Add and modify calls for generateTransportData()

- move call for seed species from initialize() to
addSeedMechanismToCore()
- call getTransportData() for reactions found in reaction libraries in
addReactionLibraryToEdge()
Add function updateLonePairs() and call in fromRDKitMol()

- setting the number of lone electron pairs
- also fixes fromSMILES and similar functions using fromRDKitMol()
Merge pull request #167 from bbuesser/master

Add and modify calls for generateTransportData() and add updateLonePairs to fix adjacency lists generated by fromSMILES
Add label removeLonePairs to toAdjacencyList()

- enables printing adjacency lists without the number of lone electron
pairs per atom
- helpfulr for RMG-Java database query
Merge branch 'master' of https://github.com/bbuesser/RMG-Py
Add label saturateH to fromAdjacencyList()

- enables reading old Java-Style libraries for kinetics search on
website
Merge branch 'master' of https://github.com/bbuesser/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.