ReleaseNotes0120

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

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).

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