Log Message:

	Update new version
	------------------------------------------------------------------------------
??/??/13  orbeckst, jandom, zhuyi.xue, xdeupi, tyler.je.reddy,
          manuel.nuno.melo, danny.parton, sebastien.buchoux, denniej0,
	  rmcgibbo, richardjgowers, lennardvanderfeltz, alejandro.bernardin

  * 0.8.0

  Enhancements

  * Merge AtomGroups into a new Universe (Issue 157)
  * TPR parser (currently limited to versions 58, 73 and 83 of the
    Gromacs TPR format (Gromacs 4.0 to 4.6.1), see Issue 2)
  * fast XTC seeking (Issue 127)
  * changing resid (set_resid()) or segid (set_segid()) changes the
    topology and lists of resids/segids can be assigned to 
    groups of objects (AtomGroup, ResidueGroup)
  * helanal: additional output of local bend and unit twist angles
    (Issue 133)
  * added support for reading DMS files (DESRES molecular structure)
  * bond connectivity information can be guessed from a PDB file if
    the bond=True keyword is set in Universe (Issue 23)
  * MDAnalysis.analysis.rms.RMSD: calculation of additional RMSDs
  * Plugin to generate nucleic acid helicoidal parameters using X3DNA;
    (must install working version 2.1 of X3DNA independently)
  * can use advanced slicing (with arbitrary lists or arrays) at all
    levels of the hierarchy (Issue 148)
  * coordinate readers and writers can be used as context managers
    with the 'with' statement
  * Can load multiple trajectories as Universe(topology, traj2, traj2,
    ...) in addition to providing all trajectories as a list,
    i.e. Universe(topology, [traj1, traj2, ...])
  * added support for YASP and IBIsCO formats (.trz) (Issue 152)
  * new methods for AtomGroup: packintobox() (only orthorhombic boxes)
  * added non-standard "extended" PDB format (XPDB) that reads
    five-digit residue numbers
  * util.convert_aa_code() recognizes non-standard residue names such
    as HSE, GLUH, GLH, ...
  * added new geometrics selections: sphlayer, sphzone, cylayer, cyzone
  * added TopologyDict and TopologyGroup classes for bond analysis

  Changes

  * dropped support for Python 2.5; minimum requirement is Python 2.6
    (Issue 130)
  * almost all methods of AtomGroup return NumPy arrays
  * slicing and indexing of AtomGroup, Residue, ResidueGroup, Segment,
    SegmentGroup will now always return an appropriate object and
    never a simple list
  * removed Timeseries.principleAxis (probably was never working)
  * dependent on Biopython >= 1.59 (Issue 147)
  * Hydrogen bond analysis defaults to updating selection 1 and 2 for
    every timestep in order to avoid unexpected behavior (Issue 138)

  Fixes

  * fixed incorrect computation of distances in serial and parallel 
    distance_array() with PBC (Issue 151)
  * fixed Issue 129 (hole.py module pipe/file closure)
  * fixed array comparison bug in MDAnalysis.analysis.helanal
    and various enhancements to the helanal module
  * fixed MDAnalysis.analysis.rms.RMSD.run(): gave incorrect results
    if ref_frame != 0
  * alignto() now checks that the two selections describe the same
    atoms (fixes Issue 143)
  * slicing of ResidueGroup will now produce a ResidueGroup, and
    slicing of a SegmentGroup will produce a SegmentGroup, not a list
    as before (fixes Issue 135)
  * detect OpenMP-capable compiler during setup (Issue 145), which should allow
    users of Mac OS X 10.7 and 10.8 to build MDAnalysis using Apple's
    C-compiler (clang) (Issue 142) although they will not get a parallel
    version of distance_array.
  * PDB with blank lines gave IndexError (Issue 158)
 

12/24/12 danny.parton, jandom, orbeckst, jjlights03, jphillips, \ 
naveen.michaudagrawal, andy.somogyi, sebastien.buchoux

  * 0.7.7

  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 https://code.google.com/p/mdanalysis/wiki/netcdf)

06/30/12 orbeckst, joshua.adelman, andy.somogyi, tyler.je.reddy, lukas.grossar, \ 
denniej0, danny.parton

  * 0.7.6 

  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

  * selectAtoms: updated *nucleic* and *nucleicxstal* selection definition
    *nucleic* includes the two-letter NA code that follows gromacs topolgy
    format and *nucleicxstal* allows for the one-letter NA code that follows
    the PDB Database code.
  * 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)