Work on the TS estimation moved to qm folder.

The code was stored in data/kinetics, but has been
placed in a created qm/reaction.py file.
Began building the QMReaction class in qm/reaction.py

Set up some methods which should be useful. More need 
to be added and the generateTransitionState method needs
heavy triming, editing, and possibly moving in the future.
Removed QM thermo generation from this branch.

The thermo generation has exception handling issues, 
and has been removed to focus on TS build.
More methods added to qm/reaction.py
Removed the old generate3dTS method.

This was the first attempt some time back, which was
abandoned. There were some issues with 1-->1 reactions.
Added call from KineticsFamily to generateTransitionState.
Further development to reaction.py.
Fixes to make generateTransitionState compatible with qm.

Had to change the way geometries are made and stored.
Edits to qm/reaction.py

Creating methods to handle the bounds matrix editing.
Fixed bounds matrix TS generation bugs for some reaction familes.

For reactions with 2 products from 1 reactant, and 1
product from 2 reactants.
Set up to generate TS geometry estimates and send to mopac.

The geometries can now be estimated and sent to run. This
gets working code to test the TS estimates being worked on.
The current successful run test is based on the TD properties
version, so more needs to be added for the TS search. Also the 
keywords need to be expanded.
Added fixes to TS geometry estimation for more reaction families.

Reactions involving 2 reactants and 2 products have been
cleaned up. The embedding needs to be added, but issues
with the sorting label editting need to be resolved first.
Small changes to comments.
Moved ts geometry manipulation to qm/reaction.py

The geometry editing is not unique to mopac, and will
be used for all transition state geometry estimates. 
Having it in reaction will enable all methods to inherit
the geometry editing.
Fixed error in bounds matrix editing.
Added deep copy method to prevent editing of rmg molecules.
Completed the geometry setup for 2 by 2 reactions.
Started the build for 1 to 1 reactions.

The process may require the matching of reactant and
product atoms. This would be unavoidable in any case
as we want to add 2 ended searches to the TS searching.
Attempt to match atoms in reactants and products for 2 ended search.
Different approach to the 2 ended method.