ReleaseNotes075

Changes

0.7.5 release date: 02/11/12

MDAnalysis can now be found on PyPI (MDAnalysis), allowing simple installation from the internet. Metadata was added to setup to facilitate PyPI upload and pages on the wiki describe how to do this. In addition, Debian/Ubuntu packages are also available.

Note that in order to run UnitTests one needs the separate package MDAnalysisTests (with the same release number 0.7.5).

Enhancements

• new method OtherWriter() for trajectory readers to generate a writer for any format that has been initialised for the common basic values
• new simple Residue.chi1_selection() selection
• new distances.between() function (EXPERIMENTAL)
• support LAMMPS non-standard DCD files (Issue 84; EXPERIMENTAL)
• read and write multi-frame PDB files (Issue 77; EXPERIMENTAL)
• extend the PDB parsing, support CONECT and REMARK entries
• new GNM-based trajectory analysis module (Issue 90)
• Read/Write velocities with TRR, new attribute Atom.velocity and AtomGroup.velocities() (Issue 91)
• hydrogen bond analysis detects a range of GLYCAM atom types and utils.convert_aa_code will also accept GLYCAM-style residue names (Issue 92)
• XYZ reader: can set timestep (Issue 92)

Changes

• The UnitTests are now integrated with the separate test data in a separate Python package named MDAnalysisTests; to run the tests for 0.7.5 one will need MDAnalysisTests-0.7.5 (Issue 87).
• install a range of analysis dependencies right away: networkx, biopython, GridDataFormats (usually all painless); leave scipy and matplotlib to the user and the local package manager
• When writing a trajectory and converting units, effectively a copy of the timestep is made and the in-memory timestep is not altered. In his way, analysis after writing a frame will still see the coordinates in MDAnalysis units and not converted units.

Fixes

• analysis.align.rms_fit_traj(): can output fitted trajectory to any supported format not just the input format
• fixed ProgressMeter: default format string was broken
• fixed: ResidueGroup and SegmentGroup indexing (did not work with numpy.int64 etc) and now raise TypeError if it does not fit
• fixed HydrogenBondingAnalysis backbone donor list: had C but should have been O (this was supposed to be fixed with r849 in 0.7.4 but a typo crept in). NOTE: analysis might have produced partially wrong results.
• fixed: dihedral() and other methods using core.util.angle() sometimes returned nan instead of +pi or -pi
• fixed: writing a trajectory from chained CRD files gave garbage coordinates (Issue 81)
• fixed: support files for docs are now in included in the source distribution (thanks to Sebastien Buchoux; Issue 82)
• fixed: core.util.iterable() would wrongly detect unicode strings as "iterable"; this lead the Reader autodections and then the ChainReader fail with "Runtime Error: Maximum recursion depth exceeded" for single filenames provided as a unicode string.
• fixed: HBond analysis pickling of tables (Issue 92)

Authors

orbeckst, sebastien.buchoux, jandom, hallben, lukasgrossar