deprecate BiLayerGrapheneGenerator rotation_angle parameter.

Replacing rotation_angle with layer_rotation_angle kwarg in
BiLayerGrapheneGenerator constructor.
updating command-line arg for BiLayerGrapheneGenerator.

Changing rotation-angle to layer-rotation-angle.
Adding __iter__ methods to Point and Vector classes
Adding __len__ methods to Point and Vector classes
Several updates to transform functions.

Cleaned up code and fixed a few bugs in rotation_matrix,
transformation_matrix, and rotate_point functions.
Adding code for StoneWalesDefectGenerator class
Take advantage of Point iterator container method
replacing vac/defect bounds OrderedDict with None
adding vac_bounds kwarg to generate_vacancy_structure method
changing van der Waals distance to 3.35 angstroms
renaming _structure_generator_atom(s) to _structure_atom(s)
updating imports for structure_atom(s) modules
updating docstrings
replacing LAMMPSAtoms with StructureAtoms class
updating docstrings
renaming and moving _polyhedra module to tools._geometric_shapes
updating imports and docstrings for _geometric_shapes module
changing order of function defs
updating docstring modules
adding doc sources and modules for new tools sub-packages.

Adding two new sub-packages to sknano.tools: geometric_shapes and
symmetry_groups for defining abstract data structures describing
geometric shapes and symmetric groups, respectively.