@Override public IAtomContainer shallowCopy() { return new AtomContainer2(this); }
@Override public IAtomContainer shallowCopy() { return new AtomContainer2(this); }
/** * {@inheritDoc} */ @Override public IAtomContainer newAtomContainer() { if (CDK_LEGACY_AC) return new AtomContainer(0,0,0,0); else return new AtomContainer2(0,0,0,0); } }
/** * {@inheritDoc} */ @Override public IAtomContainer newAtomContainer() { if (CDK_LEGACY_AC) return new AtomContainer(0,0,0,0); else return new AtomContainer2(0,0,0,0); } }
@Override public IChemObject newTestObject() { return new AtomContainer2(); } });
@Test public void testAtomContainer() { // create an empty container with in the constructor defined array lengths IAtomContainer container = new AtomContainer2(); Assert.assertEquals(0, container.getAtomCount()); Assert.assertEquals(0, container.getBondCount()); // test whether the ElectronContainer is correctly initialized IAtom c1 = container.getBuilder().newInstance(IAtom.class, "C"); IAtom c2 = container.getBuilder().newInstance(IAtom.class, "C"); IAtom n = container.getBuilder().newInstance(IAtom.class, "N"); container.addAtom(c1); container.addAtom(c2); container.addAtom(n); container.addBond(container.getBuilder().newInstance(IBond.class, c1, c2, IBond.Order.DOUBLE)); container.addLonePair(container.getBuilder().newInstance(ILonePair.class, n)); }
@Test public void testAtomContainer_int_int_int_int() { // create an empty container with predefined // array lengths IAtomContainer container = new AtomContainer2(5, 6, 1, 2); Assert.assertEquals(0, container.getAtomCount()); Assert.assertEquals(0, container.getElectronContainerCount()); // test whether the ElectronContainer is correctly initialized IAtom c1 = container.getBuilder().newInstance(IAtom.class, "C"); IAtom c2 = container.getBuilder().newInstance(IAtom.class, "C"); IAtom n = container.getBuilder().newInstance(IAtom.class, "N"); container.addAtom(c1); container.addAtom(c2); container.addAtom(n); container.addBond(container.getBuilder().newInstance(IBond.class, c1, c2, IBond.Order.DOUBLE)); container.addLonePair(container.getBuilder().newInstance(ILonePair.class, n)); }
@Test public void testAtomContainer_IAtomContainer() { IAtomContainer acetone = newChemObject().getBuilder().newInstance(IAtomContainer.class); IAtom c1 = acetone.getBuilder().newInstance(IAtom.class, "C"); IAtom c2 = acetone.getBuilder().newInstance(IAtom.class, "C"); IAtom o = acetone.getBuilder().newInstance(IAtom.class, "O"); IAtom c3 = acetone.getBuilder().newInstance(IAtom.class, "C"); acetone.addAtom(c1); acetone.addAtom(c2); acetone.addAtom(c3); acetone.addAtom(o); IBond b1 = acetone.getBuilder().newInstance(IBond.class, c1, c2, IBond.Order.SINGLE); IBond b2 = acetone.getBuilder().newInstance(IBond.class, c1, o, IBond.Order.DOUBLE); IBond b3 = acetone.getBuilder().newInstance(IBond.class, c1, c3, IBond.Order.SINGLE); acetone.addBond(b1); acetone.addBond(b2); acetone.addBond(b3); IAtomContainer container = new AtomContainer2(acetone); Assert.assertEquals(4, container.getAtomCount()); Assert.assertEquals(3, container.getBondCount()); }