/** * Constructs an empty, forward reaction. */ public Reaction() { this.reactants = getBuilder().newInstance(IAtomContainerSet.class); this.products = getBuilder().newInstance(IAtomContainerSet.class); this.agents = getBuilder().newInstance(IAtomContainerSet.class); this.map = new Mapping[growArraySize]; mappingCount = 0; reactionDirection = IReaction.Direction.FORWARD; }
@Override public void startDocument() { super.startDocument(); // cdo.startObject("Frame"); currentChemModel = currentChemFile.getBuilder().newInstance(IChemModel.class); }
private IChemFile readChemFile(IChemFile chemFile) throws CDKException { IChemSequence sequence = readChemSequence(chemFile.getBuilder().newInstance(IChemSequence.class)); chemFile.addChemSequence(sequence); return chemFile; }
/** * Gets the polarizabilitiyFactorForAtom. * *@param atomContainer AtomContainer *@param atom atom for which the factor should become known *@return The polarizabilitiyFactorForAtom value */ public double getPolarizabilitiyFactorForAtom(IAtomContainer atomContainer, IAtom atom) { IAtomContainer acH = atomContainer.getBuilder().newInstance(IAtomContainer.class, atomContainer); addExplicitHydrogens(acH); return getKJPolarizabilityFactor(acH, atom); }
/** * Makes a single carbon atom, centered on the origin. * * @return an atom container with a single atom */ public IAtomContainer makeSingleAtom() { IAtomContainer container = builder.newInstance(IAtomContainer.class); container.addAtom(builder.newInstance(IAtom.class, "C", new Point2d(0, 0))); return container; }
/** * {@inheritDoc} */ @Override public void addSingleElectron(int idx) { ISingleElectron electron = getBuilder().newInstance(ISingleElectron.class); electron.setAtom(getAtom(idx)); addSingleElectron(electron); }
/** * {@inheritDoc} */ @Override public void addBond(int atom1, int atom2, IBond.Order order) { IBond bond = getBuilder().newInstance(IBond.class, getAtom(atom1), getAtom(atom2), order); addBond(bond); /* * no notifyChanged() here because addBond(bond) does it already */ }
/** * {@inheritDoc} */ @Override public void addBond(int atom1, int atom2, IBond.Order order, IBond.Stereo stereo) { IBond bond = getBuilder().newInstance(IBond.class, getAtom(atom1), getAtom(atom2), order, stereo); addBond(bond); }
/** * {@inheritDoc} */ @Override public void addBond(int atom1, int atom2, IBond.Order order) { IBond bond = getBuilder().newInstance(IBond.class, getAtom(atom1), getAtom(atom2), order); addBond(bond); }
@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); } }
@Test public void testEmptyContainer() { IAtomContainer emptyContainer = super.builder.newInstance(IAtomContainer.class); // nothing should be made IRenderingElement root = generator.generate(emptyContainer, model); List<IRenderingElement> elements = elementUtil.getAllSimpleElements(root); Assert.assertEquals(0, elements.size()); }
@Test public void testEmptyContainer() { IAtomContainer emptyContainer = super.builder.newInstance(IAtomContainer.class); // nothing should be made IRenderingElement root = generator.generate(emptyContainer, model); List<IRenderingElement> elements = elementUtil.getAllSimpleElements(root); Assert.assertEquals(0, elements.size()); }
@Test public void testEmptyReaction() { IReaction singleReaction = super.builder.newInstance(IReaction.class); // nothing should be made IRenderingElement root = generator.generate(singleReaction, model); List<IRenderingElement> elements = elementUtil.getAllSimpleElements(root); Assert.assertEquals(0, elements.size()); }
@Test public void testEmptyContainer() { IAtomContainer emptyContainer = super.builder.newInstance(IAtomContainer.class); // nothing should be made IRenderingElement root = generator.generate(emptyContainer, model); List<IRenderingElement> elements = elementUtil.getAllSimpleElements(root); Assert.assertEquals(1, elements.size()); }
@Test public void testEmptyReaction() { IReaction singleReaction = super.builder.newInstance(IReaction.class); // nothing should be made IRenderingElement root = generator.generate(singleReaction, model); List<IRenderingElement> elements = elementUtil.getAllSimpleElements(root); Assert.assertEquals(0, elements.size()); }
@Test public void testEmptyContainer() { IAtomContainer emptyContainer = super.builder.newInstance(IAtomContainer.class); // nothing should be made IRenderingElement root = generator.generate(emptyContainer, model); List<IRenderingElement> elements = elementUtil.getAllSimpleElements(root); Assert.assertEquals(0, elements.size()); }
@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()); }
@Test public void testSingleTripletRadical() throws Exception { InputStream in = ClassLoader.getSystemResourceAsStream("data/mdl/singleTripletRadical.mol"); MDLV2000Reader reader = new MDLV2000Reader(in); IAtomContainer molecule = DefaultChemObjectBuilder.getInstance().newInstance(IAtomContainer.class); molecule = reader.read(molecule); reader.close(); assertThat(molecule.getConnectedSingleElectronsCount(molecule.getAtom(1)), is(2)); }
@Test public void testBond_IAtom_IAtom() { IChemObject object = newChemObject(); IAtom c = object.getBuilder().newInstance(IAtom.class, "C"); IAtom o = object.getBuilder().newInstance(IAtom.class, "O"); IBond bond = new Bond(c, o); Assert.assertEquals(2, bond.getAtomCount()); Assert.assertEquals(c, bond.getBegin()); Assert.assertEquals(o, bond.getEnd()); Assert.assertEquals(IBond.Order.SINGLE, bond.getOrder()); Assert.assertEquals(IBond.Stereo.NONE, bond.getStereo()); }
@Test public void testPartialFilledStructureMerger4() throws Exception { SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance()); IAtomContainerSet acs = DefaultChemObjectBuilder.getInstance().newInstance(IAtomContainerSet.class); acs.addAtomContainer(sp.parseSmiles("[C]CCC[CH2]")); acs.addAtomContainer(sp.parseSmiles("[C]CC[CH2]")); acs.addAtomContainer(sp.parseSmiles("[CH2]")); PartialFilledStructureMerger pfsm = new PartialFilledStructureMerger(); IAtomContainer result = pfsm.generate(acs); Assert.assertTrue(ConnectivityChecker.isConnected(result)); Assert.assertTrue(new SaturationChecker().allSaturated(result)); }