private static void replaceReferencesWithClones(final IChemModel chemModel)
throws CDKException {
// we make references in products/reactants clones, since same compounds
// in different reactions need separate layout (different positions etc)
if (chemModel.getReactionSet() != null) {
for (final IReaction reaction : chemModel.getReactionSet()
.reactions()) {
int i = 0;
final IAtomContainerSet products = reaction.getProducts();
for (final IAtomContainer product : products.atomContainers()) {
try {
products.replaceAtomContainer(i, product.clone());
} catch (final CloneNotSupportedException e) {
}
i++;
}
i = 0;
final IAtomContainerSet reactants = reaction.getReactants();
for (final IAtomContainer reactant : reactants.atomContainers()) {
try {
reactants.replaceAtomContainer(i, reactant.clone());
} catch (final CloneNotSupportedException e) {
}
i++;
}
}
}
}
/**
* Get the container which the bond is found on resonance from a IMolecule. It is based on looking
* if the order of the bond changes. Return null is any is found.
*
* @param molecule The IMolecule to analyze
* @param bond The IBond
* @return The container with the bond
*/
@TestMethod("testGetContainer_IMolecule_IBond")
public IAtomContainer getContainer(IMolecule molecule, IBond bond) {
IAtomContainerSet setOfCont = getContainers(molecule);
if (setOfCont == null) return null;
for (IAtomContainer container : setOfCont.atomContainers()) {
if (container.contains(bond)) return container;
}
return null;
}
/**
* Generates a shortest path based BitSet fingerprint for the given AtomContainer.
*
* @param ac The AtomContainer for which a fingerprint is generated
* @exception CDKException if there error in aromaticity perception or other CDK functions
* @return A {@link BitSet} representing the fingerprint
*/
@Override
public IBitFingerprint getBitFingerprint(IAtomContainer ac) throws CDKException {
IAtomContainer atomContainer = null;
try {
atomContainer = (IAtomContainer) ac.clone();
} catch (CloneNotSupportedException ex) {
logger.error("Failed to clone the molecule:", ex);
}
Aromaticity.cdkLegacy().apply(atomContainer);
BitSet bitSet = new BitSet(fingerprintLength);
if (!ConnectivityChecker.isConnected(atomContainer)) {
IAtomContainerSet partitionedMolecules =
ConnectivityChecker.partitionIntoMolecules(atomContainer);
for (IAtomContainer container : partitionedMolecules.atomContainers()) {
addUniquePath(container, bitSet);
}
} else {
addUniquePath(atomContainer, bitSet);
}
return new BitSetFingerprint(bitSet);
}
/**
* 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();
}
private List<IAtomContainer> toList(IAtomContainerSet set) {
return FluentIterable.from(set.atomContainers()).toList();
}