/** * {@inheritDoc} */ @Override public void addBond(IBond bond) { logger.debug("Adding bond: ", bond); super.addBond(bond); }
/** * {@inheritDoc} */ @Override public void addBond(int atom1, int atom2, IBond.Order order, IBond.Stereo stereo) { logger.debug("Adding bond: atom1=" + atom1 + " atom2=" + atom2, " order=" + order + " stereo=" + stereo); super.addBond(atom1, atom2, order, stereo); }
/** * {@inheritDoc} */ @Override public void addBond(int atom1, int atom2, IBond.Order order) { logger.debug("Adding bond: atom1=" + atom1 + " atom2=" + atom2, " order=" + order); super.addBond(atom1, atom2, order); }
/** * {@inheritDoc} */ @Override public void addElectronContainer(IElectronContainer electronContainer) { if (electronContainer instanceof IBond) this.addBond((IBond) electronContainer); if (electronContainer instanceof ILonePair) this.addLonePair((ILonePair) electronContainer); if (electronContainer instanceof ISingleElectron) this.addSingleElectron((ISingleElectron) electronContainer); }
/** * {@inheritDoc} */ @Override public void addElectronContainer(IElectronContainer electronContainer) { if (electronContainer instanceof IBond) this.addBond((IBond) electronContainer); if (electronContainer instanceof ILonePair) this.addLonePair((ILonePair) electronContainer); if (electronContainer instanceof ISingleElectron) this.addSingleElectron((ISingleElectron) electronContainer); }
/** * {@inheritDoc} */ @Override public void addBond(int atom1, int atom2, IBond.Order order) { IBond bond = getBuilder().newInstance(IBond.class, getAtom(atom1), getAtom(atom2), order); addBond(bond); /* * no notifyChanged() here because addBond(bond) does it already */ }
/** * {@inheritDoc} */ @Override public void addBond(int atom1, int atom2, IBond.Order order, IBond.Stereo stereo) { IBond bond = getBuilder().newInstance(IBond.class, getAtom(atom1), getAtom(atom2), order, stereo); addBond(bond); /* * no notifyChanged() here because addBond(bond) does it already */ }
/** * {@inheritDoc} */ @Override public void addBond(int atom1, int atom2, IBond.Order order, IBond.Stereo stereo) { IBond bond = getBuilder().newInstance(IBond.class, getAtom(atom1), getAtom(atom2), order, stereo); addBond(bond); /* * no notifyChanged() here because addBond(bond) does it already */ }
/** * {@inheritDoc} */ @Override public void addBond(int atom1, int atom2, IBond.Order order) { IBond bond = getBuilder().newInstance(IBond.class, getAtom(atom1), getAtom(atom2), order); addBond(bond); /* * no notifyChanged() here because addBond(bond) does it already */ }
C24D6D.addBond(0, 1, IBond.Order.SINGLE); // 1 C24D6D.addBond(0, 5, IBond.Order.SINGLE); // 2 C24D6D.addBond(0, 11, IBond.Order.SINGLE); // 3 C24D6D.addBond(1, 2, IBond.Order.SINGLE); // 4 C24D6D.addBond(1, 10, IBond.Order.SINGLE); // 5 C24D6D.addBond(2, 3, IBond.Order.SINGLE); // 6 C24D6D.addBond(2, 9, IBond.Order.SINGLE); // 7 C24D6D.addBond(3, 4, IBond.Order.SINGLE); // 8 C24D6D.addBond(3, 8, IBond.Order.SINGLE); // 9 C24D6D.addBond(4, 5, IBond.Order.SINGLE); // 10 C24D6D.addBond(4, 7, IBond.Order.SINGLE); // 11 C24D6D.addBond(5, 6, IBond.Order.SINGLE); // 12 C24D6D.addBond(6, 16, IBond.Order.SINGLE); // 13 C24D6D.addBond(6, 17, IBond.Order.SINGLE); // 14 C24D6D.addBond(7, 15, IBond.Order.SINGLE); // 15 C24D6D.addBond(7, 16, IBond.Order.SINGLE); // 16 C24D6D.addBond(8, 14, IBond.Order.SINGLE); // 17 C24D6D.addBond(8, 15, IBond.Order.SINGLE); // 18 C24D6D.addBond(9, 13, IBond.Order.SINGLE); // 19 C24D6D.addBond(9, 14, IBond.Order.SINGLE); // 20 C24D6D.addBond(10, 12, IBond.Order.SINGLE); // 21 C24D6D.addBond(10, 13, IBond.Order.SINGLE); // 22 C24D6D.addBond(11, 12, IBond.Order.SINGLE); // 23 C24D6D.addBond(11, 17, IBond.Order.SINGLE); // 24 C24D6D.addBond(12, 19, IBond.Order.SINGLE); // 25 C24D6D.addBond(13, 20, IBond.Order.SINGLE); // 26 C24D6D.addBond(14, 21, IBond.Order.SINGLE); // 27 C24D6D.addBond(15, 22, IBond.Order.SINGLE); // 28 C24D6D.addBond(16, 23, IBond.Order.SINGLE); // 29
C40C3V.addBond(0, 1, IBond.Order.SINGLE); // 1 C40C3V.addBond(0, 5, IBond.Order.SINGLE); // 2 C40C3V.addBond(0, 8, IBond.Order.SINGLE); // 3 C40C3V.addBond(1, 2, IBond.Order.SINGLE); // 4 C40C3V.addBond(1, 25, IBond.Order.SINGLE); // 5 C40C3V.addBond(2, 3, IBond.Order.SINGLE); // 6 C40C3V.addBond(2, 6, IBond.Order.SINGLE); // 7 C40C3V.addBond(3, 4, IBond.Order.SINGLE); // 8 C40C3V.addBond(3, 24, IBond.Order.SINGLE); // 9 C40C3V.addBond(4, 7, IBond.Order.SINGLE); // 10 C40C3V.addBond(4, 8, IBond.Order.SINGLE); // 11 C40C3V.addBond(5, 21, IBond.Order.SINGLE); // 12 C40C3V.addBond(5, 28, IBond.Order.SINGLE); // 13 C40C3V.addBond(6, 22, IBond.Order.SINGLE); // 14 C40C3V.addBond(6, 27, IBond.Order.SINGLE); // 15 C40C3V.addBond(7, 20, IBond.Order.SINGLE); // 16 C40C3V.addBond(7, 23, IBond.Order.SINGLE); // 17 C40C3V.addBond(8, 26, IBond.Order.SINGLE); // 18 C40C3V.addBond(9, 12, IBond.Order.SINGLE); // 19 C40C3V.addBond(9, 37, IBond.Order.SINGLE); // 20 C40C3V.addBond(9, 39, IBond.Order.SINGLE); // 21 C40C3V.addBond(10, 14, IBond.Order.SINGLE); // 22 C40C3V.addBond(10, 38, IBond.Order.SINGLE); // 23 C40C3V.addBond(10, 39, IBond.Order.SINGLE); // 24 C40C3V.addBond(11, 13, IBond.Order.SINGLE); // 25 C40C3V.addBond(11, 36, IBond.Order.SINGLE); // 26 C40C3V.addBond(11, 39, IBond.Order.SINGLE); // 27 C40C3V.addBond(12, 35, IBond.Order.SINGLE); // 28 C40C3V.addBond(12, 38, IBond.Order.SINGLE); // 29
@Test public void testCountAtomPermutation() { AtomContainer ac = new AtomContainer(); ac.addAtom(new Atom("C")); ac.addAtom(new Atom("N")); ac.addAtom(new Atom("P")); ac.addAtom(new Atom("O")); ac.addAtom(new Atom("S")); ac.addAtom(new Atom("Br")); ac.addBond(0, 1, IBond.Order.SINGLE); ac.addBond(1, 2, IBond.Order.SINGLE); ac.addBond(2, 3, IBond.Order.SINGLE); ac.addBond(3, 4, IBond.Order.SINGLE); ac.addBond(4, 5, IBond.Order.SINGLE); AtomContainerAtomPermutor acap = new AtomContainerAtomPermutor(ac); int counter = 0; while (acap.hasNext()) { counter++; acap.next(); } Assert.assertEquals(719, counter); }
@Test public void testBondPermutation() { AtomContainer ac = new AtomContainer(); ac.addAtom(new Atom("C")); ac.addAtom(new Atom("N")); ac.addAtom(new Atom("P")); ac.addAtom(new Atom("O")); ac.addAtom(new Atom("S")); ac.addAtom(new Atom("Br")); ac.addBond(0, 1, IBond.Order.SINGLE); ac.addBond(1, 2, IBond.Order.DOUBLE); ac.addBond(2, 3, IBond.Order.TRIPLE); ac.addBond(3, 4, IBond.Order.QUADRUPLE); ac.addBond(4, 5, IBond.Order.SINGLE); // was 5.0 ! AtomContainerBondPermutor acap = new AtomContainerBondPermutor(ac); int counter = 0; while (acap.hasNext()) { counter++; acap.next(); } Assert.assertEquals(119, counter); }
@Test public void testBondPermutation() { AtomContainer ac = new org.openscience.cdk.AtomContainer(); AtomContainer result; String bonds = new String(""); ac.addAtom(new Atom("C")); ac.addAtom(new Atom("N")); ac.addAtom(new Atom("P")); ac.addAtom(new Atom("O")); ac.addAtom(new Atom("S")); ac.addAtom(new Atom("Br")); ac.addBond(0, 1, IBond.Order.SINGLE); ac.addBond(1, 2, IBond.Order.DOUBLE); ac.addBond(2, 3, IBond.Order.TRIPLE); ac.addBond(3, 4, IBond.Order.QUADRUPLE); ac.addBond(4, 5, IBond.Order.SINGLE); // was 5.0 ! AtomContainerBondPermutor acap = new AtomContainerBondPermutor(ac); int counter = 0; while (acap.hasNext()) { counter++; bonds = ""; result = (AtomContainer) acap.next(); for (int f = 0; f < result.getBondCount(); f++) { bonds += result.getBond(f).getOrder(); } //logger.debug(bonds); } Assert.assertEquals(119, counter); }
@Test public void testAtomPermutation() { AtomContainer ac = new org.openscience.cdk.AtomContainer(); AtomContainer result; String atoms = new String(""); ac.addAtom(new Atom("C")); ac.addAtom(new Atom("N")); ac.addAtom(new Atom("P")); ac.addAtom(new Atom("O")); ac.addAtom(new Atom("S")); ac.addAtom(new Atom("Br")); ac.addBond(0, 1, IBond.Order.SINGLE); ac.addBond(1, 2, IBond.Order.SINGLE); ac.addBond(2, 3, IBond.Order.SINGLE); ac.addBond(3, 4, IBond.Order.SINGLE); ac.addBond(4, 5, IBond.Order.SINGLE); AtomContainerAtomPermutor acap = new AtomContainerAtomPermutor(ac); int counter = 0; while (acap.hasNext()) { counter++; atoms = ""; result = (AtomContainer) acap.next(); for (int f = 0; f < result.getAtomCount(); f++) { atoms += result.getAtom(f).getSymbol(); } } Assert.assertEquals(719, counter); }
/** * @cdk.bug 1875946 */ @Test public void testPreservingFormalCharge() throws Exception { AtomContainer mol = new AtomContainer(); mol.addAtom(new Atom(Elements.OXYGEN)); mol.getAtom(0).setFormalCharge(-1); mol.addAtom(new Atom(Elements.CARBON)); mol.addBond(0, 1, IBond.Order.SINGLE); addImplicitHydrogens(mol); SmilesGenerator generator = new SmilesGenerator(); generator.create(new AtomContainer(mol)); Assert.assertEquals(-1, mol.getAtom(0).getFormalCharge().intValue()); // mmm, that does not reproduce the bug findings yet :( }