Fix calculateCyclicSymmetryNumber() function

Function was modifying original molecule's bond by changing them
to benzene bonds.  Now we make a copy of the molecule to start with (this uses
up a little extra memory but right now we just need to get it working.)

Also use a try and except block for converting to RDKit Mol, since it can
fail for some nitrogen cases.
Getting rid of fitting warnings in thermo because they clog the log file.
Get rid of warning for overlapping children.

It is clogging up the log file.  Eventually we will want to clean up the
overlapping children in the databases altogether.
Only write shortDesc and longDesc in database entries if they aren't blank.
No longer read or write groups in rules.py.  Load them from groups.py instead.
Remove duplicate "Library reaction" declaration for Multikinetics in chemkin commentary.
Remove storing of kinetic comments from kinetic library upon loading.

Indication of which library the kinetics came from is already done
in chemkin when given a LibraryReaction.  The short and longDesc may
also be too long to be presented in chemkin files.  We don't use those
from the rules so we shouldn't use them here.  As long as the user
knows it's from a particular library, they can look up long commentary in
the database.
Work in progress: load and save kinetic libraries with separate dictionary files.
Move saveDictionary and getSpecies functions from KineticsLibraries to Database class.

So that the KineticsDepository can also use this function to save species dictionaries
separate from their kinetics.
Save and load depositories into folders  separated by reactions.py and dictionary.txt