improve/expand tests for FeaturizedAtoms, encoding

[rkurchin]

They also probably need to be reorganized a bit in light of the addition of the FeaturizedAtoms type...

[thazhemadam]

On a slightly related note, the documentation may also need some reorganization.

[rkurchin]

renamed issue because realized we also need tests in the AtomGraph tests that the keyword arguments work. Currently those are only tested in the utils tests for graph-building, but then when a semicolon got lost in the AtomGraph constructor such that all keyword arguments accidentally became positional, it didn't break anything...