Where things stand as of 15 Nov 2005
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The MMP files from Damian are minimized structures. So the idea for
the tests is that for each structure, we generate a perturbed version
and then we want the minimizer to bring it back to the minimized
shape. So the MMP files we have right now are essentially outputs of
the tests, or references for how the outputs should look.

The immediate need for MmpFile.py is in helping to perturb the MMP
structures supplied by Damian. Later, it might help with merging
position information from other file formats into an MMP file. This
would be helpful when we get GAMESS data in something like an XYZ or a
PDB file. There is already some effort in that direction, see
sim/src/tests/scripts/xyzmerge.py and
sim/src/tests/scripts/XyzFile.py.

It makes sense to have Python classes representing a few different
file formats that we are likely to be using. That's why I used names
like XyzFile.py and MmpFile.py.