ReleaseNotes077

CHANGELOG

• 0.7.7
• released 24 December, 2012

Enhancements

• multithreaded distance_array() (Issue 80, experimental); see the new core.parallel.distance module
• MDAnalysis.analysis.rms for simple RMSD analysis
• format of input coordinates can be set as (filename, format) tuples (Issue 76)
• new AtomGroup.asphericity() and AtomGroup.shapeParameter() methods to compute shape descriptors.
• access to forces (AtomGroup.forces with get_forces() and set_forces(); the default unit for force is kJ/(mol*A) and it is automatically converted from/to native). Currently, only the TRR Reader/Writer support forces.
• all element masses
• logger reports current version when starting

Fixes

• fixed Issue 115 (GROReader now uses fixed-column width format to read GRO files)
• fixed Issue 116 (Failed to write AMBER netcdf trajectory from AtomGroup)
• fixed Issue 117 (could not write Gromacs XTC/TRR from AMBER netcdf)
• fixed Issue 120 (DCDWriter: wrote wrong unitcell information)
• fixed Issue 121 (PSFParser would fail with IndexError for files without SEGID)
• Issue 122 (made installation of netCDF4 library optional, which means that users of the AMBER netcdf Reader/Writer will have to manually install the library and its dependencies netcdf and HDF5, see the wiki page on netcdf)

Authors

danny.parton, jandom, orbeckst, jjlights03, jphillips, naveen.michaudagrawal, andy.somogyi