code: public static double getTotalCharge(IAtomContainer atomContainer) {
          double charge = 0.0;
          for (IAtom atom : atomContainer.atoms()) {
              // we assume CDKConstant.UNSET is equal to 0
              Double thisCharge = atom.getCharge();
              if (thisCharge != CDKConstants.UNSET) charge += thisCharge;
          }
          return charge;
      }
docs: Get the summed charge of all atoms in an AtomContainer
  
  @param  atomContainer The IAtomContainer to manipulate
  @return The summed charges of all atoms in this AtomContainer.