src/test/data/mdl/butadiene.mol @@ -548,8 +548,16 @@ public class MDLV2000Reader extends DefaultChemObjectReader { // MDL down bond stereo = IBond.Stereo.DOWN; } else if (mdlStereo == 0) { - // bond has no stereochemistry - stereo = IBond.Stereo.NONE; + if (order == 2) { + // double bond stereo defined by coordinates + stereo = IBond.Stereo.E_Z_BY_COORDINATES; + } else { + // bond has no stereochemistry + stereo = IBond.Stereo.NONE; + } + } else if (mdlStereo == 3 && order == 2) { + // unknown E/Z stereochemistry + stereo = IBond.Stereo.E_OR_Z; } else if (mdlStereo == 4) { //MDL bond undefined stereo = (IBond.Stereo)CDKConstants.UNSET; src/main/org/openscience/cdk/io/MDLV2000Reader.java @@ -587,4 +587,60 @@ public class MDLV2000ReaderTest extends SimpleChemObjectReaderTest { container.getBond(0).getStereo() ); } + + @Test public void testReadStereoBonds() throws Exception { + String mdl = + "cyclopropane.mol\n" + + "\n" + + "\n" + + " 9 9 0 0 0 1 V2000\n" + + " -0.0073 -0.5272 0.9655 C 0 0 0 0 0\n" + + " -0.6776 -0.7930 -0.3498 C 0 0 0 0 0\n" + + " 0.2103 0.4053 -0.1891 C 0 0 0 0 0\n" + + " 0.8019 -1.1711 1.2970 H 0 0 0 0 0\n" + + " -0.6000 -0.2021 1.8155 H 0 0 0 0 0\n" + + " -1.7511 -0.6586 -0.4435 H 0 0 0 0 0\n" + + " -0.3492 -1.6277 -0.9620 H 0 0 0 0 0\n" + + " 1.1755 0.4303 -0.6860 H 0 0 0 0 0\n" + + " -0.2264 1.3994 -0.1675 H 0 0 0 0 0\n" + + " 1 2 1 6 0 0\n" + + " 1 3 1 6 0 0\n" + + " 1 4 1 0 0 0\n" + + " 1 5 1 1 0 0\n" + + " 2 3 1 0 0 0\n" + + " 2 6 1 0 0 0\n" + + " 2 7 1 6 0 0\n" + + " 3 8 1 6 0 0\n" + + " 3 9 1 0 0 0\n" + + "M END\n"; + MDLV2000Reader reader = new MDLV2000Reader(new StringReader(mdl)); + IMolecule mol = (IMolecule) reader.read(new Molecule()); + Assert.assertNotNull(mol); + Assert.assertEquals(9, mol.getAtomCount()); + Assert.assertEquals(9, mol.getBondCount()); + Assert.assertEquals(IBond.Stereo.DOWN, mol.getBond(0).getStereo()); + Assert.assertEquals(IBond.Stereo.UP, mol.getBond(3).getStereo()); + } + + @Test public void testStereoDoubleBonds() throws Exception { + String filename = "data/mdl/butadiene.mol"; + logger.info("Testing: " + filename); + InputStream ins = this.getClass().getClassLoader() + .getResourceAsStream(filename); + MDLV2000Reader reader = new MDLV2000Reader(ins, Mode.STRICT); + ChemFile chemFile = (ChemFile)reader.read((ChemObject)new ChemFile()); + Assert.assertNotNull(chemFile); + List<IAtomContainer> containersList = + ChemFileManipulator.getAllAtomContainers(chemFile); + Assert.assertEquals(1, containersList.size()); + IAtomContainer container = containersList.get(0); + Assert.assertEquals( + IBond.Stereo.E_Z_BY_COORDINATES, + container.getBond(0).getStereo() + ); + Assert.assertEquals( + IBond.Stereo.E_OR_Z, + container.getBond(2).getStereo() + ); + } } src/test/org/openscience/cdk/io/MDLV2000ReaderTest.java 024499e7c26bd423c22cc0856027d48389bb50f7 cb824f1896fd6a41f5d526699d1e433241b03e6c Rajarshi Guha rajarshi.guha@gmail.com http://github.com/egonw/cdk/commit/ffe9576b02a941d076fd6f1d44d542d6c5b41b95 ffe9576b02a941d076fd6f1d44d542d6c5b41b95 2009-11-01T09:20:42-08:00 2009-11-01T09:20:42-08:00 Merge branch 'stereo' d9bfb7b1925098fc9229aa37b127fb3c3c2a4a4d Rajarshi Guha rajarshi.guha@gmail.com