Adding atom energies for BMK/cbsb7

Note:These energies were calculated by Aaron Vandeputte
Avoid mutating adjacency lists from training reaction sets.

This fixes the issue of starred atoms getting erased in the
website for training reactions, and therefore database
edits through the website leading to errors.  This is because we try to
match reaction templates to the training reactions, mutating
the adjacency lists while doing so.  Therefore, deepcopy
all the reaction information before proceeding.  Though
this increases the time spent, it will only be necessary
at the start of a job or website load.
Fixed the smallest set of smallest rings algorithm
Merge remote-tracking branch from Victor
Adding script files for running RMG-Py examples files.
Added transportData class,  CriticalPointGroupContribution class and TransportLibrary class

These classes work together to allow the access of data from the transport libraries and the estimation of the properties via group additivity methods.  Still in progress
added methods for extraction of transport properties from libraries

Still need to add the method for approximation of transport properties from group additivity

deleted unneccessary get functions from transport files
added group additivity functions for transport properties

uses the Joback group additivity method to approximate the transport properties sigma and epsilon
Fixed group additivity methods for transport properties

Cleaned up errors and used averaging of critical point properties for each molecule in a species
Began test file for transport data classes

Test file verifies the working of the transportData, CriticalPointGroupContribution, and TransportDatabase class.  TransportDatabase class test is not finished
Fixed issue with determining the sigma value of transport properties from group estimates

Sigma estimates use the total number of groups used which was incorrectly calculated previously

Fixed counting of atoms for transport estimation by groups
Original version only counted non hydrogen atoms
Added units for polarizability C*m^2*V^-1
Added units to variables that make up a transport object
Added test for the group estimation of transport properties
Added load function to the TransportLibrary and TransportDatabase classes and optimized transport estimation
Fixed units for creation of transportData object and file path for loading from database

If you run this test on your own computer make sure to make the file paths match
Changed units of transport epsilon property to J/mol and added test for acetone to verify estimation methods
Changed leonnardJones to TransportData in chemkin, species, and model files to work with updated transport files
Updated pressure Dependent calculations to use transportData sigma and epsilon values instead of makeshift lennardJones class
Added transport libraries to the RMGdatabase class to allow calculation of transport properties alongside thermo data during pDep reactions