code: public static StereoElementFactory using3DCoordinates(IAtomContainer container) {
          EdgeToBondMap bondMap = EdgeToBondMap.withSpaceFor(container);
          int[][] graph = GraphUtil.toAdjList(container, bondMap);
          return new StereoElementFactory3D(container, graph, bondMap).checkSymmetry(true);
      }
docs: Create a stereo element factory for creating stereo elements using 3D
  coordinates and depiction labels (up/down, wedge/hatch).
  
  @param container the structure to create the factory for
  @return the factory instance