Lots of comments
Added new c++ and python classes to measure distances in periodic boundary conditions during NEB runs. Added a mindist class for periodic rigid body systems (not yet complete).
New system class for OTP molecules with periodic boundary conditions.
Updated test routine
More updated tests
More updates to test routines, including alignment tests and structure visualisation (ongoing)
More updates to testing and visualisation
Edited testing routines and trying to fix rigid periodic mindist class
Experimenting with periodic get_dist routine
Tidied up testing and mindist classes, checked that they work and removed unnecessary comments
Tidying periodic_exact_match.py
Tidy minpermdist_stochastic.py
Added a method for passing in a (single) configuration from a file
Merge branch 'master' into periodic_boundaries

Conflicts:
	pele/angleaxis/_otp_cluster.py
	pele/angleaxis/aamindist.py
	pele/angleaxis/aasystem.py
	pele/angleaxis/aatopology.py
	pele/angleaxis/rigidbody.py
	pele/mindist/minpermdist_stochastic.py
	pele/mindist/periodic_exact_match.py
	pele/utils/rbtools.py
Merge branch 'periodic_boundaries' of https://github.com/sniblett402/pele into periodic_boundaries

Conflicts:
	pele/mindist/periodic_exact_match.py
refactor aatopology.h to deal with periodic bounds

RigidFragment now accepts another paramter

std::shared_ptr<DistanceInterface> distance_function

Both CartesianDistanceWrapper and PeriodicDistanceWrapper inherit from
DistanceInterface, so either of those can be used as the distance
function.

I could have done it by templating RigidFragment, which would have been
faster, but the code ends up simpler using interfaces.  The distance
function is called over and over again, so the loss of speed may end up
being a problem.  I think it will be fine, but we should user profiling
to test for sure.
fix bug where array_wrap_np was ignoring exceptions

I forgot to add except * to the end of the cdef function.  This is
needed because the cdef function returns a pure c object.
add periodic distances to _cpp_aa.pyx
Moved the rigid-body measure, transform and mindist functions to new files in more logical locations, and improved the documentation for all the new functions
Merge branch 'periodic_boundaries' of https://github.com/sniblett402/pele into periodic_boundaries