/**
* Constructs an AtomContainer with a copy of the atoms and electronContainers of another
* AtomContainer (A shallow copy, i.e., with the same objects as in the original AtomContainer).
*
* @param container An AtomContainer to copy the atoms and electronContainers from
*/
public AtomContainer(IAtomContainer container) {
this.atomCount = container.getAtomCount();
this.bondCount = container.getBondCount();
this.lonePairCount = container.getLonePairCount();
this.singleElectronCount = container.getSingleElectronCount();
this.atoms = new IAtom[this.atomCount];
this.bonds = new IBond[this.bondCount];
this.lonePairs = new ILonePair[this.lonePairCount];
this.singleElectrons = new ISingleElectron[this.singleElectronCount];
stereoElements = new HashSet<IStereoElement>(atomCount / 2);
for (IStereoElement element : container.stereoElements()) {
addStereoElement(element);
}
for (int f = 0; f < container.getAtomCount(); f++) {
atoms[f] = container.getAtom(f);
container.getAtom(f).addListener(this);
}
for (int f = 0; f < this.bondCount; f++) {
bonds[f] = container.getBond(f);
container.getBond(f).addListener(this);
}
for (int f = 0; f < this.lonePairCount; f++) {
lonePairs[f] = container.getLonePair(f);
container.getLonePair(f).addListener(this);
}
for (int f = 0; f < this.singleElectronCount; f++) {
singleElectrons[f] = container.getSingleElectron(f);
container.getSingleElectron(f).addListener(this);
}
}
/**
* Adds all atoms and electronContainers of a given atomcontainer to this container.
*
* @param atomContainer The atomcontainer to be added
*/
public void add(IAtomContainer atomContainer) {
for (int f = 0; f < atomContainer.getAtomCount(); f++) {
if (!contains(atomContainer.getAtom(f))) {
addAtom(atomContainer.getAtom(f));
}
}
for (int f = 0; f < atomContainer.getBondCount(); f++) {
if (!contains(atomContainer.getBond(f))) {
addBond(atomContainer.getBond(f));
}
}
for (int f = 0; f < atomContainer.getLonePairCount(); f++) {
if (!contains(atomContainer.getLonePair(f))) {
addLonePair(atomContainer.getLonePair(f));
}
}
for (int f = 0; f < atomContainer.getSingleElectronCount(); f++) {
if (!contains(atomContainer.getSingleElectron(f))) {
addSingleElectron(atomContainer.getSingleElectron(f));
}
}
for (IStereoElement se : atomContainer.stereoElements()) stereoElements.add(se);
notifyChanged();
}
/**
* Convenience method for labelling all stereo elements. The {@link CIP_CHIRALITY} is determined
* for each element and stored as as {@link String} on the {@link CDKConstants#CIP_DESCRIPTOR}
* property key. Atoms/bonds that are not stereocenters have no label assigned and the property
* will be null.
*
* @param container structure to label
*/
public static void label(IAtomContainer container) {
for (IStereoElement stereoElement : container.stereoElements()) {
if (stereoElement instanceof ITetrahedralChirality) {
ITetrahedralChirality tc = (ITetrahedralChirality) stereoElement;
tc.getChiralAtom()
.setProperty(CDKConstants.CIP_DESCRIPTOR, getCIPChirality(container, tc).toString());
} else if (stereoElement instanceof IDoubleBondStereochemistry) {
IDoubleBondStereochemistry dbs = (IDoubleBondStereochemistry) stereoElement;
dbs.getStereoBond()
.setProperty(CDKConstants.CIP_DESCRIPTOR, getCIPChirality(container, dbs).toString());
}
}
}