code: private IAtomContainer setAntiFlags(IAtomContainer container, IAtomContainer ac, int number, boolean b) {
          IBond bond = ac.getBond(number);
          if (!container.contains(bond)) {
              bond.setFlag(CDKConstants.REACTIVE_CENTER, b);
              bond.getBegin().setFlag(CDKConstants.REACTIVE_CENTER, b);
              bond.getEnd().setFlag(CDKConstants.REACTIVE_CENTER, b);
          } else
              return null;
          return ac;
      }
docs: Set the Flags to atoms and bonds which are not contained
  in an atomContainer.
  
  @param container Container with the flags
  @param ac        Container to put the flags
  @param b         True, if the the flag is true
  @return          Container with added flags