mdtraj/mdtraj 0.8.0 on GitHub

What's New

New parser for AMBER PRMTOP topology files.
Removed dependency on netCDF4 and the c libnetcdf. We're now exclusively using
the pure python NetCDF3 implementation in scipy.io, which is now a dependency.
Removed dependency on simtk.unit as an external package
Fixed a behavior where "default" unit cell dimensions were being saved in trajectories without periodic boundary conditions in XTC, DCD and TRR, which when loaded up later were interpreted as being "real" periodic boundary conditions.
Better ResSeq preservation in HDF5 files.
More detailed repr and str on Trajectory.
Load pdb files directly from a URL.
Unicode fixes for python3.
Bugfixes in OpenMM reporters
New theme for the documentation with IPython notebooks for the examples
Improvements to DCD seek()
Reorganized the internal layout of the code for easier navigation, IPython tab completion.

Thanks to everyone who contributed to this release: Robert T. McGibbon, Kyle A. Beauchamp, Carlos Hernandez, TJ Lane, Gert Kiss, and Matt Harrigan.