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);
}
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 AddFormulaToItself()
{
ChemicalFormula formulaA = new ChemicalFormula("C2H3NO");
ChemicalFormula formulaB = new ChemicalFormula("C4H6N2O2");
formulaA.Add(formulaA);
Assert.AreEqual(formulaA, formulaB);
}
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 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 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));
}
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);
}
/// <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 RemoveElementCompletelyFromFromula()
{
ChemicalFormula formulaA = new ChemicalFormula("C2H3NO");
ChemicalFormula formulaB = new ChemicalFormula("C2NO");
formulaA.Remove(Element.PeriodicTable["H"]);
Assert.AreEqual(formulaA, formulaB);
}
public void ParsingFormulaWithSpacesAtEnd()
{
ChemicalFormula formulaA = new ChemicalFormula("C2H3NO ");
ChemicalFormula formulaB = new ChemicalFormula("C2H3NO");
Assert.AreEqual(formulaA, formulaB);
}
public static void HillNotationNoCarbonNoHydrogen()
{
ChemicalFormula formulaA = ChemicalFormula.ParseFormula("Ca5O14Br6");
Assert.AreEqual("Br6Ca5O14", formulaA.Formula);
}
public static void HillNotationNoHydrogen()
{
ChemicalFormula formulaA = ChemicalFormula.ParseFormula("NC2O");
Assert.AreEqual("C2NO", formulaA.Formula);
}
public static void ContainsSpecificIsotope()
{
ChemicalFormula formulaA = ChemicalFormula.ParseFormula("C2H5NOO{16}");
Assert.IsTrue(formulaA.ContainsSpecificIsotope(PeriodicTable.GetElement("O")[16]));
}
public static void HashCodeImmutableEquality()
{
ChemicalFormula formulaA = ChemicalFormula.ParseFormula("C2H3NO");
Assert.AreEqual(formulaA.GetHashCode(), formulaA.GetHashCode());
}
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 static void UniqueIsotopesWithHeavyIsotope()
{
ChemicalFormula formulaA = ChemicalFormula.ParseFormula("CC{13}H3NO");
Assert.AreEqual(1, formulaA.NumberOfUniqueIsotopes);
}
public static void UniqueIsotopes()
{
ChemicalFormula formulaA = ChemicalFormula.ParseFormula("C2H3NO");
Assert.AreEqual(0, formulaA.NumberOfUniqueIsotopes);
}
public static void UniqueElementsWithHeavyIsotope()
{
ChemicalFormula formulaA = ChemicalFormula.ParseFormula("CC{13}H3NO");
Assert.AreEqual(4, formulaA.NumberOfUniqueElementsByAtomicNumber);
}
public static void UniqueElements()
{
ChemicalFormula formulaA = ChemicalFormula.ParseFormula("C2H3NO");
Assert.AreEqual(4, formulaA.NumberOfUniqueElementsByAtomicNumber);
}
public static void AverageMass()
{
ChemicalFormula formulaA = ChemicalFormula.ParseFormula("C");
Assert.AreEqual(PeriodicTable.GetElement("C").AverageMass, formulaA.AverageMass);
}
public static void TotalProtons2()
{
ChemicalFormula formulaA = ChemicalFormula.ParseFormula("C{12}2H3NO");
Assert.AreEqual(30, formulaA.ProtonCount);
}
public static void HydrogenCarbonRatio()
{
ChemicalFormula formulaA = ChemicalFormula.ParseFormula("C8H4");
Assert.AreEqual(0.5, formulaA.HydrogenCarbonRatio);
}
public void RemoveElementCompletelyFromFromulaWithHeavyIsotope()
{
ChemicalFormula formulaA = new ChemicalFormula("C2C{13}H3NO");
ChemicalFormula formulaB = new ChemicalFormula("H3NO");
formulaA.Remove(Element.PeriodicTable["C"]);
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 static void ContainsIsotopesOfYe()
{
ChemicalFormula formulaA = ChemicalFormula.ParseFormula("CC{13}H3NO");
Assert.IsTrue(formulaA.ContainsIsotopesOf(PeriodicTable.GetElement("C")));
}
public static void EqualsFalse()
{
ChemicalFormula formulaA = ChemicalFormula.ParseFormula("OCHHCHN");
Assert.IsFalse(formulaA.Equals("C"));
}
public static void BadFormula()
{
Assert.Throws <MzLibException>(() => { ChemicalFormula.ParseFormula("!@#$"); }, "Input string for chemical formula was in an incorrect format");
}
public static void TestIsotopicDistribution2()
{
IsotopicDistribution.GetDistribution(ChemicalFormula.ParseFormula("AlO{16}"));
}
public static void Equals()
{
ChemicalFormula formulaA = ChemicalFormula.ParseFormula("OCHHCHN");
Assert.AreEqual(formulaA, formulaA);
}
public static void NumberOfAtoms()
{
ChemicalFormula formulaA = ChemicalFormula.ParseFormula("C2H3NO");
Assert.AreEqual(7, formulaA.AtomCount);
}
public static void CatchProbStuff()
{
ChemicalFormula formula = (ChemicalFormula.ParseFormula("C50O50"));
IsotopicDistribution.GetDistribution(formula, 0.001, 1e-50, 1e-15);
}
public static void HillNotationWithHeavyIsotopeNegativeCount()
{
ChemicalFormula formulaA = ChemicalFormula.ParseFormula("H3NC2C{13}-2O");
Assert.AreEqual("C2C{13}-2H3NO", formulaA.Formula);
}
public static void TestAnotherFormula()
{
ChemicalFormula formulaA = ChemicalFormula.ParseFormula("H{1}CC{13}2H3NO{16}");
Assert.AreEqual("CC{13}2H3H{1}NO{16}", formulaA.Formula);
}
public static void NeutronCount()
{
ChemicalFormula formulaA = ChemicalFormula.ParseFormula("C{12}O{16}");
Assert.AreEqual(14, formulaA.NeutronCount());
}
public static void NeutronCountFail()
{
ChemicalFormula formulaA = ChemicalFormula.ParseFormula("CO");
Assert.Throws <MzLibException>(() => { formulaA.NeutronCount(); }, "Cannot know for sure what the number of neutrons is!");
}
public void ParsingFormulaWithDeuterium()
{
ChemicalFormula formulaA = new ChemicalFormula("C2D3H3NO");
ChemicalFormula formulaB = new ChemicalFormula("C2H{2}3H3NO");
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 static void HillNotationNoCarbon()
{
ChemicalFormula formulaA = ChemicalFormula.ParseFormula("BrH");
Assert.AreEqual("HBr", formulaA.Formula);
}
public void TotalNeutrons()
{
ChemicalFormula formulaA = new ChemicalFormula("C2H3NO");
Assert.AreEqual(19, formulaA.GetNeutronCount());
}
public void RemoveElementCompletelyFromFromulaBySymbol()
{
ChemicalFormula formulaA = new ChemicalFormula("C2H3NO");
ChemicalFormula formulaB = new ChemicalFormula("C2NO");
formulaA.Remove("H");
Assert.AreEqual(formulaA, formulaB);
}
public void UniqueElements()
{
ChemicalFormula formulaA = new ChemicalFormula("C2H3NO");
Assert.AreEqual(4, formulaA.ElementCount);
}
public void RemoveEmptyFormulaFromFromula()
{
ChemicalFormula formulaA = new ChemicalFormula("C2H3NO");
ChemicalFormula formulaB = new ChemicalFormula("C2H3NO");
formulaA.Remove(EmptyFormula);
Assert.AreEqual(formulaA, formulaB);
}
public void UniqueIsotopes()
{
ChemicalFormula formulaA = new ChemicalFormula("C2H3NO");
Assert.AreEqual(4, formulaA.IsotopeCount);
}
public void RemoveIsotopeFromFromulaEquality()
{
ChemicalFormula formulaA = new ChemicalFormula("C2H3NO");
ChemicalFormula formulaB = new ChemicalFormula("C2H3O");
formulaA.Remove("N", 1);
Assert.AreEqual(formulaA, formulaB);
}
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);
}
static void Main(string[] args)
{
Loaders.LoadElements(@"elements.dat");
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;
for (int i = 11; i <= 11; i++)
{
double factor = Math.Pow(2, 0.5 * i);
Console.WriteLine("Approx number of amino acids: " + Convert.ToInt32(factor));
ChemicalFormula chemicalFormula = new ChemicalFormula();
chemicalFormula.Add("C", Convert.ToInt32(averageC * factor));
chemicalFormula.Add("H", Convert.ToInt32(averageH * factor));
chemicalFormula.Add("O", Convert.ToInt32(averageO * factor));
chemicalFormula.Add("N", Convert.ToInt32(averageN * factor));
chemicalFormula.Add("S", Convert.ToInt32(averageS * factor));
Console.WriteLine("Formula," + chemicalFormula.Formula);
Console.WriteLine("Monoisotopic mass," + chemicalFormula.MonoisotopicMass);
Console.WriteLine("Average mass," + chemicalFormula.AverageMass);
var numPeaks = MathNet.Numerics.Combinatorics.Combinations(Convert.ToInt32(averageC * factor) + 1, 1) *
MathNet.Numerics.Combinatorics.Combinations(Convert.ToInt32(averageH * factor) + 1, 1) *
MathNet.Numerics.Combinatorics.Combinations(Convert.ToInt32(averageO * factor) + 2, 2) *
MathNet.Numerics.Combinatorics.Combinations(Convert.ToInt32(averageN * factor) + 1, 1) *
MathNet.Numerics.Combinatorics.Combinations(Convert.ToInt32(averageS * factor) + 3, 3);
Console.WriteLine("Combinatorial number of peaks," + numPeaks);
IsotopicDistribution ye;
double fineRes;
#region Find lowest possible width that is same as widest one for zero min prob
fineRes = Math.Pow(2, -1);
ye = new IsotopicDistribution(chemicalFormula, fineRes, 0);
int firstCount = ye.Intensities.Count;
do
{
fineRes /= 2;
ye = new IsotopicDistribution(chemicalFormula, fineRes, 0);
} while (ye.Intensities.Count <= firstCount);
fineRes *= 2;
ye = new IsotopicDistribution(chemicalFormula, fineRes, 0);
Console.WriteLine(" fineRes" + ", " + fineRes);
OutputMassesAndIntensities(ye, fineRes, 0, ye.Masses.Count);
for (int j = 0; j < ye.Masses.Count - 1; j++)
{
Console.Write((j + 1) + ",");
}
Console.WriteLine("");
for (int j = 0; j < ye.Masses.Count - 1; j++)
{
Console.Write((ye.Masses[j + 1] - ye.Masses[j]) + ",");
}
Console.WriteLine("");
#endregion
#region Redo with only high probabilities
var maxIntensity = ye.Intensities.Max();
fineRes = Math.Pow(2, -1);
ye = new IsotopicDistribution(chemicalFormula, fineRes, maxIntensity / 10000);
firstCount = ye.Intensities.Count;
do
{
fineRes /= 2;
ye = new IsotopicDistribution(chemicalFormula, fineRes, maxIntensity / 10000);
} while (ye.Intensities.Count <= firstCount);
fineRes *= 2;
ye = new IsotopicDistribution(chemicalFormula, fineRes, maxIntensity / 10000);
Console.WriteLine(" fineRes" + ", " + fineRes);
OutputMassesAndIntensities(ye, fineRes, 0, ye.Masses.Count);
#endregion
//#region For 0 min probability try to reach numPeaks
//fineRes = Math.Pow(2, -2);
//do
//{
// ye = new IsotopicDistribution(chemicalFormula, fineRes, 0);
// Console.WriteLine(ye.Intensities.Count);
// fineRes /= 2;
//} while (ye.Intensities.Count < numPeaks);
//#endregion
#region For a given high resolution, use lowest allowed probability
fineRes = Math.Pow(2, -18);
double minProb = maxIntensity / 10000;
ye = new IsotopicDistribution(chemicalFormula, fineRes, minProb);
Console.WriteLine(" minProbability" + ", " + minProb);
Console.WriteLine(" fineRes" + ", " + fineRes);
OutputMassesAndIntensities(ye, fineRes, 0, ye.Masses.Count);
#endregion
#region For the selected run, zoom in
var maxInt = ye.Intensities.Skip(1).Max();
var indexOfMax = ye.Intensities.IndexOf(maxInt);
var massOfMax = ye.Masses[indexOfMax];
var filteredMasses = ye.Masses.Where(b => b > massOfMax - 0.5 && b < massOfMax + 0.5);
var lowestIndex = ye.Masses.IndexOf(filteredMasses.First());
var highestIndex = ye.Masses.IndexOf(filteredMasses.Last());
Console.WriteLine("Zoomed in:");
OutputMassesAndIntensities(ye, fineRes, lowestIndex, highestIndex);
#endregion
}
Console.WriteLine("done");
Console.Read();
}
public static void NumberOfAtomsOfNegativeFormula()
{
ChemicalFormula formulaA = ChemicalFormula.ParseFormula("C-2H-3N-1O-1");
Assert.AreEqual(-7, formulaA.AtomCount);
}
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 ProteoformRelation(Proteoform pf1, Proteoform pf2, ProteoformComparison relation_type, double delta_mass, string current_directory)
{
connected_proteoforms[0] = pf1;
connected_proteoforms[1] = pf2;
RelationType = relation_type;
DeltaMass = delta_mass;
InstanceId = instanceCounter;
lock (Sweet.lollipop) instanceCounter += 1; //Not thread safe
if (CH2 == null || HPO3 == null)
{
CH2 = ChemicalFormula.ParseFormula("C1 H2");
HPO3 = ChemicalFormula.ParseFormula("H1 O3 P1");
}
if (Sweet.lollipop.neucode_labeled)
{
lysine_count = pf1.lysine_count;
}
List <PtmSet> candidate_sets = new List <PtmSet>();
if (Sweet.lollipop.et_use_notch && (relation_type == ProteoformComparison.ExperimentalTheoretical || relation_type == ProteoformComparison.ExperimentalDecoy))
{
if (Sweet.lollipop.et_use_notch && !Sweet.lollipop.et_notch_ppm)
{
double mass = delta_mass - Sweet.lollipop.notch_tolerance_et;
while (mass <= delta_mass + Sweet.lollipop.notch_tolerance_et)
{
Sweet.lollipop.theoretical_database.possible_ptmset_dictionary_notches.TryGetValue(
Math.Round(mass, 1), out List <PtmSet> candidates);
if (candidates != null)
{
candidate_sets.AddRange(candidates);
}
mass += 0.1;
}
candidate_sets = candidate_sets.Distinct().ToList();
}
else
{
Sweet.lollipop.theoretical_database.possible_ptmset_dictionary_notches.TryGetValue(Math.Round(delta_mass, 1), out candidate_sets);
}
if (candidate_sets != null)
{
candidate_sets = candidate_sets.Where(s => Sweet.lollipop.et_notch_ppm
? Math.Abs(s.mass - delta_mass) * 1e6 / pf1.modified_mass <
Sweet.lollipop.notch_tolerance_et
: Math.Abs(s.mass - delta_mass) < Sweet.lollipop.notch_tolerance_et).ToList();
candidate_ptmset = candidate_sets.OrderBy(s => s.ptm_rank_sum).FirstOrDefault();
}
}
else if (Sweet.lollipop.ee_use_notch &&
(relation_type == ProteoformComparison.ExperimentalExperimental ||
relation_type == ProteoformComparison.ExperimentalFalse))
{
if (Sweet.lollipop.ee_use_notch && !Sweet.lollipop.ee_notch_ppm)
{
double mass = delta_mass - Sweet.lollipop.notch_tolerance_ee;
while (mass <= delta_mass + Sweet.lollipop.notch_tolerance_ee)
{
Sweet.lollipop.theoretical_database.possible_ptmset_dictionary_notches.TryGetValue(
Math.Round(mass, 1), out List <PtmSet> candidates);
if (candidates != null)
{
candidate_sets.AddRange(candidates);
}
mass += 0.1;
}
candidate_sets = candidate_sets.Distinct().ToList();
}
else
{
Sweet.lollipop.theoretical_database.possible_ptmset_dictionary_notches.TryGetValue(Math.Round(delta_mass, 1), out candidate_sets);
}
if (candidate_sets != null)
{
candidate_sets = candidate_sets.Where(s => Sweet.lollipop.ee_notch_ppm
? Math.Abs(s.mass - delta_mass) * 1e6 / pf1.modified_mass <
Sweet.lollipop.notch_tolerance_ee
: Math.Abs(s.mass - delta_mass) < Sweet.lollipop.notch_tolerance_ee).ToList();
candidate_ptmset = candidate_sets.OrderBy(s => s.ptm_rank_sum).FirstOrDefault();
}
}
else if
(relation_type == ProteoformComparison.ExperimentalTheoretical ||
relation_type == ProteoformComparison.ExperimentalDecoy)
{
if (Sweet.lollipop.peak_width_base_et > 0.09)
{
double mass = delta_mass - Sweet.lollipop.peak_width_base_et;
while (mass <= delta_mass + Sweet.lollipop.peak_width_base_et)
{
Sweet.lollipop.theoretical_database.possible_ptmset_dictionary.TryGetValue(
Math.Round(mass, 1), out List <PtmSet> candidates);
if (candidates != null)
{
candidate_sets.AddRange(candidates);
}
mass += 0.1;
}
candidate_sets = candidate_sets.Distinct().ToList();
}
else
{
Sweet.lollipop.theoretical_database.possible_ptmset_dictionary.TryGetValue(
Math.Round(delta_mass, 1), out candidate_sets);
}
if (pf2 as TheoreticalProteoform != null && candidate_sets != null && candidate_sets.Count > 0)
{
List <PtmSet> narrower_range_of_candidates = new List <PtmSet>();
if (Sweet.lollipop.et_use_notch)
{
narrower_range_of_candidates = candidate_sets;
}
else
{
narrower_range_of_candidates = candidate_sets
.Where(s => Math.Abs(s.mass - delta_mass) < Sweet.lollipop.peak_width_base_et).ToList();
}
TheoreticalProteoform t = pf2 as TheoreticalProteoform;
candidate_ptmset = Proteoform.generate_possible_added_ptmsets(narrower_range_of_candidates,
Sweet.lollipop.theoretical_database.all_mods_with_mass, t, pf2.begin, pf2.end,
pf2.ptm_set,
Sweet.lollipop.mod_rank_first_quartile, false).OrderBy(x =>
x.ptm_rank_sum +
Math.Abs(Math.Abs(x.mass) - Math.Abs(delta_mass)) *
10E-6) // major score: delta rank; tie breaker: deltaM, where it's always less than 1
.FirstOrDefault();
}
}
// Start the model (0 Da) at the mass defect of CH2 or HPO3 itself, allowing the peak width tolerance on either side
double half_peak_width = RelationType == ProteoformComparison.ExperimentalTheoretical || RelationType == ProteoformComparison.ExperimentalDecoy ?
Sweet.lollipop.peak_width_base_et / 2 :
Sweet.lollipop.peak_width_base_ee / 2;
double low_decimal_bound = half_peak_width + ((CH2.MonoisotopicMass - Math.Truncate(CH2.MonoisotopicMass)) / CH2.MonoisotopicMass) * (Math.Abs(delta_mass) <= CH2.MonoisotopicMass ? CH2.MonoisotopicMass : Math.Abs(delta_mass));
double high_decimal_bound = 1 - half_peak_width + ((HPO3.MonoisotopicMass - Math.Ceiling(HPO3.MonoisotopicMass)) / HPO3.MonoisotopicMass) * (Math.Abs(delta_mass) <= HPO3.MonoisotopicMass ? HPO3.MonoisotopicMass : Math.Abs(delta_mass));
double delta_mass_decimal = Math.Abs(delta_mass - Math.Truncate(delta_mass));
outside_no_mans_land = delta_mass_decimal <= low_decimal_bound || delta_mass_decimal >= high_decimal_bound ||
high_decimal_bound <= low_decimal_bound;
if (Sweet.lollipop.et_use_notch && (relation_type == ProteoformComparison.ExperimentalTheoretical || relation_type == ProteoformComparison.ExperimentalDecoy))
{
outside_no_mans_land = true;
}
if (Sweet.lollipop.ee_use_notch && (relation_type == ProteoformComparison.ExperimentalExperimental || relation_type == ProteoformComparison.ExperimentalFalse))
{
outside_no_mans_land = true;
}
}
public void TotalProtons()
{
ChemicalFormula formulaA = new ChemicalFormula("C2H3NO");
Assert.AreEqual(22, formulaA.GetProtonCount());
}
public void IsotopesTest()
{
var provider = new MockElementProvider();
IElement h = provider.GetElement(1);
IElement h1 = provider.GetElement(1, 1);
IElement h2 = provider.GetElement(1, 2);
// These two are equal.
ChemicalFormula formula0 = new ChemicalFormula(new[]
{
new EntityCardinality <IElement>(h, 2)
});
ChemicalFormula formula1 = new ChemicalFormula(new[]
{
new EntityCardinality <IElement>(h, 2)
});
ChemicalFormula formula2 = new ChemicalFormula(new[]
{
new EntityCardinality <IElement>(h1, 2)
});
// These two are equal.
ChemicalFormula formula3 = new ChemicalFormula(new[]
{
new EntityCardinality <IElement>(h, 1),
new EntityCardinality <IElement>(h1, 1)
});
ChemicalFormula formula4 = new ChemicalFormula(new[]
{
new EntityCardinality <IElement>(h1, 1),
new EntityCardinality <IElement>(h, 1)
});
ChemicalFormula formula5 = new ChemicalFormula(new[]
{
new EntityCardinality <IElement>(h1, 1),
new EntityCardinality <IElement>(h2, 1)
});
ChemicalFormula[] formulas = new[]
{
formula0, formula1, formula2, formula3, formula4, formula5,
};
for (int i = 0; i < 6; i++)
{
for (int j = i; j < 6; j++)
{
ChemicalFormula fi = formulas[i];
ChemicalFormula fj = formulas[j];
if (
i == j ||
(i == 0 && j == 1) ||
(i == 3 && j == 4)
)
{
Assert.IsTrue(fi.Equals(fj));
}
else
{
Assert.IsFalse(fi.Equals(fj));
}
}
}
}
public void UniqueElementsWithHeavyIsotope()
{
ChemicalFormula formulaA = new ChemicalFormula("CC{13}H3NO");
Assert.AreEqual(4, formulaA.ElementCount);
}
public static void TestChemicalFormulaWithIsotopesTMT(string formula, double mass)
{
ChemicalFormula cf = ChemicalFormula.ParseFormula(formula);
Assert.AreEqual(mass, ClassExtensions.RoundedDouble(cf.MonoisotopicMass));
}
public void UniqueIsotopesWithHeavyIsotope()
{
ChemicalFormula formulaA = new ChemicalFormula("CC{13}H3NO");
Assert.AreEqual(5, formulaA.IsotopeCount);
}
public static void TestPeptideWithSetModifications()
{
var prot = new Protein("M", null);
DigestionParams digestionParams = new DigestionParams(maxMissedCleavages: 0, minPeptideLength: 1, maxModsForPeptides: 3); // if you pass Custom Protease7 this test gets really flakey.
List <Modification> variableModifications = new List <Modification>();
ModificationMotif.TryGetMotif("M", out ModificationMotif motif);
variableModifications.Add(new Modification(_originalId: "ProtNmod", _target: motif, _locationRestriction: "N-terminal.", _chemicalFormula: ChemicalFormula.ParseFormula("H"), _monoisotopicMass: GetElement(1).PrincipalIsotope.AtomicMass));
variableModifications.Add(new Modification(_originalId: "pepNmod", _target: motif, _locationRestriction: "Peptide N-terminal.", _chemicalFormula: ChemicalFormula.ParseFormula("H"), _monoisotopicMass: GetElement(1).PrincipalIsotope.AtomicMass));
variableModifications.Add(new Modification(_originalId: "resMod", _target: motif, _locationRestriction: "Anywhere.", _chemicalFormula: ChemicalFormula.ParseFormula("H"), _monoisotopicMass: GetElement(1).PrincipalIsotope.AtomicMass));
variableModifications.Add(new Modification(_originalId: "PepCmod", _target: motif, _locationRestriction: "Peptide C-terminal.", _chemicalFormula: ChemicalFormula.ParseFormula("H"), _monoisotopicMass: GetElement(1).PrincipalIsotope.AtomicMass));
variableModifications.Add(new Modification(_originalId: "ProtCmod", _target: motif, _locationRestriction: "C-terminal.", _chemicalFormula: ChemicalFormula.ParseFormula("H"), _monoisotopicMass: GetElement(1).PrincipalIsotope.AtomicMass));
var ye = prot.Digest(digestionParams, new List <Modification>(), variableModifications).ToList();
Assert.AreEqual(3 * 2 * 3, ye.Count);
Assert.AreEqual("[H]M[H][H]", ye.Last().SequenceWithChemicalFormulas);
double m1 = 5 * GetElement("H").PrincipalIsotope.AtomicMass + Residue.ResidueMonoisotopicMass['M'] + GetElement("O").PrincipalIsotope.AtomicMass;
m1 = Math.Round(m1, 9, MidpointRounding.AwayFromZero);
double m2 = ye.Last().MonoisotopicMass;
double m3 = m1 - m2;
Assert.IsTrue(m3 < 1e-9);
}
public override void SetValue(string fieldName, string value)
{
if (MzTab.NullFieldText.Equals(value))
return;
switch (fieldName)
{
case Fields.Identifier:
Identifiers = value.Split('|').ToList();
return;
case Fields.ChemicalFormula:
ChemicalFormula = new ChemicalFormula(value);
return;
case Fields.Smiles:
Smiles = value;
return;
case Fields.InChIKey:
InChIKeys = value.Split('|').ToList();
return;
case Fields.Description:
Description = value;
return;
case Fields.ExperimentMZ:
ExperimentalMZ = double.Parse(value, CultureInfo.CurrentCulture);
return;
case Fields.TheoreticalMZ:
TheoreticalMZ = double.Parse(value, CultureInfo.CurrentCulture);
return;
case Fields.Charge:
Charge = int.Parse(value);
return;
case Fields.RetentionTime:
RetentionTimes = value.Split('|').Select(double.Parse).ToList();
return;
case Fields.TaxID:
TaxID = int.Parse(value);
return;
case Fields.Species:
Species = value;
return;
case Fields.Database:
Database = value;
return;
case Fields.DatabaseVersion:
DatabaseVersion = value;
return;
case Fields.Reliability:
Reliability = (MzTab.MetabolomicsReliabilityScore) int.Parse(value);
return;
case Fields.Uri:
Uri = new Uri(value);
return;
case Fields.SpectralReference:
SpectralReference = value;
return;
case Fields.SearchEngine:
SearchEngines = value.Split('|').Select(v => new CVParamater(v)).ToList();
return;
case Fields.Modifications:
Modifications = value;
return;
}
if (fieldName.Contains("["))
{
string condensedFieldName;
List<int> indices = MzTab.GetFieldIndicies(fieldName, out condensedFieldName);
switch (condensedFieldName)
{
case Fields.BestSearchEngineScores:
SetListValue(ref _bestSearchEngineScores, indices[0], double.Parse(value, CultureInfo.CurrentCulture));
return;
case Fields.SearchEngineScorePerMsRun:
SetListValue(ref _searchEngineScorePerMsRun, indices[0], indices[1], double.Parse(value, CultureInfo.CurrentCulture));
return;
case Fields.AbundanceAssay:
SetListValue(ref _abundanceAssays, indices[0], double.Parse(value, CultureInfo.CurrentCulture));
return;
case Fields.AbundanceStudyVariable:
SetListValue(ref _abundanceStudyVariables, indices[0], double.Parse(value, CultureInfo.CurrentCulture));
return;
case Fields.AbundanceStDevStudyVariable:
SetListValue(ref _abundanceStdevStudyVariables, indices[0], double.Parse(value, CultureInfo.CurrentCulture));
return;
case Fields.AbudnanceStdErrorStudyVariable:
SetListValue(ref _abundanceStandardErrorStudyVariables, indices[0], double.Parse(value, CultureInfo.CurrentCulture));
return;
}
}
if (fieldName.StartsWith(MzTab.OptionalColumnPrefix))
{
SetOptionalData(fieldName, value);
return;
}
throw new ArgumentException("Unexpected field name: " + fieldName);
}
public static void TestPeptideWithFixedModifications()
{
var prot = new Protein("M", null);
DigestionParams digestionParams = new DigestionParams(maxMissedCleavages: 0, minPeptideLength: 1, maxModsForPeptides: 3); // if you pass Custom Protease7 this test gets really flakey.
List <Modification> fixedMods = new List <Modification>();
ModificationMotif.TryGetMotif("M", out ModificationMotif motif);
fixedMods.Add(new Modification(_originalId: "ProtNmod", _target: motif, _locationRestriction: "N-terminal.", _chemicalFormula: ChemicalFormula.ParseFormula("H"), _monoisotopicMass: GetElement(1).PrincipalIsotope.AtomicMass));
fixedMods.Add(new Modification(_originalId: "pepNmod", _target: motif, _locationRestriction: "Peptide N-terminal.", _chemicalFormula: ChemicalFormula.ParseFormula("H"), _monoisotopicMass: GetElement(1).PrincipalIsotope.AtomicMass));
fixedMods.Add(new Modification(_originalId: "resMod", _target: motif, _locationRestriction: "Anywhere.", _chemicalFormula: ChemicalFormula.ParseFormula("H"), _monoisotopicMass: GetElement(1).PrincipalIsotope.AtomicMass));
fixedMods.Add(new Modification(_originalId: "PepCmod", _target: motif, _locationRestriction: "Peptide C-terminal.", _chemicalFormula: ChemicalFormula.ParseFormula("H"), _monoisotopicMass: GetElement(1).PrincipalIsotope.AtomicMass));
fixedMods.Add(new Modification(_originalId: "ProtCmod", _target: motif, _locationRestriction: "C-terminal.", _chemicalFormula: ChemicalFormula.ParseFormula("H"), _monoisotopicMass: GetElement(1).PrincipalIsotope.AtomicMass));
var ok = prot.Digest(digestionParams, fixedMods, new List <Modification>()).ToList();
Assert.AreEqual(1, ok.Count);
Assert.AreEqual("[:pepNmod on M]M[:resMod on M][:ProtCmod on M]", ok.First().FullSequence);
Assert.AreEqual("[H]M[H][H]", ok.First().SequenceWithChemicalFormulas);
Assert.AreEqual(5 * GetElement("H").PrincipalIsotope.AtomicMass + Residue.ResidueMonoisotopicMass['M'] + GetElement("O").PrincipalIsotope.AtomicMass, ok.Last().MonoisotopicMass, 1e-9);
}
