Added traj.select_atoms()
Updated test to account for atom reindexing behavior
Fix bonds and changed name
Moved restrict() to topology, added test for number of bonds after restriction
Merge pull request #55 from kyleabeauchamp/restrict_atoms

Added traj.select_atoms()
change the way the topology is saved in the hdf5 files
small change to hdf5 reporter to supress a useless warning
Merge branch 'master' of github.com:rmcgibbo/mdtraj
Merge pull request #57 from rmcgibbo/hdf5topology

Change the way the topology is saved in the hdf5 files
changed the test to show the breakage -- suppling a report interval other than 1 in the test suite
fixed issue
Merge pull request #59 from rmcgibbo/reportinterval

reportInterval isn't supposed to be a bool. Fix for issue #58