Test parsing of nt level data

This now can extract RsR(z) data from the quality XML data. This has tests for
the basic extraction of RsR level data for nts. This is pretty simple but may
work once I have a working database schema.
Ignore todo.txt
Add some test files
Add initial pass at LoopLoopCorresopndence

This loader will compute the correspondences between loops of two structures. We
will also compute discrepancy for loops that are exact. This is then stored in
the database. Much of this code comes from some previous work I did to make a
quick and dirty test of this method. This needs many more tests.
Ignore my .tasks directory
Allow store to store nested iterators

Sometimes I have iterators that produce iterators as the input data to store.
This should make it a bit easier by allowing me to use such things
transparently.
Use new store method
Tests and bug fixes for loop_loop

I added some tests and fixed mistakes in the loop_loop_correspondence module.
Specifically there were problems with the utility functions. This fixes them so
we can get the PDBs and loops correctly.
Move mapping method to utils and test

I added tests for the mapping method as well as placing it in the utils class.
It feels like a general utilities sort of thing to do. In doing so I found bugs
and have fixed them.
Remove extra comment
Add error checking and use utility class

I added some logic for complaining when given bad inputs. This should not occur
but it doesn't hurt to be safe. Examples are when we get empty loop ids. I also
have this use the utility class I wrote.
Use utils path loading and minor bug fix

We should use utils.py path handling code. In addition, I upper case pdbs so we
don't have problems when giving a lower case one. We should always have
normalized pdb case.
WebRequestHelper should subclass RetryHelper

In addition we need to be a little smarter about handling iterators or nested
iterators when saving.
Fixes for new database naming/scheme

In addition, I improved error handling.
Use module specific loggers

We should use a logger for each module as this makes it easier to find where
each logging statement is coming from. This change covers nearly all classes and
modules.