/**
* 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();
}
/**
* Initiates the process for the given mechanism. The atoms to apply are mapped between reactants
* and products.
*
* @param atomContainerSet
* @param atomList The list of atoms taking part in the mechanism. Only allowed two atoms. The
* first atom is the atom which contains the ISingleElectron and the second third is the atom
* which will be removed the first atom
* @param bondList The list of bonds taking part in the mechanism. Only allowed one bond. It is
* the bond which is moved
* @return The Reaction mechanism
*/
@TestMethod(value = "testInitiate_IAtomContainerSet_ArrayList_ArrayList")
public IReaction initiate(
IAtomContainerSet atomContainerSet, ArrayList<IAtom> atomList, ArrayList<IBond> bondList)
throws CDKException {
CDKAtomTypeMatcher atMatcher = CDKAtomTypeMatcher.getInstance(atomContainerSet.getBuilder());
if (atomContainerSet.getAtomContainerCount() != 1) {
throw new CDKException("RadicalSiteIonizationMechanism only expects one IMolecule");
}
if (atomList.size() != 3) {
throw new CDKException("RadicalSiteIonizationMechanism expects three atoms in the ArrayList");
}
if (bondList.size() != 2) {
throw new CDKException(
"RadicalSiteIonizationMechanism only expect one bond in the ArrayList");
}
IAtomContainer molecule = atomContainerSet.getAtomContainer(0);
IAtomContainer reactantCloned;
try {
reactantCloned = (IAtomContainer) molecule.clone();
} catch (CloneNotSupportedException e) {
throw new CDKException("Could not clone IMolecule!", e);
}
IAtom atom1 = atomList.get(0); // Atom containing the ISingleElectron
IAtom atom1C = reactantCloned.getAtom(molecule.getAtomNumber(atom1));
IAtom atom2 = atomList.get(1); // Atom
IAtom atom2C = reactantCloned.getAtom(molecule.getAtomNumber(atom2));
IAtom atom3 = atomList.get(2); // Atom to be saved
IAtom atom3C = reactantCloned.getAtom(molecule.getAtomNumber(atom3));
IBond bond1 = bondList.get(0); // Bond to increase the order
int posBond1 = molecule.getBondNumber(bond1);
IBond bond2 = bondList.get(1); // Bond to remove
int posBond2 = molecule.getBondNumber(bond2);
BondManipulator.increaseBondOrder(reactantCloned.getBond(posBond1));
reactantCloned.removeBond(reactantCloned.getBond(posBond2));
List<ISingleElectron> selectron = reactantCloned.getConnectedSingleElectronsList(atom1C);
reactantCloned.removeSingleElectron(selectron.get(selectron.size() - 1));
atom1C.setHybridization(null);
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(reactantCloned);
IAtomType type = atMatcher.findMatchingAtomType(reactantCloned, atom1C);
if (type == null) return null;
atom2C.setHybridization(null);
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(reactantCloned);
type = atMatcher.findMatchingAtomType(reactantCloned, atom2C);
if (type == null) return null;
reactantCloned.addSingleElectron(new SingleElectron(atom3C));
atom3C.setHybridization(null);
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(reactantCloned);
type = atMatcher.findMatchingAtomType(reactantCloned, atom3C);
if (type == null) return null;
IReaction reaction = DefaultChemObjectBuilder.getInstance().newInstance(IReaction.class);
reaction.addReactant(molecule);
/* mapping */
for (IAtom atom : molecule.atoms()) {
IMapping mapping =
DefaultChemObjectBuilder.getInstance()
.newInstance(
IMapping.class, atom, reactantCloned.getAtom(molecule.getAtomNumber(atom)));
reaction.addMapping(mapping);
}
IAtomContainerSet moleculeSetP = ConnectivityChecker.partitionIntoMolecules(reactantCloned);
for (int z = 0; z < moleculeSetP.getAtomContainerCount(); z++)
reaction.addProduct((IAtomContainer) moleculeSetP.getAtomContainer(z));
return reaction;
}