Update atomtyper.py to use networkX 2.X methods
Update atomtyper.py to use networkX 2.X methods

Upgrading to networkX >= 2.4 removes the nx.Graph.node method, breaking
atomtyper.py.

NetworkX recently updated to 2.4 and the way we access nodes have been
removed: G.node –> use G.nodes. This was only present in `atomtyper.py`,
the rest of our node calls were using the new syntax.

Updating to handle the new syntax restores expected behavior, and all
unit tests pass.

mosdef-hub/foyer,iModels/foyer,mosdef-hub/foyer,iModels/foyer