ReleaseNotes072

Release 0.7.2 of MDAnalysis (31 March 2011).

Changes

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

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)

orbeckst, dcaplan, naveen.michaudagrawal