CCTBX Conversion: Transformation/F-calc function

[stephaniewankowicz]

Change the functions in the transformer.py file.
The functions here are essentially f-calc. Throughout the qFit code, we take our sampled conformers and convert them to density to do our optimization functions.

The input to these functions will be arrays or 'conformer' objects that will contain coordinates, b-factors, and occupancy.

The output of this function will need to include the ability to get the array only values of the density which will be fed into the QP/MIQP step.

On top of changing the functions within transformer.py, the following functions in qfit.py will need to be altered with the new required input/output:

_update_transformer
_subtract_transformer
_convert
write_maps