Merge pull request #3 from jchodera/alldrugs

Added test for all drugs database (Zdd) from ZINC.  Test currently reveals some possible issues.
Merge pull request #5 from jchodera/master

Fixed some pathnames in `drugs` test.
Added init.py
By default, do not force symmetry upon protons attached to same heavy atom.
Updated adjacency graph calculation to symmetrize.
Added basic logging.
Added logger to test-drugs.py
Use no constraints in test-drugs.py.  Noted this requirement in SystemChecker docstring.
Use no constraints in test-drugs.py.  Noted this requirement in SystemChecker docstring.
Check for zero force constant when comparing harmonic angle forces.
Take care not to divide by zero charge when calculating relative error.
Merge pull request #6 from kyleabeauchamp/fixing_drugs

[WIP] Starting work to fix drugs...
Started adding docstrings and cleaning up.
More docstrings and cleanup for system_checker
Minor fixes.
PEP8
pyflakes, pep8, and docstrings for gafftools.py
Fixed some pyflakes bugs in amber_parser
minor docstring update in amber_parser.py
Major overhaul of test_drugs, now seems to be working with nose.  Major cleanup still required.