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);
}
/// <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 void TestGetMaximalFormula_MolecularFormulaRange_IChemObjectBuilder()
{
var mf1 = new MolecularFormula(); /* C4H12NO4 */
mf1.Add(builder.NewIsotope("C"), 4);
mf1.Add(builder.NewIsotope("H"), 12);
mf1.Add(builder.NewIsotope("N"), 1);
mf1.Add(builder.NewIsotope("O"), 4);
var mf2 = new MolecularFormula(); /* C7H20N4O2 */
mf2.Add(builder.NewIsotope("C"), 7);
mf2.Add(builder.NewIsotope("H"), 20);
mf2.Add(builder.NewIsotope("N"), 4);
mf2.Add(builder.NewIsotope("O"), 2);
var mf3 = new MolecularFormula(); /* C9H5O7 */
mf3.Add(builder.NewIsotope("C"), 9);
mf3.Add(builder.NewIsotope("H"), 5);
mf3.Add(builder.NewIsotope("O"), 7);
var mfSet = new MolecularFormulaSet
{
mf1,
mf2,
mf3
};
MolecularFormulaRange mfRange = MolecularFormulaRangeManipulator.GetRange(mfSet);
IMolecularFormula formula = MolecularFormulaRangeManipulator.GetMaximalFormula(mfRange, builder);
/* Result: C4-9H5-20N0-4O2-7 */
Assert.AreEqual(4, mfRange.GetIsotopes().Count());
Assert.AreEqual(formula.GetCount(builder.NewIsotope("C")),
mfRange.GetIsotopeCountMax(builder.NewIsotope("C")));
Assert.AreEqual(formula.GetCount(builder.NewIsotope("H")),
mfRange.GetIsotopeCountMax(builder.NewIsotope("H")));
Assert.AreEqual(formula.GetCount(builder.NewIsotope("N")),
mfRange.GetIsotopeCountMax(builder.NewIsotope("N")));
Assert.AreEqual(formula.GetCount(builder.NewIsotope("O")),
mfRange.GetIsotopeCountMax(builder.NewIsotope("O")));
}
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);
}
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);
}
/// <summary>
/// Adds an molecularFormula to this MolecularFormula.
/// </summary>
/// <param name="formula">The molecularFormula to be added to this chemObject</param>
/// <returns>The IMolecularFormula</returns>
public IMolecularFormula Add(IMolecularFormula formula)
{
foreach (var newIsotope in formula.Isotopes)
{
Add(newIsotope, formula.GetCount(newIsotope));
}
if (formula.Charge != null)
{
if (Charge != null)
{
Charge += formula.Charge;
}
else
{
Charge = formula.Charge;
}
}
return(this);
}
/// <summary>
/// Method to extract the Ring Double Bond Equivalents (RDB) value. It test all possible
/// oxidation states.
/// </summary>
/// <param name="formula">The IMolecularFormula object</param>
/// <returns>The RDBE value</returns>
public virtual IReadOnlyList <double> GetRDBEValue(IMolecularFormula formula)
{
var RDBEList = new List <double>();
// The number of combinations with repetition
// (v+n-1)!/[n!(v-1)!]
int nE = 0; // number of elements to change
var nV = new List <int>(); // number of valence changing
foreach (var isotope in formula.Isotopes)
{
int[] valence = GetOxidationState(formula.Builder.NewAtom(isotope.Symbol));
if (valence.Length != 1)
{
for (int i = 0; i < valence.Length; i++)
{
nV.Add(valence[i]);
}
nE += MolecularFormulaManipulator.GetElementCount(formula, ChemicalElement.OfSymbol(isotope.Symbol));
}
}
double RDBE = 0;
if (nE == 0)
{
foreach (var isotope in formula.Isotopes)
{
var valence = GetOxidationState(formula.Builder.NewAtom(isotope.Symbol));
var value = (valence[0] - 2) * formula.GetCount(isotope) / 2.0;
RDBE += value;
}
RDBE += 1;
RDBEList.Add(RDBE);
}
else
{
double RDBE_1 = 0;
foreach (var isotope in formula.Isotopes)
{
var valence = GetOxidationState(formula.Builder.NewAtom(isotope.Symbol));
var value = (valence[0] - 2) * formula.GetCount(isotope) * 0.5;
RDBE_1 += value;
}
var valences = new string[nV.Count];
for (int i = 0; i < valences.Length; i++)
{
valences[i] = nV[i].ToString(NumberFormatInfo.InvariantInfo);
}
var c = new Combinations(valences, nE);
while (c.HasMoreElements())
{
double RDBE_int = 0.0;
var combo = (object[])c.NextElement();
for (int i = 0; i < combo.Length; i++)
{
var value = (int.Parse((string)combo[i], NumberFormatInfo.InvariantInfo) - 2) / 2;
RDBE_int += value;
}
RDBE = 1 + RDBE_1 + RDBE_int;
RDBEList.Add(RDBE);
}
}
return(RDBEList);
}
