/** {@inheritDoc} */ @Override public void setMassNumber(Integer massNumber) { logger.debug("Setting mass number: ", massNumber); super.setMassNumber(massNumber); }
@Test public void testOutput() throws Exception { StringWriter writer = new StringWriter(); IAtomContainer molecule = new AtomContainer(); Atom atom = new Atom("C"); atom.setMassNumber(14); molecule.addAtom(atom); CDKSourceCodeWriter sourceWriter = new CDKSourceCodeWriter(writer); sourceWriter.write(molecule); sourceWriter.close(); String output = writer.toString(); String newline = "\n"; assertThat(output, is("{" + newline + " IChemObjectBuilder builder = DefaultChemObjectBuilder.getInstance();" + newline + " IAtomContainer mol = builder.newInstance(IAtomContainer.class);" + newline + " IAtom a1 = builder.newInstance(IAtom.class,\"C\");" + newline + " a1.setFormalCharge(0);" + newline + " mol.addAtom(a1);" + newline + "}" + newline)); } }
/** * Test example with one explicit carbon, writing of MassNumber * */ @Test public void testMassNumber() throws Exception { StringWriter writer = new StringWriter(); IAtomContainer mol = new AtomContainer(); Atom atom = new Atom("C"); atom.setMassNumber(new Integer(12)); mol.addAtom(atom); CMLWriter cmlWriter = new CMLWriter(writer); cmlWriter.write(mol); cmlWriter.close(); logger.debug("****************************** testMAssNumber()"); logger.debug(writer.toString()); logger.debug("******************************"); Assert.assertTrue(writer.toString().indexOf("isotopeNumber=\"12\"") != -1); }
/** * @cdk.bug 1212219 */ @Test public void testBug1212219() throws Exception { StringWriter writer = new StringWriter(); IAtomContainer molecule = new AtomContainer(); Atom atom = new Atom("C"); atom.setMassNumber(14); molecule.addAtom(atom); MDLV2000Writer mdlWriter = new MDLV2000Writer(writer); mdlWriter.write(molecule); mdlWriter.close(); String output = writer.toString(); //logger.debug("MDL output for testBug1212219: " + output); Assert.assertTrue(output.indexOf("M ISO 1 1 14") != -1); }
/** * Test roundtripping of MassNumber. * @throws Exception */ @Test public void testMassNumber() throws Exception { IAtomContainer mol = new AtomContainer(); Atom atom = new Atom("C"); atom.setMassNumber(new Integer(12)); mol.addAtom(atom); Assert.assertEquals(12, atom.getMassNumber().intValue()); IAtomContainer roundTrippedMol = CMLRoundTripTool.roundTripMolecule(convertor, mol); Assert.assertEquals(1, roundTrippedMol.getAtomCount()); IAtom roundTrippedAtom = roundTrippedMol.getAtom(0); Assert.assertEquals(atom.getMassNumber(), roundTrippedAtom.getMassNumber()); }
@Test public void testIsotope() throws Exception { IAtomContainer mol = new AtomContainer(); Atom atom = new Atom("C"); atom.setMassNumber(13); mol.addAtom(atom); IAtomContainer roundTrippedMol = CMLRoundTripTool.roundTripMolecule(convertor, mol); Assert.assertEquals(1, roundTrippedMol.getAtomCount()); IAtom roundTrippedAtom = roundTrippedMol.getAtom(0); Assert.assertEquals(atom.getMassNumber(), roundTrippedAtom.getMassNumber()); }
/** * @cdk.bug 590236 */ @Test public void testBug590236() throws Exception { String smiles = ""; IAtomContainer molecule = new AtomContainer(); SmilesGenerator sg = SmilesGenerator.isomeric(); molecule.addAtom(new Atom("C")); Atom carbon2 = new Atom("C"); carbon2.setMassNumber(13); molecule.addAtom(carbon2); molecule.addBond(0, 1, IBond.Order.SINGLE); fixCarbonHCount(molecule); smiles = sg.create(molecule); Assert.assertEquals("C[13CH3]", smiles); }