Merge pull request #167 from bbuesser/master

Add and modify calls for generateTransportData() and add updateLonePairs to fix adjacency lists generated by fromSMILES
Merge branch 'master' of https://github.com/bbuesser/RMG-Py
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