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