/** * {@inheritDoc} */ @Override public int getAtomCount() { return bond.getAtomCount(); }
/** * {@inheritDoc} */ @Override public int getAtomCount() { return bond.getAtomCount(); }
/** * Constructs an array of Atom objects from Bond. * @param container The Bond object. * @return The array of Atom objects. */ public static IAtom[] getAtomArray(IBond container) { IAtom[] ret = new IAtom[container.getAtomCount()]; for (int i = 0; i < ret.length; ++i) ret[i] = container.getAtom(i); return ret; }
/** * Constructs an array of Atom objects from Bond. * @param container The Bond object. * @return The array of Atom objects. */ public static IAtom[] getAtomArray(IBond container) { IAtom[] ret = new IAtom[container.getAtomCount()]; for (int i = 0; i < ret.length; ++i) ret[i] = container.getAtom(i); return ret; }
Edge toBeamEdge(IBond b, Map<IAtom, Integer> indices) throws CDKException { checkArgument(b.getAtomCount() == 2, "Invalid number of atoms on bond"); int u = indices.get(b.getBegin()); int v = indices.get(b.getEnd()); return toBeamEdgeLabel(b, this.flavour).edge(u, v); }
private List<List<Integer>> order1(IAtomContainer atomContainer) throws CDKException { List<List<Integer>> fragments = new ArrayList<List<Integer>>(); for (IBond bond : atomContainer.bonds()) { if (bond.getAtomCount() != 2) throw new CDKException("We only consider 2 center bonds"); List<Integer> tmp = new ArrayList<Integer>(); tmp.add(atomContainer.indexOf(bond.getBegin())); tmp.add(atomContainer.indexOf(bond.getEnd())); fragments.add(tmp); } return fragments; }
private List<List<Integer>> order1(IAtomContainer atomContainer) throws CDKException { List<List<Integer>> fragments = new ArrayList<List<Integer>>(); for (IBond bond : atomContainer.bonds()) { if (bond.getAtomCount() != 2) throw new CDKException("We only consider 2 center bonds"); List<Integer> tmp = new ArrayList<Integer>(); tmp.add(atomContainer.indexOf(bond.getBegin())); tmp.add(atomContainer.indexOf(bond.getEnd())); fragments.add(tmp); } return fragments; }
private int bondOrderBioType(int bidx) { IBond bond = mol.getBond(bidx); if (bond.getAtomCount() != 2) return 0; final int a1 = mol.indexOf(bond.getBegin()), a2 = mol.indexOf(bond.getEnd()); if (maskAro[a1] && maskAro[a2]) return -1; return bondOrder[bidx]; }
@Test public void testSetAtom_SomeNull() { IBond b = (IBond) newChemObject(); b.setAtom(b.getBuilder().newInstance(IAtom.class, "C"), 0); Assert.assertEquals(1, b.getAtomCount()); }
@Override public DescriptorValue calculate(IBond bond, IAtomContainer ac) { ensureIsotopeFactory(); if (bond.getAtomCount() != 2) { return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(), new DoubleResult( Double.NaN), NAMES, new CDKException("Only 2-center bonds are considered")); } IAtom[] atoms = BondManipulator.getAtomArray(bond); return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(), new DoubleResult( Math.abs(factory.getElement(atoms[0].getSymbol()).getAtomicNumber() - factory.getElement(atoms[1].getSymbol()).getAtomicNumber())), NAMES); }
@Test public void testBond() { IBond bond = new Bond(); Assert.assertEquals(0, bond.getAtomCount()); Assert.assertNull(bond.getBegin()); Assert.assertNull(bond.getEnd()); Assert.assertNull(bond.getOrder()); Assert.assertEquals(IBond.Stereo.NONE, bond.getStereo()); }
@Test public void testBond() { IBond bond = new Bond(); Assert.assertEquals(0, bond.getAtomCount()); Assert.assertNull(bond.getBegin()); Assert.assertNull(bond.getEnd()); Assert.assertNull(bond.getOrder()); Assert.assertEquals(IBond.Stereo.NONE, bond.getStereo()); }
@Test public void testDebugBond() { IBond bond = new DebugBond(); Assert.assertEquals(0, bond.getAtomCount()); Assert.assertNull(bond.getBegin()); Assert.assertNull(bond.getEnd()); Assert.assertNull(bond.getOrder()); Assert.assertEquals(IBond.Stereo.NONE, bond.getStereo()); }
@Test public void testSetAtoms_arrayIAtom() { IBond b = (IBond) newChemObject(); IAtom[] atomsToAdd = new IAtom[2]; atomsToAdd[0] = b.getBuilder().newInstance(IAtom.class, "C"); atomsToAdd[1] = b.getBuilder().newInstance(IAtom.class, "O"); b.setAtoms(atomsToAdd); Assert.assertEquals(2, b.getAtomCount()); Assert.assertEquals(atomsToAdd[0], b.getBegin()); Assert.assertEquals(atomsToAdd[1], b.getEnd()); }
@Test public void testBond_IAtom_IAtom() { IChemObject object = newChemObject(); IAtom c = object.getBuilder().newInstance(IAtom.class, "C"); IAtom o = object.getBuilder().newInstance(IAtom.class, "O"); IBond bond = new Bond(c, o); Assert.assertEquals(2, bond.getAtomCount()); Assert.assertEquals(c, bond.getBegin()); Assert.assertEquals(o, bond.getEnd()); Assert.assertEquals(IBond.Order.SINGLE, bond.getOrder()); Assert.assertEquals(IBond.Stereo.NONE, bond.getStereo()); }
@Test public void testBond_IAtom_IAtom_IBond_Order() { IChemObject object = newChemObject(); IAtom c = object.getBuilder().newInstance(IAtom.class, "C"); IAtom o = object.getBuilder().newInstance(IAtom.class, "O"); IBond bond = new Bond(c, o, IBond.Order.DOUBLE); Assert.assertEquals(2, bond.getAtomCount()); Assert.assertEquals(c, bond.getBegin()); Assert.assertEquals(o, bond.getEnd()); Assert.assertTrue(bond.getOrder() == IBond.Order.DOUBLE); Assert.assertEquals(IBond.Stereo.NONE, bond.getStereo()); }
@Test public void testBond_IAtom_IAtom() { IChemObject object = newChemObject(); IAtom c = object.getBuilder().newInstance(IAtom.class, "C"); IAtom o = object.getBuilder().newInstance(IAtom.class, "O"); IBond bond = new Bond(c, o); Assert.assertEquals(2, bond.getAtomCount()); Assert.assertEquals(c, bond.getBegin()); Assert.assertEquals(o, bond.getEnd()); Assert.assertEquals(IBond.Order.SINGLE, bond.getOrder()); Assert.assertEquals(IBond.Stereo.NONE, bond.getStereo()); }
@Test public void testBond_IAtom_IAtom_IBond_Order_IBond_Stereo() { IChemObject object = newChemObject(); IAtom c = object.getBuilder().newInstance(IAtom.class, "C"); IAtom o = object.getBuilder().newInstance(IAtom.class, "O"); IBond bond = new Bond(c, o, IBond.Order.SINGLE, IBond.Stereo.UP); Assert.assertEquals(2, bond.getAtomCount()); Assert.assertEquals(c, bond.getBegin()); Assert.assertEquals(o, bond.getEnd()); Assert.assertTrue(bond.getOrder() == IBond.Order.SINGLE); Assert.assertEquals(IBond.Stereo.UP, bond.getStereo()); }
@Test public void testBond_IAtom_IAtom_IBond_Order_IBond_Stereo() { IChemObject object = newChemObject(); IAtom c = object.getBuilder().newInstance(IAtom.class, "C"); IAtom o = object.getBuilder().newInstance(IAtom.class, "O"); IBond bond = new Bond(c, o, IBond.Order.SINGLE, IBond.Stereo.UP); Assert.assertEquals(2, bond.getAtomCount()); Assert.assertEquals(c, bond.getBegin()); Assert.assertEquals(o, bond.getEnd()); Assert.assertTrue(bond.getOrder() == IBond.Order.SINGLE); Assert.assertEquals(IBond.Stereo.UP, bond.getStereo()); }
@Test public void testBond_IAtom_IAtom_IBond_Order() { IChemObject object = newChemObject(); IAtom c = object.getBuilder().newInstance(IAtom.class, "C"); IAtom o = object.getBuilder().newInstance(IAtom.class, "O"); IBond bond = new Bond(c, o, IBond.Order.DOUBLE); Assert.assertEquals(2, bond.getAtomCount()); Assert.assertEquals(c, bond.getBegin()); Assert.assertEquals(o, bond.getEnd()); Assert.assertTrue(bond.getOrder() == IBond.Order.DOUBLE); Assert.assertEquals(IBond.Stereo.NONE, bond.getStereo()); }