code: public Point3d geometricCenterAllPlacedAtoms(IAtomContainer molecule) {
          IAtomContainer allPlacedAtoms = getAllPlacedAtoms(molecule);
          return GeometryUtil.get3DCenter(allPlacedAtoms);
      }
docs: Calculates the geometric center of all placed atoms in the atomcontainer.
  
  @param molecule
  @return    Point3d the geometric center