeRatio = new double[7];
            for (int i = 0; i < 7; i++)
            {
                isotopeRatio[i] = Peaks[i].Intensity;
            }
            double[] CorrectedIntensities = (double[] )argIntensities.Clone();

            //Isotope Correction
            for (int i = 0; i <= 2; i++)
            {
                double Ratio = CorrectedIntensities[i]/ isotopeRatio[0];
                for (int j = i; j < 7; j++)
                {
                    CorrectedIntensities[j] = CorrectedIntensities[j] - (isotopeRatio[j-i] * Ratio );
                }
            }

            double isotopeCorrectionFactor = CorrectedIntensities[3] / argIntensities[3];

            // Purity Correction
            //double PurityCorrection = Math.Pow(argPurity, argNumOfLabelingSite);

            return isotopeCorrectionFactor;
        }

        public void RemoveZeroIsotopeFromFromula()
        {
            ChemicalFormula formulaA = new ChemicalFormula("C2H3NO");
            ChemicalFormula formulaB = new ChemicalFormula("C2H3NO");

            formulaA.Remove(Element.PeriodicTable["H"][1], 0);

            Assert.AreEqual(formulaA, formulaB);
        }

        public void RemoveNullIsotopeFromFromula()
        {
            ChemicalFormula formulaA = new ChemicalFormula("C2H3NO");
            ChemicalFormula formulaB = new ChemicalFormula("C2H3NO");

            formulaA.Remove(NullIsotope);

            Assert.AreEqual(formulaA, formulaB);
        }

        public void RemoveNonExistantIsotopeFromFromula()
        {
            ChemicalFormula formulaA = new ChemicalFormula("C2H5NO2");
            ChemicalFormula formulaB = new ChemicalFormula("Fe");
            ChemicalFormula formulaC = new ChemicalFormula("C2H5Fe-1NO2");

            formulaA.Remove(formulaB);

            Assert.AreEqual(formulaA, formulaC);
        }

        public void RemoveIsotopeFromFromulaEquality()
        {
            ChemicalFormula formulaA = new ChemicalFormula("C2H3NO");
            ChemicalFormula formulaB = new ChemicalFormula("C2H3O");

            formulaA.Remove("N", 1);

            Assert.AreEqual(formulaA, formulaB);
        }

        public void RemoveFormulaFromFromula()
        {
            ChemicalFormula formulaA = new ChemicalFormula("C2H5NO2");
            ChemicalFormula formulaB = new ChemicalFormula("H2O");
            ChemicalFormula formulaC = new ChemicalFormula("C2H3NO");

            formulaA.Remove(formulaB);

            Assert.AreEqual(formulaA, formulaC);
        }

        public void AddLargeIsotopeToFormula()
        {
            ChemicalFormula formulaA = new ChemicalFormula("C2H3NO");
            ChemicalFormula formulaB = new ChemicalFormula("C2H3NOFe");

            Isotope fe = Element.PeriodicTable["Fe"].PrincipalIsotope;

            formulaA.Add(fe, 1);

            Assert.AreEqual(formulaA, formulaB);
        }

        public void UniqueIsotopes()
        {
            ChemicalFormula formulaA = new ChemicalFormula("C2H3NO");

            Assert.AreEqual(4, formulaA.IsotopeCount);
        }

        public void UniqueElements()
        {
            ChemicalFormula formulaA = new ChemicalFormula("C2H3NO");

            Assert.AreEqual(4, formulaA.ElementCount);
        }

        public void TotalNeutrons()
        {
            ChemicalFormula formulaA = new ChemicalFormula("C2H3NO");

            Assert.AreEqual(19, formulaA.GetNeutronCount());
        }