/** @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();
}
/**
* Removes the given atom and all connected electronContainers from the AtomContainer.
*
* @param atom The atom to be removed
*/
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;
}
}
removeAtom(position);
}
notifyChanged();
}
/**
* Removes all atoms and electronContainers of a given atomcontainer from this container.
*
* @param atomContainer The atomcontainer to be removed
*/
public void remove(IAtomContainer atomContainer) {
for (int f = 0; f < atomContainer.getAtomCount(); f++) {
removeAtom(atomContainer.getAtom(f));
}
for (int f = 0; f < atomContainer.getBondCount(); f++) {
removeBond(atomContainer.getBond(f));
}
for (int f = 0; f < atomContainer.getLonePairCount(); f++) {
removeLonePair(atomContainer.getLonePair(f));
}
for (int f = 0; f < atomContainer.getSingleElectronCount(); f++) {
removeSingleElectron(atomContainer.getSingleElectron(f));
}
}
public void removeAtom(IAtom atom) {
logger.debug("Removing atom: ", atom);
super.removeAtom(atom);
}
public void removeAtom(int position) {
logger.debug("Removing atom: ", position);
super.removeAtom(position);
}
/**
* Removes the given atom from the AtomContainer. Note that the electronContainers are unaffected:
* you also have to take care of removing all electronContainers to this atom from the container.
*
* @param atom The atom to be removed
*/
public void removeAtom(IAtom atom) {
int position = getAtomNumber(atom);
if (position != -1) {
removeAtom(position);
}
}