CCTBX Conversion: Write PDB File

[stephaniewankowicz]

Change the writing of PDBs from qFit infrastructure to CCTBX.

This will change the function of tofile(). The input of this function will be a structure object (either a protein, ligand, or residue) and the output should be a PDB file written to the output directory.

There should be options in the function to write out header information. There should also be options to change the file name output. We do not need this for ligand or residue outputs but want it for the entire protein.

This function is used extensively in qfit.py (for intermediate or debugging outputs) as well as qfit_protein, qfit_residue, and qfit_ligand.

Note this function name should be changed to tofilePDB (or something like this) to differentiate between the tofile PDB and tofile for maps.