ReleaseNotes0170

MDAnalysis 0.17.0 release

• release date: 01/24/18
• release announcement

CHANGELOG

Enhancements

• added support for GSD format topology/trajectory parser (PR #1693)
• spherical selections tokens can use the periodic KDTree (PR #1733)
• added Amber residue names to 'protein' atom selection (PR #1704)
• KDTree for neighbor search on periodic systems (PR #1660, #1692)
• Python versions 3.4 and upwards are now supported (Issue #260)
• added Universe.empty to allow Universes of custom size to be constructed without any files (PR #1533)
• add minimal topology reader that is able to load coordinate/trajectory files on their own without requiring a topology file (Issue #1371)
• added "parse_n_atoms" to Reader API and implemented this for DCD, INPCRD, NCDF, TRR and XTC formats (PR #1533)
• added 'all_coordinates' keyword to Universe to also load the topology file as a frame of the reader together with the trajectory files (PR #1533)
• add low level lib.formats.libdcd module for reading/writing DCD (PR #1372)
• replace old DCD reader with a Python 3 ready DCD reader (Issue #659)
• about 20% speed improvements for GNM analysis. (PR #1579)
• added support for Tinker TXYZ and ARC files
• libmdaxdr and libdcd classes can now be pickled (PR #1680)
• speed up atomgroup.rotate when point = (0, 0, 0) (Issue #1707)
• introduce the water bridge analysis module (PR #1722)
• Universe.add_TopologyAttr now accepts strings to add a given attribute to the Universe (Issue #1092, PR #1186)
• The TPR parser populate the moltypes and molnums topology attributes; the moltype and molnum selection keyword are added (Issue #1555, PR #1578)
• use gridDataFormats >= 0.4.0 for new 'type' kwarg in analysis.density.Density.export() to enable writing DX files compatible with (buggy) PyMOL (#1725)

Deprecations

• HydrogenBondAnalysis detect_hydrogens=heuristic is marked for deprecation in 1.0
• timeseries keyword format is replaced by order. The format keyword is marked for deprecation in 1.0

Fixes

• Fixed analysis.psa.dist_mat_to_vec not returning int values (Issue #1507)
• Fixed triclinic PBC transform for a- and b- axes (Issue #1697)
• Fixed nuclinfo.tors() not converting delta (Issue #1572)
• Changed _calc_dihedral and Dihedral.value() to match IUPAC convention (Issue #1565)
• Fixed _calc_dihedral returning negative angles as positive (Issue #1554)
• correctly read little-endian TRZ files on big-endian architectures (issue #1424)
• Fixed type matching and inclusion compilation warnings for the ENCORE analysis package (issue #1390)
• Fix extra deprecation warnings for instant segment and residue selectors (Issue #1476)
• Accessing segments from a universe with an instant selector now issues a deprecation warning as expected (Issue #1478)
• Fixed Angle.angle method return NaN values when angle was very close to 180 degrees (Issue #1556)
• Fixed analysis.rms.RMSD failure with select != "all" (Issue #1487)
• Fixed analysis.rms.RMSD: group RMSD calculation does not superimpose groupselections anymore (issue #720)
• XDR files now avoid offset recalculation on a rewind (PR #1667)
• Universe creation doesn't Matryoshka NamedStream anymore (PR #1669)
• Fixed triclinic unit cell distances for box edges (Issue #1475)
• Fixed analysis.rms.RMSD: selections are now applied to atomgroup, not to atomgroup.universe
• Default filename argument for AlignTraj works again (Issue #1713)
• Fixed analysis.rms.RMSD failed when selection is unicode (PR #1710)
• Fixed analysis.align.AlignTraj failed when step > 1 (Issue #1714)

Changes

• generate pairwise distance matrix, analysis.psa.PSAnalysis.D, by default when analysis.psa.PSAnalysis.run_pairs_analysis is run (Issue #1507)
• remove deprecated TimeSeriesCollection
• remove deprecated analysis.align.rms_fit_trj
• remove deprecated analysis.contacts.ContactAnalysis
• remove deprecated analysis.contacts.ContactAnalysis1
• remove deprecated analysis.hbonds.hbond_analysis 1-indexing
• remove deprecated analysis.rms target keyword from functions
• remove deprecated analysis.rms.RMSD mass_weighted keyword
• remove deprecated analysis.align mass_weighted keyword from classes
• remove deprecated analysis.psa mass_weighted keyword from classes
• use fast scipy.io.netcdf pure python implementation for reading of Amber netcdf3 trajctories instead of netCDF4 but use netCDF4 for fast writing (if available) or fall back to netcdf (see also Issue #506)
• libmdaxdr classes now accept more argument types for a write (PR #1442)
• libmdaxdr classes now raise EOFError when accessing another frame after the end of the file. Used to raise IOError.
• Universe.load_new() now returns the universe itself instead of tuple (filename_or_array, trajectory_type) (Issue #1613)
• docs: URLs to (www|docs).mdanalysis.org now link to SSL-encrypted site (see issue MDAnalysis/MDAnalysis.github.io#61)
• attributes can not be assigned to AtomGroups (and similar objects) unless they are part of the Universe topology (Issue #1092 PR #1186)

Authors

richardjgowers, rathann, orbeckst, tylerjereddy, mtiberti, kain88-de, jbarnoud, nestorwendt, mmattaNU, jmborr, sobuelow, seyler, rcortini, xiki-tempula, manuel.nuno.melo