@Test
public void s_penta_2_3_diene_expl_h() throws Exception {
IAtomContainer m = new AtomContainer(5, 4, 0, 0);
m.addAtom(new Atom("C"));
m.addAtom(new Atom("C"));
m.addAtom(new Atom("C"));
m.addAtom(new Atom("C"));
m.addAtom(new Atom("C"));
m.addAtom(new Atom("H"));
m.addAtom(new Atom("H"));
m.addBond(0, 1, IBond.Order.SINGLE);
m.addBond(1, 2, IBond.Order.DOUBLE);
m.addBond(2, 3, IBond.Order.DOUBLE);
m.addBond(3, 4, IBond.Order.SINGLE);
m.addBond(1, 5, IBond.Order.SINGLE);
m.addBond(3, 6, IBond.Order.SINGLE);
int[][] atoms =
new int[][] {
{0, 5, 6, 4},
{5, 0, 6, 4},
{5, 0, 4, 6},
{0, 5, 4, 6},
{4, 6, 5, 0},
{4, 6, 0, 5},
{6, 4, 0, 5},
{6, 4, 5, 0},
};
Stereo[] stereos =
new Stereo[] {
Stereo.CLOCKWISE,
Stereo.ANTI_CLOCKWISE,
Stereo.CLOCKWISE,
Stereo.ANTI_CLOCKWISE,
Stereo.CLOCKWISE,
Stereo.ANTI_CLOCKWISE,
Stereo.CLOCKWISE,
Stereo.ANTI_CLOCKWISE
};
for (int i = 0; i < atoms.length; i++) {
IStereoElement element =
new ExtendedTetrahedral(
m.getAtom(2),
new IAtom[] {
m.getAtom(atoms[i][0]),
m.getAtom(atoms[i][1]),
m.getAtom(atoms[i][2]),
m.getAtom(atoms[i][3])
},
stereos[i]);
m.setStereoElements(Collections.singletonList(element));
assertThat(convert(m).toSmiles(), is("CC(=[C@]=C(C)[H])[H]"));
}
}
@Test
public void s_penta_2_3_diene_impl_h() throws Exception {
IAtomContainer m = new AtomContainer(5, 4, 0, 0);
m.addAtom(new Atom("C"));
m.addAtom(new Atom("C"));
m.addAtom(new Atom("C"));
m.addAtom(new Atom("C"));
m.addAtom(new Atom("C"));
m.addBond(0, 1, IBond.Order.SINGLE);
m.addBond(1, 2, IBond.Order.DOUBLE);
m.addBond(2, 3, IBond.Order.DOUBLE);
m.addBond(3, 4, IBond.Order.SINGLE);
IStereoElement element =
new ExtendedTetrahedral(
m.getAtom(2),
new IAtom[] {m.getAtom(0), m.getAtom(1), m.getAtom(3), m.getAtom(4)},
CLOCKWISE);
m.setStereoElements(Collections.singletonList(element));
assertThat(convert(m).toSmiles(), is("CC=[C@@]=CC"));
}
/**
* 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;
}
