ReleaseNotes076

CHANGELOG

Enhancements

GRO file velocities may be accessed as AtomGroup.velocities() or Atom.velocity (Issue 102)
PrimitivePDBReader can be sliced
AMBER NetCDF (binary trajectory) reader and writer, supporting coordinates and velocities; requires netcdf4-python (Issue 109)
additional attributes and methods for AtomGroup to consolidate the interface to the Timestep: attribute 'positions' and 'get_positions()' can be used instead of the 'coordinates()' method. get/set methods for both positions and velocities.
almost all Readers now support some form of slicing; unsupported slicing operations will raise a TypeError
additional analysis for Nucleic Acid order parameters (MDAnalysis.analysis.nuclinfo)
AMBER TOPParser now able to do both amber10 and amber12 formats (Issue 100)

Changes

HydrogenBondAnalysis: multiple enhancements and changes (Issue 103)
- many new analysis functions (see docs)
- run() does not return the results anymore; results are simply stored as attribute timeseries (similar to other analysis tools)
- only write per-frame debugging messages to the logfile when the new verbose keyword is set to True
- more reliable detection of hydrogens bonded to heavy atoms
- remove duplicate hydrogen bonds from the output
removed CHO and EAM (formyl and ethanol termini of gA in CHARMM) from the set of residues recognized as protein (collision with commonly used CHO for cholesterol)
PrimitivePDBWriter: special segid SYSTEM is translated to empty chainID
In order to write multi frame PDB files, the multiframe=True keyword must be supplied or use the MultiPDBWriter
empty AtomGroup can be constructed or can result from a selection without matches; it does not raise NoDataError anymore (Issue 12)
all single frame readers denote the first (and only) frame as frame number 1 (i.e. ts.frame == 1); it used to be 0 but 1 is consistent with the way this is is handled with real trajectories
requires Biopython >= 1.51 (fixes for Issue 112 and Issue 113)
Atom.type is always stored as a string.

Fixes

HydrogenBondAnalysis: NH1 and NH2 were not recognized
GROWriter: enforce maximum resname and atomname length of 5 chars
Universe.load_new() raised a NameError (thanks to JiyongPark.77)
fixed Issue 105 (trajectory snapshots could not be written to PDB)
fixed Issue 107 (NAMD/VMD space delimited PSF files can be autodetected and read); important when using CGENFF atom types (thanks to JiyongPark.77 for initial patch)
fixed Issue 101 (could not write single frame to trr file)
fixed: permissive=True flag was ignored in Universe and hence the PrimitivePDBReader was always selected even if the Biopython one was desired
fixed Issue 112 (used removed Biopython constructs in MDAnalysis.analysis.align.fasta2select; thanks to francesco.oteri for a test case and fix)
fixed failing 'type' selection for topology formats that read an atom type as an integer (such as the AMBER parser)
fixed Issue 111 (NAN in pycpqrot and RMSD calculation)
fixed Issue 113 (replaced outdated Biopython to call ClustalW)

orbeckst, joshua.adelman, andy.somogyi, tyler.je.reddy, lukas.grossar, denniej0