/** * @cdk.bug 2984581 * @throws Exception */ @Test public void testAromaticRingsLine() throws Exception { String filename = "data/hin/bug2984581.hin"; InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename); ISimpleChemObjectReader reader = new HINReader(ins); IChemFile content = reader.read(new ChemFile()); reader.close(); List<IAtomContainer> cList = ChemFileManipulator.getAllAtomContainers(content); Assert.assertEquals(1, cList.size()); }
@Test public void testRead_IChemObject() throws Exception { Assert.assertNotNull("No test file has been set!", testFile); boolean read = false; for (IChemObject object : acceptableChemObjects()) { if (chemObjectIO.accepts(object.getClass())) { InputStream ins = SimpleChemObjectReaderTest.class.getClassLoader().getResourceAsStream(testFile); chemObjectIO.setReader(ins); IChemObject readObject = chemObjectIO.read(object); chemObjectIO.close(); Assert.assertNotNull("Failed attempt to read the file as " + object.getClass().getName(), readObject); read = true; } } if (!read) { Assert.fail("Reading an IChemObject from the Reader did not work properly."); } }
@Test public void testIsConnectedFromHINFile() throws Exception { String filename = "data/hin/connectivity1.hin"; InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename); ISimpleChemObjectReader reader = new HINReader(ins); IChemFile content = reader.read(new ChemFile()); reader.close(); List<IAtomContainer> cList = ChemFileManipulator.getAllAtomContainers(content); IAtomContainer ac = cList.get(0); Assert.assertEquals(57, ac.getAtomCount()); Assert.assertEquals(59, ac.getBondCount()); }
@Test public void testRead_IChemObject() throws Exception { Assert.assertNotNull("No test file has been set!", testFile); boolean read = false; for (IChemObject object : acceptableChemObjects()) { if (chemObjectIO.accepts(object.getClass())) { InputStream ins = SimpleChemObjectReaderTest.class.getClassLoader().getResourceAsStream(testFile); chemObjectIO.setReader(ins); IChemObject readObject = chemObjectIO.read(object); chemObjectIO.close(); Assert.assertNotNull("Failed attempt to read the file as " + object.getClass().getName(), readObject); read = true; } } if (!read) { Assert.fail("Reading an IChemObject from the Reader did not work properly."); } }
@Test(expected = CDKException.class) public void testUndefinedPartialCharge() throws Exception { String filename = "data/mdl/burden_undefined.sdf"; InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename); ISimpleChemObjectReader reader = new MDLV2000Reader(ins); ChemFile content = reader.read(new ChemFile()); reader.close(); List<IAtomContainer> cList = ChemFileManipulator.getAllAtomContainers(content); IAtomContainer ac = cList.get(0); Assert.assertNotNull(ac); addExplicitHydrogens(ac); AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(ac); Aromaticity.cdkLegacy().apply(ac); addExplicitHydrogens(ac); AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(ac); lpcheck.saturate(ac); GasteigerMarsiliPartialCharges peoe = new GasteigerMarsiliPartialCharges(); peoe.calculateCharges(ac); } }
reader.close(); IChemSequence seq1 = chemFile1.getChemSequence(0); IChemModel model1 = seq1.getChemModel(0);
ISimpleChemObjectReader reader = new HINReader(ins); IChemFile content = reader.read(new ChemFile()); reader.close(); List<IAtomContainer> cList = ChemFileManipulator.getAllAtomContainers(content); Assert.assertEquals(1, cList.size());