void Main()
{
IAtomContainer someMolecule = null;
{
#region 1
IAtomContainer ac = someMolecule; // get an atom container somehow
BondDiscretePartitionRefiner refiner = new BondDiscretePartitionRefiner();
PermutationGroup autG = refiner.GetAutomorphismGroup(ac);
foreach (var automorphism in autG.GenerateAll())
{
// do something with the permutation
}
#endregion
}
{
#region 2
IAtomContainer ac = someMolecule; // get an atom container somehow
BondDiscretePartitionRefiner refiner = new BondDiscretePartitionRefiner();
if (refiner.IsCanonical(ac))
{
// do something with the atom container
}
#endregion
}
{
IAtomContainer ac = someMolecule;
#region 3
BondDiscretePartitionRefiner refiner = new BondDiscretePartitionRefiner();
refiner.Refine(ac);
bool isCanon = refiner.IsCanonical();
PermutationGroup autG = refiner.GetAutomorphismGroup();
#endregion
}
}
public void ResetTest()
{
string acpString1 = "C0C1C2 0:1(1),1:2(1)";
IAtomContainer ac1 = AtomContainerPrinter.FromString(acpString1, builder);
BondDiscretePartitionRefiner refiner = new BondDiscretePartitionRefiner();
refiner.Refine(ac1);
Assert.AreEqual(refiner.GetConnectivity(0, 1), 1);
Assert.AreEqual(refiner.GetVertexCount(), 2);
string acpString2 = "C0C1C2 0:1(1),0:2(1),1:2(1)";
IAtomContainer ac2 = AtomContainerPrinter.FromString(acpString2, builder);
refiner.Refine(ac2);
Assert.AreEqual(refiner.GetConnectivity(0, 2), 1);
Assert.AreEqual(refiner.GetVertexCount(), 3);
}
public void GetConnectivityTest()
{
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);
Assert.AreEqual(1, refiner.GetConnectivity(0, 1));
}
public void GetVertexCountTest()
{
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);
Assert.AreEqual(ac.Atoms.Count, refiner.GetVertexCount());
}
public void RefineTest()
{
string acpString = "C0C1O2O3 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);
PermutationGroup autG = refiner.GetAutomorphismGroup();
Assert.AreEqual(2, 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 TestBiphenyl()
{
IAtomContainer mol = TestMoleculeFactory.MakeBiphenyl();
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(mol);
Aromaticity.CDKLegacy.Apply(mol);
Assert.IsNotNull(mol, "Created molecule was null");
BondDiscretePartitionRefiner refiner = new BondDiscretePartitionRefiner();
refiner.Refine(mol);
Partition autP = refiner.GetAutomorphismPartition();
Assert.AreEqual(4, autP.Count, "Wrong number of equivalent classes");
Partition expected = Partition.FromString("0,5,7,12|1,4,8,11|2,3,9,10|6");
Assert.AreEqual(expected, autP, "Wrong class assignment");
}