public void TestReplaceIsotopes()
{
ChemicalFormula formulaA = new ChemicalFormula("CC{13}2H3NO");
formulaA.Replace(PeriodicTable.GetElement("C")[13], PeriodicTable.GetElement("C")[12]);
Assert.AreEqual("CC{12}2H3NO", formulaA.Formula);
}
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);
}
private static void BenchmarkTimeGettingElementFromPeriodicTable()
{
Console.WriteLine("Starting benchmark BenchmarkTimeGettingElementFromPeriodicTable");
int numRepetitions = 100000000;
Stopwatch stopWatch = new Stopwatch();
stopWatch.Restart();
for (int i = 0; i < numRepetitions; i++)
{
var a = PeriodicTable.GetElement(1);
var b = a.Protons + a.AverageMass + 4;
}
stopWatch.Stop();
Console.WriteLine("Time for getting by atomic number: " + stopWatch.Elapsed);
stopWatch.Restart();
for (int i = 0; i < numRepetitions; i++)
{
var a = PeriodicTable.GetElement("H");
var b = a.Protons + a.AverageMass + 4;
}
stopWatch.Stop();
Console.WriteLine("Time for getting by atomic symbol: " + stopWatch.Elapsed);
Console.WriteLine("Benchmark BenchmarkTimeGettingElementFromPeriodicTable finished");
}
public void RemoveElementCompletelyFromFromulaWithHeavyIsotope()
{
ChemicalFormula formulaA = new ChemicalFormula("C2C{13}H3NO");
ChemicalFormula formulaB = new ChemicalFormula("H3NO");
formulaA.Remove(PeriodicTable.GetElement("C"));
Assert.AreEqual(formulaA, formulaB);
}
public static void RemoveElementFromFromula()
{
ChemicalFormula formulaA = ChemicalFormula.ParseFormula("C2H3NO");
ChemicalFormula formulaB = ChemicalFormula.ParseFormula("C2HNO");
formulaA.Remove(PeriodicTable.GetElement("H"), 2);
Assert.AreEqual(formulaA, formulaB);
}
public void RemoveIsotopeCompletelyFromFromula()
{
ChemicalFormula formulaA = new ChemicalFormula("C2H3NO");
ChemicalFormula formulaB = new ChemicalFormula("C2NO");
formulaA.RemoveIsotopesOf(PeriodicTable.GetElement("H"));
Assert.AreEqual(formulaA, formulaB);
}
public void RemoveNegativeElementFromFromula()
{
ChemicalFormula formulaA = new ChemicalFormula("C2H3NO");
ChemicalFormula formulaB = new ChemicalFormula("C2H5NO");
formulaA.Remove(PeriodicTable.GetElement("H"), -2);
Assert.AreEqual(formulaA, formulaB);
}
public void AddIsotopeWithExistingMassNumber()
{
Element al = PeriodicTable.GetElement("Al");
Assert.Throws <ArgumentException>(() =>
{
al.AddIsotope(27, 28, 1);
}, "Isotope with mass number " + 28 + " already exists");
}
public void RemoveZeroIsotopeFromFromula()
{
ChemicalFormula formulaA = new ChemicalFormula("C2H3NO");
ChemicalFormula formulaB = new ChemicalFormula("C2H3NO");
formulaA.Remove(PeriodicTable.GetElement("H")[1], 0);
Assert.AreEqual(formulaA, formulaB);
}
public static void RemoveElementCompletelyFromFromula()
{
ChemicalFormula formulaA = ChemicalFormula.ParseFormula("C2H3NO");
ChemicalFormula formulaB = ChemicalFormula.ParseFormula("C2NO");
formulaA.RemoveIsotopesOf(PeriodicTable.GetElement("H"));
Assert.AreEqual(formulaB, formulaA);
}
public void ThresholdProbability()
{
ChemicalFormula formulaA = new ChemicalFormula("CO");
// Only the principal isotopes have joint probability of 0.5! So one result when calcuating isotopic distribution
var a = new IsotopicDistribution(formulaA, 0.0001, 0.5);
Assert.AreEqual(1, a.Masses.Count());
Assert.IsTrue((PeriodicTable.GetElement("C").PrincipalIsotope.AtomicMass + PeriodicTable.GetElement("O").PrincipalIsotope.AtomicMass).MassEquals(a.Masses[0]));
}
public static void ThresholdProbability()
{
ChemicalFormula formulaA = ChemicalFormula.ParseFormula("CO");
// Only the principal isotopes have joint probability of 0.5! So one result when calcuating isotopic distribution
var a = IsotopicDistribution.GetDistribution(formulaA, 0.0001, 0.5);
Assert.AreEqual(1, a.Masses.Count());
Assert.IsTrue(Math.Abs((PeriodicTable.GetElement("C").PrincipalIsotope.AtomicMass + PeriodicTable.GetElement("O").PrincipalIsotope.AtomicMass - a.Masses.First())) < 1e-9);
}
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 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 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 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 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 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);
}
public static void LoadElements()
{
// has the periodic table already been loaded?
if (PeriodicTable.GetElement(1) != null)
{
return;
}
// periodic table has not been loaded yet - load it
PeriodicTableLoader.Load();
}
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 PeptideCountElements()
{
Peptide pep = new Peptide("G");
pep.AddModification(new OldSchoolModification(1));
Assert.AreEqual(5, pep.ElementCountWithIsotopes("H"));
pep.AddModification(new OldSchoolChemicalFormulaModification(ChemicalFormula.ParseFormula("H{1}")));
Assert.AreEqual(5, pep.ElementCountWithIsotopes("H")); // NOTHING HAS BEEN ADDED!
pep.AddModification(new OldSchoolChemicalFormulaModification(ChemicalFormula.ParseFormula("H{1}"), ModificationSites.G));
Assert.AreEqual(6, pep.ElementCountWithIsotopes("H"));
Isotope isotope = PeriodicTable.GetElement("H").PrincipalIsotope;
Assert.AreEqual(1, pep.SpecificIsotopeCount(isotope));
}
/// <summary>
/// Subtract the mass of a proton for every formal charge on a modification.
/// </summary>
/// <param name="_monoisotopicMass"></param>
/// <param name="_chemicalFormula"></param>
/// <param name="_databaseReference"></param>
/// <param name="formalChargesDictionary"></param>
/// <returns></returns>
private static double AdjustMonoIsotopicMassForFormalCharge(double?_monoisotopicMass, ChemicalFormula _chemicalFormula, Dictionary <string, IList <string> > _databaseReference, Dictionary <string, int> formalChargesDictionary)
{
foreach (var dbAndAccession in _databaseReference.SelectMany(b => b.Value.Select(c => b.Key + "; " + c)))
{
if (formalChargesDictionary.ContainsKey(dbAndAccession))
{
if (_monoisotopicMass.HasValue)
{
_monoisotopicMass -= formalChargesDictionary[dbAndAccession] * Constants.ProtonMass;
}
if (_chemicalFormula != null)
{
_chemicalFormula.Remove(PeriodicTable.GetElement("H"), formalChargesDictionary[dbAndAccession]);
}
break;
}
}
return((double)_monoisotopicMass);
}
private static void BenchmarkGettingIsotopes()
{
Console.WriteLine("Starting benchmark BenchmarkGettingIsotopes");
int numRepetitions = 10000000;
Stopwatch stopWatch = new Stopwatch();
long a = 0;
stopWatch.Restart();
for (int i = 0; i < numRepetitions; i++)
{
a += PeriodicTable.GetElement(20).Isotopes.Count();
}
stopWatch.Stop();
Console.WriteLine("Time for getting isotopes1: " + stopWatch.Elapsed + " a = " + a);
Console.WriteLine("Benchmark BenchmarkGettingIsotopes finished");
}
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>
/// Get a ModificationWithLocation from string representations of a modification specification. Returns null if the string representation is not recognized.
/// </summary>
/// <param name="specification"></param>
/// <returns></returns>
private static IEnumerable <Modification> ReadMod(List <string> specification, Dictionary <string, int> formalChargesDictionary)
{
// UniProt-specific fields
string uniprotAC = null;
string uniprotFT = null;
// Other fields
string id = null;
List <string> motifs = null;
string terminusLocalizationString = null;
ChemicalFormula correctionFormula = null;
double? monoisotopicMass = null;
var externalDatabaseLinks = new Dictionary <string, IList <string> >();
List <string> keywords = null;
// Custom fields
List <double> neutralLosses = null;
List <double> diagnosticIons = null;
string modificationType = null;
foreach (string line in specification)
{
if (line.Length >= 2)
{
switch (line.Substring(0, 2))
{
case "ID": // Mandatory
id = line.Substring(5);
break;
case "AC": // Do not use! Only present in UniProt ptmlist
uniprotAC = line.Substring(5);
break;
case "FT": // Optional
uniprotFT = line.Substring(5);
break;
case "TG": // Which amino acid(s) or motifs is the modification on
motifs = new List <string>(line.Substring(5).TrimEnd('.').Split(new string[] { " or " }, StringSplitOptions.None));
break;
case "PP": // Terminus localization
terminusLocalizationString = line.Substring(5);
break;
case "CF": // Correction formula
correctionFormula = ChemicalFormula.ParseFormula(line.Substring(5).Replace(" ", string.Empty));
break;
case "MM": // Monoisotopic mass difference. Might not precisely correspond to formula!
{
if (!double.TryParse(line.Substring(5), NumberStyles.Any, CultureInfo.InvariantCulture, out double thisMM))
{
throw new MzLibException(line.Substring(5) + " is not a valid monoisotopic mass");
}
monoisotopicMass = thisMM;
}
break;
case "DR": // External database links!
{
var splitString = line.Substring(5).TrimEnd('.').Split(new string[] { "; " }, StringSplitOptions.None);
if (externalDatabaseLinks.TryGetValue(splitString[0], out IList <string> val))
{
val.Add(splitString[1]);
}
else
{
externalDatabaseLinks.Add(splitString[0], new List <string> {
splitString[1]
});
}
}
break;
case "KW": // ; Separated keywords
{
keywords = new List <string>(line.Substring(5).TrimEnd('.').Split(new string[] { "; " }, StringSplitOptions.None));
}
break;
// NOW CUSTOM FIELDS:
case "NL": // Netural Losses. If field doesn't exist, single equal to 0
try
{
neutralLosses = new List <double>(line.Substring(5).Split(new string[] { " or " }, StringSplitOptions.RemoveEmptyEntries).Select(b => ChemicalFormula.ParseFormula(b).MonoisotopicMass));
}
catch (MzLibException)
{
neutralLosses = new List <double>(line.Substring(5).Split(new string[] { " or " }, StringSplitOptions.RemoveEmptyEntries).Select(b => double.Parse(b, CultureInfo.InvariantCulture)));
}
break;
case "DI": // Masses of diagnostic ions. Might just be "DI"!!! If field doesn't exist, create an empty list!
try
{
diagnosticIons = new List <double>(line.Substring(5).Split(new string[] { " or " }, StringSplitOptions.RemoveEmptyEntries).Select(b => ChemicalFormula.ParseFormula(b).MonoisotopicMass));
}
catch (MzLibException)
{
diagnosticIons = new List <double>(line.Substring(5).Split(new string[] { " or " }, StringSplitOptions.RemoveEmptyEntries).Select(b => double.Parse(b, CultureInfo.InvariantCulture)));
}
break;
case "MT": // Modification Type. If the field doesn't exist, set to the database name
modificationType = line.Substring(5);
break;
case "//":
if (id == null)
{
throw new MzLibException("id is null");
}
if ("CROSSLNK".Equals(uniprotFT)) // Ignore crosslinks
{
break;
}
if (uniprotAC != null)
{
modificationType = "UniProt";
externalDatabaseLinks.Add("UniProt", new List <string> {
uniprotAC
});
}
if (modificationType == null)
{
throw new MzLibException("modificationType of " + id + " is null");
}
if (!monoisotopicMass.HasValue && correctionFormula != null)
{
monoisotopicMass = correctionFormula.MonoisotopicMass;
}
foreach (var dbAndAccession in externalDatabaseLinks.SelectMany(b => b.Value.Select(c => b.Key + "; " + c)))
{
if (formalChargesDictionary.ContainsKey(dbAndAccession))
{
if (monoisotopicMass.HasValue)
{
monoisotopicMass -= formalChargesDictionary[dbAndAccession] * Constants.protonMass;
}
if (correctionFormula != null)
{
correctionFormula.Remove(PeriodicTable.GetElement("H"), formalChargesDictionary[dbAndAccession]);
}
break;
}
}
if (terminusLocalizationString == null || motifs == null)
{
yield return(new Modification(id, modificationType));
}
else if (ModificationWithLocation.terminusLocalizationTypeCodes.TryGetValue(terminusLocalizationString, out TerminusLocalization terminusLocalization))
{
foreach (var singleTarget in motifs)
{
string theMotif;
if (aminoAcidCodes.TryGetValue(singleTarget, out char possibleMotifChar))
{
theMotif = possibleMotifChar.ToString();
}
else
{
theMotif = singleTarget;
}
if (ModificationMotif.TryGetMotif(theMotif, out ModificationMotif motif))
{
var idToUse = id;
// Augment id if mulitple motifs!
// Add id to keywords
if (motifs.Count != 1)
{
if (keywords == null)
{
keywords = new List <string> {
id
}
}
;
else
{
keywords.Add(id);
}
idToUse += " on " + motif;
}
// Add the modification!
if (!monoisotopicMass.HasValue)
{
// Return modification
yield return(new ModificationWithLocation(idToUse, modificationType, motif, terminusLocalization, externalDatabaseLinks, keywords));
}
else
{
if (correctionFormula == null)
{
// Return modification with mass
yield return(new ModificationWithMass(idToUse, modificationType, motif, terminusLocalization, monoisotopicMass.Value, externalDatabaseLinks,
keywords,
neutralLosses,
diagnosticIons));
}
else
{
// Return modification with complete information!
yield return(new ModificationWithMassAndCf(idToUse, modificationType, motif, terminusLocalization, correctionFormula, monoisotopicMass.Value, externalDatabaseLinks, keywords,
neutralLosses,
diagnosticIons));
}
}
}
else
{
throw new MzLibException("Could not get motif from " + singleTarget);
}
}
}
else
{
throw new MzLibException("Could not get modification site from " + terminusLocalizationString);
}
break;
}
}
}
}
public void ContainsIsotopesOfYe()
{
ChemicalFormula formulaA = new ChemicalFormula("CC{13}H3NO");
Assert.IsTrue(formulaA.ContainsIsotopesOf(PeriodicTable.GetElement("C")));
}
public void AverageMass()
{
ChemicalFormula formulaA = new ChemicalFormula("C");
Assert.AreEqual(PeriodicTable.GetElement("C").AverageMass, formulaA.AverageMass);
}
public void InvalidChemicalElement()
{
Assert.Throws <KeyNotFoundException>(() => { Element e = PeriodicTable.GetElement("Faa"); });
}
public void ContainsSpecificIsotope()
{
ChemicalFormula formulaA = new ChemicalFormula("C2H5NOO{16}");
Assert.IsTrue(formulaA.ContainsSpecificIsotope(PeriodicTable.GetElement("O")[16]));
}
public void InvalidElementIsotope()
{
Assert.IsNull(PeriodicTable.GetElement("C")[100]);
}