move mengine src to reflect new freemol directory structure

header files containg all the data from
mmff94.prm and mmxconst.prm

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.

updated readme

changes for win32

initial checkin of mpeg_encode source

draft design spec

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.

building up freemol root structure

Change to popen3 to be able to capture stderr

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.

Sample python code showing how mengine can be called using popen2

Sample file for use with mengine and mengine.py

Tag original source from https://cicc-grid.svn.sourceforge.net/svnroot/cicc-grid/cicc-grid/smi23d/trunk

Tag the original source from https://cicc-grid.svn.sourceforge.net/svnroot/cicc-grid/cicc-grid/smi23d/trunk

Create place for tagged branches

Was an old test

No need to store output file until a test suite is developed.

No need to store executables

Two mods to compile properly under mingw without
breaking linux compile.
Comments in source near /* TJO ... */
gmmx.c handle null-termination of file name string properly.
pcmod.h #include <stdio.h> to define FILE type.

test

test add

test

First Commit

First Import