ReleaseNotes0150

MDAnalysis 0.15.0 is a new release with many new features and fixes; see also the blog post.

CHANGELOG

link download_url to GitHub releases so that Depsy recognizes contributors (issue #749)
a version variable is now exposed; it is built by setup.py from the AUTHORS file (Issue #784)

rmsd doesn't superimpose by default anymore. The superposition is controlled by the 'superposition' keyword now. (see issue #562, #822)

ENT file format added to PDB Readers/Writers/Parsers (Issue #834)
rmsd now returns proper value when given array of weights (Issue #814)
change_release now finds number and dev (Issue #776)
units.py now correctly prints errors for unknown units.
test_shear_from_matrix doesn't fail for MKL builds anymore (Issue #757)
HEADER and TITLE now appear just once in the PDB. (Issue #741) (PR #761)
MOL2 files without substructure section can now be read (Issue #816)
MOL2 files can be written without substructure section (Issue #816)
GRO files with an incomplete set of velocities can now be read (Issue #820)
Fixed Atom.position/velocity/force returning a view onto Timestep array (Issue #755)
PDB files can now read a CRYST entry if it happens before model headers (Issue #849)
Fixed HistoryReader returning 1 based frame indices (Issue #851)

Added zero_based indices for HBondsAnalysis. (Issue #807)
Generalized contact analysis class Contacts added. (Issue #702)
Removed Bio.PDBParser and sloppy structure builder and all of MDAnalysis.coordinates.pdb (Issue #777)
PDB parsers/readers/writers replaced by "permissive"/"primitive" counterparts (formerly known as PrimitivePDBReader); the 'permissive' keyword for Universe is now ignored and only the native MDAnalysis PDBReader is being used (Issue #777)
PDBReader only opens a single file handle in its lifetime, previously opened & closed handle each frame (Issue #850)

Use of PrimitivePDBReader/Writer/Parser deprecated in favor of PDBReader/ Writer/Parser (Issue #777)
Deprecated all get_* and set_* methods of Groups.
Deprecation warnings for accessing atom attributes from Residue, ResidueGroup, Segment, SegmentGroup. Will not be present or will give per-level results.
Deprecation warnings for accessing plural residue attributes from Residue or Segment (will disappear), or from SegmentGroup (will give per-Segment results).
Deprecation warnings for accessing plural segment attributes from Segment (will disappear).
Deprecated Atom number, pos, centroid, universe setter
Deprecated AtomGroup serials, write_selection
Deprecated Residue name, id
Deprecated Segment id, name
Deprecated as_Universe function; not needed
Deprecated ContactAnalysis and ContactAnalysis1 classes

jandom, abhinavgupta94, orbeckst, kain88-de, hainm, jbarnoud, dotsdl, richardjgowers, BartBruininks, jdetle