public virtual void TestSort_BrokenComparator()
{
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);
set.Add(b);
// this comparator is deliberately broken but serves for the test
// - null should be a high value (Interger.MAX)
// - also, avoid boxed primitives in comparators
set.Sort(new ComparerByBroken());
// despite null being low, the two atom containers should
// still be in the first slot
Assert.IsNotNull(set[0]);
Assert.IsNotNull(set[1]);
Assert.IsTrue(set.Count == 2 || set[2] == null);
}
public void SetUp()
{
molecule1 = builder.NewAtomContainer();
atomInMol1 = builder.NewAtom("Cl");
molecule1.Atoms.Add(atomInMol1);
molecule1.Atoms.Add(builder.NewAtom("Cl"));
bondInMol1 = builder.NewBond(atomInMol1, molecule1.Atoms[1]);
molecule1.Bonds.Add(bondInMol1);
molecule2 = builder.NewAtomContainer();
atomInMol2 = builder.NewAtom("O");
atomInMol2.ImplicitHydrogenCount = 2;
molecule2.Atoms.Add(atomInMol2);
moleculeSet = builder.NewChemObjectSet <IAtomContainer>();
moleculeSet.Add(molecule1);
moleculeSet.Add(molecule2);
reaction = builder.NewReaction();
reaction.Reactants.Add(molecule1);
reaction.Products.Add(molecule2);
reactionSet = builder.NewReactionSet();
reactionSet.Add(reaction);
chemModel = builder.NewChemModel();
chemModel.MoleculeSet = moleculeSet;
chemModel.ReactionSet = reactionSet;
chemSequence1 = builder.NewChemSequence();
chemSequence1.Add(chemModel);
chemSequence2 = builder.NewChemSequence();
chemFile = builder.NewChemFile();
chemFile.Add(chemSequence1);
chemFile.Add(chemSequence2);
}
public virtual void TestGetAtomContainerCount()
{
IChemObjectSet <T> som = (IChemObjectSet <T>)NewChemObject();
som.Add(NewContainerObject());
som.Add(NewContainerObject());
som.Add(NewContainerObject());
Assert.AreEqual(3, som.Count);
}
/// <summary>
/// get all Molecules object from a set of Reactions.
/// </summary>
/// <param name="set">The set of reaction to inspect</param>
/// <returns>The IAtomContanerSet</returns>
public static IChemObjectSet <IAtomContainer> GetAllMolecules(IReactionSet set)
{
IChemObjectSet <IAtomContainer> moleculeSet = set.Builder.NewAtomContainerSet();
foreach (var reaction in set)
{
var molecules = ReactionManipulator.GetAllMolecules(reaction);
foreach (var ac in molecules)
{
bool contain = false;
foreach (var atomContainer in moleculeSet)
{
if (atomContainer.Equals(ac))
{
contain = true;
break;
}
}
if (!contain)
{
moleculeSet.Add(ac);
}
}
}
return(moleculeSet);
}
public virtual void TestSetReactants_IAtomContainerSet()
{
IReaction reaction = (IReaction)NewChemObject();
IAtomContainer sodiumhydroxide = reaction.Builder.NewAtomContainer();
IAtomContainer aceticAcid = reaction.Builder.NewAtomContainer();
IAtomContainer water = reaction.Builder.NewAtomContainer();
IChemObjectSet <IAtomContainer> reactants = reaction.Builder.NewAtomContainerSet();
reactants.Add(sodiumhydroxide);
reactants.Add(aceticAcid);
reactants.Add(water);
reaction.Reactants.AddRange(reactants);
Assert.AreEqual(3, reaction.Reactants.Count);
Assert.AreEqual(1.0, reaction.Reactants.GetMultiplier(aceticAcid).Value, 0.00001);
}
/// <summary>
/// Get all molecule objects from a set of Reactions given a <see cref="IAtomContainerSet"/> to add.
/// </summary>
/// <param name="scheme">The set of reaction to inspect</param>
/// <param name="molSet">The set of molecules to be added</param>
/// <returns>All molecules</returns>
public static IChemObjectSet <IAtomContainer> GetAllAtomContainers(IReactionScheme scheme, IChemObjectSet <IAtomContainer> molSet)
{
// A ReactionScheme can contain other IRreactionSet objects
foreach (var rm in scheme.Schemes)
{
foreach (var ac in GetAllAtomContainers(rm, molSet))
{
bool contain = false;
foreach (var atomContainer in molSet)
{
if (atomContainer.Equals(ac))
{
contain = true;
break;
}
}
if (!contain)
{
molSet.Add((IAtomContainer)(ac));
}
}
}
foreach (var reaction in scheme.Reactions)
{
var newAtomContainerSet = ReactionManipulator.GetAllAtomContainers(reaction);
foreach (var ac in newAtomContainerSet)
{
bool contain = false;
foreach (var atomContainer in molSet)
{
if (atomContainer.Equals(ac))
{
contain = true;
break;
}
}
if (!contain)
{
molSet.Add(ac);
}
}
}
return(molSet);
}
public void SetUp()
{
mol1 = builder.NewAtomContainer();
atomInMol1 = builder.NewAtom("Cl");
atomInMol1.Charge = -1.0;
atomInMol1.FormalCharge = -1;
atomInMol1.ImplicitHydrogenCount = 1;
mol1.Atoms.Add(atomInMol1);
mol1.Atoms.Add(builder.NewAtom("Cl"));
bondInMol1 = builder.NewBond(atomInMol1, mol1.Atoms[1]);
mol1.Bonds.Add(bondInMol1);
mol2 = builder.NewAtomContainer();
atomInMol2 = builder.NewAtom("O");
atomInMol2.ImplicitHydrogenCount = 2;
mol2.Atoms.Add(atomInMol2);
som.Add(mol1);
som.Add(mol2);
}