ReleaseNotes0130

Richard Gowers edited this page Jan 17, 2016 · 1 revision

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

Project Information

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GNU GPL v2 code license
Labels: python, molecular dynamics, analysis, DCD, CHARMM, LAMMPS, NAMD, Gromacs, computer simulation, atoms, coordinates, trajectory, XTC, Library, object-oriented
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