code: public IAtomContainer assignMMFF94PartialCharges(IAtomContainer ac) throws CDKException {
          if (!mmff.assignAtomTypes(ac))
              throw new CDKException("Molecule had an atom of unknown MMFF type");
          mmff.partialCharges(ac);
          mmff.clearProps(ac);
          for (IAtom atom : ac.atoms())
              atom.setProperty(MMFF_94_CHARGE, atom.getCharge());
          return ac;
      }
docs: Main method which assigns MMFF94 partial charges
  
  @param ac AtomContainer
  @return AtomContainer with MMFF94 partial charges as atom properties