Import inerts from Java kinetic libraries with normal case rather than uppercase.

This makes it consistent with other parts where we load inerts (in chemkin.py for instance.)
Add set of bath gases (Ar, Ne, He, and N2) to all RMG jobs just like Java.
Only index the reactive species, not the inerts.

We might run into some trouble in terms of nonreactive / nonbath gas species
like in liquid phase with water.  But probably they won't want that species
to be indexed anyway.
Merge pull request #274 from connie/addinerts

Add inerts to RMG jobs just like Java does.
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
Fix regular expression matching of old and intermediate adjlists.
Don't default to fromOldAdjacencyList when fromAdjacencyList function fails.

The fromAdjacencyList function may be failing from other issues.  Rely on the
regex to detect old and intermediate style adjlists properly.
Raise InvalidAdjacencyListError if wildcards get assigned in a molecule adjlist.

Wildcards like x should only be used to construct groups.  We construct atoms
for a molecule like so:

atom = Atom(atomType[0], unpairedElectrons[0], partialCharges[0], label, lonePairs[0])

However, we should actually ensure that each list has only a single item and does not
include wildcards.

Also includes a wildcard adjlist unit test to ensure the proper error is raised.
Change CO representation to SMILES='[C-]#[O+]', which is the true ground state.

We probably want resonance to the double bonded state later through charge resonance.
However [C+]#[O-] is completely wrong.
Consistency check for molecule adjlists by checking valency against p,u,c values.

Prior to this, the lone pairs were calculated using the given number of
radical electrons, and the charges were then set automatically with complete
disregard to user-specified charge.  Now, assume u and c to be implicitly zero
unless otherwise specified.  Therefore, if either u or c are nonzero,
they must be explicitly indicated or else they will fail the valency check.

We may want some group checks in the future.

Also includes fixes to unit tests to include these explicit charges and lone pairs.
Make a unit test for an incorrect new-style adjlist.