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.
Add saturateH=True to fromAdjacencyList() in loadOldDictionary()
Merge remote-tracking branch 'GreenGroup/master'
Merge branch 'GreenGroup/master'
change loop length over PdepNetworks in search for maximum leak rates

- numPdepNetworks = self.networkCount was the number of PdepNetworks
ever created in that model

- len(self.networkList) is the number of actually existing PdepNetworks
at any time

fixes #176
Limit the search for electronic states to atoms involved in reaction

- limit search on labeled atoms
- this is currently RMG-specific to track electronic states as attribute
of single atoms, we have to consider moving on to tracking it as a
species
property
Bug fix for internal mode projection for Cantherm

We were not following the Gaussian white paper formulae and this resulted
in some cases where our projection was completely wrong.

This bug fix has been provided by @agvandeputte
Correcting the ZPE after projection

After projecting the hindered rotors we need to recalculate the ZPE
according to the projected frequencies. Since  'ideally" only the modes with
a small wave number are projected out this should not be that different from
the ZPE coming before projections.
Add new ketoenol family to list of unimolecular kinetic families.
Encode in UTF-8 otherwise we run into errors for unicode symbols.

If that fails, then encode in ascii and omit the symbols completely.
We run into too many errors otherwise.
Crash RMG when identical molecular structures and labels are found thermo libraries.

Don't let user go unaware if thermo entry is being overwritten (when labels are
identical).  Also raise error if identical adjlists are found, since only
the first entry would be used in RMG.  This will probably cause database to
load a little slower, but is a preventative measure.
Make more stringent checks for unlabeled duplicate reactions in reaction libraries.

Previously, RMG would only throw an error for reactions in the same direction,
as well as same order of reactants and products.  Now using the built-in
reaction isomorphism check for both directions and all permutations.
Fix 00c8765 - do not check if own reaction is duplicate.
Add saturateH=True to fromAdjacencyList() in loadOldDictionary()
change loop length over PdepNetworks in search for maximum leak rates

- numPdepNetworks = self.networkCount was the number of PdepNetworks
ever created in that model

- len(self.networkList) is the number of actually existing PdepNetworks
at any time

fixes #176
Limit the search for electronic states to atoms involved in reaction

- limit search on labeled atoms
- this is currently RMG-specific to track electronic states as attribute
of single atoms, we have to consider moving on to tracking it as a
species
property
Merge branch 'master' of https://github.com/bbuesser/RMG-Py
Merge remote-tracking branch 'GreenGroup/master'

Conflicts:
	rmgpy/data/base.py
Unit test (failing) for reading old-style adjacency lists.

See issue #180