@Test
public void testCalculateMissingHydrogens_Aromatic() throws Exception {
IAtomContainer pyrrole = MoleculeFactory.makePyrrole();
IAtom n = pyrrole.getAtom(1);
IRingSet rs = (new SSSRFinder(pyrrole)).findSSSR();
IRing ring = (IRing) rs.getAtomContainer(0);
for (int j = 0; j < ring.getBondCount(); j++) {
ring.getBond(j).setFlag(CDKConstants.ISAROMATIC, true);
}
Assert.assertEquals(5, ring.getBondCount());
Assert.assertEquals(1, satcheck.calculateNumberOfImplicitHydrogens(n, pyrrole));
}
@Test
public void testFingerprinter_int_int() throws java.lang.Exception {
ShortestPathFingerprinter fingerprinter = new ShortestPathFingerprinter(1024);
Assert.assertNotNull(fingerprinter);
IAtomContainer mol = MoleculeFactory.makeIndole();
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol);
BitSet bs = fingerprinter.getBitFingerprint(mol).asBitSet();
IAtomContainer frag1 = MoleculeFactory.makePyrrole();
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(frag1);
BitSet bs1 = fingerprinter.getBitFingerprint(frag1).asBitSet();
Assert.assertTrue(FingerprinterTool.isSubset(bs, bs1));
}
@Test
public void testRegression() throws Exception {
IAtomContainer mol1 = MoleculeFactory.makeIndole();
IAtomContainer mol2 = MoleculeFactory.makePyrrole();
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol1);
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol2);
ShortestPathFingerprinter fingerprinter = new ShortestPathFingerprinter();
IBitFingerprint bs1 = fingerprinter.getBitFingerprint(mol1);
Assert.assertEquals(
"Seems the fingerprint code has changed. This will cause a number of other tests to fail too!",
22,
bs1.cardinality());
IBitFingerprint bs2 = fingerprinter.getBitFingerprint(mol2);
Assert.assertEquals(
"Seems the fingerprint code has changed. This will cause a number of other tests to fail too!",
11,
bs2.cardinality());
}
