public static IChemModel emptyModel() {
final IChemModel chemModel = DefaultChemObjectBuilder.getInstance()
.newInstance(IChemModel.class);
chemModel.setMoleculeSet(chemModel.getBuilder().newInstance(
IAtomContainerSet.class));
chemModel.getMoleculeSet().addAtomContainer(
chemModel.getBuilder().newInstance(IAtomContainer.class));
return chemModel;
}
private static void removeDuplicateAtomContainers(final IChemModel chemModel) {
// we remove molecules which are in AtomContainerSet as well as in a
// reaction
final IReactionSet reactionSet = chemModel.getReactionSet();
final IAtomContainerSet moleculeSet = chemModel.getMoleculeSet();
if (reactionSet != null && moleculeSet != null) {
final List<IAtomContainer> aclist = ReactionSetManipulator
.getAllAtomContainers(reactionSet);
for (int i = moleculeSet.getAtomContainerCount() - 1; i >= 0; i--) {
for (int k = 0; k < aclist.size(); k++) {
final String label = moleculeSet.getAtomContainer(i)
.getID();
if (aclist.get(k).getID().equals(label)) {
chemModel.getMoleculeSet().removeAtomContainer(i);
break;
}
}
}
}
}
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 && m instanceof IAtomContainer) {
setOfMolecules.addAtomContainer((IAtomContainer) m);
}
chemModel.setMoleculeSet(setOfMolecules);
return chemModel;
}
private IMolecule checkForXMoleculeFile(IChemFile chemFile, int numberOfMolecules) {
Assert.assertNotNull(chemFile);
Assert.assertEquals(chemFile.getChemSequenceCount(), 1);
org.openscience.cdk.interfaces.IChemSequence seq = chemFile.getChemSequence(0);
Assert.assertNotNull(seq);
Assert.assertEquals(seq.getChemModelCount(), 1);
org.openscience.cdk.interfaces.IChemModel model = seq.getChemModel(0);
Assert.assertNotNull(model);
org.openscience.cdk.interfaces.IMoleculeSet moleculeSet = model.getMoleculeSet();
Assert.assertNotNull(moleculeSet);
Assert.assertEquals(moleculeSet.getMoleculeCount(), numberOfMolecules);
IMolecule mol = null;
for (int i = 0; i < numberOfMolecules; i++) {
mol = moleculeSet.getMolecule(i);
Assert.assertNotNull(mol);
}
return mol;
}
private static void removeEmptyAtomContainers(final IChemModel chemModel) {
final IAtomContainerSet moleculeSet = chemModel.getMoleculeSet();
if (moleculeSet != null && moleculeSet.getAtomContainerCount() == 0) {
chemModel.setMoleculeSet(null);
}
}
/**
* Inserts a molecule into the current set, usually from Combobox or Insert
* field, with possible shifting of the existing set.
*
* @param chemPaintPanel
* @param molecule
* @param generateCoordinates
* @param shiftPanel
* @throws CDKException
*/
public static void generateModel(
final AbstractJChemPaintPanel chemPaintPanel,
IAtomContainer molecule, final boolean generateCoordinates,
final boolean shiftPasted) throws CDKException {
if (molecule == null) {
return;
}
final IChemModel chemModel = chemPaintPanel.getChemModel();
IAtomContainerSet moleculeSet = chemModel.getMoleculeSet();
if (moleculeSet == null) {
moleculeSet = new AtomContainerSet();
}
// On copy & paste on top of an existing drawn structure, prevent the
// pasted section to be drawn exactly on top or to far away from the
// original by shifting it to a fixed position next to it.
if (shiftPasted) {
double maxXCurr = Double.NEGATIVE_INFINITY;
double minXPaste = Double.POSITIVE_INFINITY;
for (final IAtomContainer atc : moleculeSet.atomContainers()) {
// Detect the right border of the current structure..
for (final IAtom atom : atc.atoms()) {
if (atom.getPoint2d().x > maxXCurr) {
maxXCurr = atom.getPoint2d().x;
}
}
// Detect the left border of the pasted structure..
for (final IAtom atom : molecule.atoms()) {
if (atom.getPoint2d().x < minXPaste) {
minXPaste = atom.getPoint2d().x;
}
}
}
if (maxXCurr != Double.NEGATIVE_INFINITY
&& minXPaste != Double.POSITIVE_INFINITY) {
// Shift the pasted structure to be nicely next to the existing
// one.
final int MARGIN = 1;
final double SHIFT = maxXCurr - minXPaste;
for (final IAtom atom : molecule.atoms()) {
atom.setPoint2d(new Point2d(atom.getPoint2d().x + MARGIN
+ SHIFT, atom.getPoint2d().y));
}
}
}
if (generateCoordinates) {
// now generate 2D coordinates
final StructureDiagramGenerator sdg = new StructureDiagramGenerator();
sdg.setTemplateHandler(new TemplateHandler(moleculeSet.getBuilder()));
try {
sdg.setMolecule(molecule);
sdg.generateCoordinates(new Vector2d(0, 1));
molecule = sdg.getMolecule();
} catch (final Exception exc) {
JOptionPane.showMessageDialog(chemPaintPanel,
GT._("Structure could not be generated"));
throw new CDKException("Cannot depict structure");
}
}
if (moleculeSet.getAtomContainer(0).getAtomCount() == 0) {
moleculeSet.getAtomContainer(0).add(molecule);
} else {
moleculeSet.addAtomContainer(molecule);
}
final IUndoRedoFactory undoRedoFactory = chemPaintPanel.get2DHub()
.getUndoRedoFactory();
final UndoRedoHandler undoRedoHandler = chemPaintPanel.get2DHub()
.getUndoRedoHandler();
if (undoRedoFactory != null) {
final IUndoRedoable undoredo = undoRedoFactory
.getAddAtomsAndBondsEdit(chemPaintPanel.get2DHub()
.getIChemModel(), molecule, null, "Paste",
chemPaintPanel.get2DHub());
undoRedoHandler.postEdit(undoredo);
}
chemPaintPanel.getChemModel().setMoleculeSet(moleculeSet);
chemPaintPanel.updateUndoRedoControls();
chemPaintPanel.get2DHub().updateView();
}