public void GetConnectivityTest()
{
string acpString = "C0C1C2C3 0:1(1),0:3(1),1:2(2),2:3(1)";
IAtomContainer ac = AtomContainerPrinter.FromString(acpString, builder);
AtomDiscretePartitionRefiner refiner = new AtomDiscretePartitionRefiner();
refiner.Refine(ac);
IBond bond = ac.GetBond(ac.Atoms[1], ac.Atoms[2]);
int orderN = bond.Order.Numeric();
Assert.AreEqual(orderN, refiner.GetConnectivity(1, 2));
}
public void GetAutomorphismGroup_StartingGroupTest()
{
string acpString = "C0C1C2C3 0:1(1),0:2(1),1:3(1),2:3(1)";
IAtomContainer ac = AtomContainerPrinter.FromString(acpString, builder);
Permutation flip = new Permutation(1, 0, 3, 2);
PermutationGroup autG = new PermutationGroup(4, new[] { flip });
AtomDiscretePartitionRefiner refiner = new AtomDiscretePartitionRefiner();
refiner.GetAutomorphismGroup(ac, autG);
Assert.IsNotNull(autG);
Assert.AreEqual(8, autG.Order());
}
public void Refine_IgnoreBondOrderTest()
{
string acpString = "C0C1C2C3 0:1(2),0:3(1),1:2(1),2:3(2)";
IAtomContainer ac = AtomContainerPrinter.FromString(acpString, builder);
bool ignoreBondOrder = true;
BondDiscretePartitionRefiner refiner = new BondDiscretePartitionRefiner(ignoreBondOrder);
refiner.Refine(ac);
PermutationGroup autG = refiner.GetAutomorphismGroup();
Assert.AreEqual(8, autG.Order());
}
public void Refine_StartingPartitionTest()
{
Partition partition = Partition.FromString("0,1|2,3");
string acpString = "C0C1C2C3 0:1(1),0:3(1),1:2(1),2:3(1)";
IAtomContainer ac = AtomContainerPrinter.FromString(acpString, builder);
BondDiscretePartitionRefiner refiner = new BondDiscretePartitionRefiner();
refiner.Refine(ac, partition);
PermutationGroup autG = refiner.GetAutomorphismGroup();
Assert.AreEqual(2, autG.Order());
}
public void ReSetTest()
{
string acpString1 = "C0C1 0:1(1)";
IAtomContainer ac1 = AtomContainerPrinter.FromString(acpString1, builder);
AtomDiscretePartitionRefiner refiner = new AtomDiscretePartitionRefiner();
refiner.Refine(ac1);
Assert.AreEqual(refiner.GetConnectivity(0, 1), 1);
Assert.AreEqual(refiner.GetVertexCount(), 2);
string acpString2 = "C0C1C2 0:1(2),1:2(1)";
IAtomContainer ac2 = AtomContainerPrinter.FromString(acpString2, builder);
refiner.Refine(ac2);
Assert.AreEqual(refiner.GetConnectivity(0, 1), 2);
Assert.AreEqual(refiner.GetVertexCount(), 3);
}
/// <summary>
/// This test is checking all permutations of an atom container to see
/// if the refiner gives the canonical labelling map (effectively).
/// </summary>
/// <param name="atomContainer"></param>
public void CheckForCanonicalForm(IAtomContainer atomContainer)
{
AtomContainerAtomPermutor permutor = new AtomContainerAtomPermutor(atomContainer);
AtomDiscretePartitionRefiner refiner = new AtomDiscretePartitionRefiner();
refiner.Refine(atomContainer);
Permutation best = refiner.GetBest().Invert();
string cert = AtomContainerPrinter.ToString(atomContainer, best, true);
while (permutor.MoveNext())
{
IAtomContainer permutedContainer = permutor.Current;
refiner.Refine(permutedContainer);
best = refiner.GetBest().Invert();
string permCert = AtomContainerPrinter.ToString(permutedContainer, best, true);
Assert.AreEqual(cert, permCert);
}
}
private BondRefinable Refinable(string acpString)
{
return(new BondRefinable(AtomContainerPrinter.FromString(acpString, builder)));
}
public void NapthaleneB()
{
Test(AtomContainerPrinter.FromString("C0C1C2C3C4C5C6C7C8C9 0:1(1),1:2(2),2:3(1),3:4(1),4:5(2),"
+ "5:6(1),6:7(2),7:8(1),3:8(2),8:9(1),0:9(2)", CDK.Builder), 4);
}
public void CycloButadiene()
{
Test(AtomContainerPrinter.FromString("C0C1C2C3 0:1(2),1:2(1),2:3(2),0:3(1)", builder), 4);
}
public static string ToString(IAtomContainer atomContainer)
{
return(AtomContainerPrinter.ToString(atomContainer, new Permutation(atomContainer.Atoms.Count)));
}
public static void Print(IAtomContainer atomContainer)
{
Console.Out.WriteLine(AtomContainerPrinter.ToString(atomContainer));
}