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v0.1.2.dev2

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@hainm hainm released this 21 Apr 11:40
· 5095 commits to master since this release

what's new

  • add "groupby" method for DataSetList
  • directly access "calc_..." methods from FrameArray and TrajReadOnly (traj.calc_COM, ...)
  • "tolist" in Traj should return 3D list (n_frame, n_atoms, 3)
  • "tolist" of Frame should return 2D list (n_atoms, 3)
  • add "tolist" for DataSet_Vector
  • add "keys()" to DataSetList class. Now we can use this as a list and a dict
  • support Grid calculation (calc_volmap, ...)
  • enhance speed of AtomMask selection (about 5 times faster)
  • add set_error_silent to turn-off (and on) cpptraj' warning
  • add attribute indices for AtomMask object (shorter than selected_indices method's name
  • support loading MDAnalysis objects (Universe)
  • add method load_pseudo_parm to load ParmEd and mdtraj Topology objects
  • fully compat with cpptraj, user can get CpptrajState from trajin.in file
    (pytraj.io.load_cpptraj_file)
  • add to_ndarray for DataSet, Frame, Vec3,... objects
  • introduce memoryview for DataSet
  • fix memory for calculate method
  • add simple wrapper to pysander to be used with pandas' DataFrame
  • add calc_multidihedral for quickly scanning dihedral
  • improve code for AtomMask: add_selected_indices could accept memview
  • add _frame_iter_master to iterate anything that results Frame objects
  • add frame_iter with atom indices (before: only support atom mask): traj(mask=index_array)