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Incoporate the parameter files mmff94.prm and mmxconst.prm into the mengine code by turning them into header files. Each line becomes a string array element that is parsed in place of lines in the .prm files. The .prm files are no longer needed, but are not deleted from the repository.
Add -a switch to cause H atoms to be added, deleting existing ones. With -a, mengine behaves as the original. Formal charges are not always preserved, by the original or the modified mengine with or without the -a switch. It appears that negative charges are preserved (benzoic acid). A positive charge on a N atom (an amine) is not preserved. Charges are recognized in CHG records and in atom records. Charges are output only in atom records.
Add back the command line options -d -i -x for dipole moment, vibrational data and logp. Have error.log directed to stdout.
Create new main program, mengine.c to replace gmmx.c simplifying command line parsing (none). Make mengine read stdin (sdf) and write stdout (sdf) instead of files. Makefile reflects change from gmmx to mengine.
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