Use pdbs given pdbs if any

If we are given a list of PDBs recalculate the units for we will do so.
Otherwise we default to all rna containing pdb files.
Filter out all obsolete files

We do not need loops from any obsoleted files. They may also not have an unit
ids and cause some unneeded warnings when running the pipeline. This way we
exclude them and avoid these warnings.
We should report the motif assignment in export

When we export we should report the current motif assignment. If no motif is
assigned then we give an empty string as the assignment.
Don't really need the motif_id variable

We can just set the resulting dict directly, no need to store the value
temporarily.
Never attempt to search for junction loop releases

We never look for junction loop releases because they will never exist. We
check this by seeing if the loop type is in the dict of releases. If not we
skip.