/// <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 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");
}
public void ChemicalFormulaCompareTest()
{
var provider = new MockElementProvider();
var formula = ChemicalFormula.Water(provider);
var formula2 = ChemicalFormula.Water(provider);
IElement h = provider.GetElement("H");
IElement o = provider.GetElement("O");
var formula3 = new ChemicalFormula(new[]
{
new EntityCardinality <IElement>(h, 1),
new EntityCardinality <IElement>(o, 2),
});
Assert.AreEqual(formula, formula2);
Assert.AreNotEqual(formula, formula3);
// Equality when element object is different.
IElement anotherH = new Element(1, "H", h.Isotopes);
IElement anotherO = new Element(1, "O", o.Isotopes);
ChemicalFormula formula4 = new ChemicalFormula(new[]
{
new EntityCardinality <IElement>(anotherH, 2),
new EntityCardinality <IElement>(anotherO, 1),
});
Assert.IsTrue(formula.Equals(formula4));
Assert.IsTrue(formula2.Equals(formula4));
Assert.IsFalse(formula3.Equals(formula4));
}
public override bool Equals(object o)
{
ModificationWithMassAndCf m = o as ModificationWithMassAndCf;
return(m != null &&
base.Equals(m) &&
chemicalFormula.Equals(m.chemicalFormula));
}
public static void Multiply()
{
ChemicalFormula formulaA = ChemicalFormula.ParseFormula("C2H3NO");
formulaA.Multiply(2);
ChemicalFormula formulaB = ChemicalFormula.ParseFormula("C4H6N2O2");
Assert.AreEqual(formulaA, formulaB);
Assert.IsFalse(formulaA.Equals(null));
}
/// <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 PsiModIsotope()
{
var parser = new PsiModOboParser();
PsiModTerm[] modifications = parser.Parse(PsiModOboParserTest.GetFilePath()).ToArray();
PsiModTerm psiMod402 = modifications.Single(x => x.Id == "MOD:00402");
IProteoformModificationLookup psiModLookup = PsiModModificationLookup.CreateFromModifications(new[] { psiMod402 },
_elementProvider);
this.FindById(psiModLookup, ProFormaKey.Identifier, ProFormaEvidenceType.PsiMod, 402, "MOD:");
var mod = psiModLookup.GetModification(new ProFormaDescriptor(ProFormaKey.Identifier,
ProFormaEvidenceType.PsiMod, "MOD:00402"));
ChemicalFormula chemicalFormula = new ChemicalFormula(
new IEntityCardinality <IElement>[]
{
new EntityCardinality <IElement>(_elementProvider.GetElement("C"), 22),
new EntityCardinality <IElement>(_elementProvider.GetElement("H", 1), 30),
new EntityCardinality <IElement>(_elementProvider.GetElement("H", 2), 8),
new EntityCardinality <IElement>(_elementProvider.GetElement("N"), 4),
new EntityCardinality <IElement>(_elementProvider.GetElement("O"), 6),
new EntityCardinality <IElement>(_elementProvider.GetElement("S"), 1),
});
Assert.IsInstanceOf(typeof(IHasChemicalFormula), mod);
var formulaMod = (IHasChemicalFormula)mod;
Assert.IsTrue(chemicalFormula.Equals(formulaMod.GetChemicalFormula()));
Assert.IsInstanceOf(typeof(IIdentifiable), mod);
var idMod = (IIdentifiable)mod;
Assert.AreEqual("MOD:00402", idMod.Id);
Assert.AreEqual("Gygi ICAT(TM) d8 modified cysteine", idMod.Name);
}
public void EqualsFalse()
{
ChemicalFormula formulaA = new ChemicalFormula("OCHHCHN");
Assert.IsFalse(formulaA.Equals("C"));
}
public void TestEquality()
{
ChemicalFormula formulaB = new ChemicalFormula("CO");
Assert.IsTrue(formulaB.Equals(formulaB));
}
public static void EqualsFalse()
{
ChemicalFormula formulaA = ChemicalFormula.ParseFormula("OCHHCHN");
Assert.IsFalse(formulaA.Equals("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 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));
}
}
}
}