AtomTests.java

public class AtomTests {
	
	public final static IChemObjectBuilder builder = DefaultChemObjectBuilder.getInstance(); 

	@Test
	public void one_four_cyclohexadiene() throws InvalidSmilesException {
		String acpString = "C0C1C2C3C4C5 0:1(2),0:5(1),1:2(1),2:3(1),3:4(2),4:5(1)";
		IAtomContainer cyclohexadiene = AtomContainerPrinter.fromString(acpString, builder);
		AtomDiscretePartitionRefiner refiner = new AtomDiscretePartitionRefiner();
		PermutationGroup aut = refiner.getAutomorphismGroup(cyclohexadiene);
		for (Permutation automorphism : aut.all()) {
			System.out.println(automorphism.toCycleString());
		}
	}
	
	@Test
	public void four_H_pyran() throws InvalidSmilesException {
		String acpString = "C0C1C2C3C4O5 0:1(2),0:5(1),1:2(1),2:3(1),3:4(2),4:5(1)";
		IAtomContainer cyclohexadiene = AtomContainerPrinter.fromString(acpString, builder);
		AtomDiscretePartitionRefiner refiner = new AtomDiscretePartitionRefiner();
		PermutationGroup aut = refiner.getAutomorphismGroup(cyclohexadiene);
		for (Permutation automorphism : aut.all()) {
			System.out.println(automorphism.toCycleString());
		}
	}

}