public void fullPermutationTest(IAtomContainer mol) {
AtomContainerAtomPermutor permutor = new AtomContainerAtomPermutor(mol);
String expected = new MoleculeSignature(mol).toCanonicalString();
int numberOfPermutationsTried = 0;
while (permutor.hasNext()) {
IAtomContainer permutation = permutor.next();
String actual = new MoleculeSignature(permutation).toCanonicalString();
numberOfPermutationsTried++;
String msg = "Failed on permutation " + numberOfPermutationsTried;
Assert.assertEquals(msg, expected, actual);
}
}
@Test
public void testAtomPermutation() throws CDKException {
IAtomContainer pamine = makePropylAmine();
ShortestPathFingerprinter fp = new ShortestPathFingerprinter();
IBitFingerprint bs1 = fp.getBitFingerprint(pamine);
AtomContainerAtomPermutor acp = new AtomContainerAtomPermutor(pamine);
while (acp.hasNext()) {
IAtomContainer container = acp.next();
IBitFingerprint bs2 = fp.getBitFingerprint(container);
Assert.assertTrue(bs1.equals(bs2));
}
}
@Test
public void testAtomPermutation2() throws CDKException {
IAtomContainer pamine = TestMoleculeFactory.makeCyclopentane();
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(pamine);
ShortestPathFingerprinter fp = new ShortestPathFingerprinter();
IBitFingerprint bs1 = fp.getBitFingerprint(pamine);
AtomContainerAtomPermutor acp = new AtomContainerAtomPermutor(pamine);
while (acp.hasNext()) {
IAtomContainer container = acp.next();
IBitFingerprint bs2 = fp.getBitFingerprint(container);
Assert.assertTrue(bs1.equals(bs2));
}
}
/** A unit test for JUnit */
@Test
public void testAtomPermutation() {
IAtomContainer mol = new AtomContainer();
mol.addAtom(new Atom("S"));
mol.addAtom(new Atom("O"));
mol.addAtom(new Atom("O"));
mol.addAtom(new Atom("O"));
mol.addAtom(new Atom("O"));
mol.addBond(0, 1, IBond.Order.DOUBLE);
mol.addBond(0, 2, IBond.Order.DOUBLE);
mol.addBond(0, 3, IBond.Order.SINGLE);
mol.addBond(0, 4, IBond.Order.SINGLE);
mol.getAtom(3).setImplicitHydrogenCount(1);
mol.getAtom(4).setImplicitHydrogenCount(1);
AtomContainerAtomPermutor acap = new AtomContainerAtomPermutor(mol);
SmilesGenerator sg = new SmilesGenerator();
String smiles = "";
String oldSmiles = sg.createSMILES(mol);
while (acap.hasNext()) {
smiles = sg.createSMILES(new AtomContainer((AtomContainer) acap.next()));
// logger.debug(smiles);
Assert.assertEquals(oldSmiles, smiles);
}
}