model = sequence.getBuilder().newInstance(IChemModel.class); try { readCoordinates(model); model = sequence.getBuilder().newInstance(IChemModel.class); readCoordinates(model); } else if (line.indexOf("SCF Done:") >= 0) {
model = sequence.getBuilder().newInstance(IChemModel.class); try { readCoordinates(model); model = sequence.getBuilder().newInstance(IChemModel.class); readCoordinates(model); } else if (line.indexOf("SCF Done:") >= 0) {
@Test public void testGrowChemModelArray() { IChemSequence cs = (IChemSequence) newChemObject(); cs.addChemModel(cs.getBuilder().newInstance(IChemModel.class)); cs.addChemModel(cs.getBuilder().newInstance(IChemModel.class)); cs.addChemModel(cs.getBuilder().newInstance(IChemModel.class)); Assert.assertEquals(3, cs.getChemModelCount()); cs.addChemModel(cs.getBuilder().newInstance(IChemModel.class)); cs.addChemModel(cs.getBuilder().newInstance(IChemModel.class)); cs.addChemModel(cs.getBuilder().newInstance(IChemModel.class)); // this one should enfore array grow Assert.assertEquals(6, cs.getChemModelCount()); }
@Test public void testGetChemModelCount() { IChemSequence cs = (IChemSequence) newChemObject(); cs.addChemModel(cs.getBuilder().newInstance(IChemModel.class)); cs.addChemModel(cs.getBuilder().newInstance(IChemModel.class)); cs.addChemModel(cs.getBuilder().newInstance(IChemModel.class)); Assert.assertEquals(3, cs.getChemModelCount()); }
@Test public void testGetChemModel_int() { IChemSequence cs = (IChemSequence) newChemObject(); cs.addChemModel(cs.getBuilder().newInstance(IChemModel.class)); IChemModel second = cs.getBuilder().newInstance(IChemModel.class); cs.addChemModel(second); cs.addChemModel(cs.getBuilder().newInstance(IChemModel.class)); Assert.assertEquals(second, cs.getChemModel(1)); }
@Test public void testAddChemModel_IChemModel() { IChemSequence cs = (IChemSequence) newChemObject(); cs.addChemModel(cs.getBuilder().newInstance(IChemModel.class)); cs.addChemModel(cs.getBuilder().newInstance(IChemModel.class)); cs.addChemModel(cs.getBuilder().newInstance(IChemModel.class)); Assert.assertEquals(3, cs.getChemModelCount()); }
@Test public void testChemModels() { IChemSequence cs = (IChemSequence) newChemObject(); cs.addChemModel(cs.getBuilder().newInstance(IChemModel.class)); cs.addChemModel(cs.getBuilder().newInstance(IChemModel.class)); cs.addChemModel(cs.getBuilder().newInstance(IChemModel.class)); Assert.assertEquals(3, cs.getChemModelCount()); Iterator<IChemModel> models = cs.chemModels().iterator(); int count = 0; while (models.hasNext()) { Assert.assertNotNull(models.next()); ++count; } Assert.assertEquals(3, count); }
@Test public void testRemoveChemModel_int() { IChemSequence cs = (IChemSequence) newChemObject(); cs.addChemModel(cs.getBuilder().newInstance(IChemModel.class)); cs.addChemModel(cs.getBuilder().newInstance(IChemModel.class)); cs.addChemModel(cs.getBuilder().newInstance(IChemModel.class)); Assert.assertEquals(3, cs.getChemModelCount()); cs.removeChemModel(1); Assert.assertEquals(2, cs.getChemModelCount()); }
private IChemSequence readChemSequence(IChemSequence sequence) throws CDKException, IOException { IChemModel chemModel = sequence.getBuilder().newInstance(IChemModel.class); ICrystal crystal = null; crystal = sequence.getBuilder().newInstance(ICrystal.class); chemModel = sequence.getBuilder().newInstance(IChemModel.class); throw new CDKException("Could not determine element symbol!", exception); IAtom atom = sequence.getBuilder().newInstance(IAtom.class, symbol); atom.setAtomicNumber(atomType[i]);
@Test @Override public void testStateChanged_IChemObjectChangeEvent() { ChemObjectListenerImpl listener = new ChemObjectListenerImpl(); IChemSequence chemObject = (IChemSequence) newChemObject(); chemObject.addListener(listener); chemObject.addChemModel(chemObject.getBuilder().newInstance(IChemModel.class)); Assert.assertTrue(listener.changed); }
@Test public void testClone_IChemModel() throws Exception { IChemSequence sequence = (IChemSequence) newChemObject(); sequence.addChemModel(sequence.getBuilder().newInstance(IChemModel.class)); // 1 sequence.addChemModel(sequence.getBuilder().newInstance(IChemModel.class)); // 2 sequence.addChemModel(sequence.getBuilder().newInstance(IChemModel.class)); // 3 sequence.addChemModel(sequence.getBuilder().newInstance(IChemModel.class)); // 4 IChemSequence clone = (IChemSequence) sequence.clone(); Assert.assertEquals(sequence.getChemModelCount(), clone.getChemModelCount()); for (int f = 0; f < sequence.getChemModelCount(); f++) { for (int g = 0; g < clone.getChemModelCount(); g++) { Assert.assertNotNull(sequence.getChemModel(f)); Assert.assertNotNull(clone.getChemModel(g)); Assert.assertNotSame(sequence.getChemModel(f), clone.getChemModel(g)); } } } }