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
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
Merge remote-tracking branch 'GreenGroup/master'
Log warning if reading adjacency list without lone electron pairs.

The official python style database contains only adjacency lists with
either lone electron pair definitions or all hydrogen atoms explicitly.
The saturateH label was intended to read the Java style database where
neither lone electron pair definitions nor all explicit hydrogen atoms
are defined.