public void TestNullArguments()
{
ChemicalFormula formulaA = new ChemicalFormula("CO");
IHasChemicalFormula ok = null;
Assert.AreEqual("item", Assert.Throws <ArgumentNullException>(() => { formulaA.Add(ok); }).ParamName);
ChemicalFormula ok2 = null;
Assert.AreEqual("formula", Assert.Throws <ArgumentNullException>(() => { formulaA.Add(ok2); }).ParamName);
Assert.AreEqual("other", Assert.Throws <ArgumentNullException>(() => { new ChemicalFormula(ok2); }).ParamName);
Element ok3 = null;
Assert.AreEqual("element", Assert.Throws <ArgumentNullException>(() => { formulaA.AddPrincipalIsotopesOf(ok3, 0); }).ParamName);
Assert.AreEqual("item", Assert.Throws <ArgumentNullException>(() => { formulaA.Remove(ok); }).ParamName);
Assert.AreEqual("formula", Assert.Throws <ArgumentNullException>(() => { formulaA.Remove(ok2); }).ParamName);
Assert.AreEqual("formula", Assert.Throws <ArgumentNullException>(() => { formulaA.IsSubsetOf(ok2); }).ParamName);
Assert.AreEqual("formula", Assert.Throws <ArgumentNullException>(() => { formulaA.IsSupersetOf(ok2); }).ParamName);
Assert.AreEqual("element", Assert.Throws <ArgumentNullException>(() => { formulaA.CountWithIsotopes(ok3); }).ParamName);
Assert.AreEqual("element", Assert.Throws <ArgumentNullException>(() => { formulaA.CountSpecificIsotopes(ok3, 0); }).ParamName);
Assert.IsFalse(formulaA.Equals(ok2));
IEnumerable <IHasChemicalFormula> ok4 = null;
Assert.AreEqual("formulas", Assert.Throws <ArgumentNullException>(() => { ChemicalFormula.Combine(ok4); }).ParamName);
Assert.AreEqual("element", Assert.Throws <ArgumentNullException>(() => { PeriodicTable.Add(ok3); }).ParamName);
Assert.AreEqual("formula", Assert.Throws <ArgumentNullException>(() => { new IsotopicDistribution(ok2); }).ParamName);
IHasMass ok5 = null;
Assert.AreEqual("objectWithMass", Assert.Throws <ArgumentNullException>(() => { ok5.ToMZ(0); }).ParamName);
var ok7 = new PhysicalObjectWithChemicalFormula("C");
}
/// <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);
}
/// <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 ChemicalForulaMyTest()
{
ChemicalFormula formula = new ChemicalFormula();
formula.Add(new ChemicalFormula("C3H5NO"));
Assert.AreEqual(PeriodicTable.GetElement("C").PrincipalIsotope.AtomicMass * 3 + PeriodicTable.GetElement("H").PrincipalIsotope.AtomicMass * 5 + PeriodicTable.GetElement("N").PrincipalIsotope.AtomicMass + PeriodicTable.GetElement("O").PrincipalIsotope.AtomicMass, formula.MonoisotopicMass);
}
public void TestAddChemicalFormula()
{
ChemicalFormula formulaB = new ChemicalFormula("C");
ChemicalFormula formulaA = new ChemicalFormula("C{12}");
formulaB.Add(formulaA);
Assert.AreEqual("CC{12}", formulaB.Formula);
}
/// <summary>
/// Combine isotope pattern
/// </summary>
/// <param name="argNumberPermethlationSite"></param>
/// <param name="argStartPurity"></param>
/// <param name="argIntensities"></param>
/// <returns></returns>
public static float Estimater3(COL.GlycoLib.GlycanCompound argCompond, int argTheoreticalMonoIdx, float[] argIntensities)
{
double[] isotopeRatio = new double[argIntensities.Length];
for (int i = 0; i < isotopeRatio.Length; i++)
{
isotopeRatio[i] = 0;
}
ChemicalFormula MonoChemFormula = new ChemicalFormula();
MonoChemFormula.Add("C", argCompond.Carbon);
MonoChemFormula.Add("H", argCompond.Hydrogen);
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);
}
double[] IsotopeDist = MonoChemFormula.GetIsotopicDistribution(10);
return(0.0f);
}
public void AddZeroSymbolToFormula()
{
ChemicalFormula formulaA = new ChemicalFormula("C2H3NO");
ChemicalFormula formulaB = new ChemicalFormula("C2H3NO");
formulaA.Add("H", 0);
Assert.AreEqual(formulaA, formulaB);
}
public void AddNullIChemicalFormulaToFormula()
{
ChemicalFormula formulaA = new ChemicalFormula("C2H3NO");
ChemicalFormula formulaB = new ChemicalFormula("C2H3NO");
formulaA.Add(NullIChemicalFormula);
Assert.AreEqual(formulaA, formulaB);
}
public void AddFormulaToItself()
{
ChemicalFormula formulaA = new ChemicalFormula("C2H3NO");
ChemicalFormula formulaB = new ChemicalFormula("C4H6N2O2");
formulaA.Add(new ChemicalFormula(formulaA));
Assert.AreEqual(formulaA, formulaB);
}
public void AddELementByAtomicNumber()
{
ChemicalFormula formulaA = new ChemicalFormula("C2H2NO");
ChemicalFormula formulaB = new ChemicalFormula("C2HNO");
formulaB.Add(1, 1);
Assert.AreEqual(formulaA, formulaB);
}
public void AddFormulaToItself()
{
ChemicalFormula formulaA = new ChemicalFormula("C2H3NO");
ChemicalFormula formulaB = new ChemicalFormula("C4H6N2O2");
formulaA.Add(formulaA);
Assert.AreEqual(formulaA, formulaB);
}
public static void TestAddLargeNegative()
{
ChemicalFormula f = ChemicalFormula.ParseFormula("CO");
f.Add("O", -10);
Assert.That(f.Formula == "C");
Assert.That(f.NumberOfUniqueElementsByAtomicNumber == 1);
Assert.That(f.MonoisotopicMass == 12);
}
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 AddIChemicalFormulaToFormula()
{
ChemicalFormula formulaA = new ChemicalFormula("C2H3NO");
IHasChemicalFormula formulaB = new PhysicalObjectWithChemicalFormula("H2O");
ChemicalFormula formulaC = new ChemicalFormula("C2H5NO2");
formulaA.Add(formulaB);
Assert.AreEqual(formulaA, formulaC);
}
public void AddNegativeFormulaToFormula()
{
ChemicalFormula formulaA = new ChemicalFormula("C2H3NO");
ChemicalFormula formulaB = new ChemicalFormula("C-1H-2");
ChemicalFormula formulaC = new ChemicalFormula("CHNO");
formulaA.Add(formulaB);
Assert.AreEqual(formulaA, formulaC);
}
public void TestChemicalFormula()
{
Residue.GetResidue('A');
Peptide A = new Peptide("A");
Residue.GetResidue('A');
ChemicalFormula ok = new ChemicalFormula(Residue.GetResidue('A').ThisChemicalFormula);
ok.Add(new ChemicalFormulaTerminus(ChemicalFormula.ParseFormula("OH")));
ok.Add(new ChemicalFormulaTerminus(ChemicalFormula.ParseFormula("H")));
Residue.GetResidue('A');
Residue.GetResidue('A');
Assert.AreEqual(ok, A.GetChemicalFormula());
}
public static void AddFormulaToFormula()
{
ChemicalFormula formulaA = ChemicalFormula.ParseFormula("C2H3NO");
ChemicalFormula formulaB = ChemicalFormula.ParseFormula("H2O");
ChemicalFormula formulaC = ChemicalFormula.ParseFormula("C2H5NO2");
formulaA.Add(formulaB);
Assert.AreEqual(formulaA, formulaC);
}
public void AddFormulaToFormula()
{
ChemicalFormula formulaA = new ChemicalFormula("C2H3NO");
ChemicalFormula formulaB = new ChemicalFormula("H2O");
ChemicalFormula formulaC = new ChemicalFormula("C2H5NO2");
formulaA.Add(formulaB);
Assert.AreEqual(formulaA, formulaC);
}
public void AddNegativeIsotopeToFormula()
{
ChemicalFormula formulaA = new ChemicalFormula("C2HH{1}2NO");
ChemicalFormula formulaB = new ChemicalFormula("C2HNO");
Isotope h1 = PeriodicTable.GetElement("H")[1];
formulaA.Add(h1, -2);
Assert.AreEqual(formulaA, formulaB);
}
public void AddZeroIsotopeToFormula()
{
ChemicalFormula formulaA = new ChemicalFormula("C2H3NO");
ChemicalFormula formulaB = new ChemicalFormula("C2H3NO");
Isotope h1 = PeriodicTable.GetElement("H")[1];
formulaA.Add(h1, 0);
Assert.AreEqual(formulaA, formulaB);
}
public static void AddIsotopeToFormula()
{
ChemicalFormula formulaA = ChemicalFormula.ParseFormula("C2H3NO");
ChemicalFormula formulaB = ChemicalFormula.ParseFormula("C2H3H{1}NO");
Isotope h1 = PeriodicTable.GetElement("H")[1];
formulaA.Add(h1, 1);
Assert.AreEqual(formulaA, formulaB);
}
public static void AddElementToFormula()
{
ChemicalFormula formulaA = ChemicalFormula.ParseFormula("C2H3NO");
ChemicalFormula formulaB = ChemicalFormula.ParseFormula("C2H3N2O");
Element n = PeriodicTable.GetElement(7);
formulaA.Add(n, 1);
Assert.AreEqual(formulaA, formulaB);
}
public void AddLargeElementToFormula()
{
ChemicalFormula formulaA = new ChemicalFormula("C2H3NO");
ChemicalFormula formulaB = new ChemicalFormula("C2H3NOFe");
Element fe = PeriodicTable.GetElement("Fe");
formulaA.Add(fe, 1);
Assert.AreEqual(formulaA, formulaB);
}
public void AddZeroElementToFormula()
{
ChemicalFormula formulaA = new ChemicalFormula("C2H3NO");
ChemicalFormula formulaB = new ChemicalFormula("C2H3NO");
Element n = PeriodicTable.GetElement("N");
formulaA.Add(n, 0);
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);
}
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 AddLargeIsotopeToFormula()
{
ChemicalFormula formulaA = new ChemicalFormula("C2H3NO");
ChemicalFormula formulaB = new ChemicalFormula("C2H3NOFe");
Isotope fe = PeriodicTable.GetElement("Fe").PrincipalIsotope;
formulaA.Add(fe, 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>
/// Gets the chemical formula of this amino acid polymer.
/// </summary>
/// <returns></returns>
public ChemicalFormula GetChemicalFormula()
{
var formula = new ChemicalFormula();
// Handle Modifications
if (ContainsModifications())
{
for (int i = 0; i < Length + 2; i++)
{
if (_modifications[i] == null)
{
continue;
}
IHasChemicalFormula chemMod = _modifications[i] as IHasChemicalFormula;
if (chemMod == null)
{
throw new MzLibException("Modification " + _modifications[i] + " does not have a chemical formula!");
}
formula.Add(chemMod.ThisChemicalFormula);
}
}
// Handle N-Terminus
formula.Add(NTerminus.ThisChemicalFormula);
// Handle C-Terminus
formula.Add(CTerminus.ThisChemicalFormula);
// Handle Amino Acid Residues
for (int i = 0; i < Length; i++)
{
formula.Add(residues[i].ThisChemicalFormula);
}
return(formula);
}
static IsoDecon()
{
//AVERAGINE
const double averageC = 4.9384;
const double averageH = 7.7583;
const double averageO = 1.4773;
const double averageN = 1.3577;
const double averageS = 0.0417;
const double fineRes = 0.125;
const double minRes = 1e-8;
for (int i = 0; i < numAveraginesToGenerate; i++)
{
double averagineMultiplier = (i + 1) / 2.0;
//Console.Write("numAveragines = " + numAveragines);
ChemicalFormula chemicalFormula = new ChemicalFormula();
chemicalFormula.Add("C", Convert.ToInt32(averageC * averagineMultiplier));
chemicalFormula.Add("H", Convert.ToInt32(averageH * averagineMultiplier));
chemicalFormula.Add("O", Convert.ToInt32(averageO * averagineMultiplier));
chemicalFormula.Add("N", Convert.ToInt32(averageN * averagineMultiplier));
chemicalFormula.Add("S", Convert.ToInt32(averageS * averagineMultiplier));
{
var chemicalFormulaReg = chemicalFormula;
IsotopicDistribution ye = IsotopicDistribution.GetDistribution(chemicalFormulaReg, fineRes, minRes);
var masses = ye.Masses.ToArray();
var intensities = ye.Intensities.ToArray();
Array.Sort(intensities, masses);
Array.Reverse(intensities);
Array.Reverse(masses);
mostIntenseMasses[i] = masses[0];
diffToMonoisotopic[i] = masses[0] - chemicalFormulaReg.MonoisotopicMass;
allMasses[i] = masses;
allIntensities[i] = intensities;
}
}
}
public ChemicalFormulaModification ToHeavyModification(bool c, bool n)
{
var formula = new ChemicalFormula();
if (c)
{
Element carbon = PeriodicTable.GetElement("C");
int carbon12 = ChemicalFormula.Count(carbon[12]);
formula.Add(carbon[12], -carbon12);
formula.Add(carbon[13], carbon12);
}
if (n)
{
Element nitrogen = PeriodicTable.GetElement("N");
int nitrogen14 = ChemicalFormula.Count(nitrogen[14]);
formula.Add(nitrogen[14], -nitrogen14);
formula.Add(nitrogen[15], nitrogen14);
}
return(new ChemicalFormulaModification(formula, "#", Site));
}
/// <summary>
/// Resolve Methods()
/// if all 'values' are the same this returns the one value otherwise you get a separated list of all values in their original order.
/// for example:
/// Notches 1,1,1,1 returns as 1
/// Notches 1,0,1,0 returns as 1|0|1|0
/// </summary>
internal static (string ResolvedString, ChemicalFormula ResolvedValue) Resolve(IEnumerable <IEnumerable <Modification> > enumerable)
{
var list = enumerable.ToList();
ChemicalFormula firstChemFormula = new ChemicalFormula();
foreach (var firstMods in list[0])
{
if (firstMods == null || firstMods.ChemicalFormula == null)
{
return("unknown", null);
}
firstChemFormula.Add(firstMods.ChemicalFormula);
}
bool equals = true;
List <ChemicalFormula> formulas = new List <ChemicalFormula>();
foreach (var anEnum in list)
{
ChemicalFormula fhere = new ChemicalFormula();
foreach (var mod in anEnum)
{
if (mod == null || mod.ChemicalFormula == null)
{
return("unknown", null);
}
fhere.Add(mod.ChemicalFormula);
}
if (!firstChemFormula.Equals(fhere))
{
equals = false;
}
formulas.Add(fhere);
}
if (!equals)
{
var returnString = GlobalVariables.CheckLengthOfOutput(string.Join("|", formulas.Select(b => b.Formula)));
return(returnString, null);
}
else
{
return(firstChemFormula.Formula, firstChemFormula);
}
}
private static (string, ChemicalFormula) Resolve(IEnumerable <IEnumerable <ModificationWithMassAndCf> > enumerable)
{
ChemicalFormula f = new ChemicalFormula();
{
var firstEnum = enumerable.First();
foreach (var mod in firstEnum)
{
if (mod == null)
{
return("unknown", null);
}
f.Add(mod.chemicalFormula);
}
}
bool equals = true;
List <ChemicalFormula> formulas = new List <ChemicalFormula>();
foreach (var anEnum in enumerable)
{
ChemicalFormula fhere = new ChemicalFormula();
foreach (var mod in anEnum)
{
if (mod == null)
{
return("unknown", null);
}
fhere.Add(mod.chemicalFormula);
}
if (!f.Equals(fhere))
{
equals = false;
}
formulas.Add(fhere);
}
if (!equals)
{
var returnString = GlobalVariables.CheckLengthOfOutput(string.Join("|", formulas.Select(b => b.Formula)));
return(returnString, null);
}
else
{
return(f.Formula, f);
}
}
public void AddNullIsotopeToFormula()
{
ChemicalFormula formulaA = new ChemicalFormula("C2H3NO");
ChemicalFormula formulaB = new ChemicalFormula("C2H3NO");
formulaA.Add(NullIsotope, 1);
Assert.AreEqual(formulaA, formulaB);
}
public void AddZeroSymbolToFormula()
{
ChemicalFormula formulaA = new ChemicalFormula("C2H3NO");
ChemicalFormula formulaB = new ChemicalFormula("C2H3NO");
formulaA.Add("H", 0);
Assert.AreEqual(formulaA, formulaB);
}
public void AddNegativeFormulaToFormula()
{
ChemicalFormula formulaA = new ChemicalFormula("C2H3NO");
ChemicalFormula formulaB = new ChemicalFormula("C-1H-2");
ChemicalFormula formulaC = new ChemicalFormula("CHNO");
formulaA.Add(formulaB);
Assert.AreEqual(formulaA, formulaC);
}
public void AddNonExistentSymbolToFormula()
{
ChemicalFormula formulaA = new ChemicalFormula("C2H3NO");
formulaA.Add("Faa", 1);
}
public void AddZeroIsotopeToFormula()
{
ChemicalFormula formulaA = new ChemicalFormula("C2H3NO");
ChemicalFormula formulaB = new ChemicalFormula("C2H3NO");
Isotope h1 = PeriodicTable.GetElement("H")[1];
formulaA.Add(h1, 0);
Assert.AreEqual(formulaA, formulaB);
}
internal static IEnumerable <Modification> ReadMods(string unimodLocation)
{
var unimodSerializer = new XmlSerializer(typeof(unimod_t));
var deserialized = unimodSerializer.Deserialize(new FileStream(unimodLocation, FileMode.Open, FileAccess.Read, FileShare.Read)) as unimod_t;
Dictionary <string, string> positionConversion = new Dictionary <string, string>()
{
{ "Anywhere", "Anywhere." },
{ "AnyNterm", "Peptide N-terminal." },
{ "AnyCterm", "Peptide C-terminal." },
{ "ProteinNterm", "N-terminal." },
{ "ProteinCterm", "C-terminal." }
};
foreach (var mod in deserialized.modifications)
{
var id = mod.title;
var ac = mod.record_id;
ChemicalFormula cf = new ChemicalFormula();
foreach (var el in mod.delta.element)
{
try
{
cf.Add(el.symbol, int.Parse(el.number));
}
catch
{
var tempCF = ChemicalFormula.ParseFormula(DictOfElements[el.symbol]);
tempCF.Multiply(int.Parse(el.number));
cf.Add(tempCF);
}
}
//TODO Add "on motif" to the ID field
foreach (var target in mod.specificity)
{
var tg = target.site;
if (tg.Length > 1)
{
tg = "X"; //I think that we should allow motifs here using the trygetmotif
}
ModificationMotif.TryGetMotif(tg, out ModificationMotif motif);
if (positionConversion.TryGetValue(target.position.ToString(), out string pos))
{
//do nothing, the new string value should be there
}
else
{
pos = null;
}
Dictionary <string, IList <string> > dblinks = new Dictionary <string, IList <string> >
{
{ "Unimod", new List <string> {
ac.ToString()
} },
};
if (target.NeutralLoss == null)
{
yield return(new Modification(_originalId: id, _modificationType: "Unimod", _target: motif, _locationRestriction: pos, _chemicalFormula: cf, _databaseReference: dblinks));
}
else
{
Dictionary <MassSpectrometry.DissociationType, List <double> > neutralLosses = null;
foreach (var nl in target.NeutralLoss)
{
ChemicalFormula cfnl = new ChemicalFormula();
if (nl.mono_mass == 0)
{
if (neutralLosses == null)
{
neutralLosses = new Dictionary <MassSpectrometry.DissociationType, List <double> >
{
{ MassSpectrometry.DissociationType.AnyActivationType, new List <double> {
0
} }
};
}
else
{
if (neutralLosses.ContainsKey(MassSpectrometry.DissociationType.AnyActivationType))
{
if (!neutralLosses[MassSpectrometry.DissociationType.AnyActivationType].Contains(0))
{
neutralLosses[MassSpectrometry.DissociationType.AnyActivationType].Add(0);
}
}//we don't need an else cuz it's already there
}
}
else
{
foreach (var el in nl.element)
{
try
{
cfnl.Add(el.symbol, int.Parse(el.number));
}
catch
{
var tempCF = ChemicalFormula.ParseFormula(DictOfElements[el.symbol]);
tempCF.Multiply(int.Parse(el.number));
cfnl.Add(tempCF);
}
}
if (neutralLosses == null)
{
neutralLosses = new Dictionary <MassSpectrometry.DissociationType, List <double> >
{
{ MassSpectrometry.DissociationType.AnyActivationType, new List <double> {
cfnl.MonoisotopicMass
} }
};
}
else
{
if (neutralLosses.ContainsKey(MassSpectrometry.DissociationType.AnyActivationType))
{
if (!neutralLosses[MassSpectrometry.DissociationType.AnyActivationType].Contains(cfnl.MonoisotopicMass))
{
neutralLosses[MassSpectrometry.DissociationType.AnyActivationType].Add(cfnl.MonoisotopicMass);
}
}//we don't need an else cuz it's already there
}
}
}
yield return(new Modification(_originalId: id, _target: motif, _locationRestriction: "Anywhere.", _modificationType: "Unimod", _chemicalFormula: cf, _databaseReference: dblinks, _neutralLosses: neutralLosses));
}
}
}
}
public void AddZeroElementToFormula()
{
ChemicalFormula formulaA = new ChemicalFormula("C2H3NO");
ChemicalFormula formulaB = new ChemicalFormula("C2H3NO");
Element n = PeriodicTable.GetElement("N");
formulaA.Add(n, 0);
Assert.AreEqual(formulaA, formulaB);
}
public void AddNonExistentSymbolToFormula()
{
ChemicalFormula formulaA = new ChemicalFormula("C2H3NO");
Assert.Throws<KeyNotFoundException>(() => formulaA.Add("Faa", 1), "The element symbol 'Faa' is not found in the periodic table");
}
public void AddNonExistentSymbolToFormula()
{
ChemicalFormula formulaA = new ChemicalFormula("C2H3NO");
Assert.Throws <KeyNotFoundException>(() => formulaA.Add("Faa", 1), "The element symbol 'Faa' is not found in the periodic table");
}
public ChemicalFormulaModification ToHeavyModification(bool c, bool n)
{
var formula = new ChemicalFormula();
if (c)
{
Element carbon = PeriodicTable.GetElement("C");
int carbon12 = ChemicalFormula.Count(carbon[12]);
formula.Add(carbon[12], -carbon12);
formula.Add(carbon[13], carbon12);
}
if (n)
{
Element nitrogen = PeriodicTable.GetElement("N");
int nitrogen14 = ChemicalFormula.Count(nitrogen[14]);
formula.Add(nitrogen[14], -nitrogen14);
formula.Add(nitrogen[15], nitrogen14);
}
return new ChemicalFormulaModification(formula, "#", Site);
}
public IEnumerable <Fragment> Fragment(FragmentTypes types, int minIndex, int maxIndex, bool calculateChemicalFormula)
{
foreach (FragmentTypes type in types.GetIndividualFragmentTypes())
{
bool isChemicalFormula = calculateChemicalFormula;
ChemicalFormula capFormula = type.GetIonCap();
bool isCTerminal = type.GetTerminus() == Terminus.C;
double monoMass = capFormula.MonoisotopicMass;
ChemicalFormula formula = new ChemicalFormula(capFormula);
IHasChemicalFormula terminus = isCTerminal ? CTerminus : NTerminus;
monoMass += terminus.MonoisotopicMass;
if (isChemicalFormula)
{
formula.Add(terminus);
}
bool first = true;
bool hasMod = _modifications != null;
for (int i = 0; i <= maxIndex; i++)
{
int aaIndex = isCTerminal ? Length - i : i - 1;
// Handle the terminus mods first in a special case
IHasMass mod;
if (first)
{
first = false;
if (hasMod)
{
mod = _modifications[aaIndex + 1];
if (mod != null)
{
monoMass += mod.MonoisotopicMass;
if (isChemicalFormula)
{
if (mod is IHasChemicalFormula modFormula)
{
formula.Add(modFormula);
}
else
{
isChemicalFormula = false;
}
}
}
}
continue;
}
monoMass += residues[aaIndex].MonoisotopicMass;
formula.Add(residues[aaIndex]);
if (hasMod)
{
mod = _modifications[aaIndex + 1];
if (mod != null)
{
monoMass += mod.MonoisotopicMass;
if (isChemicalFormula)
{
if (mod is IHasChemicalFormula modFormula)
{
formula.Add(modFormula);
}
else
{
isChemicalFormula = false;
}
}
}
}
if (i < minIndex)
{
continue;
}
if (isChemicalFormula)
{
yield return(new ChemicalFormulaFragment(type, i, formula, this));
}
else
{
yield return(new Fragment(type, i, monoMass, this));
}
}
}
}
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);
}
/// <summary>
/// Combine isotope pattern
/// </summary>
/// <param name="argNumberPermethlationSite"></param>
/// <param name="argStartPurity"></param>
/// <param name="argIntensities"></param>
/// <returns></returns>
public static float Estimater3(COL.GlycoLib.GlycanCompound argCompond,int argTheoreticalMonoIdx, float[] argIntensities)
{
double[] isotopeRatio = new double[argIntensities.Length];
for (int i = 0; i < isotopeRatio.Length; i++)
{
isotopeRatio[i] = 0;
}
ChemicalFormula MonoChemFormula = new ChemicalFormula();
MonoChemFormula.Add("C", argCompond.Carbon);
MonoChemFormula.Add("H", argCompond.Hydrogen);
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);
}
double[] IsotopeDist = MonoChemFormula.GetIsotopicDistribution(10);
return 0.0f;
}
