code: @Override
      public void setChemFilters(boolean stereoFilter, boolean fragmentFilter, boolean energyFilter) {
  
          if (firstAtomMCS != null) {
              ChemicalFilters chemFilter = new ChemicalFilters(allMCS, allAtomMCS, firstSolution, firstAtomMCS,
                      getReactantMolecule(), getProductMolecule());
  
              if (stereoFilter && firstAtomMCS.size() > 1) {
                  try {
                      chemFilter.sortResultsByStereoAndBondMatch();
                      this.stereoScore = chemFilter.getStereoMatches();
                  } catch (CDKException ex) {
                      LOGGER.error(Level.SEVERE, null, ex);
                  }
              }
              if (fragmentFilter) {
                  chemFilter.sortResultsByFragments();
                  this.fragmentSize = chemFilter.getSortedFragment();
              }
              if (energyFilter) {
                  try {
                      chemFilter.sortResultsByEnergies();
                      this.bEnergies = chemFilter.getSortedEnergy();
                  } catch (CDKException ex) {
                      LOGGER.error(Level.SEVERE, null, ex);
                  }
              }
          }
      }
docs: {@inheritDoc}