code: Entry<String, Point2d[]> createEntry(final IAtomContainer container) {
          try {
  
              final int n = container.getAtomCount();
              final int[] ordering = new int[n];
              final String smiles = cansmi(container, ordering);
  
              // build point array that is in the canonical output order
              final Point2d[] points = new Point2d[n];
              for (int i = 0; i < n; i++) {
                  Point2d point = container.getAtom(i).getPoint2d();
  
                  if (point == null) {
                      logger.warn("Atom at index ", i, " did not have coordinates.");
                      return null;
                  }
  
                  points[ordering[i]] = point;
              }
  
              return new SimpleEntry<String, Point2d[]>(smiles, points);
  
          } catch (CDKException e) {
              logger.warn("Could not encode container as SMILES: ", e);
          }
  
          return null;
      }
docs: Create a library entry from an atom container. Note the entry is not added to the library.
  
  @param container structure representation
  @return a new library entry (not stored).
  @see #add(java.util.Map.Entry)