@Override public IPseudoAtom clone() throws CloneNotSupportedException { return (IPseudoAtom) super.clone(); } }
@Override public IPseudoAtom clone() throws CloneNotSupportedException { return (IPseudoAtom) super.clone(); } }
/** {@inheritDoc} */ @Override public IAtom clone() throws CloneNotSupportedException { Object clone = null; try { clone = super.clone(); } catch (Exception exception) { logger.error("Could not clone DebugAtom: " + exception.getMessage(), exception); logger.debug(exception); } return (IAtom) clone; }
@Test public void testSFBug956923_nonAromatic() throws Exception { String smiles = ""; IAtomContainer molecule = new AtomContainer(); SmilesGenerator sg = new SmilesGenerator(); Atom sp2CarbonWithOneHydrogen = new Atom("C"); sp2CarbonWithOneHydrogen.setHybridization(IAtomType.Hybridization.SP2); sp2CarbonWithOneHydrogen.setImplicitHydrogenCount(1); molecule.addAtom(sp2CarbonWithOneHydrogen); molecule.addAtom((Atom) sp2CarbonWithOneHydrogen.clone()); molecule.addAtom((Atom) sp2CarbonWithOneHydrogen.clone()); molecule.addAtom((Atom) sp2CarbonWithOneHydrogen.clone()); molecule.addAtom((Atom) sp2CarbonWithOneHydrogen.clone()); molecule.addAtom((Atom) sp2CarbonWithOneHydrogen.clone()); molecule.addBond(0, 1, IBond.Order.SINGLE); molecule.addBond(1, 2, IBond.Order.SINGLE); molecule.addBond(2, 3, IBond.Order.SINGLE); molecule.addBond(3, 4, IBond.Order.SINGLE); molecule.addBond(4, 5, IBond.Order.SINGLE); molecule.addBond(5, 0, IBond.Order.SINGLE); smiles = sg.create(molecule); Assert.assertEquals("[CH]1[CH][CH][CH][CH][CH]1", smiles); }
/** * A bug reported for JChemPaint. * * @cdk.bug 956923 */ @Test public void testSFBug956923_aromatic() throws Exception { String smiles = ""; IAtomContainer molecule = new AtomContainer(); SmilesGenerator sg = new SmilesGenerator().aromatic(); Atom sp2CarbonWithOneHydrogen = new Atom("C"); sp2CarbonWithOneHydrogen.setHybridization(IAtomType.Hybridization.SP2); sp2CarbonWithOneHydrogen.setImplicitHydrogenCount(1); molecule.addAtom(sp2CarbonWithOneHydrogen); molecule.addAtom((Atom) sp2CarbonWithOneHydrogen.clone()); molecule.addAtom((Atom) sp2CarbonWithOneHydrogen.clone()); molecule.addAtom((Atom) sp2CarbonWithOneHydrogen.clone()); molecule.addAtom((Atom) sp2CarbonWithOneHydrogen.clone()); molecule.addAtom((Atom) sp2CarbonWithOneHydrogen.clone()); molecule.addBond(0, 1, IBond.Order.SINGLE); molecule.addBond(1, 2, IBond.Order.SINGLE); molecule.addBond(2, 3, IBond.Order.SINGLE); molecule.addBond(3, 4, IBond.Order.SINGLE); molecule.addBond(4, 5, IBond.Order.SINGLE); molecule.addBond(5, 0, IBond.Order.SINGLE); AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molecule); Aromaticity.cdkLegacy().apply(molecule); smiles = sg.create(molecule); Assert.assertEquals("c1ccccc1", smiles); }