public void TestSimpleCarbonOxygenCompound()
{
string acpString = "O0C1C2 0:1(2),1:2(1)";
IAtomContainer ac = AtomContainerPrinter.FromString(acpString, builder);
CheckForCanonicalForm(ac);
}
public void TestDisconnectedBondsCarbonCompound()
{
string acpString = "C0C1C2C3 0:2(1),1:3(2)";
IAtomContainer ac = AtomContainerPrinter.FromString(acpString, builder);
CheckForCanonicalForm(ac);
}
public void TestCyclicCarbonOxygenCompound()
{
string acpString = "O0C1O2C3 0:1(1),0:3(1),1:2(1),2:3(1)";
IAtomContainer ac = AtomContainerPrinter.FromString(acpString, builder);
CheckForCanonicalForm(ac);
}
public void TestDoubleBondCyclicCarbonCompound()
{
string acpString = "C0C1C2C3 0:1(1),0:3(2),1:2(2),2:3(1)";
IAtomContainer ac = AtomContainerPrinter.FromString(acpString, builder);
CheckForCanonicalForm(ac);
}
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));
}
private IAtomContainer Cubene()
{
string acpString = "C0C1C2C3C4C5C6C7 0:1(1),0:2(2),0:4(1),1:3(1),"
+ "1:5(1),2:3(1),2:6(1),3:7(1),"
+ "4:5(1),4:6(1),5:7(2),6:7(1)";
return(AtomContainerPrinter.FromString(acpString, builder));
}
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 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 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 GetConnectivity()
{
string acpString = "C0C1C2C3 0:1(1),1:2(2),2:3(3)";
IAtomContainer ac = AtomContainerPrinter.FromString(acpString, builder);
AtomRefinable refinable = new AtomRefinable(ac);
Assert.AreEqual(1, refinable.GetConnectivity(0, 1));
Assert.AreEqual(2, refinable.GetConnectivity(1, 2));
Assert.AreEqual(3, refinable.GetConnectivity(2, 3));
}
public void GetBondPartitionTest()
{
string acpString = "C0C1C2C3O4 0:1(2),0:4(1),1:2(1),2:3(2),3:4(1)";
IAtomContainer ac = AtomContainerPrinter.FromString(acpString, builder);
BondRefinable refinable = new BondRefinable(ac);
Partition bondPartition = refinable.GetInitialPartition();
Partition expected = Partition.FromString("0,3|1,4|2");
Assert.AreEqual(expected, bondPartition);
}
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 NeighboursInBlockForMultipleBondsIgnoringBondOrders()
{
string acpString = "C0C1C2C3C4 0:1(1),0:2(2),0:3(1),1:4(1),2:4(1),3:4(2)";
IAtomContainer ac = AtomContainerPrinter.FromString(acpString, builder);
AtomRefinable refinable = new AtomRefinable(ac, false, true);
IInvariant invariant = refinable.NeighboursInBlock(Set(1, 2), 0);
Assert.IsTrue(invariant is IntegerInvariant);
Assert.AreEqual(new IntegerInvariant(2), invariant);
}
public void NeighboursInBlockForSingleBonds()
{
string acpString = "C0C1C2C3 0:1(1),0:3(1),1:2(1),2:3(1)";
IAtomContainer ac = AtomContainerPrinter.FromString(acpString, builder);
AtomRefinable refinable = new AtomRefinable(ac);
IInvariant invariant = refinable.NeighboursInBlock(Set(0, 2), 1);
Assert.IsTrue(invariant is IntegerInvariant);
Assert.AreEqual(new IntegerInvariant(2), invariant);
}
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 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 GetElementPartitionTest()
{
string acpString = "C0N1C2P3C4N5";
Partition expected = Partition.FromString("0,2,4|1,5|3");
IAtomContainer ac = AtomContainerPrinter.FromString(acpString, builder);
AtomRefinable refinable = new AtomRefinable(ac);
Partition elPartition = refinable.GetInitialPartition();
Assert.AreEqual(expected, elPartition);
}
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 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 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 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);
}
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);
}
