Added MM3* Hess. Added Jaguar Hess. mass-weighting

Added options to calculate.process_args and the rest of the script
to handle getting the MM3* Hessian. Also modified the Jaguar Hessian
method in calculate.extract_data to account for mass-weighting.

Modified the Hessian methods of filetypes.FileType to make them more
convenient.

The current method appears to work, but it feels sloppy. I think that
we should make a class for the Hessian that does a better job at
converting between mass-weighted versions, inversion, etc.
Modified bond/angle extraction

Bonds and angles are now only included as reference data if there
is a FF term that directly relates to them. However, this distinction
requires the mmo file. Each line pertaining to a bond or angle in the
mmo file has a comment at the end. For substructures in MM3*, that
comment refers to the substructure's name.

Right now, all bonds and angles are eliminated based on the keyword
"OPT", which must appear the in the substructure's name. It would be
nice to auto-detect the substructure name.
Slightly modified bonds and angles

Added an option to calculate.process_args to eliminate bonds and
angles if they are not included in the substructure. This is no
longer the default behavior.