CCTBX Conversion: Re-write all structure objects

[stephaniewankowicz]

This is the largest change to the qFit code. The following structure objects need to be converted from qFit to CCBTX:

1. structure
2. conformer
3. coordinate arrays (coor_set)
4. b-factor arrays
5. occupancy arrays

The functionality of structure objects sits within the structure folder.

We need to implement new ways to:

1. extract specific residues based on resi/chain or icode
2. extract and store coordinates, b-factors, and/or occupancies in separate arrays
3. be able to mask out certain parts of a conformer object (for sampling purposes)
4. assign values from each array back into a structure-like object
5. combine conformers to create a larger structure object

This code exists in
qFit_protein.py
qFit_residue.py
qFit_ligand.py
qfit.py

The following functions in qfit.py will need to be changed:

get_conformers
update_conformers