ReleaseNotes0100

Oliver Beckstein edited this page Jul 9, 2015 · 1 revision

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

  • 0.10.0
  • released 06/01/15

Enhancements

  • 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)

Changes

  • 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()

Fixes

  • 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.

Authors

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

Project Information

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GNU GPL v2 code license
Labels: python, molecular dynamics, analysis, DCD, CHARMM, LAMMPS, NAMD, Gromacs, computer simulation, atoms, coordinates, trajectory, XTC, Library, object-oriented
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