/**
* Adds a LonePair to this Atom.
*
* @param atomID The atom number to which the LonePair is added in [0,..]
*/
public void addLonePair(int atomID) {
ILonePair lonePair = getBuilder().newInstance(ILonePair.class, atoms[atomID]);
lonePair.addListener(this);
addLonePair(lonePair);
/* no notifyChanged() here because addElectronContainer() does
it already */
}
/**
* Removes the lone pair at the given position from the AtomContainer.
*
* @param position The position of the LonePair to be removed.
*/
public ILonePair removeLonePair(int position) {
ILonePair lp = lonePairs[position];
lp.removeListener(this);
for (int i = position; i < lonePairCount - 1; i++) {
lonePairs[i] = lonePairs[i + 1];
}
lonePairs[lonePairCount - 1] = null;
lonePairCount--;
notifyChanged();
return lp;
}
/**
* Clones this AtomContainer object and its content.
*
* @return The cloned object
* @see #shallowCopy
*/
public IAtomContainer clone() throws CloneNotSupportedException {
// this is pretty wasteful as we need to delete most the data
// we can't simply create an empty instance as the sub classes (e.g. AminoAcid)
// would have a ClassCastException when they invoke clone
IAtomContainer clone = (IAtomContainer) super.clone();
// remove existing elements - we need to set the stereo elements list as list.clone() doesn't
// work as expected and will also remove all elements from the original
clone.setStereoElements(new ArrayList<IStereoElement>(stereoElements.size()));
clone.removeAllElements();
// create a mapping of the original atoms/bonds to the cloned atoms/bonds
// we need this mapping to correctly clone bonds, single/paired electrons
// and stereo elements
// - the expected size stop the map be resized - method from Google Guava
Map<IAtom, IAtom> atomMap =
new HashMap<IAtom, IAtom>(atomCount >= 3 ? atomCount + atomCount / 3 : atomCount + 1);
Map<IBond, IBond> bondMap =
new HashMap<IBond, IBond>(bondCount >= 3 ? bondCount + bondCount / 3 : bondCount + 1);
// clone atoms
IAtom[] atoms = new IAtom[this.atomCount];
for (int i = 0; i < atoms.length; i++) {
atoms[i] = (IAtom) this.atoms[i].clone();
atomMap.put(this.atoms[i], atoms[i]);
}
clone.setAtoms(atoms);
// clone bonds using a the mappings from the original to the clone
IBond[] bonds = new IBond[this.bondCount];
for (int i = 0; i < bonds.length; i++) {
IBond original = this.bonds[i];
IBond bond = (IBond) original.clone();
int n = bond.getAtomCount();
IAtom[] members = new IAtom[n];
for (int j = 0; j < n; j++) {
members[j] = atomMap.get(original.getAtom(j));
}
bond.setAtoms(members);
bondMap.put(this.bonds[i], bond);
bonds[i] = bond;
}
clone.setBonds(bonds);
// clone lone pairs (we can't use an array to buffer as there is no setLonePairs())
for (int i = 0; i < lonePairCount; i++) {
ILonePair original = this.lonePairs[i];
ILonePair pair = (ILonePair) original.clone();
if (pair.getAtom() != null) pair.setAtom(atomMap.get(original.getAtom()));
clone.addLonePair(pair);
}
// clone single electrons (we can't use an array to buffer as there is no setSingleElectrons())
for (int i = 0; i < singleElectronCount; i++) {
ISingleElectron original = this.singleElectrons[i];
ISingleElectron electron = (ISingleElectron) original.clone();
if (electron.getAtom() != null) electron.setAtom(atomMap.get(original.getAtom()));
clone.addSingleElectron(electron);
}
// map each stereo element to a new instance in the clone
for (IStereoElement element : stereoElements) {
clone.addStereoElement(element.map(atomMap, bondMap));
}
return clone;
}
@Override
public BoundsTree layout(IAtom atom, Graphics2D g) {
Rectangle2D idBounds;
this.currentObject = atom;
String id = atom.getID();
IAtomContainer molecule = null;
if (this.parent != null) {
molecule = (IAtomContainer) this.parent.getCurrentObject();
}
this.boundsTree = new BoundsTree(atom.getID());
if (molecule == null || this.shouldDraw(atom, molecule)) {
Integer implicitHydrogenCount;
this.boundsTree.add(id + ":symbol", this.layoutAtomSymbol(atom, g));
if (this.isCharged(atom)) {
Rectangle2D chargeBounds = this.layoutCharge(atom, g);
this.boundsTree.add(id + ":charge", chargeBounds);
}
if (this.params.drawImplicitHydrogens
&& (implicitHydrogenCount = atom.getImplicitHydrogenCount()) != null
&& implicitHydrogenCount > 0) {
int align = 1;
if (molecule != null) {
GeometryTools.getBestAlignmentForLabel((IAtomContainer) molecule, (IAtom) atom);
}
LabelManager.AnnotationPosition suggestedPosition =
this.labelManager.alignmentToAnnotationPosition(align);
if (atom.getSymbol().equals("O")
&& (molecule == null || molecule.getConnectedAtomsCount(atom) == 0)) {
suggestedPosition = LabelManager.AnnotationPosition.W;
}
if (this.labelManager.isUsed(atom, suggestedPosition)) {
suggestedPosition = this.labelManager.getNextSparePosition(atom);
}
this.labelManager.setUsedPosition(atom, suggestedPosition);
Rectangle2D hBounds =
this.layoutImplicitHydrogens(atom, implicitHydrogenCount, suggestedPosition, g);
if (hBounds != null) {
this.boundsTree.add(id + ":hs", hBounds);
}
}
} else if (this.params.drawRS && this.chiralMap.containsKey(atom)) {
this.boundsTree.add(
id + ":chiral", this.layoutChiralSymbol(atom, this.chiralMap.get(atom), g));
} else {
Point2d p = atom.getPoint2d();
this.boundsTree.add(id + ":symbol", new Point2D.Double(p.x, p.y));
}
if (this.params.drawAtomID
&& molecule != null
&& (idBounds = this.layoutAtomID(atom, molecule, g)) != null) {
this.boundsTree.add(id + ":id", idBounds);
}
if (this.params.drawLonePairs && molecule != null) {
int lonePairCount = 0;
for (ILonePair lonePair : molecule.lonePairs()) {
if (!lonePair.contains(atom)) {
continue;
}
++lonePairCount;
}
if (lonePairCount > 0) {
Stroke stroke = g.getStroke();
g.setStroke(new BasicStroke(0.05f));
this.layoutElectronPairs(atom, molecule, lonePairCount, g);
g.setStroke(stroke);
}
}
return this.boundsTree;
}