/** * @param set The collection of IAtomContainer objects * @return The summed charges of all atoms in this set. */ public static double getTotalCharge(IAtomContainerSet set) { double charge = 0; for (int i = 0; i < set.getAtomContainerCount(); i++) { int thisCharge = AtomContainerManipulator.getTotalFormalCharge(set.getAtomContainer(i)); double stoich = set.getMultiplier(i); charge += stoich * thisCharge; } return charge; }
/** * @param set The collection of IAtomContainer objects * @return The summed formal charges of all atoms in this set. */ public static double getTotalFormalCharge(IAtomContainerSet set) { int charge = 0; for (int i = 0; i < set.getAtomContainerCount(); i++) { int thisCharge = AtomContainerManipulator.getTotalFormalCharge(set.getAtomContainer(i)); double stoich = set.getMultiplier(i); charge += stoich * thisCharge; } return charge; }
IAtomContainer container = (IAtomContainer) arg0; writer.write(mopacCommands.getSetting()); int formalCharge = AtomContainerManipulator.getTotalFormalCharge(container); if (formalCharge != 0) writer.write(" CHARGE=" + formalCharge); writer.write('\n');
IAtomContainer container = (IAtomContainer) arg0; writer.write(mopacCommands.getSetting()); int formalCharge = AtomContainerManipulator.getTotalFormalCharge(container); if (formalCharge != 0) writer.write(" CHARGE=" + formalCharge); writer.write('\n');
&& getTotalFormalCharge(ac1) == getTotalFormalCharge(ac2)) {
/** * Test total formal charge. * */ @Test public void testGetTotalFormalCharge_IAtomContainer() throws Exception { SmilesParser parser = new SmilesParser(DefaultChemObjectBuilder.getInstance()); IAtomContainer mol = parser.parseSmiles("[O-]C([N+])C([N+])C"); int totalCharge = AtomContainerManipulator.getTotalFormalCharge(mol); Assert.assertEquals(1, totalCharge); }
@Test public void testReadProton() throws Exception { String mdl = "proton.mol\n" + "\n" + "\n" + " 1 0 0 0 0 1 V2000\n" + " -0.0073 -0.5272 0.9655 H 0 0 0 0 0\n" + "M CHG 1 1 1\n" + "M END\n"; MDLV2000Reader reader = new MDLV2000Reader(new StringReader(mdl)); IAtomContainer mol = reader.read(new AtomContainer()); reader.close(); Assert.assertNotNull(mol); Assert.assertEquals(1, mol.getAtomCount()); Assert.assertEquals(0, mol.getBondCount()); Assert.assertEquals(1, AtomContainerManipulator.getTotalFormalCharge(mol)); IAtom atom = mol.getAtom(0); Assert.assertEquals(1, atom.getFormalCharge().intValue()); }