code: private void setActiveCenters(IAtomContainer reactant) throws CDKException {
          Iterator<IBond> bonds = reactant.bonds().iterator();
          while (bonds.hasNext()) {
              IBond bondi = bonds.next();
              IAtom atom1 = bondi.getBegin();
              IAtom atom2 = bondi.getEnd();
              if (bondi.getOrder() == IBond.Order.SINGLE
                      && (atom1.getFormalCharge() == CDKConstants.UNSET ? 0 : atom1.getFormalCharge()) == 0
                      && (atom2.getFormalCharge() == CDKConstants.UNSET ? 0 : atom2.getFormalCharge()) == 0
                      && reactant.getConnectedSingleElectronsCount(atom1) == 0
                      && reactant.getConnectedSingleElectronsCount(atom2) == 0) {
                  bondi.setFlag(CDKConstants.REACTIVE_CENTER, true);
                  atom1.setFlag(CDKConstants.REACTIVE_CENTER, true);
                  atom2.setFlag(CDKConstants.REACTIVE_CENTER, true);
              }
          }
      }
docs: Set the active center for this molecule. The active center will be single bonds.
  As default is only those atoms without charge and between a sigma bond.
  
  @param reactant The molecule to set the activity
  @throws CDKException