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@hainm hainm released this 26 May 14:18
· 4196 commits to master since this release
v0.1.2.dev4
86d1a87

What's new?

  • add pretty print for DataSetList when having pandas
  • enhance speed for frame_iter and chunk_iter
  • add 'merge_traj'
  • add apply method to change traj's internal data
  • add basic math for Trajectory
  • add XYZ class as a simple wrapper for numpy ndarray
    traj.xyz is no longer ndarray, just a read-only wrapper
  • add TrajectoryMDAnalysisIterator
  • add read_data for DataFile and DataSetList
  • add frame swap for Trajectory
  • add atom coords assignment traj['@ca'] = xyz
  • add stack for DataSetList to join 2 datasets
  • rename set_frame_m to set_frame_mass
  • update to_amber_mask to convert integer array-like to string mask
  • add autoimage and rmsfit_to for chunk_iter and frame_iter
  • tune speed for chunk_iter and frame_iter for TrajectoryIterator
  • add plot method for DataSet
  • add write_to_cpptraj_format
  • add array for Frame
  • introduce array interface to numpy for cpptraj's DataSet
  • add median, std, ... for DataSetList
  • update run_all_and_find_fails.py for capturing segmetation fault
  • add Trajectory joining (traj += traj)
  • optimize slicing for TrajectoryIterator
  • optimize strip_atoms (1000 times speed up)
  • add copy method for DataSet
  • add fancy indexing for DataSetList
  • add _fast_slice for Trajectory (1000 times faster)
  • add regular expression for groupby
  • add to_pickle, to_json, read_pickle, read_json
  • add _guess_filetype
  • change fit_to to rmsfit_to
  • enhance smart _frame_iter_master
  • create alias rmsd for calc_rmsd in common_actions module
  • update loading hd5f file without going through mdtraj
  • correctly handle box in api.Trajectory
  • add TrajectoryREMDIterator class to handal REMD
  • change io.load_remd_iterator to io.iterload_remd
  • add io._iterload_from_filelist and io._load_from_filelist
  • add count for DataSet_integer
  • API CHANGE (05-06-2015):
    • change FrameArray to Trajectory
    • change TrajReadOnly to TrajectoryIterator (issue #262)
      (#262)
    • io.load will return Trajectory instead of TrajectoryIterator
    • io.iterload will return TrajectoryIterator
  • add "legend" as property of DataSet
  • remove "get_box" from Frame. use "box"
  • support autoimage when loading mdtraj object
  • bugfix for io.loadpdb_rcsb
  • add 'calc_rdf'
  • trick to add reference to Action
    • Example: calc_abcxyz([[ref,], traj], command), where ref is a Frame object, abcxyz is a specific action.
  • add option to load coords from ParmEd object
  • add align_principal_axis
  • fix iteration in api.Trajectory: 2 orders of magniture faster
  • add "as_ndmatrix" for Matrix_3x3
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