Fix superclass call
Add function to setup logging

We need to do some more complicated things when logging so it's easier to have a
nice setup function for them.
Use logging function and refactor running

We should run each stage within a try expect and then log as needed. This way we
never write to standard out when we should be logging exceptions to a file.
Also, no errors bubble up to the top this way.
Improvements to core

It is better to define a logger property for core. This means we can set it's
name to be the name of the stage we are running. This way the logging messages
are clear as to what is happening. Though this does obscure the source of the
error, which may prove to be an issue for people unfamiliar with the structure.
However, it does make it much easier for someone who is familiar to the
structure to know what stage is running and what has failed.

Also, we change transform to provide a list. This lets me improve the logging
messages to include things like how far along the process we are. This is
very useful when watching the pipeline.

Finally, I add skip exceptions. These allow a stage to skip parts when needed.
This is meant to be used when we have run into an error condition that prevents
the stage from continuing with this specific input but we still want to keep
going. For example we may require nt level data on a stage, but we haven't
imported it for a particular PDB. In this case we should no longer process the
PDB but keep trying with the rest of the PDBs. There are two types of skip
exceptions, SkipPdb which skips an entire PDB and SkipValue which skips only a
single transformed value for a PDB.
Make downloader extend core.Loader

The generic Loader is a pretty good framework for all stages including
downloading. This alters download to use the generic framework.
Remove unneeded and unused file
Add a stage to compute the summary interactions

For the wire's 2014 paper we computed helix to loop interactions. We decided
this was a useful thing to compute and have added it as part of the pipeline. We
can now compute this data for all structures.
Update utils