code: private IAtomContainer getAllPlacedAtoms(IAtomContainer molecule) {
          IAtomContainer placedAtoms = new AtomContainer();
          for (int i = 0; i < molecule.getAtomCount(); i++) {
              if (molecule.getAtom(i).getFlag(CDKConstants.ISPLACED)) {
                  placedAtoms.addAtom(molecule.getAtom(i));
              }
          }
          return placedAtoms;
      }
docs: Gets the allPlacedAtoms attribute of the AtomPlacer3D object.
  
  @return    The allPlacedAtoms value