ReleaseNotes0150

Richard Gowers edited this page May 16, 2016 · 1 revision

MDAnalysis 0.15.0 is a new release with many new features and fixes; see also the blog post.

  • release: 0.15.0
  • release date: 05/15/16

CHANGELOG

Metadata

  • link download_url to GitHub releases so that Depsy recognizes contributors (issue #749)
  • a version variable is now exposed; it is built by setup.py from the AUTHORS file (Issue #784)

API Changes

  • rmsd doesn't superimpose by default anymore. The superposition is controlled by the 'superposition' keyword now. (see issue #562, #822)

Enhancements

  • Add conda build scripts (Issue #608)
  • Added read-only property giving Universe init kwargs (Issue #292)
  • Added 'crdbox' as AMBER Trj format extension (Issue #846)
  • Iteration and seeking in PDB files made faster (Issue #848)

Fixes

  • ENT file format added to PDB Readers/Writers/Parsers (Issue #834)
  • rmsd now returns proper value when given array of weights (Issue #814)
  • change_release now finds number and dev (Issue #776)
  • units.py now correctly prints errors for unknown units.
  • test_shear_from_matrix doesn't fail for MKL builds anymore (Issue #757)
  • HEADER and TITLE now appear just once in the PDB. (Issue #741) (PR #761)
  • MOL2 files without substructure section can now be read (Issue #816)
  • MOL2 files can be written without substructure section (Issue #816)
  • GRO files with an incomplete set of velocities can now be read (Issue #820)
  • Fixed Atom.position/velocity/force returning a view onto Timestep array (Issue #755)
  • PDB files can now read a CRYST entry if it happens before model headers (Issue #849)
  • Fixed HistoryReader returning 1 based frame indices (Issue #851)

Changes

  • Added zero_based indices for HBondsAnalysis. (Issue #807)
  • Generalized contact analysis class Contacts added. (Issue #702)
  • Removed Bio.PDBParser and sloppy structure builder and all of MDAnalysis.coordinates.pdb (Issue #777)
  • PDB parsers/readers/writers replaced by "permissive"/"primitive" counterparts (formerly known as PrimitivePDBReader); the 'permissive' keyword for Universe is now ignored and only the native MDAnalysis PDBReader is being used (Issue #777)
  • PDBReader only opens a single file handle in its lifetime, previously opened & closed handle each frame (Issue #850)

Deprecations (Issue #599)

  • Use of PrimitivePDBReader/Writer/Parser deprecated in favor of PDBReader/ Writer/Parser (Issue #777)
  • Deprecated all get_* and set_* methods of Groups.
  • Deprecation warnings for accessing atom attributes from Residue, ResidueGroup, Segment, SegmentGroup. Will not be present or will give per-level results.
  • Deprecation warnings for accessing plural residue attributes from Residue or Segment (will disappear), or from SegmentGroup (will give per-Segment results).
  • Deprecation warnings for accessing plural segment attributes from Segment (will disappear).
  • Deprecated Atom number, pos, centroid, universe setter
  • Deprecated AtomGroup serials, write_selection
  • Deprecated Residue name, id
  • Deprecated Segment id, name
  • Deprecated as_Universe function; not needed
  • Deprecated ContactAnalysis and ContactAnalysis1 classes

Authors

jandom, abhinavgupta94, orbeckst, kain88-de, hainm, jbarnoud, dotsdl, richardjgowers, BartBruininks, jdetle

Project Information

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