Started on reactions

Laid some of the groundwork for reactions, especially acid_base.
Very weird, very cool metaclassing

I have no idea if this is something I should pursue.  But it is
intriguing enough that I want to keep pursuing it for educational
purposes.
Started working out acids and bases

- Minor changes to metaclassing, dropping it for a while. After sleeping
on it and looking at it again I don't see the point
- More functionality in base_reactions and acid_base, and appropriate
changes to testing
- Realized how hard this next part is going to be
Full isomorphisms

- Missing support for subgraphs and those isomorphisms
- More stuff for reactions
Playing around a bit

I'm still working out the kinks of how I want to set up reactions.  I
foresee myself rewriting reaction stuff many times
File structure

In progress work on how my directory is organized and how to best import
things from within the package
Improving directory structure

- Removed unnecessary sphinx docs
- Restructured directory, imports
- Significant improvements to __init__ files and to runtests.py
Molfiles

- Some more minor fixes to testing
- Laid the foundation for mol file parsing
molfile v2000

Started working on the (older) molfile format
MolV2000 object

- Added functionality to parsing molfiles (v2000) (maybe 70% done?)
- Stuck more closely to the abstraction in runtests (use vars not
__dict__, I should change everything that uses __dict__)
- Improved how main is called
- MolV2000Parser is implemented as a wrapper on MolV2000
- Tests for MolV2000 objects
more molv2000

- reorganized test directory molecules
- fixed unit tests accordingly
- expanded molv2000 capabilities
Spring cleaning

Adding some of my helper functions from python_tools into the parent
directory just so people see where they're coming from.  Using them to
clean up
Working on acid base

- Improved conditions
- Continued working on acid-base reactions
- Started using properties for my trickier setters
Ton of work on acid_base

- Working on a setup script
- Improved how reactions are handled
- Completed (initial) implementation of an acid base reaction
- Start of testing acid-base and helper methods, needs to be much more
comprehensive
Merge pull request #20 from Dannnno/acid_base

Acid base