public virtual void TestInstance_IIsotope()
{
IMolecularFormula mf = Builder.NewMolecularFormula();
IIsotope carb = Builder.NewIsotope("C");
IIsotope flu = Builder.NewIsotope("F");
IIsotope h1 = Builder.NewIsotope("H");
mf.Add(carb);
mf.Add(flu);
mf.Add(h1, 3);
IEnumerator <IIsotope> istoIter = mf.Isotopes.GetEnumerator();
Assert.IsNotNull(istoIter);
Assert.IsTrue(istoIter.MoveNext());
IIsotope next = istoIter.Current;
Assert.IsTrue(next is IIsotope);
// Assert.AreEqual(carb, next);
Assert.IsTrue(istoIter.MoveNext());
next = istoIter.Current;
Assert.IsTrue(next is IIsotope);
// Assert.AreEqual(flu, next);
Assert.IsTrue(istoIter.MoveNext());
next = istoIter.Current;
Assert.IsTrue(next is IIsotope);
// Assert.AreEqual(h1, next);
Assert.IsFalse(istoIter.MoveNext());
}
public virtual void TestGetIsotope_Number_Clone()
{
IMolecularFormula mf = Builder.NewMolecularFormula();
IIsotope carb = Builder.NewIsotope("C");
IIsotope flu = Builder.NewIsotope("F");
IIsotope h1 = Builder.NewIsotope("H");
mf.Add(carb);
mf.Add(flu);
mf.Add(h1, 3);
object clone = mf.Clone();
Assert.IsTrue(clone is IMolecularFormula);
IMolecularFormula cloneFormula = (IMolecularFormula)clone;
Assert.AreEqual(1, cloneFormula.GetCount(carb));
Assert.AreEqual(1, cloneFormula.GetCount(flu));
Assert.AreEqual(3, cloneFormula.GetCount(h1));
// In a List the objects are not stored in the same order than called
// Assert.AreEqual("C", cloneFormula.Isotopes[0].Symbol);
// Assert.AreEqual("F", cloneFormula.Isotopes[1].Symbol);
// Assert.AreEqual("H", cloneFormula.Isotopes[2].Symbol);
}
public virtual void TestClone_IMolecualrFormula()
{
IMolecularFormulaSet mfS = Builder.NewMolecularFormulaSet();
IMolecularFormula mf1 = Builder.NewMolecularFormula();
IIsotope carb = Builder.NewIsotope("C");
IIsotope flu = Builder.NewIsotope("F");
IIsotope h1 = Builder.NewIsotope("H");
mf1.Add(carb);
mf1.Add(flu);
mf1.Add(h1, 3);
mfS.Add(mf1);
IMolecularFormula mf2 = Builder.NewMolecularFormula();
IIsotope carb2 = Builder.NewIsotope("C");
IIsotope iode = Builder.NewIsotope("I");
IIsotope h2 = Builder.NewIsotope("H");
mf2.Add(carb2);
mf2.Add(iode, 2);
mf2.Add(h2, 2);
mfS.Add(mf2);
object clone = mfS.Clone();
Assert.IsTrue(clone is IMolecularFormulaSet);
Assert.AreNotSame(mfS, clone);
Assert.AreEqual(mfS.Count(), ((IMolecularFormulaSet)clone).Count());
Assert.AreEqual(mfS[0].IsotopesCount, ((IMolecularFormulaSet)clone)
[0].IsotopesCount);
Assert.AreEqual(mfS[1].IsotopesCount, ((IMolecularFormulaSet)clone)
[1].IsotopesCount);
}
public virtual void TestSetCharge_Integer()
{
IMolecularFormula mf = Builder.NewMolecularFormula();
mf.Charge = 1;
mf.Add(Builder.NewAtom("C"));
mf.Add(Builder.NewAtom("F"));
mf.Add(Builder.NewAtom("H"), 3);
Assert.AreEqual(1.0, mf.Charge.Value, 0.001);
}
public virtual void TestGetCharge()
{
IMolecularFormula mf = Builder.NewMolecularFormula();
mf.Charge = 1;
mf.Add(Builder.NewAtom("C"));
mf.Add(Builder.NewAtom("F"));
mf.Add(Builder.NewAtom("H"), 3);
Assert.AreEqual(3, mf.IsotopesCount);
Assert.AreEqual(1.0, mf.Charge.Value, 0.001);
}
public virtual void TestGetIsotopeCount()
{
IMolecularFormula mf = Builder.NewMolecularFormula();
mf.Add(Builder.NewIsotope("C"));
mf.Add(Builder.NewIsotope("H"));
mf.Add(Builder.NewIsotope("H"));
mf.Add(Builder.NewIsotope("H"));
mf.Add(Builder.NewIsotope("H"));
Assert.AreEqual(2, mf.IsotopesCount);
}
public virtual void TestAddIsotope_IIsotope()
{
IMolecularFormula mf = Builder.NewMolecularFormula();
mf.Add(Builder.NewIsotope("C"));
mf.Add(Builder.NewIsotope("H"));
IIsotope hy = Builder.NewIsotope("C");
hy.Abundance = 2.00342342;
mf.Add(hy);
Assert.AreEqual(3, mf.IsotopesCount);
}
public virtual void TestRemoveAllIsotopes()
{
IMolecularFormula mf = Builder.NewMolecularFormula();
IIsotope carb = Builder.NewIsotope("C");
IIsotope flu = Builder.NewIsotope("F");
IIsotope h1 = Builder.NewIsotope("H");
mf.Add(carb);
mf.Add(flu);
mf.Add(h1, 3);
// remove the Fluorine
mf.Clear();
Assert.AreEqual(0, mf.IsotopesCount);
}
/// <summary>
/// Clear the isotope information from isotopes that are major (e.g.
/// <sup>12</sup>C, <sup>1</sup>H, etc).
/// </summary>
/// <param name="formula">the formula</param>
public static void ClearMajorIsotopes(IMolecularFormula formula)
{
var isotopesToRemove = new List <IIsotope>();
var isotopesToAdd = new List <Tuple <IIsotope, int> >();
foreach (var iso in formula.Isotopes.Where(n => IsMajor(n)))
{
var count = formula.GetCount(iso);
isotopesToRemove.Add(iso);
iso.MassNumber = null;
// may be immutable
var iso_ = iso;
if (iso_.MassNumber != null)
{
iso_ = formula.Builder.NewIsotope(iso_.Symbol);
}
iso_.ExactMass = null;
iso_.Abundance = null;
isotopesToAdd.Add(new Tuple <IIsotope, int>(iso_, count));
}
foreach (var isotope in isotopesToRemove)
{
formula.Remove(isotope);
}
foreach (var t in isotopesToAdd)
{
formula.Add(t.Item1, t.Item2);
}
}
public virtual void TestGetIsotopeCount_IIsotope_Occurr()
{
IMolecularFormula mf = Builder.NewMolecularFormula();
IIsotope carb = Builder.NewIsotope("C");
IIsotope flu = Builder.NewIsotope("F");
IIsotope h1 = Builder.NewIsotope("H");
mf.Add(carb);
mf.Add(flu);
mf.Add(h1, 3);
Assert.AreEqual(3, mf.IsotopesCount);
Assert.AreEqual(1, mf.GetCount(carb));
Assert.AreEqual(1, mf.GetCount(flu));
Assert.AreEqual(3, mf.GetCount(h1));
}
public virtual void TestMolecularFormula_NullCharge()
{
IMolecularFormula mf = Builder.NewMolecularFormula();
IMolecularFormula mf2 = Builder.NewMolecularFormula();
mf2.Charge = 0;
mf.Add(mf2);
}
public virtual void TestContains_IIsotope()
{
IMolecularFormula mf = Builder.NewMolecularFormula();
IIsotope carb = Builder.NewIsotope("C");
IIsotope h1 = Builder.NewIsotope("H");
IIsotope h2 = Builder.NewIsotope("H");
h2.ExactMass = 2.0004;
mf.Add(carb);
mf.Add(h1);
Assert.IsTrue(mf.Contains(carb));
Assert.IsTrue(mf.Contains(h1));
Assert.IsFalse(mf.Contains(h2));
}
public virtual void TestIsotopes()
{
IMolecularFormula mf = Builder.NewMolecularFormula();
mf.Add(Builder.NewIsotope("C"));
mf.Add(Builder.NewIsotope("F"));
mf.Add(Builder.NewIsotope("H"), 3);
IEnumerator <IIsotope> istoIter = mf.Isotopes.GetEnumerator();
int counter = 0;
while (istoIter.MoveNext())
{
counter++;
}
Assert.AreEqual(3, counter);
}
public virtual void TestContains_IMolecularFormula()
{
IMolecularFormulaSet mfS = Builder.NewMolecularFormulaSet();
IMolecularFormula mf = Builder.NewMolecularFormula();
IIsotope carb = Builder.NewIsotope("C");
IIsotope h1 = Builder.NewIsotope("H");
IIsotope h2 = Builder.NewIsotope("H");
h2.ExactMass = 2.00055;
mf.Add(carb);
mf.Add(h1);
mfS.Add(mf);
Assert.IsTrue(mfS.Contains(mf));
}
public virtual void TestAdd_IMolecularFormula()
{
IMolecularFormula acetone = Builder.NewMolecularFormula();
acetone.Add(Builder.NewIsotope("C"), 3);
IIsotope oxig = Builder.NewIsotope("O");
acetone.Add(oxig);
Assert.AreEqual(2, acetone.IsotopesCount);
IMolecularFormula water = Builder.NewMolecularFormula();
water.Add(Builder.NewIsotope("H"), 2);
water.Add(oxig);
acetone.Add(water);
Assert.AreEqual(3, acetone.IsotopesCount);
}
/// <summary>
/// Returns the maximal occurrence of the IIsotope into IMolecularFormula
/// from this MolelecularFormulaRange.
/// </summary>
/// <param name="mfRange">The MolecularFormulaRange to analyze</param>
/// <returns>A IMolecularFormula containing the maximal occurrence of each isotope</returns>
public static IMolecularFormula GetMaximalFormula(MolecularFormulaRange mfRange, IChemObjectBuilder builder)
{
IMolecularFormula formula = builder.NewMolecularFormula();
foreach (var isotope in mfRange.GetIsotopes())
{
formula.Add(isotope, mfRange.GetIsotopeCountMax(isotope));
}
return(formula);
}
public virtual void TestSetCharge_Double()
{
IMolecularFormula mf = Builder.NewMolecularFormula();
Assert.AreEqual(null, mf.Charge);
mf.Charge = 1;
Assert.AreEqual(1.0, mf.Charge.Value, 0.001);
mf.Add(mf);
Assert.AreEqual(2.0, mf.Charge.Value, 0.001);
}
public virtual void TestAddIsotope_IIsotope_int()
{
IMolecularFormula mf = Builder.NewMolecularFormula();
IIsotope carb = Builder.NewIsotope("C");
IIsotope flu = Builder.NewIsotope("F");
IIsotope h1 = Builder.NewIsotope("H");
mf.Add(carb);
mf.Add(flu);
mf.Add(h1, 3);
Assert.AreEqual(3, mf.IsotopesCount);
Assert.AreEqual(1, mf.GetCount(carb));
Assert.AreEqual(1, mf.GetCount(flu));
Assert.AreEqual(3, mf.GetCount(h1));
// In a List the objects are not stored in the same order than called
// Assert.AreEqual("C", mf.Isotopes[0].Symbol);
// Assert.AreEqual("F", mf.Isotopes[1].Symbol);
// Assert.AreEqual("H", mf.Isotopes[2].Symbol);
}
internal IMolecularFormula GenerateCurrentMolecularFormula(IChemObjectBuilder builder)
{
IMolecularFormula formula = builder.NewMolecularFormula();
for (int k = 0; k < buffer.Length; ++k)
{
if (buffer[k] > 0)
{
formula.Add(GetCharacterAt(k), buffer[k]);
}
}
return(formula);
}
/// <summary>
/// Generates a MolecularFormula object that contains the isotopes in the
/// isotopes[] array with counts in the currentCounts[] array. In other
/// words, generates a proper CDK representation of the currently examined
/// formula.
/// </summary>
private IMolecularFormula GenerateFormulaObject()
{
IMolecularFormula formulaObject = builder.NewMolecularFormula();
for (int i = 0; i < isotopes.Length; i++)
{
if (currentCounts[i] == 0)
{
continue;
}
formulaObject.Add(isotopes[i], currentCounts[i]);
}
return(formulaObject);
}
public virtual void TestClone_Isotopes()
{
IMolecularFormula mf = Builder.NewMolecularFormula();
IIsotope carb = Builder.NewIsotope("C");
IIsotope flu = Builder.NewIsotope("F");
IIsotope h1 = Builder.NewIsotope("H");
mf.Add(carb);
mf.Add(flu);
mf.Add(h1, 3);
Assert.AreEqual(3, mf.IsotopesCount);
Assert.AreEqual(1, mf.GetCount(carb));
Assert.AreEqual(1, mf.GetCount(flu));
Assert.AreEqual(3, mf.GetCount(h1));
object clone = mf.Clone();
Assert.IsTrue(clone is IMolecularFormula);
Assert.AreEqual(mf.IsotopesCount, ((IMolecularFormula)clone).IsotopesCount);
Assert.AreEqual(3, ((IMolecularFormula)clone).IsotopesCount);
}
public virtual void TestCharge_rest()
{
IMolecularFormula mf = Builder.NewMolecularFormula();
Assert.AreEqual(null, mf.Charge);
mf.Charge = 1;
Assert.AreEqual(1.0, mf.Charge.Value, 0.001);
IMolecularFormula mf2 = Builder.NewMolecularFormula();
mf2.Charge = -1;
mf.Add(mf2);
Assert.AreEqual(0.0, mf.Charge.Value, 0.001);
}
public virtual void TestGetIsotopeCount_Sum_Isotope()
{
var add = Builder.NewAdductFormula();
Assert.AreEqual(0, add.GetIsotopes().Count());
var adduct1 = Builder.NewMolecularFormula();
var C = Builder.NewIsotope("C");
adduct1.Add(C);
var h = Builder.NewIsotope("H");
adduct1.Add(h, 4);
add.Add(adduct1);
IMolecularFormula adduct2 = Builder.NewMolecularFormula();
adduct2.Add(h);
add.Add(adduct2);
Assert.AreEqual(1, add.GetCount(C));
Assert.AreEqual(5, add.GetCount(h));
}
