Removing lingering references to LenardJones class

Cantherm was failing because it was still refering to LenardJones
class which is now removed after the transport branch has been merged.

Made the writing of output of measure also consistent to use
TransportModel
Fix to make standalone Cantherm work

Commit 5c4a2da0aec8e7abcc0153e4bfd62f84fe9f88d6 would
modify the label in the input file causing Cantherm to crash
when its trying to calculate kinetics for that reaction.
Fix typo in function name convertInitialKeysToSpeciesObjects
Save mole fractions instead of concentrations (easier comparison with chemkin)
Do not compute reverse rate coefficients in solver if the rxn is irreversible.

Apparently we were still considering reactions as reversible even when
they are irreversible.
Change "debug" logging level messages to level 1.

For some reason logging.log(0,"message") doesn't log anything
even if you have set the logger level to 0 with the --debug option.
Making these messages level 1 seems to fix it.
There are probably other places this should be fixed too.
More warning messages logged when failed to match template
More debug logging messages when generating reverse templates
Tweak database path in input documentation

This is still entirely wrong, in terms of how you enter the 
reaction libraries, but serves to show how easy it is
to update the documentation online :-)
Molepro imported to canther statmech

The Cantherm example uses a molepro output file, leading to
a failure in the cantherm example. This change fixes the failure,
however there are possibly further fixes needed for correct
implementation in StatMechJob.
Unit tests for pickle use the highest protocol.

If we change some stuff to use __slots__ then this will be necessary.
In the mean time it should just make it faster.
Improved debug logging for reaction family templates
More honest error message in when failing to draw species.

It used to assume the error was lack of molecular structure,
when in fact it could be anything.
Unit tests for molecule drawing.

We don't test a lot, but it should help check it doesn't crash.
Update molecule drawing unit tests.

I think older versions of the pycario libraries cannot create surfaces
without a temporary file. This makes most tests work with that scenario,
and adds another test for it.
Fix scipy.optimize.fmin call in statmech/conformer.pyx

This was giving trouble with a certain version of scipy.
Fix typo in arrheniusTest.py
TransportDatabase has no loadOld function.  Don't try to import old transport groups.
Use RDKit instead of Openbabel in toSMILES() for N2 species

fixes #175
Speed up the SMILES generation by looking up small molecules, and test it.

The previous algorithm checked the molecular formula anyway, so we may as well
use that to shortcut a bunch of things that can be uniquely identified that way,
to avoid calling OpenBabel or RDKit.

I also made a unit test that we get back the same SMILES we started with.

Inspired by and closes #175