What’s New?

These are new features and improvements of note in each release.

v0.8.0 (March 10, 2014)

  • 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.

v0.7.0 (February 21, 2014)

  • New geometry functions md.compute_contacts and md.geometry.squareform for residue-residue contact maps
  • Fix segfault in md.rmsd when using the optional atom_indices kwarg
  • md.compute_phi, md.compute_psi, and md.compute_omega now return the correct atom indices, as their docstring always said.
  • Topology Element instances are now properly immutable
  • Small bugfixes to baker_hubbard, and better docstring
  • Automatic installation of pandas and simtk.unit via setuptools’ install_requires.
  • Small bugfix to mdcrd loading with stride
  • superpose now correctly translates the final structure, and doesn’t recenter the reference structure

v0.6.1 (February 11, 2014)

  • Trajectory.join(discard_overlapping_frames=True) is criterion for detecting overlapping frames is more realistic
  • We now support installation via conda, and are supplying conda binaries
  • md.load() is much faster when loading multiple trajectory files
  • Bug-fixes for pandas 0.13.0 release, detection of zinc atoms in PDB files
  • Geometry functions are more resilient to segfaults from bad user parameters
  • Fix intermittent RMSD segfaults from invalid memory access
  • Fix RMSD centering bug with memory alignment after restrict_atoms

v0.6.0 (January 21, 2014)

  • md.rmsd() signature changed to be more understandable
  • All file objects now have a __len__ function.
  • Small bugfixes related to vsites.

v0.5.1 (January 4, 2014)

  • Minor bug fix when no dihedrals match specification
  • Add __str__ to Topology parts
  • More examples sections in docstrings

v0.5.0 (January 3, 2014)

  • Numerous bug fixes
  • Much improved coverage of the test suite.
  • Removed cffi dependency for accelerated geometry code
  • Faster multi-trajectory loading
  • MSMBuilder2 LH5 format support
  • Change license from GPL to LGPL
  • More convenience methods on Topology
  • PDB writer writes connect records
  • Hydrogen bond identification with baker_hubbard
  • Rotation/translation to superpose trajectories
  • New RMSD API. It’s much simpler and much more memory efficient
  • Full support for computing all of the chi angles
  • Add seek/tell methods to all of the trajectory file objects
  • New top level memory efficient iterload method for chunked trajectory loading
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