Added Command_Line interface for GULP
Merge branch 'master' of https://github.com/materialsproject/pymatgen
Merge branch 'master' of https://github.com/materialsproject/pymatgen
Modifications to the VoronoiConnectivity code, added a method to find
Voronoi Connectivity and distance between Voronoi Connected objects
Merge branch 'master' of https://github.com/materialsproject/pymatgen
	Merge branch 'master' of https://github.com/materialsproject/pymatgen
Added method get_connections:

Returns a list of site pairs that are Voronoi Neighbors, along
        with their real-space distances.

Also made cutoff distance in VoronoiConnectivity a possible input variable.
Default is 10, should be backwards compatible.
Cleanup.
Removed gulp_caller, kept in Pymatpro until ready.
Merge branch 'master' of https://github.com/materialsproject/pymatgen

Conflicts:
	pymatgen/command_line/gulp_caller.py
Update dev version number.
 Code cleanup
Merge remote-tracking branch 'mpmaster/master'
I have no idea what I'm doing
Substitution of functional groups
cleanup of SubstitutionProbability. Addition of SubstitutionPredictor, which
does half of what the Substitutor currently does, but more cleanly.
refactor SubstitutionPredictorTransformation to use SubstitutionPredictor
instead of Substitutor
minor changes to substitutor for compatibility with modified
SubstitutionProbability
added method to get underlying element object from specie
clean up anonymous formula