Added profiling option for thermoEstimator
Added makeProfileGraph as a script to be able to modify profile graphics with different thresholds
Moved generateQMData to higher QMMolecule class along with minor modifications
Merge branch 'master' of https://github.com/GreenGroup/RMG-Py
Limit lone pair drawing to Nitrogen atoms only.

There are still some issues with positioning of the lone pairs.  For instance
1 N 1 1 {2,S} {3,S}
2 H 0 0 {1,S}
3 H 0 0 {1,S}

Will draw the long pair on the hydrogen rather than the N.  But for now, we can
avoid drawing lone pairs on oxygens and such where it is not needed.
Draw lone electron pairs only for nitrogen containing species
Make transport writing compatible with Python 2.6

The format syntax where you omit the field numbers 
was introduced in Python 2.7.
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()
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.