Oliver Beckstein edited this page Jan 31, 2018 · 3 revisions

MDAnalysis 0.17.0 release



  • 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)


  • 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


  • 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)


  • 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 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) now link to SSL-encrypted site (see issue MDAnalysis/
  • attributes can not be assigned to AtomGroups (and similar objects) unless they are part of the Universe topology (Issue #1092 PR #1186)


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

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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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