public void undo() { if(som!=null) chemModel.setMoleculeSet(som); if(sor!=null) chemModel.setReactionSet(sor); }
private static void removeEmptyMolecules(IChemModel chemModel) { IAtomContainerSet moleculeSet = chemModel.getMoleculeSet(); if (moleculeSet != null && moleculeSet.getAtomContainerCount() == 0) { chemModel.setMoleculeSet(null); } }
/** * Create a new chem model for a single {@link IAtomContainer}. * * @param container the container to create the model for * @return a new {@link IChemModel} */ private static IChemModel newModel(final IAtomContainer container) { if (container == null) throw new NullPointerException("cannot create chem model for a null container"); final IChemObjectBuilder builder = container.getBuilder(); final IChemModel model = builder.newInstance(IChemModel.class); final IAtomContainerSet containers = builder.newInstance(IAtomContainerSet.class); containers.addAtomContainer(container); model.setMoleculeSet(containers); return model; }
public void undo() { if (chemModelRelay != null) { for (IAtomContainer ac : oldsom.atomContainers()) { chemModelRelay.updateAtoms(ac, ac.atoms()); } } chemModel.setMoleculeSet(oldsom); chemModel.setReactionSet(oldsor); }
public void redo() { if (chemModelRelay != null) { for (IAtomContainer ac : newsom.atomContainers()) { chemModelRelay.updateAtoms(ac, ac.atoms()); } } chemModel.setMoleculeSet(newsom); chemModel.setReactionSet(newsor); }
public void select(IAtomContainer atomContainer) { this.chemModel = atomContainer.getBuilder().newInstance(IChemModel.class); IAtomContainerSet molSet = atomContainer.getBuilder().newInstance(IAtomContainerSet.class); molSet.addAtomContainer(atomContainer); this.chemModel.setMoleculeSet(molSet); }
/** * Create a new ChemModel containing an IAtomContainer. It will create an * {@link IAtomContainer} from the passed IAtomContainer when needed, which may cause * information loss. * * @param atomContainer The AtomContainer to have inside the ChemModel. * @return The new IChemModel object. */ public static IChemModel newChemModel(IAtomContainer atomContainer) { IChemModel model = atomContainer.getBuilder().newInstance(IChemModel.class); IAtomContainerSet moleculeSet = model.getBuilder().newInstance(IAtomContainerSet.class); moleculeSet.addAtomContainer(atomContainer); model.setMoleculeSet(moleculeSet); return model; }
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 = 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 = 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 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()); }
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); }
/** * Test if we get the expected {@link IllegalArgumentException} when we pass * an {@link IAtomContainer} without 2D coordinates. */ @Test(expected = IllegalArgumentException.class) public void testCalculateBounds_IChemModel_SingleAtom() { IAtomContainer container = new AtomContainer(); container.addAtom(container.getBuilder().newInstance(IAtom.class, "C")); IAtomContainerSet set = container.getBuilder().newInstance(IAtomContainerSet.class); set.addAtomContainer(container); IChemModel model = container.getBuilder().newInstance(IChemModel.class); model.setMoleculeSet(set); BoundsCalculator.calculateBounds(model); }
@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 if we get the expected {@link IllegalArgumentException} when we pass * an {@link IAtomContainer} without 2D coordinates. */ @Test(expected = IllegalArgumentException.class) public void testCalculateBounds_IChemModel() { IAtomContainer container = new AtomContainer(); container.addAtom(container.getBuilder().newInstance(IAtom.class, "C")); container.addAtom(container.getBuilder().newInstance(IAtom.class, "C")); IAtomContainerSet set = container.getBuilder().newInstance(IAtomContainerSet.class); set.addAtomContainer(container); IChemModel model = container.getBuilder().newInstance(IChemModel.class); model.setMoleculeSet(set); BoundsCalculator.calculateBounds(model); }
@Test public void testMoleculeSet() throws Exception { IAtomContainerSet list = new AtomContainerSet(); list.addAtomContainer(new AtomContainer()); list.addAtomContainer(new AtomContainer()); IChemModel model = new ChemModel(); model.setMoleculeSet(list); IChemModel roundTripped = CMLRoundTripTool.roundTripChemModel(convertor, model); IAtomContainerSet newList = roundTripped.getMoleculeSet(); Assert.assertNotNull(newList); Assert.assertEquals(2, newList.getAtomContainerCount()); Assert.assertNotNull(newList.getAtomContainer(0)); Assert.assertNotNull(newList.getAtomContainer(1)); }