Document and throw more exceptions.

We throw some exceptions if we can't find sequence or 2D locations when parsing
the postscript.
Remove BioPython as a testing dependecy.

That was just lazyness and it's not a good idea to have BioPython required for
one silly function in testing.
Update README
Outline the align module

This is a module to generate alignments and their correlations. This introduces
a dependency on BioPython. This has not yet been tested but is the general
format and documentation that this package will contain.
Outline a simple Sequence object.

The sequence object is just a simple way to have a string that has a names
property. Names is useful for associating ids with the characters in a sequence.
Add first tox.ini
Ignore files added by tox
Have long_description be a string

It was causing problems for tox to have long_description be read from the
readme.
SSL work around for python 2.5
Add tox task
Add methods to get first and last nt in a polymer

These are simple convience methods, but they are useful when we only care about
the location of the chain breaks.
Reorder so we use _count after it is defined

Some tests were failing because I did not define _count before trying to use
it.
Limit number of pythons we test on
Make tests a module

This makes it easier to run tests with nose as it likes looking for test
packages. The reorganization is pretty simple, the only big thing was moving
the test files out of test and into files.
Fix UNAfold failures

UNAfold was failing because I was not matching against the files correctly.
This corrects that. I've also added a case to test if there are any matched
files, if not it assumes folding failed somehow. I don't know how to trick the
program into doing that but it is a good check for the future.
Clean up some warnings
Remove Mfold folder

Mfold is no longer suggested for usage. The suggested program is UNAfold. I
remove mfold from the folders class because we should not be using it. If
needed I can add it back, but I don't see the point of maintaining code that
shouldn't be run.
Limit envs to 2.5 and 2.7

I'll work on comptability with python 3 once I no longer have to deal with 2.5.
In addition, pypy was complaning about virtualenv or something. It's not
important right now so I'll deal with that later.
Increase 2.5 compatibility

This is now sort of compatible with python 2.5. The one thing limiting this is
mutable sequence. I should change results set to not need this as it is just
for convenience. However, tox will still fail because I can't get it to install
the pdbx package from github which is needed for the cif file wrappers. I
should ask if pdb is going to release that as a package, which would make
things a lot easier.
Version bump