ReleaseNotes0140

MDAnalysis 0.14.0 is a new release with many new features and fixes; see also the blog post.

Authors

tyler.je.reddy, kain88-de, jbarnoud, richardjgowers, orbeckst, manuel.nuno.melo, Balasubra, Saxenauts, mattihappy

Offsets files for Gromacs trajectory formats have been changed to a numpy style format '.npz'. Offsets files will be regenerated when you load a xtc/trr trajectory again. (Issue #441)
rotation_matrix now accepts array-likes as input

XDR file seeking errors now report system errno. (PR #678)
Offsets reading for xtc/trr files has been sped up. (Issue #441)
select_atoms now implicitly ORs multiple values after a keyword for many types of selections (Issue #345)
Performance improvements for the PDBReader of about 10%
LinearDensity analysis module added, which allows to compute linear mass and charge density profiles along the three cartesian axes of the cell. Works for orthorombic, fixed volume cells only. (Issue #670)
Trajectories can now be sliced using a boolean array (Issue #725)

xdrlib was rebranded libmdaxdr. (Issue #679)
xdrlib has been ported to cython. (Issue #441)
util.NamedStream no longer inherits from basestring (Issue #649)
Short TRZ titles are striped from trailing spaces. A friendlier error message is raised when the TRZ writer is asked to write a title longer than 80 characters. (Issue #689)
PDB doesn't save charge information anymore
coordinates.core.get_writer_for uses the user defined format if provided before trying to deduce the format from file extension. (Issue #712)

Syntax error corrected in psa.py (Issue #738)
XDR file seeking and telling working again for large files (Issue #677).
ContactAnalysis1 run method now starts at frame index 0 by default (Issue #624)
Fixed PrimitivePDBWriter alignment of the atom name. (Issue #639 and #647)
The 'atom' selection keyword returns an empty selection rather than an error when no atoms are are found. (Issue #644)
nucleic selection will now detect nucleic residue names suffixed with 3 or 5 (Issue #461)
Fixed Reader returning all frames with stop in slice was 0 (Issue #672)
Fixed NCDFReader not reading dt (Issue #676)
Fixed PDB-Topology read bonds for atom ids larger then 10000 (Issue #693)
Fixed Type Error in qcprot.pyx when no rotation can be fond (Issue #705)
Fixed cyzone selection failing in orthogonal systems (Issue #710)
Fixed Error in calculation of average grid density (Issue #716)
Fixed indexing an AtomGroup using a list of bools now working (Issue #729)