/** @inheritDoc */
public void removeAtomAndConnectedElectronContainers(IAtom atom) {
int position = getAtomNumber(atom);
if (position != -1) {
for (int i = 0; i < bondCount; i++) {
if (bonds[i].contains(atom)) {
removeBond(i);
--i;
}
}
for (int i = 0; i < lonePairCount; i++) {
if (lonePairs[i].contains(atom)) {
removeLonePair(i);
--i;
}
}
for (int i = 0; i < singleElectronCount; i++) {
if (singleElectrons[i].contains(atom)) {
removeSingleElectron(i);
--i;
}
}
List<IStereoElement> atomElements = new ArrayList<IStereoElement>(3);
for (IStereoElement element : stereoElements) {
if (element.contains(atom)) atomElements.add(element);
}
stereoElements.removeAll(atomElements);
removeAtom(position);
}
notifyChanged();
}
/**
* Returns a one line string representation of this Container. This method is conform RFC #9.
*
* @return The string representation of this Container
*/
public String toString() {
StringBuffer stringContent = new StringBuffer(64);
stringContent.append("AtomContainer(");
stringContent.append(this.hashCode());
if (getAtomCount() > 0) {
stringContent.append(", #A:").append(getAtomCount());
for (int i = 0; i < getAtomCount(); i++) {
stringContent.append(", ").append(getAtom(i).toString());
}
}
if (getBondCount() > 0) {
stringContent.append(", #B:").append(getBondCount());
for (int i = 0; i < getBondCount(); i++) {
stringContent.append(", ").append(getBond(i).toString());
}
}
if (getLonePairCount() > 0) {
stringContent.append(", #LP:").append(getLonePairCount());
for (int i = 0; i < getLonePairCount(); i++) {
stringContent.append(", ").append(getLonePair(i).toString());
}
}
if (getSingleElectronCount() > 0) {
stringContent.append(", #SE:").append(getSingleElectronCount());
for (int i = 0; i < getSingleElectronCount(); i++) {
stringContent.append(", ").append(getSingleElectron(i).toString());
}
}
if (stereoElements.size() > 0) {
stringContent.append(", ST:[#").append(stereoElements.size());
for (IStereoElement elements : stereoElements) {
stringContent.append(", ").append(elements.toString());
}
stringContent.append(']');
}
stringContent.append(')');
return stringContent.toString();
}
/**
* 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;
}