@Override public void startDocument() { logger.info("Start XML Doc"); // cdo.startDocument(); currentChemSequence = currentChemFile.getBuilder().newInstance(IChemSequence.class); currentChemModel = currentChemFile.getBuilder().newInstance(IChemModel.class); currentMoleculeSet = currentChemFile.getBuilder().newInstance(IAtomContainerSet.class); currentMolecule = currentChemFile.getBuilder().newInstance(IAtomContainer.class); atomEnumeration = new HashMap<String, IAtom>(); moleculeCustomProperty = new ArrayList<String>(); newMolecule(); BUILTIN = ""; curRef = 0; }
@Override public void startDocument() { logger.info("Start XML Doc"); // cdo.startDocument(); currentChemSequence = currentChemFile.getBuilder().newInstance(IChemSequence.class); currentChemModel = currentChemFile.getBuilder().newInstance(IChemModel.class); currentMoleculeSet = currentChemFile.getBuilder().newInstance(IAtomContainerSet.class); currentMolecule = currentChemFile.getBuilder().newInstance(IAtomContainer.class); atomEnumeration = new HashMap<String, IAtom>(); moleculeCustomProperty = new ArrayList<String>(); newMolecule(); BUILTIN = ""; curRef = 0; }
@Override public void startDocument() { super.startDocument(); // cdo.startObject("Frame"); currentChemModel = currentChemFile.getBuilder().newInstance(IChemModel.class); }
@Override public void startDocument() { super.startDocument(); // cdo.startObject("Frame"); currentChemModel = currentChemFile.getBuilder().newInstance(IChemModel.class); }
@Override public void startDocument() { super.startDocument(); // cdo.startObject("Frame"); currentChemModel = currentChemFile.getBuilder().newInstance(IChemModel.class); }
@Override public void startDocument() { super.startDocument(); // cdo.startObject("Frame"); currentChemModel = currentChemFile.getBuilder().newInstance(IChemModel.class); }
/** * Read a ChemFile from a file in MDL RDF format. * * @param chemFile The IChemFile * @return The IChemFile that was read from the RDF file. */ private IChemFile readChemFile(IChemFile chemFile) throws CDKException { IChemSequence chemSequence = chemFile.getBuilder().newInstance(IChemSequence.class); IChemModel chemModel = chemFile.getBuilder().newInstance(IChemModel.class); chemSequence.addChemModel(readChemModel(chemModel)); chemFile.addChemSequence(chemSequence); return chemFile; }
/** * Read the ShelX from input. Each ShelX document is expected to contain * one crystal structure. * * @return a ChemFile with the coordinates, charges, vectors, etc. */ private IChemFile readChemFile(IChemFile file) throws IOException { IChemSequence seq = file.getBuilder().newInstance(IChemSequence.class); IChemModel model = file.getBuilder().newInstance(IChemModel.class); ICrystal crystal = readCrystal(file.getBuilder().newInstance(ICrystal.class)); model.setCrystal(crystal); seq.addChemModel(model); file.addChemSequence(seq); return file; }
/** * Read the ShelX from input. Each ShelX document is expected to contain * one crystal structure. * * @return a ChemFile with the coordinates, charges, vectors, etc. */ private IChemFile readChemFile(IChemFile file) throws IOException { IChemSequence seq = file.getBuilder().newInstance(IChemSequence.class); IChemModel model = file.getBuilder().newInstance(IChemModel.class); ICrystal crystal = readCrystal(file.getBuilder().newInstance(ICrystal.class)); model.setCrystal(crystal); seq.addChemModel(model); file.addChemSequence(seq); return file; }
private IChemFile readChemFile(IChemFile file) throws CDKException, IOException { IChemSequence seq = readChemSequence(file.getBuilder().newInstance(IChemSequence.class)); file.addChemSequence(seq); return file; }
private IChemFile readChemFile(IChemFile chemFile) throws CDKException { IChemSequence sequence = readChemSequence(chemFile.getBuilder().newInstance(IChemSequence.class)); chemFile.addChemSequence(sequence); return chemFile; }
private IChemFile readChemFile(IChemFile chemFile) throws CDKException { IChemSequence sequence = readChemSequence(chemFile.getBuilder().newInstance(IChemSequence.class)); chemFile.addChemSequence(sequence); return chemFile; }
@Test public void testGrowChemSequenceArray() { IChemFile cs = (IChemFile) newChemObject(); cs.addChemSequence(cs.getBuilder().newInstance(IChemSequence.class)); cs.addChemSequence(cs.getBuilder().newInstance(IChemSequence.class)); cs.addChemSequence(cs.getBuilder().newInstance(IChemSequence.class)); Assert.assertEquals(3, cs.getChemSequenceCount()); cs.addChemSequence(cs.getBuilder().newInstance(IChemSequence.class)); cs.addChemSequence(cs.getBuilder().newInstance(IChemSequence.class)); cs.addChemSequence(cs.getBuilder().newInstance(IChemSequence.class)); // this one should enfore array grow Assert.assertEquals(6, cs.getChemSequenceCount()); }
@Test public void testAddChemSequence_IChemSequence() { IChemFile cs = (IChemFile) newChemObject(); cs.addChemSequence(cs.getBuilder().newInstance(IChemSequence.class)); cs.addChemSequence(cs.getBuilder().newInstance(IChemSequence.class)); cs.addChemSequence(cs.getBuilder().newInstance(IChemSequence.class)); Assert.assertEquals(3, cs.getChemSequenceCount()); }
@Test public void testGetChemSequenceCount() { IChemFile cs = (IChemFile) newChemObject(); cs.addChemSequence(cs.getBuilder().newInstance(IChemSequence.class)); cs.addChemSequence(cs.getBuilder().newInstance(IChemSequence.class)); cs.addChemSequence(cs.getBuilder().newInstance(IChemSequence.class)); Assert.assertEquals(3, cs.getChemSequenceCount()); }
@Test public void testGetChemSequence_int() { IChemFile cs = (IChemFile) newChemObject(); cs.addChemSequence(cs.getBuilder().newInstance(IChemSequence.class)); IChemSequence second = cs.getBuilder().newInstance(IChemSequence.class); cs.addChemSequence(second); cs.addChemSequence(cs.getBuilder().newInstance(IChemSequence.class)); Assert.assertEquals(second, cs.getChemSequence(1)); }
@Test public void testChemSequences() { IChemFile cs = (IChemFile) newChemObject(); cs.addChemSequence(cs.getBuilder().newInstance(IChemSequence.class)); cs.addChemSequence(cs.getBuilder().newInstance(IChemSequence.class)); cs.addChemSequence(cs.getBuilder().newInstance(IChemSequence.class)); Assert.assertNotNull(cs.chemSequences()); Assert.assertEquals(3, cs.getChemSequenceCount()); }
@Test public void testRemoveChemSequence_int() { IChemFile cs = (IChemFile) newChemObject(); cs.addChemSequence(cs.getBuilder().newInstance(IChemSequence.class)); cs.addChemSequence(cs.getBuilder().newInstance(IChemSequence.class)); cs.addChemSequence(cs.getBuilder().newInstance(IChemSequence.class)); Assert.assertEquals(3, cs.getChemSequenceCount()); cs.removeChemSequence(1); Assert.assertEquals(2, cs.getChemSequenceCount()); }
@Test @Override public void testStateChanged_IChemObjectChangeEvent() { ChemObjectListenerImpl listener = new ChemObjectListenerImpl(); IChemFile chemObject = (IChemFile) newChemObject(); chemObject.addListener(listener); chemObject.addChemSequence(chemObject.getBuilder().newInstance(IChemSequence.class)); Assert.assertTrue(listener.changed); }
@Test public void testClone_ChemSequence() throws Exception { IChemFile file = (IChemFile) newChemObject(); file.addChemSequence(file.getBuilder().newInstance(IChemSequence.class)); // 1 file.addChemSequence(file.getBuilder().newInstance(IChemSequence.class)); // 2 file.addChemSequence(file.getBuilder().newInstance(IChemSequence.class)); // 3 file.addChemSequence(file.getBuilder().newInstance(IChemSequence.class)); // 4 IChemFile clone = (IChemFile) file.clone(); Assert.assertEquals(file.getChemSequenceCount(), clone.getChemSequenceCount()); for (int f = 0; f < file.getChemSequenceCount(); f++) { for (int g = 0; g < clone.getChemSequenceCount(); g++) { Assert.assertNotNull(file.getChemSequence(f)); Assert.assertNotNull(clone.getChemSequence(g)); Assert.assertNotSame(file.getChemSequence(f), clone.getChemSequence(g)); } } } }