/** * {@inheritDoc} */ @Override public void setOrder(Order order) { bond.setOrder(order); }
/** * {@inheritDoc} */ @Override public void setOrder(Order order) { bond.setOrder(order); }
/** * Resets the bond order of the Bond to 1.0. */ public void unsaturateBonds(IAtomContainer container) { for (IBond bond : container.bonds()) bond.setOrder(Order.SINGLE); }
/** * Resets the bond orders of all atoms to 1.0. */ public void unsaturate(IAtomContainer atomContainer) { for (IBond bond : atomContainer.bonds()) bond.setOrder(Order.SINGLE); }
/** * Increment the bond order of this bond. * * @param bond The bond whose order is to be incremented * @see #increaseBondOrder(org.openscience.cdk.interfaces.IBond.Order) * @see #decreaseBondOrder(org.openscience.cdk.interfaces.IBond.Order) * @see #decreaseBondOrder(org.openscience.cdk.interfaces.IBond) */ public static void increaseBondOrder(IBond bond) { bond.setOrder(increaseBondOrder(bond.getOrder())); }
/** * Decrease the order of a bond. * * @param bond The bond in question * @see #decreaseBondOrder(org.openscience.cdk.interfaces.IBond.Order) * @see #increaseBondOrder(org.openscience.cdk.interfaces.IBond.Order) * @see #increaseBondOrder(org.openscience.cdk.interfaces.IBond.Order) */ public static void decreaseBondOrder(IBond bond) { bond.setOrder(decreaseBondOrder(bond.getOrder())); }
/** * Decrease the order of a bond. * * @param bond The bond in question * @see #decreaseBondOrder(org.openscience.cdk.interfaces.IBond.Order) * @see #increaseBondOrder(org.openscience.cdk.interfaces.IBond.Order) * @see #increaseBondOrder(org.openscience.cdk.interfaces.IBond.Order) */ public static void decreaseBondOrder(IBond bond) { bond.setOrder(decreaseBondOrder(bond.getOrder())); }
public boolean unsaturateByDecreasingBondOrder(IBond bond) { if (bond.getOrder() != IBond.Order.SINGLE) { bond.setOrder(BondManipulator.decreaseBondOrder(bond.getOrder())); return true; } else { return false; } }
@Test public void testGetMinimumBondOrder_HigherOrders() { List<IBond> bonds = new ArrayList<IBond>(); IBond bond = new Bond(); bond.setOrder(IBond.Order.QUINTUPLE); bonds.add(bond); bond = new Bond(); bond.setOrder(IBond.Order.SEXTUPLE); bonds.add(bond); Assert.assertEquals(IBond.Order.QUINTUPLE, BondManipulator.getMinimumBondOrder(bonds.iterator())); }
/** * {@inheritDoc} */ @Override public void addBond(int beg, int end, Order order, Stereo stereo) { IBond bond = getBuilder().newBond(); bond.setAtoms(new IAtom[]{getAtom(beg), getAtom(end)}); bond.setOrder(order); bond.setStereo(stereo); addBond(bond); }
/** * {@inheritDoc} */ @Override public void addBond(int beg, int end, Order order, Stereo stereo) { IBond bond = getBuilder().newBond(); bond.setAtoms(new IAtom[]{getAtom(beg), getAtom(end)}); bond.setOrder(order); bond.setStereo(stereo); addBond(bond); }
/** * {@inheritDoc} */ @Override public void addBond(int beg, int end, Order order, Stereo stereo) { IBond bond = getBuilder().newBond(); bond.setAtoms(new IAtom[]{getAtom(beg), getAtom(end)}); bond.setOrder(order); bond.setStereo(stereo); addBond(bond); }
@Test public void testPyridine_SingleOrDouble() throws Exception { String[] expectedTypes = {"C.sp2", "N.sp2", "C.sp2", "C.sp2", "C.sp2", "C.sp2"}; IAtomContainer molecule = TestMoleculeFactory.makePyridine(); for (IBond bond : molecule.bonds()) { bond.setOrder(IBond.Order.UNSET); bond.setFlag(CDKConstants.SINGLE_OR_DOUBLE, true); } assertAtomTypes(testedAtomTypes, expectedTypes, molecule); }
@Test public void testSetOrder_IBond_Order() { IBond b = (IBond) newChemObject(); IAtom c = b.getBuilder().newInstance(IAtom.class, "C"); IAtom o = b.getBuilder().newInstance(IAtom.class, "O"); b.setAtom(c, 0); b.setAtom(o, 1); b.setOrder(Order.DOUBLE); Assert.assertEquals(IBond.Order.DOUBLE, b.getOrder()); b.setOrder(IBond.Order.SINGLE); Assert.assertEquals(IBond.Order.SINGLE, b.getOrder()); }
@Test public void testGetAtomCount() { IBond b = (IBond) newChemObject(); IAtom c = b.getBuilder().newInstance(IAtom.class, "C"); IAtom o = b.getBuilder().newInstance(IAtom.class, "O"); b.setAtom(c, 0); b.setAtom(o, 1); b.setOrder(Order.SINGLE); Assert.assertEquals(2.0, b.getAtomCount(), 0.001); }
@Test public void testClone_Order() throws Exception { IChemObject object = newChemObject(); IAtom atom1 = object.getBuilder().newInstance(IAtom.class, "C"); IAtom atom2 = object.getBuilder().newInstance(IAtom.class, "O"); IBond bond = object.getBuilder().newInstance(IBond.class, atom1, atom2, IBond.Order.SINGLE); IBond clone = (IBond) bond.clone(); // test cloning of bond order bond.setOrder(IBond.Order.DOUBLE); Assert.assertEquals(IBond.Order.SINGLE, clone.getOrder()); }
@Test public void testContains_IAtom() { IBond b = (IBond) newChemObject(); IAtom c = b.getBuilder().newInstance(IAtom.class, "C"); IAtom o = b.getBuilder().newInstance(IAtom.class, "O"); b.setAtom(c, 0); b.setAtom(o, 1); b.setOrder(Order.SINGLE); Assert.assertTrue(b.contains(c)); Assert.assertTrue(b.contains(o)); }