ReleaseNotes072

Oliver Beckstein edited this page Sep 26, 2015 · 4 revisions

Release 0.7.2 of MDAnalysis (31 March 2011).

Changes

  • Release 0.7.2
  • NOTE: minimum Python version required is 2.5 (since 0.6.3)

Enhancements

  • loading from a PDB sets segid to the chain id if it exists
  • PrimitivePDBWriter uses first letter of segid as PDB chain id
  • aliased segment.name to segment.id
  • new method AtomGroup.bbox() that returns the orthorhombic bounding box
  • enhancements of the analysis.density module (build density from B-factors with density_from_PDB)
  • PQR radius is now an attribute of Atom; AtomGroup.radii() returns the radii as a NumPy array; internally B-factor has also become an attribute of each Atom.
  • recognise many more OPLS/AA and Amber residue names as "protein"
  • recognise more atom masses (taken from CHARMM27 and Gromacs) and atom types (from CHARMM, Amber, OPLS, GROMOS) and moved masses and types into new module topology.tables; the type recognition is still incomplete but can be easily enhanced in tables
  • analysis.align: convenience functions rotation_matrix() and alignto()
  • TrajectoryReader gained Writer() method which returns an appropriate TrajectoryWriter instance that can be used for processing this trajectory (enhancement of the Trajectory API); if no Writer is known then a NotImplementedError is raised
  • doc improvements

Fixes

  • installation: removed dependency on Cython; developer should use setup_developer.py instead of setup.py (Issue 66)
  • Fixed a problem with the strict PDBReader: raised exception when the pdb did not contain a segid
  • Support for PDBs with 4 character resnames and segID output when writing (Issue 63) --- makes the (default) PrimitivePDBReader/Writer more suitable for NAMD/CHARMM but breaks strict PDB standard. If you need full PDB reading capabilities, use the strict PDBReader (i.e. use Universe(..., permissive=False)).
  • fixed bug in (experimental) phi and psi selections
  • fixed bugs in reading of unit cells (Issue 60, Issue 61, Issue 34)
  • universe.trajectory.delta returns the full precision dt value instead of a value rounded to 4 decimals (Issue 64)
  • fixed bug in DCDWriter (XTC->DCD was broken, Issue 59)

Authors

orbeckst, dcaplan, naveen.michaudagrawal

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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