/** * 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; }