ReleaseNotes061

Oliver Beckstein edited this page Sep 26, 2015 · 4 revisions

Availability

You can download the tar ball for the MDAnalysis 0.6.1 from MDAnalysis-0.6.1.tar.gz or check out

svn checkout http://mdanalysis.googlecode.com/svn/branches/release-0-6-1 mdanalysis-0.6.1

Major additions

It is now possible to read Gromacs xtc and trr trajectories using the native Gromacs xdrfile library (included). You can provide a pdb file instead of a psf to define the atoms (although this does not generate the bonds yet).

There are also test cases included for automated unit tests. The test trajectories were taken from one of our recent papers (see docs for details). This makes the tar ball much bigger than before (16 MiB) but allows you to check the functionality by doing

import MDAnalysis.tests
MDAnalysis.tests.test()

(In later releases we will add additional test cases and possibly factor the testing framework out of the standard package.)

Changes

CHANGELOG

  • 0.6.1 release
  • can build a simple Universe from a PDB file (FIXES Issue 11)
  • can read Gromacs XTC and TRR files (FIXES Issue 1) but no Timeseries or Collections yet for those formats
  • removed Universe.load_new_dcd() and Universe.load_new_pdb() --- use the generic Universe.load_new() (MIGHT BREAK OLD CODE)
  • removed deprecated Universe._dcd attribute (MIGHT BREAK OLD CODE)
  • FIXED bug in PDB.PDBWriter and CRD.CRDWriter
  • use SloppyPDB in order to cope with large PDB files
  • core.distances.self_distance_array() is now behaving the same way as distance_array()
  • defined Trajectory API (see MDAnalysis/coordinates/__init__.py)
  • renamed _dcdtest to dcdtimeseries (will not affect old code)
  • unit tests added (still need more test cases)

Source code

We are also changing the develop workflow. From now on, most of the development will be done on the svn trunk so in order to follow development so please do not use /svn/branches/development-UNSTABLE-orbeckst anymore but simply do a

svn checkout http://mdanalysis.googlecode.com/svn/trunk/ mdanalysis

(Developers should remove their old mdanalysis directory and do

svn checkout --username USER https://mdanalysis.googlecode.com/svn/trunk/ mdanalysis    

to contribute to the main development line. See also DevelopmentWorkflow )

We'll try to keep the trunk reasonably clean (using unit tests). Releases will be found on /svn/branches from now on.

Please report problems through the Issue Tracker or the mailing list.

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
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