What’s New

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

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 overlappign 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
  • Bugfixes for pandas 0.13.0 release, detection of zinc atoms in PDB files
  • Geometry functions are more resiliant 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
Versions