ReleaseNotes081

This is a major new release of MDAnalysis, more than 1 year after 0.7.7. In addition to bug fixes it contains many new features (such as improvements in handling Gromacs data such as a fast random access trajectory reader and TPR reading capability), new analysis modules, and it introduces the MDAnalysis.visualization module, which collects code aiding in visualizing MD data.

There are a number of potentially backwards-incompatible changes, including a minimum requirement for Python 2.6 and some methods have become managed attributes.

From this release onwards, source code distributions are exclusively hosted on the Python Package index at https://pypi.python.org/pypi/MDAnalysis and pre-built packages for a range of distributions can be found at http://download.opensuse.org/repositories/home:/MDyNMR-FTW:/MDAnalysis/

CHANGELOG

• 0.8.1
• released 1 April, 2014

(Note that we effectively skipped 0.8.0.)

Enhancements

• Named selections can now be passed to selectAtoms (Issue 174)
• (experimental) MDAnalysis.visualization namespace added along with 2D/3D streamplot modules & documentation for them
• TRR file handling is now fully aware of missing coordinate/velocity/force information when reading and writing frames.
• MDAnalysis.analysis.contacts.ContactAnalysis1 run() method now allows trajectory slicing (Issue 161)
• 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([inplace=True])
• 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
• added calc_bonds, calc_angles and calc_torsions cython functions to core.distances for quickly calculating bond information
• added applyPBC(coords, box) function to core.distances to move coordinates to within the primary unit cell
• many AtomGroup methods now support 'pbc' flag to move atoms to within primary unitcell before calculation. This behaviour can also be toggled using the core.flags['use_pbc'] flag (Issue 156)
• MDAnalysis.analysis.rms.rmsd(): new center keyword so that one can immediately calculate the minimum rmsd of two rigid-body superimposed structures

Changes

• libxdrfile2 is now used instead of libxdrfile. libxdrfile2 is distributed under GPLv2
• 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)
• AtomGroup.velocities is now a (managed) attribute and not a method anymore: replace 'ag.velocities()' with 'ag.velocities'
• changed the name of the flag 'convert_gromacs_lengths' to 'convert_lengths'

Fixes

• asUniverse now also accepts any instance that inherits from MDAnalysis.Universe (Issue 176)
• fixed XDR writer incorrect use of delta parameter (Issue 154)
• 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)
• fixed AtomGroup.ts Timestep instance not containing all available information (Issue 163)
• fixed Timestep copy method returning a base Timestep rather than appropriate format (Issue 164)

Authors

orbeckst, jandom, zhuyi.xue, xdeupi, tyler.je.reddy, manuel.nuno.melo, danny.parton, sebastien.buchoux, denniej0, rmcgibbo, richardjgowers, lennardvanderfeltz, bernardin.alejandro, matthieu.chavent