Ignore my notes directory
Uncomment WebRequestHelper

This is a useful class to help make web requests and retry as needed.
Add some docs and raise if web requests all fail

We should raise an exception if all attempts at getting some data have failed.
This now does that. In addition, I added a few small docs on exceptions and
classes.
Add first pass at computing nt-nt correspondences

I've added a module that contains logic for computing the nt-nt correspondences.
The basic idea is that we get a PDB, get the representative pdb then align the
sequences of the two structures. We use the longest chain of each for the
alignment. The actual alignment is done in a java program. We access it by
sending a web request. The python code handles figuring out what to align sends
the data and then stores the alignment. This is simply a first pass at the
structure that has some tests to show basic parts seem to work.

Also, there is some sql written as a string. This may not be ideal, but the
reason I'm using it is because sqlalchemy refuses to reflect in views. This is
annoying but injection and the like isn't a risk here as this isn't user facing.
Plus it does escape and such for us. A bit annoying but not the end of the
world.
Make sure we don't return the same pdb as rep

We shouldn't try to correlate to the same PDB as both reference and target, as
that is silly. So we prevent that by never returning it.
Set config in CIFFileFinder