code: public void saturate(IAtomContainer atomContainer) throws CDKException {
          logger.info("Saturating atomContainer by adjusting lone pair electrons...");
          boolean allSaturated = allSaturated(atomContainer);
          if (!allSaturated) {
              for (int i = 0; i < atomContainer.getAtomCount(); i++) {
                  saturate(atomContainer.getAtom(i), atomContainer);
              }
          }
      }
docs: Saturates a molecule by setting appropriate number lone pair electrons.