code: private static void makeElevationMap(IAtom atom, List<IBond> bonds, Map<IAtom, Integer> map) {
          map.clear();
          for (IBond bond : bonds) {
  
              int elevation = 0;
              switch (bond.getStereo()) {
                  case UP:
                  case DOWN_INVERTED:
                      elevation = +1;
                      break;
                  case DOWN:
                  case UP_INVERTED:
                      elevation = -1;
                      break;
              }
  
              // change elevation depending on which end of the wedge/hatch
              // the atom is on
              if (bond.getBegin().equals(atom)) {
                  map.put(bond.getEnd(), elevation);
              } else {
                  map.put(bond.getBegin(), -1 * elevation);
              }
          }
      }
docs: Maps the input bonds to a map of Atom->Elevation where the elevation is
  whether the bond is off the plane with respect to the central atom.
  
  @param atom  central atom
  @param bonds bonds connected to the central atom
  @param map   map to load with elevation values (can be reused)