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- released 06/01/15
- 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
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