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>
/// 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 RemoveIsotopeFromFromulaEquality()
{
ChemicalFormula formulaA = new ChemicalFormula("C2H3NO");
ChemicalFormula formulaB = new ChemicalFormula("C2H3O");
formulaA.Remove("N", 1);
Assert.AreEqual(formulaB, formulaA);
}
public void RemoveEmptyFormulaFromFromula()
{
ChemicalFormula formulaA = new ChemicalFormula("C2H3NO");
ChemicalFormula formulaB = new ChemicalFormula("C2H3NO");
formulaA.Remove(new ChemicalFormula());
Assert.AreEqual(formulaA, formulaB);
}
public void TestRemoveObjectFromChemicalFormula()
{
ChemicalFormula formulaB = new ChemicalFormula("CO");
var ok = new PhysicalObjectWithChemicalFormula("C");
formulaB.Remove(ok);
Assert.AreEqual("O", formulaB.Formula);
}
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 RemoveNullIsotopeFromFromula()
{
ChemicalFormula formulaA = new ChemicalFormula("C2H3NO");
ChemicalFormula formulaB = new ChemicalFormula("C2H3NO");
formulaA.Remove(NullIsotope);
Assert.AreEqual(formulaA, formulaB);
}
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 void RemoveElementCompletelyFromFromulaBySymbol()
{
ChemicalFormula formulaA = new ChemicalFormula("C2H3NO");
ChemicalFormula formulaB = new ChemicalFormula("C2NO");
formulaA.Remove("H");
Assert.AreEqual(formulaA, formulaB);
}
public void RemoveElementCompletelyFromFromula()
{
ChemicalFormula formulaA = new ChemicalFormula("C2H3NO");
ChemicalFormula formulaB = new ChemicalFormula("C2NO");
formulaA.Remove(PeriodicTable.GetElement("H"));
Assert.AreEqual(formulaA, formulaB);
}
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 void RemoveNegativeElementFromFromula()
{
ChemicalFormula formulaA = new ChemicalFormula("C2H3NO");
ChemicalFormula formulaB = new ChemicalFormula("C2H5NO");
formulaA.Remove(PeriodicTable.GetElement("H"), -2);
Assert.AreEqual(formulaA, formulaB);
}
public void RemoveFormulaFromFromula()
{
ChemicalFormula formulaA = new ChemicalFormula("C2H5NOO{16}");
ChemicalFormula formulaB = new ChemicalFormula("H2O{16}");
ChemicalFormula formulaC = new ChemicalFormula("C2H3NO");
formulaA.Remove(formulaB);
Assert.AreEqual(formulaA, formulaC);
}
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);
}
/// <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);
}
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 RemoveEmptyFormulaFromFromula()
{
ChemicalFormula formulaA = new ChemicalFormula("C2H3NO");
ChemicalFormula formulaB = new ChemicalFormula("C2H3NO");
formulaA.Remove(EmptyFormula);
Assert.AreEqual(formulaA, formulaB);
}
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 RemoveElementCompletelyFromFromulaBySymbol()
{
ChemicalFormula formulaA = new ChemicalFormula("C2H3NO");
ChemicalFormula formulaB = new ChemicalFormula("C2NO");
formulaA.Remove("H");
Assert.AreEqual(formulaA, formulaB);
}
public void RemoveElementCompletelyFromFromula()
{
ChemicalFormula formulaA = new ChemicalFormula("C2H3NO");
ChemicalFormula formulaB = new ChemicalFormula("C2NO");
formulaA.Remove(Element.PeriodicTable["H"]);
Assert.AreEqual(formulaA, formulaB);
}
/// <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 RemoveZeroIsotopeFromFromula()
{
ChemicalFormula formulaA = new ChemicalFormula("C2H3NO");
ChemicalFormula formulaB = new ChemicalFormula("C2H3NO");
formulaA.Remove(PeriodicTable.GetIsotope("H", 1), 0);
Assert.AreEqual(formulaA, formulaB);
}
public void RemoveNegativeIsotopeFromFromula()
{
ChemicalFormula formulaA = new ChemicalFormula("C2H3NO");
ChemicalFormula formulaB = new ChemicalFormula("C2H5NO");
formulaA.Remove(PeriodicTable.GetElement("H")[1], -2);
Assert.AreEqual(formulaA, formulaB);
}
public void RemoveIsotopeCompletelyFromFromula()
{
ChemicalFormula formulaA = new ChemicalFormula("C2H3NO");
ChemicalFormula formulaB = new ChemicalFormula("C2NO");
formulaA.Remove(PeriodicTable.GetElement("H")[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));
}