code: @Override
      public Object[] toArray() {
          IAtomContainer[] ret = new IAtomContainer[coordinates.size()];
          int index = 0;
          for (Point3d[] coords : coordinates) {
              try {
                  IAtomContainer conf = (IAtomContainer) atomContainer.clone();
                  for (int i = 0; i < coords.length; i++) {
                      IAtom atom = conf.getAtom(i);
                      atom.setPoint3d(coords[i]);
                  }
                  ret[index++] = conf;
              } catch (CloneNotSupportedException e) {
                  e.printStackTrace();
              }
          }
          return ret;
      }
docs: Returns the conformers in the form of an array of IAtomContainers.
  
  Beware that if you have a large number of conformers you may run out
  memory during construction of the array since IAtomContainer's are not
  light weight objects!
  
  @return The conformers as an array of individual IAtomContainers.