ReleaseNotes0100

This is a new minor release of MDAnalysis, which contains a large number of enhancements, changes to the API and a few bug fixes.

CHANGELOG

Improved performance of PDB Reading. Up to 3x faster. (Issue #212)
Added the 'same ... as' selection keyword (Issue #217)
Added guess_bonds keyword argument to Universe creation. This will attempt to guess all topology information on Universe creation. (Issue #245)
Added guess_bonds method to AtomGroup. (Issue #245)
All TopologyObjects (Bond, Angle etc) now have is_guessed attribute
TopologyGroup now has alternate constructor method, .from_indices()
Added TopologyObject.indices property
Amber netCDF4 Reader will now read Forces (Issue #257)
Amber netCDF4 Writer will now write Velocities and Forces
Added Amber coordinate/restart file reader (Issue #262)
Structural superpositions (MDAnalysis.analysis.align) can work with partial matches of atoms.
new path similarity analysis module MDAnalysis.analysis.psa
AtomGroup and TopologyGroup can now be indexed by numpy boolean arrays works identically to numpy masks. (Issue #282)

TopologyGroup can now have zero length, and will evaluate to False when empty.
Renamed TopologyGroup.dump_contents to "to_indices"
Deprecated 'bonds' keyword from Universe and replaced with 'guess_bonds'
PrimitivePDBReader now requires the numatoms keyword
Structural superpositions (MDAnalysis.analysis.align) use partial matches of atoms by default (use strict=True for old behavior)
Function rmsd() was removed from MDAnalysis.analysis.align name space and should be accessed as MDAnalysis.analysis.rms.rmsd()

bynum selections now work from AtomGroup instances (Issue #275)
Cylinder selections now work from AtomGroup instances and honor PBC (Issue #274)
NetCDFWriter previously always wrote velocities/forces if found in timestep, rather than following how the Writer was created.

richardjgowers, caio s. souza, manuel.nuno.melo, orbeckst, sseyler