Fix naming issue

The tool to get all pdbs is not named Pdb, but QueryHelper.
Fix QueryHelper

QueryHelper did not correctly send requests. It used the wrong keyword arguments
for both the request and for setting the parser.
Remove duplicate class and fix getting rna pdbs

There was an issue where I did not get all RNA containing pdbs because the
content-type was not set correctly. This has been corrected. In addition, I had
a class (QueryHelper) which did the same thing as RnaPdbsHelper. I've removed
QueryHelper.
Use RnaPdbsHelper

This is the correct way of getting all rna containing pdbs.
Update downloader to only use cif files

The downloader should only get cif files because those are the only ones we need
to analyze.
Silence webrequest when failure is allowed
Downloader should never fail