@Test public void testAccepts() throws Exception { SMILESWriter reader = new SMILESWriter(); Assert.assertTrue(reader.accepts(AtomContainer.class)); Assert.assertTrue(reader.accepts(AtomContainerSet.class)); }
private void initIOSettings() { useAromaticityFlag = addSetting(new BooleanIOSetting("UseAromaticity", IOSetting.Importance.LOW, "Should aromaticity information be stored in the SMILES?", "false")); }
@Test public void testWriteSMILESFile() throws Exception { StringWriter stringWriter = new StringWriter(); IAtomContainer benzene = TestMoleculeFactory.makeBenzene(); addImplicitHydrogens(benzene); SMILESWriter smilesWriter = new SMILESWriter(stringWriter); smilesWriter.write(benzene); smilesWriter.close(); Assert.assertTrue(stringWriter.toString().contains("C=C")); }
@Test public void testWriteAromatic() throws Exception { StringWriter stringWriter = new StringWriter(); IAtomContainer benzene = TestMoleculeFactory.makeBenzene(); addImplicitHydrogens(benzene); AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(benzene); Aromaticity.cdkLegacy().apply(benzene); SMILESWriter smilesWriter = new SMILESWriter(stringWriter); Properties prop = new Properties(); prop.setProperty("UseAromaticity", "true"); PropertiesListener listener = new PropertiesListener(prop); smilesWriter.addChemObjectIOListener(listener); smilesWriter.customizeJob(); smilesWriter.write(benzene); smilesWriter.close(); Assert.assertFalse(stringWriter.toString().contains("C=C")); Assert.assertTrue(stringWriter.toString().contains("ccc")); } }
@BeforeClass public static void setup() { setChemObjectIO(new SMILESWriter()); }
@Override public boolean accepts(Class<? extends IChemObject> classObject) { if (IAtomContainer.class.equals(classObject)) return true; if (IAtomContainerSet.class.equals(classObject)) return true; Class<?>[] interfaces = classObject.getInterfaces(); for (int i = 0; i < interfaces.length; i++) { if (IAtomContainerSet.class.equals(interfaces[i])) return true; if (IAtomContainer.class.equals(interfaces[i])) return true; } Class superClass = classObject.getSuperclass(); if (superClass != null) return this.accepts(superClass); return false; }
try (SMILESWriter smilesWriter = new SMILESWriter(stringWriter)) { smilesWriter.write(mcsmolecule); smilesWriter.close();
outFile = new File(fileName); cow = new SMILESWriter(new FileWriter(outFile)); if (cow != null && askIOSettings())
SMILESWriter sw = new SMILESWriter(smilesString); sw.write(ac); sw.close(); cs.setSMILES(smilesString.toString());
SMILESWriter sw = new SMILESWriter(smilesString); sw.write(ac); sw.close(); cs.setSMILES(smilesString.toString());