github MDAnalysis/mdanalysis package-2.5.0
Release 2.5.0 of MDAnalysis
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latest releases: package-2.7.0, release-2.7.0, package-2.6.1...
11 months ago

Release 2.5.0 of MDAnalysis

This a minor release of MDAnalysis.

The minimum Python version has been raised to 3.9 and NumPy to 1.21.0 as per NEP29. We also now package wheels for both linux and osx arm64 machines on PyPi.

Supported Python versions:

  • 3.9, 3.10, 3.11

Major changes:

See the CHANGELOG and our release blog post for more details.

Fixes:

  • Fixed an issue where transformations were not being properly applied to
    Universes with multiple trajectories (i.e. using the ChainReader)
    (Issue #3657 #4008 PR #3906)
  • Fixed an issue with the the heavy distance_type for WaterBridgeAnalysis
    where distance was not correctly assigned when more than one hydrogen
    was bonded to a heavy atom (Issue #4040, PR #4066).
  • PDB topology parser no longer fails when encountering unknown formal
    charges and instead simply does not populate attribute (Issue #4027)
  • Fixed an issue where using the between keyword of HydrogenBondAnalysis
    led to incorrect donor-atom distances being returned (PR #4092, Issue #4091)
  • Fixed an issue where chi1_selections() ignored atom names CG1 OG OG1 SG
    and incorrectly returned None for amino acids CYS, ILE, SER, THR, VAL
    (Issue #4108, PR #4109)
  • Fix H5MD reader to read box vectors rather than returning None as the
    dimensions (Issue #4075, PR #4076)
  • Fix to allow reading NetCDF trajectories which do not have the time
    variable defined (Issue #4073, PR #4074)
  • Allows shape_parameter and asphericity to yield per residue quantities
    (Issue #3002, PR #3905)
  • Fix EDRReader failing when parsing single-frame EDR files (Issue #3999)
  • Add 'PairIJ Coeffs' to the list of sections in LAMMPSParser.py
    (Issue #3336)
  • PDBReader now defaults atom values for ts.data['occupancy'] to 0.0, rather
    than the previous default of 1.0. This now matches the default used when
    setting Universe Topology attributes using the first frame's information (PR #3988)

Enchancements:

  • ARM64 (osx and linux) wheels are now provided via PyPi (Issue #4054)
  • Addition of a new analysis class analysis.atomicdistances.AtomicDistances
    to provide distances between two atom groups over a trajectory.
    (Issue #3654, PR #4105)
  • Add kwarg n_frames to class method empty() in
    MDAnalysis.core.universe, enabling creation of a blank Universe with
    multiple frames (PR #4140)
  • PDBReader now populates ts.data['tempfactor'] with the tempfactor for
    each atom for each frame. If an entry is missing for a given atom,
    this will default to a 1.0 value. Note, this does not affect the
    topology, i.e. AtomGroup.tempfactors is not dynamically updated.
    (Issue #3825, PR #3988)
  • Add writing u.trajectory.ts.data['molecule_tag'] as molecule tags to
    LAMMPS data file (Issue #3548)
  • Add progressbar_kwargs parameter to AnalysisBase.run method, allowing
    to modify description, position etc of tqdm progressbars. (PR #4085)
  • Add a nojump transformation, which unwraps trajectories so that particle
    paths are continuous. (Issue #3703, PR #4031)
  • Added AtomGroup TopologyAttr to calculate gyration moments (Issue #3904,
    PR #3905)
  • Add support for TPR files produced by Gromacs 2023 (Issue #4047)
  • Add distopia distance calculation library bindings as a selectable backend
    for calc_bonds in MDA.lib.distances. (Issue #3783, PR #3914)
  • AuxReaders are now pickle-able and copy-able (Issue #1785, PR #3887)
  • Add pickling support for Atom, Residue, Segment, ResidueGroup
    and SegmentGroup. (PR #3953)

Changes:

  • As per NEP29 the minimum supported Python version has been raised to 3.9
    and NumPy has been raised to 1.21 (note: in practice later versions of NumPy
    may be required depending on your architecture, operating system, or Python
    version) (PRs #4115 and #3983).
  • Add progress bars to track the progress of mds.EinsteinMSD _conclude()
    methods (_conclude_simple() and _conclude_fft()) (Issue #4070, PR #4072)
  • The deprecated direct indexing and times from the results attribute of
    analysis.nucleicacids' NucPairDist and WatsonCrickDist classes has been
    removed. Please use the results.pair_distances and times attributes
    instead (Issue #3744)
  • RDKitConverter changes (part of Issue #3996):
    • moved some variables (MONATOMIC_CATION_CHARGES and
      STANDARDIZATION_REACTIONS) out of the related functions to allow users
      fine tuning them if necessary.
    • changed the sorting of heavy atoms when inferring bond orders and
      charges: previously only based on the number of unpaired electrons, now
      based on this and the number of heavy atom neighbors.
    • use RDKit's RunReactantInPlace for the standardization reactions, which
      should result in a significant speed improvement as we don't need to use
      bespoke code to transfer atomic properties from the non-standardized mol
      to the standardized one.

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