Input script to run reactions from an RMG generated model

The mechanism as well as the species dictionary should
be provided (see 10.1016/j.combustflame.2013.10.019).

The current setup works for intra_H_migration, H_Abstraction,
and R_Addition_MultipleBond families.
Copy groups from kinetics to make TS_groups.py

Copies the groups and creates an empty distanceData
object. Currently the tree, recipe, and template need to
be commented from the groups.py file, and the tree copied
to the TS_groups.py after. This needs to be fixed.
Scripts to handle TS_training data.

`databasePrep.py` collates all reactions from the
current training set as well as the new data being
added, while removing any duplicate reactions (both
forward and reverse).

`duplicate.py` should be run after `databasePrep.py`
for reaction families that are its own reverse. It
duplicates every entry in the training data.