code: @Override
      public boolean isStereoMisMatch() {
          boolean flag = false;
          IAtomContainer reactant = getReactantMolecule();
          IAtomContainer product = getProductMolecule();
          int score = 0;
  
          for (Map.Entry<IAtom, IAtom> mappingI : firstAtomMCS.entrySet()) {
              IAtom indexI = mappingI.getKey();
              IAtom indexJ = mappingI.getValue();
              for (Map.Entry<IAtom, IAtom> mappingJ : firstAtomMCS.entrySet()) {
  
                  IAtom indexIPlus = mappingJ.getKey();
                  IAtom indexJPlus = mappingJ.getValue();
                  if (!indexI.equals(indexIPlus) && !indexJ.equals(indexJPlus)) {
  
                      IAtom sourceAtom1 = indexI;
                      IAtom sourceAtom2 = indexIPlus;
  
                      IBond rBond = reactant.getBond(sourceAtom1, sourceAtom2);
  
                      IAtom targetAtom1 = indexJ;
                      IAtom targetAtom2 = indexJPlus;
                      IBond pBond = product.getBond(targetAtom1, targetAtom2);
  
                      if ((rBond != null && pBond != null) && (rBond.getStereo() != pBond.getStereo())) {
                          score++;
                      }
                  }
              }
          }
          if (score > 0) {
              flag = true;
          }
          return flag;
      }
docs: {@inheritDoc}