@Override public IChemObjectBuilder getBuilder() { return DefaultChemObjectBuilder.getInstance(); } }
public PharmacophoreQuery() { // builder should be injected but this is difficult as this class is create in static methods super(DefaultChemObjectBuilder.getInstance()); exclusionVolumes = new ArrayList<Object>(); }
private String typeHetatm(String resName, String atomName) { if (hetDictionary == null) { readHetDictionary(); cdkAtomTypeFactory = AtomTypeFactory.getInstance("org/openscience/cdk/dict/data/cdk-atom-types.owl", DefaultChemObjectBuilder.getInstance()); } String key = resName + "." + atomName; if (hetDictionary.containsKey(key)) { return hetDictionary.get(key); } return null; }
public void setDescriptor(Class<? extends T> descriptorClass) throws Exception { if (descriptor == null) { Constructor<? extends T> defaultConstructor = descriptorClass.getConstructor(); this.descriptor = defaultConstructor.newInstance(); this.descriptor.initialise(DefaultChemObjectBuilder.getInstance()); } }
/** * The JUnit setup method */ @BeforeClass public static void setUp() throws Exception { builder = DefaultChemObjectBuilder.getInstance(); setRule(RDBERule.class); }
/** * The JUnit setup method */ @BeforeClass public static void setUp() throws Exception { builder = DefaultChemObjectBuilder.getInstance(); setRule(ElementRule.class); }
@Before public void setUp() throws Exception { builder = DefaultChemObjectBuilder.getInstance(); String filename1 = "data/mdl/reaction-1.rxn"; InputStream ins1 = this.getClass().getClassLoader().getResourceAsStream(filename1); MDLRXNReader reader1 = new MDLRXNReader(ins1); set = (ReactionSet) reader1.read(new ReactionSet()); reader1.close(); }
@Test(expected=CDKException.class) public void wrongFormat() throws CDKException { InputStream in = ClassLoader.getSystemResourceAsStream("data/mdl/bug1356.sdf"); MDLReader reader = new MDLReader(in, Mode.STRICT); IChemFile chemfile = DefaultChemObjectBuilder.getInstance().newInstance(IChemFile.class); chemfile = reader.read(chemfile); } }
/** * @cdk.bug 2714283 * @throws InvalidSmilesException */ @Test(expected = InvalidSmilesException.class) public void testBadRingClosure2() throws InvalidSmilesException { SmilesParser p = new SmilesParser(DefaultChemObjectBuilder.getInstance()); p.parseSmiles("NC1=CC=C(N)C=C"); }
@Test public void testInstance() { CDKValencyChecker checker = CDKValencyChecker.getInstance(DefaultChemObjectBuilder.getInstance()); Assert.assertNotNull(checker); }
@Test public void testGetInstance_IChemObjectBuilder_int() throws Exception { CDKAtomTypeMatcher matcher = CDKAtomTypeMatcher.getInstance(DefaultChemObjectBuilder.getInstance(), CDKAtomTypeMatcher.REQUIRE_EXPLICIT_HYDROGENS); Assert.assertNotNull(matcher); }
@Test public void testH2S_Hybridization() throws Exception { IAtomContainer mol = DefaultChemObjectBuilder.getInstance().newInstance(IAtomContainer.class); IAtom s = DefaultChemObjectBuilder.getInstance().newInstance(IAtom.class, "S"); s.setHybridization(Hybridization.SP3); mol.addAtom(s); String[] expectedTypes = {"S.3"}; assertAtomTypes(testedAtomTypes, expectedTypes, mol); }
/** * No options set. */ @Test public void testGetInChIToStructure_String_IChemObjectBuilder_List() throws CDKException { InChIToStructure parser = InChIGeneratorFactory.getInstance().getInChIToStructure("InChI=1/ClH/h1H", DefaultChemObjectBuilder.getInstance(), new ArrayList<String>()); Assert.assertNotNull(parser); }
@BeforeClass public static void setup() { builder = DefaultChemObjectBuilder.getInstance(); setChemObjectIO(new RGroupQueryWriter()); }
/** * The JUnit setup method */ @BeforeClass public static void setUp() throws Exception { sdg = new StructureDiagramGenerator(); sp = new SmilesParser(DefaultChemObjectBuilder.getInstance()); }
@BeforeClass public static void setup() { builder = DefaultChemObjectBuilder.getInstance(); setChemObjectWriter(new SDFWriter()); }
@BeforeClass public static void setup() { fragmenter = new MurckoFragmenter(false, 5); smilesParser = new SmilesParser(DefaultChemObjectBuilder.getInstance()); }
@BeforeClass public static void setup() { builder = DefaultChemObjectBuilder.getInstance(); setChemObjectIO(new MDLV2000Writer()); }
@Test(expected = UnsupportedOperationException.class) public void testRemove() { String filename = "data/mdl/iterconftest.sdf"; logger.info("Testing: " + filename); InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename); IteratingMDLConformerReader reader = new IteratingMDLConformerReader(ins, DefaultChemObjectBuilder.getInstance()); reader.hasNext(); reader.next(); reader.remove(); } }
@Test public void e_butene_0D() throws Exception { InputStream in = getClass().getResourceAsStream("/data/mdl/e_butene_0d.mol"); MDLV2000Reader reader = new MDLV2000Reader(in); IAtomContainer molecule = DefaultChemObjectBuilder.getInstance().newInstance(IAtomContainer.class); molecule = reader.read(molecule); reader.close(); assertNotNull(molecule); assertFalse(molecule.stereoElements().iterator().hasNext()); }