public void timeFile(File dir, String filename) throws CDKException, IOException {
IAtomContainer atomContainer = readFile(new File(dir, filename));
long start;
start = System.currentTimeMillis();
EquivalentClassPartitioner it = new EquivalentClassPartitioner(atomContainer);
int equivalentClass[] = it.getTopoEquivClassbyHuXu(atomContainer);
Partition huXuPartition = ArrayToPartition.convert(equivalentClass, 1);
long elapsedHuXu = System.currentTimeMillis() - start;
start = System.currentTimeMillis();
AtomDiscretePartitionRefiner refiner = new AtomDiscretePartitionRefiner();
refiner.refine(atomContainer);
Partition refinedPartition = refiner.getAutomorphismPartition();
long elapsedRef = System.currentTimeMillis() - start;
long order = refiner.getAutomorphismGroup().order();
boolean partitionsEqual = refinedPartition.equals(huXuPartition);
System.out.println(
filename
+ "\t"
+ atomContainer.getAtomCount()
+ "\t"
+ elapsedRef
+ "\t"
+ elapsedHuXu
+ "\t"
+ order
+ "\t"
+ refinedPartition.size()
+ "\t"
+ partitionsEqual);
}
@Test
public void testQuinone() throws Exception {
IAtomContainer mol = MoleculeFactory.makeQuinone();
Assert.assertNotNull("Created molecule was null", mol);
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol);
CDKHueckelAromaticityDetector.detectAromaticity(mol);
EquivalentClassPartitioner partitioner = new EquivalentClassPartitioner(mol);
int[] eqCl = partitioner.getTopoEquivClassbyHuXu(mol);
Partition autP = ArrayToPartition.convert(eqCl, 1);
Assert.assertEquals("Wrong number of equivalent classes", 3, autP.size());
Partition expected = Partition.fromString("0,7|1,4|2,3,5,6");
Assert.assertEquals("Wrong class assignment", expected, autP);
}
public void compareResults(IAtomContainer atomContainer, int count) throws NoSuchAtomException {
AtomDiscretePartitionRefiner refiner = new AtomDiscretePartitionRefiner();
refiner.refine(atomContainer);
Partition refinedPartition = refiner.getAutomorphismPartition();
EquivalentClassPartitioner it = new EquivalentClassPartitioner(atomContainer);
int equivalentClass[] = it.getTopoEquivClassbyHuXu(atomContainer);
Partition huXuPartition = ArrayToPartition.convert(equivalentClass, 1);
if (refinedPartition.equals(huXuPartition)) {
System.out.println(count + " Equal");
} else {
System.out.println(count + " Failed");
System.out.println(AtomContainerPrinter.toString(atomContainer));
System.out.println(refinedPartition);
System.out.println(huXuPartition);
}
}