Change loop export proceduce

We no longer attempt to add the information about motifs, we leave that to the
motif data. In addition, we have to translate the old style ids to new style
ids. We also need to have a method to get all pdb ids with loops.
Don't pass command line options to export

We just export all loops or interactions, without using the command line
options.
Some whitespace changes.
Clean up unused imports
Some flake8 cleanups