code: private static StereoEncoder axial3DEncoder(IAtomContainer container, IAtom start, List<IBond> startBonds,
              IAtom end, List<IBond> endBonds) {
  
          Point3d[] coordinates = new Point3d[4];
  
          PermutationParity perm = new CombinedPermutationParity(fill3DCoordinates(container, start, startBonds,
                  coordinates, 0), fill3DCoordinates(container, end, endBonds, coordinates, 2));
  
          GeometricParity geom = new Tetrahedral3DParity(coordinates);
  
          int u = container.indexOf(start);
          int v = container.indexOf(end);
  
          return new GeometryEncoder(new int[]{u, v}, perm, geom);
      }
docs: Create an encoder for axial 3D stereochemistry for the given start and
  end atoms.
  
  @param container  the molecule
  @param start      start of the cumulated system
  @param startBonds bonds connected to the start
  @param end        end of the cumulated system
  @param endBonds   bonds connected to the end
  @return an encoder