SingleMapping { protected List<Map<IAtom, IAtom>> getOverLaps(IAtomContainer source, IAtomContainer target, boolean removeHydrogen) throws CDKException { mappings = new ArrayList<Map<IAtom, IAtom>>(); connectedBondOrder = new TreeMap<Integer, Double>(); this.source = source; this.target = target; if (source.getAtomCount() == 1 || (source.getAtomCount() > 0 && source.getBondCount() == 0)) { setSourceSingleAtomMap(removeHydrogen); } if (target.getAtomCount() == 1 || (target.getAtomCount() > 0 && target.getBondCount() == 0)) { setTargetSingleAtomMap(removeHydrogen); } postFilter(); return mappings; } SingleMapping();   }
@Test public void testGetOverLaps() throws CDKException { IAtom atomSource = new Atom("R"); IAtom atomTarget = new Atom("R"); IAtomContainer source = new AtomContainer(); source.addAtom(atomSource); IAtomContainer target = new AtomContainer(); target.addAtom(atomTarget); boolean removeHydrogen = false; SingleMapping instance = new SingleMapping(); assertNotNull(instance.getOverLaps(source, target, removeHydrogen)); }