public virtual void TestSort_Coefficients()
{
IChemObjectSet <T> set = (IChemObjectSet <T>)NewChemObject();
IChemObjectBuilder builder = set.Builder;
T a = NewContainerObject();
T b = NewContainerObject();
a.Atoms.Add(builder.NewAtom("C"));
a.Atoms.Add(builder.NewAtom("C"));
b.Atoms.Add(builder.NewAtom("C"));
set.Add(a, 1);
set.Add(b, 2);
Assert.AreEqual(a, set[0]);
Assert.AreEqual(1D, set.GetMultiplier(0));
Assert.AreEqual(b, set[1]);
Assert.AreEqual(2D, set.GetMultiplier(1));
// sort by atom container count
var orderedSet = set.OrderBy(n => n, new ComparerByCoefficients());
AssertAreOrderLessEqual(
new[] { a, b }.Cast <IChemObject>(),
set.Cast <IChemObject>());
Assert.IsTrue(Compares.AreDeepEqual(
new[] { 1D, 2D },
new[] { set.GetMultiplier(0), set.GetMultiplier(1) }));
}
public virtual void TestSetMultiplier_int_Double()
{
IChemObjectSet <T> som = (IChemObjectSet <T>)NewChemObject();
som.Add(NewContainerObject());
Assert.AreEqual(1.0, som.GetMultiplier(0).Value, 0.00001);
som.SetMultiplier(0, 2.0);
Assert.AreEqual(2.0, som.GetMultiplier(0).Value, 0.00001);
}
public virtual void TestSetMultiplier_IAtomContainer_Double()
{
IChemObjectSet <T> som = (IChemObjectSet <T>)NewChemObject();
T container = NewContainerObject();
som.Add(container);
Assert.AreEqual(1.0, som.GetMultiplier(container).Value, 0.00001);
som.SetMultiplier(container, 2.0);
Assert.AreEqual(2.0, som.GetMultiplier(container).Value, 0.00001);
}
/// <summary>
/// Writes a MoleculeSet to an Stream for the reaction.
/// </summary>
/// <param name="som">The MoleculeSet that is written to an Stream</param>
private void WriteAtomContainerSet(IChemObjectSet <IAtomContainer> som)
{
for (int i = 0; i < som.Count; i++)
{
IAtomContainer mol = som[i];
for (int j = 0; j < som.GetMultiplier(i); j++)
{
StringWriter sw = new StringWriter();
writer.Write("$MOL");
writer.Write('\n');
MDLV2000Writer mdlwriter = null;
try
{
mdlwriter = new MDLV2000Writer(sw);
}
catch (Exception ex)
{
Trace.TraceError(ex.Message);
Debug.WriteLine(ex);
throw new CDKException("Exception while creating MDLWriter: " + ex.Message, ex);
}
mdlwriter.Write(mol);
mdlwriter.Close();
writer.Write(sw.ToString());
}
}
}
public virtual void TestAddAtomContainer_IAtomContainer_Double()
{
IChemObjectSet <T> som = (IChemObjectSet <T>)NewChemObject();
som.Add(NewContainerObject(), 2.0);
Assert.AreEqual(1, som.Count);
Assert.AreEqual(2.0, som.GetMultiplier(0).Value, 0.00001);
}
public virtual void TestGetMultiplier_IAtomContainer()
{
IChemObjectSet <T> som = (IChemObjectSet <T>)NewChemObject();
som.Add(NewContainerObject());
Assert.AreEqual(-1.0, som.GetMultiplier(NewContainerObject()).Value, 0.00001);
}
public virtual void TestSetMultipliers_arrayDouble()
{
IChemObjectSet <T> som = (IChemObjectSet <T>)NewChemObject();
T container = NewContainerObject();
som.Add(container);
T container2 = NewContainerObject();
som.Add(container2);
Assert.AreEqual(1.0, som.GetMultiplier(0).Value, 0.00001);
Assert.AreEqual(1.0, som.GetMultiplier(1).Value, 0.00001);
double?[] multipliers = new double?[2];
multipliers[0] = 2.0;
multipliers[1] = 3.0;
som.SetMultipliers(multipliers);
Assert.AreEqual(2.0, som.GetMultiplier(0).Value, 0.00001);
Assert.AreEqual(3.0, som.GetMultiplier(1).Value, 0.00001);
}
/// <summary>
/// </summary>
/// <param name="set">The collection of IAtomContainer objects</param>
/// <returns>The summed formal charges of all atoms in this set.</returns>
public static double GetTotalFormalCharge(IChemObjectSet <IAtomContainer> set)
{
int charge = 0;
for (int i = 0; i < set.Count; i++)
{
int thisCharge = AtomContainerManipulator.GetTotalFormalCharge(set[i]);
double stoich = set.GetMultiplier(i).Value;
charge += (int)(stoich * thisCharge);
}
return(charge);
}
public virtual void TestCloneMultiplier()
{
IChemObjectSet <T> containerSet = (IChemObjectSet <T>)NewChemObject();
containerSet.Add(NewContainerObject(), 2);
object clone = containerSet.Clone();
Assert.IsTrue(clone is IChemObjectSet <T>);
IChemObjectSet <T> clonedSet = (IChemObjectSet <T>)clone;
Assert.AreNotSame(containerSet, clonedSet);
Assert.AreEqual(2, containerSet.GetMultiplier(0).Value);
Assert.AreEqual(2, clonedSet.GetMultiplier(0).Value);
}
public virtual void TestSortAtomContainers_WithMuliplier()
{
IChemObjectSet <T> som = (IChemObjectSet <T>)NewChemObject();
T ac1 = NewContainerObject();
som.Add(ac1, 2.0);
ac1.SetProperty("multiplierSortCode", "2");
T ac2 = NewContainerObject();
som.Add(ac2, 1.0);
ac2.SetProperty("multiplierSortCode", "1");
som.Sort(new CodeComparer());
Assert.AreEqual(2, som.Count);
T newFirstAC = som[0];
Assert.AreEqual(newFirstAC.GetProperty <object>("multiplierSortCode"), "1");
// OK, sorting worked as intended
// The multiplier should have been resorted too:
Assert.AreEqual(1.0, som.GetMultiplier(newFirstAC).Value, 0.00001);
}
