Attempt to refactor downloading to use webhelper

The webhelper has retries which is cleaner than the current attempt. Also, I
have run into errors that occur outside of the current try block for getting
files. This refactor moves code around we the whole thing is in a try block and
we get retries when trying to get the files.
Minor clean ups

Just moving some things around to match pep8 and such.
Allow retry helper to fail

It is possible that some attempts at getting doing things are alright if they
fail. For example, downloading a pdb file that does not exist. We add code to
allow the retry helper to fail as needed. Also, I've added some tests for retry
helper.
Allow failure when downloading files

It is ok for downloads to fail in some cases. This happens when we do not have a
pdb1 file for a structure. However, we do complain and fail if it is a cif or
pdb file that we have failed to download.