public void Test(IAtomContainer mol, int expected)
{
AtomDiscretePartitionRefiner refiner = new AtomDiscretePartitionRefiner();
PermutationGroup group = refiner.GetAutomorphismGroup(mol);
Assert.AreEqual(expected, group.Order());
}
void Main()
{
IAtomContainer someMolecule = null;
{
#region 1
IAtomContainer ac = someMolecule; // get an atom container somehow
AtomDiscretePartitionRefiner refiner = new AtomDiscretePartitionRefiner();
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
AtomDiscretePartitionRefiner refiner = new AtomDiscretePartitionRefiner();
if (refiner.IsCanonical(ac))
{
// do something with the atom container
}
#endregion
}
{
IAtomContainer ac = someMolecule;
#region 3
AtomDiscretePartitionRefiner refiner = new AtomDiscretePartitionRefiner();
refiner.Refine(ac);
bool isCanon = refiner.IsCanonical();
PermutationGroup autG = refiner.GetAutomorphismGroup();
#endregion
}
}
public void AdvancedConstructorTest()
{
bool ignoreElements = true;
bool ignoreBondOrder = true;
AtomDiscretePartitionRefiner refiner = new AtomDiscretePartitionRefiner(ignoreElements, ignoreBondOrder);
Assert.IsNotNull(refiner);
}
public void IsCanonical_FalseTest()
{
string acpString = "C0C1C2O3 0:1(2),0:3(1),1:2(1),2:3(1)";
IAtomContainer ac = AtomContainerPrinter.FromString(acpString, builder);
AtomDiscretePartitionRefiner refiner = new AtomDiscretePartitionRefiner();
Assert.IsFalse(refiner.IsCanonical(ac));
}
public void GetVertexCountTest()
{
string acpString = "C0C1C2C3 0:1(1),0:3(1),1:2(1),2:3(1)";
IAtomContainer ac = AtomContainerPrinter.FromString(acpString, builder);
AtomDiscretePartitionRefiner refiner = new AtomDiscretePartitionRefiner();
refiner.Refine(ac);
Assert.AreEqual(ac.Atoms.Count, refiner.GetVertexCount());
}
public void GetAutomorphismGroup_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);
AtomDiscretePartitionRefiner refiner = new AtomDiscretePartitionRefiner();
PermutationGroup autG = refiner.GetAutomorphismGroup(ac, partition);
Assert.AreEqual(2, autG.Order());
}
public void GetAutomorphismGroupTest()
{
string acpString = "C0C1C2O3 0:1(2),0:2(1),1:3(1),2:3(1)";
IAtomContainer ac = AtomContainerPrinter.FromString(acpString, builder);
AtomDiscretePartitionRefiner refiner = new AtomDiscretePartitionRefiner();
PermutationGroup autG = refiner.GetAutomorphismGroup(ac);
Assert.IsNotNull(autG);
Assert.AreEqual(1, autG.Order());
}
public void GetAutomorphismPartitionTest()
{
string acpString = "C0C1C2C3C4C5C6C7C8C9 0:1(2),1:2(1),2:3(2),3:4(1),"
+ "4:5(2),5:6(1),6:7(2),7:8(1),8:9(2),5:9(1),0:9(1)";
IAtomContainer ac = AtomContainerPrinter.FromString(acpString, builder);
AtomDiscretePartitionRefiner refiner = new AtomDiscretePartitionRefiner();
Partition autP = refiner.GetAutomorphismPartition(ac);
Partition expected = Partition.FromString("0|1|2|3|4|5|6|7|8|9");
Assert.AreEqual(expected, autP);
}
public void RefineTest()
{
string acpString = "C0C1O2O3 0:1(1),0:3(1),1:2(1),2:3(1)";
IAtomContainer ac = AtomContainerPrinter.FromString(acpString, builder);
AtomDiscretePartitionRefiner refiner = new AtomDiscretePartitionRefiner();
refiner.Refine(ac);
PermutationGroup autG = refiner.GetAutomorphismGroup();
Assert.AreEqual(2, autG.Order());
}
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_IgnoreElementsTest()
{
string acpString = "C0C1O2O3 0:1(1),0:3(1),1:2(1),2:3(1)";
IAtomContainer ac = AtomContainerPrinter.FromString(acpString, builder);
bool ignoreElements = true;
bool ignoreBondOrder = false;
AtomDiscretePartitionRefiner refiner = new AtomDiscretePartitionRefiner(ignoreElements, ignoreBondOrder);
refiner.Refine(ac);
PermutationGroup autG = refiner.GetAutomorphismGroup();
Assert.AreEqual(8, 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);
}
}
public void TestBiphenyl()
{
IAtomContainer mol = TestMoleculeFactory.MakeBiphenyl();
AtomContainerManipulator.PercieveAtomTypesAndConfigureAtoms(mol);
Aromaticity.CDKLegacy.Apply(mol);
Assert.IsNotNull(mol, "Created molecule was null");
AtomDiscretePartitionRefiner refiner = new AtomDiscretePartitionRefiner();
refiner.Refine(mol);
Partition autP = refiner.GetAutomorphismPartition();
Assert.AreEqual(4, autP.Count, "Wrong number of equivalent classes");
Partition expected = Partition.FromString("0,6|1,5,7,11|2,4,8,10|3,9");
Assert.AreEqual(expected, autP, "Wrong class assignment");
}
public void DefaultConstructorTest()
{
AtomDiscretePartitionRefiner refiner = new AtomDiscretePartitionRefiner();
Assert.IsNotNull(refiner);
}
