ReleaseNotes0120

Richard Gowers edited this page Oct 10, 2015 · 2 revisions

Highlights

  • Sean Seyler's Path Similarity analysis module got many more features. Check out the tutorial
  • Parsing of TPR files was vastly improved, including supporting v5.0+ of Gromacs thanks to Jonathan Barnoud
  • The installation process has been improved, any various minor annoyances removed, credit to Max Linke

CHANGELOG

API Changes

  • PrimitivePDBReader now imports occupancies into the TimeStep object. (Issue #396)
  • Atoms without a Universe now return NoDataError instead of AttributeError
  • AtomGroups of zero length or containing Atoms with no Universe raise a NoDataError when trying to access Universe
  • Atoms now keep a strong reference to Universe, meaning they do not become orphaned when the Universe goes out of scope (Issue #297)

Enhancements

  • Atom and AtomGroup now expose occupancy value as occupancy and occupancies properties (Issue #396)
  • XYZReader now supports frame indexing (Issue #428)
  • Reader objects can now be sliced using lists and arrays of indices (Issue #437)
  • PSAnalysis now includes Hausdorff pairs analysis and associated nearest neighbor plotting method (Issue #438)
  • New class PSAPair added to MDAnalysis.analysis.psa for handling Hausdorff pairs analysis (Issue #438)
  • PSAnalysis can now generate annotated heat maps (Issue #438)
  • Added three new distance functions to MDAnalysis.analysis.psa (Issue #438)
  • Additional getters added to Path and PSAnalysis (Issue #438)
  • MSD matrix function now globally available in MDAnalysis.analysis.psa (Issue #438)
  • Function for obtaining coordinate axes from numpy trajectories now globally available in MDAnalysis.analysis.psa (Issue #438)
  • TPR parser updated for Gromacs 5.0.x and 5.1 (Issue #456)
  • Setup.py now looks for some configuration values in a config file. Each config option can also be changed via environment variables if they are prefixed with 'MDA_'. Current options are 'use_cython', 'use_openmp', 'debug_cflags'

Changes

  • An AtomGroup with 0 atoms now yields an IndexError on call to AtomGroup.write (Issue #434)
  • PSA changed to PSAnalysis to reduce namespace clutter (Issue #438)
  • To build with debug-symbols use 'MDA_DEBUG_CFLAGS' instead of 'MDA_DEBUG_CFLAGS'

Fixes

  • Fixed minor issue in lib.mdamath.make_whole where if all bonds were correctly sized, it wouldn't notice that multiple fragments had been given. (Issue #445)
  • Fixed issue with PDB Topology parsing where if serials went over 100k, they wrapped to '***', breaking the parser (Issue #446)
  • Fixed AtomGroup.sequence() (Issue #451)
  • Fixed PrimitivePDBParser not detecting when resids had looped over 10,000. The original resid is stored as Atom.resnum (Issue #454)
  • Fixed TPR topology parser to treat all bonded interactions available in Gromacs 5.1 (Issue #222 and #352, pull request #463).

AUTHORS

kain88-de, richardjgowers, dotsdl, sseyler, orbeckst, jbarnoud

Project Information

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

Essentials

Applications
Downloads
Install
Release Notes
Guide for Developers
Google Summer of Code

Code of Conduct

Links

@mdanalysis on Twitter
Documentation
Tutorials
Downloads (PyPi)
Mailing Lists:
User discussion group
Developer mailing list

Clone this wiki locally
You can’t perform that action at this time.
You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session.
Press h to open a hovercard with more details.