@Override public IResourceFormat getFormat() { return MDLV2000Format.getInstance(); }
public static IResourceFormat getInstance() { if (myself == null) myself = new MDLV2000Format(); return myself; }
/** {@inheritDoc} */ @Override public String getPreferredNameExtension() { return getNameExtensions()[0]; }
/** {@inheritDoc} */ @Override public int getSupportedDataFeatures() { return getRequiredDataFeatures() | DataFeatures.HAS_2D_COORDINATES | DataFeatures.HAS_3D_COORDINATES | DataFeatures.HAS_GRAPH_REPRESENTATION; }
@Override public IResourceFormat getFormat() { return MDLV2000Format.getInstance(); }
public MDLV2000FormatTest() { super.setChemFormatMatcher((IChemFormatMatcher) MDLV2000Format.getInstance()); }
Matcher versionMatcher = MDL_VERSION.matcher(currentLine); if (versionMatcher.find()) { currentFormat = "2000".equals(versionMatcher.group(1)) ? (IChemFormat) MDLV2000Format.getInstance() : (IChemFormat) MDLV3000Format.getInstance();
@Test public void testMDLMolV2000() throws Exception { expectFormat("data/mdl/methylbenzol.mol", MDLV2000Format.getInstance()); }
@Test public void testMDLMolV2000() throws Exception { expectReader("data/mdl/methylbenzol.mol", MDLV2000Format.getInstance(), 15, 15); }
@Test public void testDetection() throws Exception { expectReader("data/mdl/withcharges.mol", MDLV2000Format.getInstance(), 9, 9); }
@Test public void testDetection() throws Exception { expectFormat("data/mdl/withcharges.mol", MDLV2000Format.getInstance()); }
@Test public void testSDF() throws Exception { String filename = "data/mdl/test2.sdf"; logger.info("Testing: " + filename); InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename); IteratingSDFReader reader = new IteratingSDFReader(ins, DefaultChemObjectBuilder.getInstance()); int molCount = 0; while (reader.hasNext()) { Object object = reader.next(); Assert.assertNotNull(object); Assert.assertTrue(object instanceof IAtomContainer); molCount++; Assert.assertEquals("Molecule # was not in MDL V2000 format: " + molCount, MDLV2000Format.getInstance(), reader.getFormat()); } Assert.assertEquals(6, molCount); reader.close(); }
@Test public void testReadTitle() throws Exception { String filename = "data/mdl/test.sdf"; logger.info("Testing: " + filename); InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename); IteratingSDFReader reader = new IteratingSDFReader(ins, DefaultChemObjectBuilder.getInstance()); //int molCount = 0; Assert.assertTrue(reader.hasNext()); Object object = reader.next(); Assert.assertNotNull(object); Assert.assertTrue(object instanceof IAtomContainer); Assert.assertEquals("2-methylbenzo-1,4-quinone", ((IAtomContainer) object).getTitle()); Assert.assertEquals(MDLV2000Format.getInstance(), reader.getFormat()); reader.close(); }
@Test public void testSDF_broken_stream() throws Exception { String filename = "data/mdl/test2.sdf"; logger.info("Testing: " + filename); InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename); InputStreamReader streamReader = new InputStreamReader(ins) { @Override public boolean ready() throws IOException { return false; } }; IteratingSDFReader reader = new IteratingSDFReader(streamReader, DefaultChemObjectBuilder.getInstance()); int molCount = 0; while (reader.hasNext()) { Object object = reader.next(); Assert.assertNotNull(object); Assert.assertTrue(object instanceof IAtomContainer); molCount++; Assert.assertEquals("Molecule # was not in MDL V2000 format: " + molCount, MDLV2000Format.getInstance(), reader.getFormat()); } Assert.assertEquals(6, molCount); reader.close(); }