ReleaseNotes0130

CHANGELOG

API Changes

• ChainReader delta keyword deprecated in favor of dt. (Issue #522)
• XYZWriter can now be used as a container format for different protein models as well as a normal trajectory. If n_atoms is None (default) MDAnalysis assumes that it is used as a container and won't give a warning if the number of atoms differs between frames.
• GROWriter.fmt strings updated to use format style (Issue #494)
• removed MDAnalysis.lib.parallel.distances; use the new backend="OpenMP" keyword for the functions in MDAnalysis.lib.distances (Issue #530)

Enhancement

• ChainReader now reports times properly summed over sub-readers (Issue #522)
• GRO file reading approximately 50% faster for large files (Issue #212)
• GRO file writing now will write velocities where possible (Issue #494)
• Added bonded selection (Issue #362)
• Spherical layer and spherical zone selections now much faster (Issue #362)
• new keyword "backend" for accelerated functions in MDAnalysis.lib.distances to select "serial" or "OpenMP"-enabled versions of the code; the default is "serial" so old code will behave as before (see Issue #530)
• Lammps data file parsing improved greatly. Should now support all files, and triclinic geometry. (Issue #139)
• Added analysis.polymer, currently with PersistenceLength tool (Issue #460)
• Added analysis.rdf, with InterRDF tool. (Issue #460)
• Made Reader.check_slice_indices a public method (Issue #604)
• analysis.helanal.helanal_main() now returns results as dict
• Added keyword to update selection every frame in density calculation (Issue #584)
• New keywords start, stop, step for density.density_from_Universe() to slice a trajectory.
• MOL2Reader now reads molecule and substructure into ts.data
• All subclasses of ProtoReader, Writer and TopologyReader are automatically added to the MDAnalysis directory of I/O (Issue #431)

Changes

• built html doc files are no longer version controlled (Issue #491)
• The lib._distances and lib_distances_openmp libraries now have a OPENMP_ENABLED boolean flag which indicates if openmp was used in compilation. (Issue #530)
• analysis.helanal.helanal_trajectory() and helanal_main() now use a logger at level INFO to output all their computed values instead of printing to stdout
• default offset for ProgressMeter was changed from 0 to 1 (to match the change from 1- to 0-based ts.frame counting)
• removed superfluous analysis.density.density_from_trajectory(); use density_from_Universe(TOPOL, TRAJ) instead.
• MOL2Writer.write now only writes a single frame (Issue #521)

Fixes

• Fixed select_atoms requiring a trajectory be loaded (Issue #270)
• AtomGroup timesteps no longer cached (Issue #606)
• GROWriter now truncates atom numbers over 99999 (Issue #550)
• AMBER netcdf writer now correctly uses float32 precision (Issue #518)
• Fixed a numpy incompatibility in analysis.leaflet.LeafletFinder. (Issue #533)
• Cleaned up MDAnalysis.Writer docs regarding dt usage. (Issue #522)
• Fixed setup-time dependency on numpy that broke pip installs. (Issue #479)
• Fixed unpickling errors due to lingering dead universes. (Issue #487)
• Fixed analysis.density modules requiring the defunct skip attribute on trajectories. (Issue #489)
• ten2eleven camelcase fixer now deals with centerOfMass (Issue #470)
• ten2eleven will now convert numatoms to n_atoms argument for writer() functions (Issue #470)
• Fixed non-compliant Amber NCDFWriter (Issue #488)
• Fixed many Timestep methods failing when positions weren't present (Issue #512)
• Fixed PointSelection using KDTree (Issue #362)
• Fixed GROParser getting tripped up by some file (Issue #548)
• Fixed writing dx files from analysis.density.density_from_Universe() (Issue #544 and #410)
• Fixed base.Reader._check_slice_indices not liking numpy ints (Issue #604)
• Fixed broken analysis.helanal.helanal_trajectory() and helanal_main()
• Fixed lib.util.greedy_splitext() (now returns full path)
• Fixed MOL2Reader not reading molecule and substructure on init (Issue #521)
• Fixed MOL2Writer rereading frames when writing them (Issue #521)
• Fixed PDBWriter not writing occupancies from atoms (Issue #620)

AUTHORS

tyler.je.reddy, kain88-de, richardjgowers, manuel.nuno.melo, orbeckst, Balasubra