/**
* Positions the aliphatic substituents of a ring system
*
* @param rs The RingSystem for which the substituents are to be laid out
* @return A list of atoms that where laid out
*/
public IAtomContainer placeRingSubstituents(IRingSet rs, double bondLength) {
logger.debug("RingPlacer.placeRingSubstituents() start");
IRing ring = null;
IAtom atom = null;
IRingSet rings = null;
IAtomContainer unplacedPartners = rs.getBuilder().newInstance(IAtomContainer.class);
IAtomContainer sharedAtoms = rs.getBuilder().newInstance(IAtomContainer.class);
IAtomContainer primaryAtoms = rs.getBuilder().newInstance(IAtomContainer.class);
IAtomContainer treatedAtoms = rs.getBuilder().newInstance(IAtomContainer.class);
Point2d centerOfRingGravity = null;
for (int j = 0; j < rs.getAtomContainerCount(); j++) {
ring = (IRing) rs.getAtomContainer(j); /* Get the j-th Ring in RingSet rs */
for (int k = 0; k < ring.getAtomCount(); k++) {
unplacedPartners.removeAllElements();
sharedAtoms.removeAllElements();
primaryAtoms.removeAllElements();
atom = ring.getAtom(k);
rings = rs.getRings(atom);
centerOfRingGravity = GeometryTools.get2DCenter(rings);
atomPlacer.partitionPartners(atom, unplacedPartners, sharedAtoms);
atomPlacer.markNotPlaced(unplacedPartners);
try {
for (int f = 0; f < unplacedPartners.getAtomCount(); f++) {
logger.debug(
"placeRingSubstituents->unplacedPartners: "
+ (molecule.getAtomNumber(unplacedPartners.getAtom(f)) + 1));
}
} catch (Exception exc) {
}
treatedAtoms.add(unplacedPartners);
if (unplacedPartners.getAtomCount() > 0) {
atomPlacer.distributePartners(
atom, sharedAtoms, centerOfRingGravity, unplacedPartners, bondLength);
}
}
}
logger.debug("RingPlacer.placeRingSubstituents() end");
return treatedAtoms;
}
/**
* 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;
}