Update ignore
Improved polymer detection

This way we find polymers by using the pdbx_unobs data which tells which
polymers are not observed. This is better than trying to infer it as I was
before. In addition, I've added several classes to represent things like models,
chains, and residues. This improves the design by allowing us to iterate over
parts of the structure to find polymers and generate unit ids.
Add residue/polymer methods

Add methods to look up a residue or polymer by index. This is useful, but
currently requires iterating over all polymers/residues each time. This is not
good and will be fixed later by memoizing the list of residues/polymers.
Correct mistakes in tests
Remove bad test and fix failing one

We now have mostly replicated the previous behavior. We don't have code to get
the resolved sequence without breaks yet, but that should be easy enough with
chaining iterators.
Add some quick code to process R3D Align output

R3DAlign doesn't yet generate unit ids. Until it does I've added this quick
barely tested code to convert the basepair correlation csv to a nt to nt
correlation list. Very simple and not very tested.
Add test file
Add tests for generating unit ids correctly

I didn't test for insertion codes and the like to make sure that we generated
the unit ids correctly. This commit fixes that by adding such code. In addition,
I change the UnitIdGenerator so that it can deal with None in the object it is
given. Before it would try to add it to the id, which is not good.
Make separate module for unit ids

Unit ids are important enough to need their own module. I've moved the generator
into it. In adddtion I've added a class to parse them as well as utility
functions to generate and parse r3d align style matlab ids to and from unit ids.
This should prove useful.
Improve unit_ids module

The unit_ids module now contains code for generating and parsing three different
style of ids, Nucleotide, Unit and Matlab. I have written tests for the
Generators of all three. The parsers are still untested. In addition, I have
code for creating a converting function, as this is something simple that we do.
Fix problems with stored properties

Properties was not instance specific for GenericMapping. This caused problems in
generating the unit ids. In addition, I've added some methods for getting the
first and last residue as well as simplifying the logic of generating the
residues.
Simplify some code
Add wrapper for SVG's produced by rnaplot

I now have a way to parse the svg files produced by RNAplot. This will prove
helpful when I finish the wrapper for RNAplot. In addition, I made changes to
make it easier to wrap RNAplot. That program does not read a file as input, but
instead reads from stdin. To deal with that I've altered the wrapper class to
support this. In addition, I renamed some of the methods for clarity and used
abc to make it clearer what has to be overridden to create a new wrapper.
Make some allowances for programs that read stdin

Somethings will read from standard in. In this case we need functions which
generate stdin and the like. We add some code that allows that.
Begin wrapper for rnaplot