public RemoveAtomsAndBondsEdit(IChemModel chemModel, IAtomContainer undoRedoContainer, String type, IChemModelRelay chemModelRelay) { this.chemModel = chemModel; this.undoRedoContainer = undoRedoContainer; this.container = chemModel.getBuilder().newInstance(IAtomContainer.class); Iterator<IAtomContainer> containers = ChemModelManipulator.getAllAtomContainers(chemModel).iterator(); while (containers.hasNext()) { container.add((IAtomContainer)containers.next()); } this.type = type; this.chemModelRelay=chemModelRelay; }
private IChemModel readChemModel(IChemModel chemModel) throws CDKException { IAtomContainerSet setOfMolecules = chemModel.getMoleculeSet(); if (setOfMolecules == null) { setOfMolecules = chemModel.getBuilder().newInstance(IAtomContainerSet.class); } IAtomContainer m = readMolecule(chemModel.getBuilder().newInstance(IAtomContainer.class)); if (m != null) { setOfMolecules.addAtomContainer(m); } chemModel.setMoleculeSet(setOfMolecules); return chemModel; }
private IChemModel readChemModel(IChemModel chemModel) throws CDKException { IAtomContainerSet setOfMolecules = chemModel.getMoleculeSet(); if (setOfMolecules == null) { setOfMolecules = chemModel.getBuilder().newInstance(IAtomContainerSet.class); } IAtomContainer m = readMolecule(chemModel.getBuilder().newInstance(IAtomContainer.class)); if (m != null) { setOfMolecules.addAtomContainer(m); } chemModel.setMoleculeSet(setOfMolecules); return chemModel; }
private IChemModel readChemModel(IChemModel chemModel) throws CDKException { IAtomContainerSet setOfMolecules = chemModel.getMoleculeSet(); if (setOfMolecules == null) { setOfMolecules = chemModel.getBuilder().newInstance(IAtomContainerSet.class); } IAtomContainer m = readAtomContainer(chemModel.getBuilder().newInstance(IAtomContainer.class)); if (m != null) { setOfMolecules.addAtomContainer(m); } chemModel.setMoleculeSet(setOfMolecules); return chemModel; }
private IChemModel readChemModel(IChemModel chemModel) throws CDKException { IAtomContainerSet setOfMolecules = chemModel.getMoleculeSet(); if (setOfMolecules == null) { setOfMolecules = chemModel.getBuilder().newInstance(IAtomContainerSet.class); } IAtomContainer m = readMolecule(chemModel.getBuilder().newInstance(IAtomContainer.class)); if (m != null) { setOfMolecules.addAtomContainer(m); } chemModel.setMoleculeSet(setOfMolecules); return chemModel; }
public IAtomContainer getConnectedAtomContainer() { if (this.chemModel != null) { IAtomContainer ac = this.chemModel.getBuilder().newInstance(IAtomContainer.class); for (IAtomContainer other : ChemModelManipulator.getAllAtomContainers(chemModel)) { ac.add(other); } return ac; } return null; }
private IChemModel readChemModel(IChemModel chemModel) throws CDKException { IAtomContainerSet setOfMolecules = chemModel.getMoleculeSet(); if (setOfMolecules == null) { setOfMolecules = chemModel.getBuilder().newInstance(IAtomContainerSet.class); } IAtomContainer m = readAtomContainer(chemModel.getBuilder().newInstance(IAtomContainer.class)); if (m != null) { setOfMolecules.addAtomContainer(m); } chemModel.setMoleculeSet(setOfMolecules); return chemModel; }
public static IChemModel emptyModel() { IChemModel chemModel = DefaultChemObjectBuilder.getInstance().newInstance(IChemModel.class); chemModel.setMoleculeSet(chemModel.getBuilder().newInstance(IAtomContainerSet.class)); chemModel.getMoleculeSet().addAtomContainer( chemModel.getBuilder().newInstance(IAtomContainer.class)); return chemModel; }
public void init() { super.init(); IChemModel chemModel = DefaultChemObjectBuilder.getInstance().newInstance(IChemModel.class); chemModel.setMoleculeSet(chemModel.getBuilder().newInstance(IAtomContainerSet.class)); chemModel.getMoleculeSet().addAtomContainer(chemModel.getBuilder().newInstance(IAtomContainer.class)); JChemPaintPanel p = new JChemPaintPanel(chemModel,GUI_APPLET,debug,this, this.blacklist); p.setName("appletframe"); p.setShowInsertTextField(true); setTheJcpp(p); this.add(p); }
/** * Returns all the AtomContainer's of a ChemModel. */ public static List<IAtomContainer> getAllAtomContainers(IChemModel chemModel) { IAtomContainerSet moleculeSet = chemModel.getBuilder().newInstance(IAtomContainerSet.class); if (chemModel.getMoleculeSet() != null) { moleculeSet.add(chemModel.getMoleculeSet()); } if (chemModel.getReactionSet() != null) { moleculeSet.add(ReactionSetManipulator.getAllMolecules(chemModel.getReactionSet())); } return MoleculeSetManipulator.getAllAtomContainers(moleculeSet); }
public void undo() { if(chemModel.getMoleculeSet()==null) chemModel.setMoleculeSet(chemModel.getBuilder().newInstance(IAtomContainerSet.class)); chemModel.getMoleculeSet().addAtomContainer(oldContainer); chemModel.getReactionSet().removeReaction(ReactionSetManipulator.getReactionByAtomContainerID(chemModel.getReactionSet(), movedContainer.getID())); }
@Test public void testSetMoleculeSet_IAtomContainerSet() { IChemModel chemModel = (IChemModel) newChemObject(); IAtomContainerSet crystal = chemModel.getBuilder().newInstance(IAtomContainerSet.class); chemModel.setMoleculeSet(crystal); Assert.assertEquals(crystal, chemModel.getMoleculeSet()); }
@Test public void testSetCrystal_ICrystal() { IChemModel chemModel = (IChemModel) newChemObject(); ICrystal crystal = chemModel.getBuilder().newInstance(ICrystal.class); chemModel.setCrystal(crystal); Assert.assertEquals(crystal, chemModel.getCrystal()); }
@Test public void testSetReactionSet_IReactionSet() { IChemModel chemModel = (IChemModel) newChemObject(); IReactionSet crystal = chemModel.getBuilder().newInstance(IReactionSet.class); chemModel.setReactionSet(crystal); Assert.assertEquals(crystal, chemModel.getReactionSet()); }
@Test public void testSetRingSet_IRingSet() { IChemModel chemModel = (IChemModel) newChemObject(); IRingSet crystal = chemModel.getBuilder().newInstance(IRingSet.class); chemModel.setRingSet(crystal); Assert.assertEquals(crystal, chemModel.getRingSet()); }
@Test public void testClone_Crystal() throws Exception { IChemModel model = (IChemModel) newChemObject(); IChemModel clone = (IChemModel) model.clone(); Assert.assertNull(clone.getCrystal()); model.setCrystal(model.getBuilder().newInstance(ICrystal.class)); clone = (IChemModel) model.clone(); Assert.assertNotNull(clone.getCrystal()); Assert.assertNotSame(model.getCrystal(), clone.getCrystal()); }
@Test public void testClone_IAtomContainerSet() throws Exception { IChemModel model = (IChemModel) newChemObject(); IChemModel clone = (IChemModel) model.clone(); Assert.assertNull(clone.getMoleculeSet()); model.setMoleculeSet(model.getBuilder().newInstance(IAtomContainerSet.class)); clone = (IChemModel) model.clone(); Assert.assertNotNull(clone.getMoleculeSet()); Assert.assertNotSame(model.getMoleculeSet(), clone.getMoleculeSet()); }
@Test public void testClone_IReactionSet() throws Exception { IChemModel model = (IChemModel) newChemObject(); IChemModel clone = (IChemModel) model.clone(); Assert.assertNull(clone.getReactionSet()); model.setReactionSet(model.getBuilder().newInstance(IReactionSet.class)); clone = (IChemModel) model.clone(); Assert.assertNotNull(clone.getReactionSet()); Assert.assertNotSame(model.getReactionSet(), clone.getReactionSet()); }
@Test public void testIsEmpty_Crystal() { IChemModel model = (IChemModel) newChemObject(); IChemObjectBuilder builder = model.getBuilder(); ICrystal crystal = builder.newInstance(ICrystal.class); model.setCrystal(crystal); Assert.assertTrue(model.isEmpty()); crystal.addAtom(builder.newInstance(IAtom.class, "C")); Assert.assertFalse(model.isEmpty()); model.setCrystal(null); Assert.assertTrue(model.isEmpty()); }
@Test public void testClone_RingSet() throws Exception { IChemModel model = (IChemModel) newChemObject(); IChemModel clone = (IChemModel) model.clone(); Assert.assertNull(clone.getRingSet()); model.setRingSet(model.getBuilder().newInstance(IRingSet.class)); clone = (IChemModel) model.clone(); Assert.assertNotNull(clone.getRingSet()); Assert.assertNotSame(model.getRingSet(), clone.getRingSet()); }