MDAnalysis Release Notes

Release 2.7.0 of MDAnalysis

This a minor release of MDAnalysis.

This release of MDAnalysis is packaged under a GPLv3+ license, additionally all contributions made from commit 44733fc214dcfdcc2b7cb3e3705258781bb491bd onwards are made under the LGPLv2.1+ license.

The minimum supported NumPy version is 1.22.3.

Supported Python versions:

  • 3.9, 3.10, 3.11, 3.12

Major changes:

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

Fixes:

  • NoJump now properly handles jumps that occur on the second frame of NPT trajectories, PR #4258

  • Fix charge reading from PDBQT files. PR #4283

  • Fixed a case where qcprot.CalcRMSDRotationalMatrix would return a RMSD of None. PR #4273

Enhancements:

  • Support was added for reading chainID from prmtop AMBER topologies (PR #4007)

  • Added support for Python 3.12 (PR #4309, #4300, #4301, #4319, #4325, #4327, #4329)

  • Added support for reading chainID from PDBQT files (PR #4284)

  • TPR reader now sets chainID from molblock (PR #4281)

  • Various improvements to the organization and performance of Major and Minor Pair analyses (PR #3735)

  • C distance backend is now exposed via libmdanalysis.pxd (PR #4342)

  • Added a GROMOS11 Reader (PR #4294)

Changes:

  • Added mda_xdrlib as a core dependency to replace the now deprecated Python xdrlib code (PR #4271)

  • ConverterBase has been moved to MDAnalysis.converters.base (PR #4253)

  • networkx is now an optional dependency of MDAnalysis (PR #4331)

  • BioPython is now an optional dependency of MDAnalysis (PR #4332)

  • Results for WatsonCrickDist nucleic acids analysis are now stored in analysis.nucleicacids.WatsonCrickDist.results.distances (PR #3735)

Deprecations:

  • Importing ConverterBase from MDAnalysis.coordinates.base will not be possible after MDAnalysis 3.0 (PR #4253)

  • Deprecation with intent of removal in MDAnalysis v3.0 of the X3DNA legacy code (PR #4333)

  • Deprecation with intent of removal in MDAnalysis v3.0 of the TRZ reader and writer (PR #4335)

  • Deprecation with intent of removal in MDAnalysis v3.0 of the MDAnalysis.lib.util.which method (PR #4340)

  • The asel argument of the timeseries attribute of Readers is now deprecated in favour of the atomgroup argument (PR #4343)

  • In nucleicacids.WatsonCrickDist, accepting lists of Residue objects was deprecated in favor of using ResidueGroup: using List[Residue] will be removed in release 3.0.0; instead use a ResidueGroup (PR #3735)

  • In nucleicacids.WatsonCrickDist the result results.pair_distances was deprecated and will be removed in 3.0.0; use results.distances instead (PR #3735)

New Contributors

  • @jennaswa made their first contribution in https://github.com/MDAnalysis/mdanalysis/pull/4289

  • @Sumit112192 made their first contribution in https://github.com/MDAnalysis/mdanalysis/pull/4346

  • @HeetVekariya made their first contribution in https://github.com/MDAnalysis/mdanalysis/pull/4359

  • @JoStoe made their first contribution in https://github.com/MDAnalysis/mdanalysis/pull/4292

  • @ljwoods2 made their first contribution in https://github.com/MDAnalysis/mdanalysis/pull/4366

Release 2.6.1 of MDAnalysis

This is a bugfix release of the 2.6.x version branch of MDAnalysis, it serves as an amendment to the earlier released version 2.6.0.

See the CHANGELOG for more details.

Bug fixes and changes

  • Reverting the v2.6.0 behaviour, builds are now again made using the oldest supported NumPy version (NumPy 1.22.3 for Python 3.9-3.10, and 1.22.3 for Python 3.11) [PR #4261]

  • Uses of numpy in1d have been replaced with isin in prepartion for NumPy 2.0 [PR #4255]

  • Cython DEF statements have been replaced with compile time integer constants as DEF statements are now deprecated in Cython 3.0 [Issue #4237, PR #4246]

  • Fix to element guessing code to more accurately interpret atom names split by numbers (i.e. N0A is now recognised as N rather than NA) [Issue #4167, PR #4168]

  • Clarification of SurvivalProbability function documentation [Issue #4247, PR #4248]1

New Contributors

  • @pillose made their first contribution in https://github.com/MDAnalysis/mdanalysis/pull/4168

Release 2.6.0 of MDAnalysis

This a minor release of MDAnalysis.

This release of MDAnalysis is packaged under a GPLv3+ license, additionally all contributions made from commit 44733fc214dcfdcc2b7cb3e3705258781bb491bd onwards are made under the LGPLv2.1+ license. More details about these license changes will be provided in an upcoming blog post.

The minimum supported NumPy version has been raised to 1.22.3 as per NEP29. Please note that package builds are now made with NumPy 1.25+ which offer backwards runtime compatibility with NEP29 supported versions of NumPy.

Supported Python versions:

  • 3.9, 3.10, 3.11

Major changes:

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

Fixes:

  • The -ffast-math compiler flag is no longer used by default at build time, avoiding inconsistent (although still scientifically correct) results seen in Intel MacOS systems when calling `AtomGroup.center_of_charge(…, unwrap=True). This also avoids potentially incorrect floating point results as detailed here. (https://github.com/MDAnalysis/mdanalysis/pull/4220)

  • DATAWriter, CRD, PQR, and PDBQT files can now be correctly written to compressed files. Before this change, any attempt to write to a compressed format (gzip or bzip2) would lead to writing out an uncompressed file. (https://github.com/MDAnalysis/mdanalysis/pull/4163)

  • Prevent accidental merging of bond/angle/dihedral types when they are defined as LAMMPS style string integers instead of tuples. This was leading to an incorrect number of bond/angle/dihedral types being written to lammps data files. (https://github.com/MDAnalysis/mdanalysis/pull/4003)

Enhancements:

  • An exclude_same argument has been added to InterRDF allowing pairs of atoms that share the same residue, segment or chain to be excluded from the calculation. (https://github.com/MDAnalysis/mdanalysis/pull/4161)

  • LAMMPS reader now supports the continuous ChainReader option. (https://github.com/MDAnalysis/mdanalysis/pull/4170)

  • AtomGroup representation now returns atom indices in the same order as they are stored in the AtomGroup. (https://github.com/MDAnalysis/mdanalysis/pull/4191)

Changes:

  • Package builds now use NumPy 1.25 or higher instead of the lowest supported NumPy version. (https://github.com/MDAnalysis/mdanalysis/pull/4198)

  • As per NEP29, the minimum supported runtime version of NumPy has been increased to 1.22.3. (https://github.com/MDAnalysis/mdanalysis/pull/4160)

  • The GSD package is now an optional dependency. (https://github.com/MDAnalysis/mdanalysis/pull/4174)

  • The MDAnalysis package now only supports GSD versions 3.0.1 or above. (https://github.com/MDAnalysis/mdanalysis/pull/4153)

  • MDAnalysis no longer officially supports 32 bit installations. (they are no longer tested in our continuous integration pipelines). Note: no code changes have been made to disable 32 bit, although it is known that new versions of most MDAnalysis core dependencies no longer release 32 bit compatible versions. (https://github.com/MDAnalysis/mdanalysis/pull/4176)

  • The package license has been updated to GPLv3+ to better reflect the compatibility of GPLv2+ with Apache and GPLv3 licensed codes. Additionally all new contributions from commit 44733fc214dcfdcc2b7cb3e3705258781bb491bd onwards are made under the LGPLv2.1+ license. (https://github.com/MDAnalysis/mdanalysis/pull/4219)

Deprecations:

  • The misspelt Boltzman_constant entry in MDAnalysis.units is now deprecated in favour the correctly spelt Boltzmann_constant. (https://github.com/MDAnalysis/mdanalysis/pull/4230 and https://github.com/MDAnalysis/mdanalysis/pull/4214)

  • MDAnalysis.analysis.hole2 is now deprecated in favour of a new HOLE2 MDAKit. (https://github.com/MDAnalysis/mdanalysis/pull/4200)

New Contributors

  • @MohitKumar020291 made their first contribution in https://github.com/MDAnalysis/mdanalysis/pull/4182

  • @Shubx10 made their first contribution in https://github.com/MDAnalysis/mdanalysis/pull/4184

  • @ztimol made their first contribution in https://github.com/MDAnalysis/mdanalysis/pull/4191

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.

New Contributors

  • @mglagolev made their first contribution in https://github.com/MDAnalysis/mdanalysis/pull/3959

  • @chrispfae made their first contribution in https://github.com/MDAnalysis/mdanalysis/pull/4009

  • @ooprathamm made their first contribution in https://github.com/MDAnalysis/mdanalysis/pull/4010

  • @MeetB7 made their first contribution in https://github.com/MDAnalysis/mdanalysis/pull/4022

  • @v-parmar made their first contribution in https://github.com/MDAnalysis/mdanalysis/pull/4032

  • @MoSchaeffler made their first contribution in https://github.com/MDAnalysis/mdanalysis/pull/4049

  • @jandom made their first contribution in https://github.com/MDAnalysis/mdanalysis/pull/4043

  • @xhgchen made their first contribution in https://github.com/MDAnalysis/mdanalysis/pull/4037

  • @DrDomenicoMarson made their first contribution in https://github.com/MDAnalysis/mdanalysis/pull/4074

  • @AHMED-salah00 made their first contribution in https://github.com/MDAnalysis/mdanalysis/pull/4059

  • @schlaicha made their first contribution in https://github.com/MDAnalysis/mdanalysis/pull/4076

  • @jvermaas made their first contribution in https://github.com/MDAnalysis/mdanalysis/pull/4031

  • @SophiaRuan made their first contribution in https://github.com/MDAnalysis/mdanalysis/pull/4072

  • @marinegor made their first contribution in https://github.com/MDAnalysis/mdanalysis/pull/4085

  • @g2707 made their first contribution in https://github.com/MDAnalysis/mdanalysis/pull/4089

  • @DanielJamesEvans made their first contribution in https://github.com/MDAnalysis/mdanalysis/pull/4109

Release 2.4.3 of MDAnalysis

This is a bugfix release of the 2.4.x version of MDAnalysis, it serves as an amendment to the earlier released version 2.4.2.

Bug fixes

  • Fixed DCD reading for large (>2Gb) files (Issue #4039). This was broken for versions 2.4.0, 2.4.1 and 2.4.2.

  • Fix element parsing from PSF files tests read via Parmed (Issue #4015)

Release 2.4.2 of MDAnalysis

This is a bugfix release of the 2.4.x version of MDAnalysis, it serves as an amendment to the earlier released version 2.4.1.

Bug fixes

  • Fixed an issue where the arguments passed to np.histogramdd in MDAnalysis.analysis.DensityAnalysis were not compatible with the 1.24 release of NumPy (PR #3976)

  • Fixed upcoming incompatibilities with NumPy 1.25 in MDAnalysis.visualization.streamlines_3D and MDAnalysis.visualization.streamlines where incorrect comparison of the truth of arrays would have led to failures (PR #3977)

Release 2.4.1 of MDAnalysis

This is a bugfix release of the 2.4.x version of MDAnalysis, it serves as an amendment to the earlier released version 2.4.0.

Bug fixes

  • The minimum version of biopython has been raised to 1.80 for pip installs

  • pytng has been added as an optional dependency

Release 2.4.0 of MDAnalysis

This a minor release of MDAnalysis, as per our once-every-three-months schedule.

The minimum NumPy and Python versions remain largely unchanged, however the minimum version of biopython has been raised to 1.80. This is also the first release to officially support Python 3.11.

Supported Python versions:

  • 3.8, 3.9, 3.10, 3.11

Major changes:

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

Fixes:

Enchancements:

  • As part of their outreachy project @umak has started adding type annotations throughout the MDAnalysis codebase

  • As part of their GSoC project @BFedder has added an auxialliary reader for EDR files (PR #3749)

  • As part of their GSoC project @aya9aladdin has fixed various issues with guessing and and attribute reading. This will be followed by the introduction of a new guesser system in a future release.

  • A reader for TNG files has been added by @hmacdope, follow up on his previous GSoC 2020 work on creating a python library for reading TNG files (PR 3765)

  • Addition of a new isolayer selection method (PR #3846)

  • Various enchancements and fixes to the LAMMPS DUMP Parser (allowing box translation on reading, allowing coordinates to be unwrapped based on dump image flags, and importing of forces and velocities) (PR #3844)

  • All readers now have a timeseries attribute (PR #3890)

  • ReaderBase file formats now accept pathlib inputs (PR #3935)

  • Added ability for hbond analysis to use types when resnames are not present (PR #3848)

Changes:

  • The deprecated setup.py extra_requires AMBER entry has been removed in favor of extra_formats (PR #3810)

  • Various issues with the auxilliary reader, this should not be much more robust (PR #3749)

  • The Cython headers have been moved to MDAnalysis.lib.libmdanalysis (PR #3913)

  • The MDAnalysis.analysis.align.sequence_alignment now uses Bio.Align.PairwiseAligner instead of the deprecated Bio.pairwise2 (PR #3951)

Deprecations:

  • The MemoryReader’s timeseries inclusive indexing will be changed to exclusive in version 3.0.0 (PR #3894)

  • The sequence_aligment() method has been deprecated and will be removed in version 3.0.0 (PR #3951)

  • MDAnalysis.analysis.nucleicacids’ direct indexing of selection indices to obtain pair distances results has been deprecated in favor of accessing results.pair_distances (PR #3958)

New Contributors

  • @jaclark5 made their first contribution in https://github.com/MDAnalysis/mdanalysis/pull/3846

  • @pgbarletta made their first contribution in https://github.com/MDAnalysis/mdanalysis/pull/3876

  • @jfennick made their first contribution in https://github.com/MDAnalysis/mdanalysis/pull/3832

  • @Hakarishirenai made their first contribution in https://github.com/MDAnalysis/mdanalysis/pull/3956

Release 2.3.0 of MDAnalysis

This a minor release of MDAnalysis, as per our once-every-three-months schedule.

The minimum NumPy version has been raised to 1.20.0 (1.21 for macosx-arm64) in line with NEP29.

Supported python versions:

  • 3.8, 3.9, 3.10

Major changes:

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

Fixes:

  • Fixed reading error when dealing with corrupt PDB CONECT records, and an issue where MDAnalysis would write out unusable CONECT records with index>100000 (Issue #988).

Enhancements:

  • Formal charges are now read from PDB files and stored in a formalcharge attribute (PR #3755).

  • A new normalizing norm parameter for the InterRDF and InterRDF_s analysis methods (Issue #3687).

  • Improved Universe serialization performance (Issue #3721, PR #3710).

Changes:

  • To install optional packages for different file formats supported by MDAnalysis, use pip install ./package[extra_formats] (Issue #3701, PR #3711).

Deprecations:

  • The extra_requires target AMBER for pip install ./package[AMBER] will be removed in 2.4.0. Use extra_formats (Issue #3701, PR #3711).

CZI EOSS Performance Improvements:

A series of performance improvements to the MDAnalysis library’s backend have been made as per planned work under MDAnalysis’ CZI EOSS4 grant. Further details about these will be provided in a future blog post.

  • MDAnalysis.lib.distances now accepts AtomGroups as well as NumPy arrays (PR #3730).

  • Timestep has been converted to a Cython Extension type (PR #3683).

Release 2.2.0 of MDAnalysis

In line with NEP29, this version of MDAnalysis drops support for Python 3.7 and raises the minimum NumPy version to 1.19.0. Minimum version support has also been changed for the following packages; networkx>=2.0, scipy>=1.5.0, gsd>=1.9.3. Further details on MDAnalysis future support strategy and NEP29 will be released shortly.

Supported python versions:

  • 3.8, 3.9, 3.10

Major changes:

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

Enhancements:

  • The frames argument was added to AnalysisBase-derived classes (i.e. modern analysis classes) allowing for specific frames to be defined when running an analysis. (PR #3415)

  • DL_POLY classic HISTORY files are now supported (Issue #3678)

  • Python wheels are now made available through PyPI for x86_64 architectures (Issue #1300, PR #3680)

  • Added a center_of_charge attribute for AtomGroups (PR #3671)

  • LinearDensity now work with UpdatingAtomGroups (Issue #2508, PR #3617)

  • Addition of a PCA transformation and an associated inverse-PCA transformation was added to the PCA analysis class (PR #3596, Issue #2703)

  • Major improvements to the RDKitConverter’s accuracy (PR #3044)

    • Accuracy of 99.14% when benchmarked against ChEMBL30

    • AtomGroups containing monatomic ion charges and edge cases with nitrogen, sulfur, phosphorus and conjugated systems should now have correctly assigned bond orders and charges.

  • Addition of a new AnalysisBase derived Watson-Crick distance analysis class (PR #3611)

Fixes:

  • Fixed issues where calling the copy method of Readers did not preserve optional arguments (Issue #3664, PR #3685)

  • Fixed several issues where iterating trajectories had undefined behaviour

    • Iterating (not in memory) SingleFrame readers now reset modified trajectory attributes (Issue #3423)

    • Iterating using defined indices did not rewind the trajectory (Issue #3416)

  • Fixed issues with competing processes writing to an XTC offset file leading to offset corruption (Issue #1988, PR #3375)

  • Fixed issue preventing OpenMMTopologyParsers from parsing systems with missing elements (Issue #3317, PR #3511)

  • Fixed issue with encore.covariance.covariance_matrix not working when providing an external reference (Issue #3539, PR #3621)

  • Fixed issue with broken code paths for “residues” and “segment” groupings for LinearDensity (Issue #3571, PR #3572)

  • Improved the flexibility of MOL2 reading, allowing for optional columns (subst_id, subst_name and charge) not to be provided (Issue #3385, PR #3598)

  • Fixed several issues related to converting AtomGroups to RDKit molecules (PR #3044):

    • Atoms are now in the same order

    • atom.GetMonomerInfor().GetName() now follows the guidelines for PDB files

    • Using NoImplicit=False no longer throws a SanitizationError

  • Fixed issues with incorrect reading of triclinic boxes from DUMP files (Issue #3386, PR #3403)

  • Fixed issue with the BAT method modifying input coordinate data (Issue #3501)

Changes:

  • The number of matches allowed when doing a smarts selection has been increased from the default 1000 to max(1000, n_atoms * 10), an additional set of smarts_kwargs can now also be passed to override this behaviour (Issue #3469, PR #3470)

  • The fasteners package is now a core dependency (PR #3375)

  • LinearDensity now saves the histogram bin edges for easier plotting as `hist_bin_edges for each dimension in the results dictionary (Issue #2508, PR #3617)

  • ContactAnalysis now accepts AtomGroups (Issue #2666, PR #3565)

Deprecations:

  • The following results attribute for LinearDensity are now deprecated: (Issue #2508, PR #3617)

    • pos is now mass_density

    • char is now charge_density

    • std entries are now stddev

Known test failures:

  • Windows builds

    • In some cases users may get permission errors with tests involving symlinks. This should not impact the behaviour of MDAnalysis but may impact the creation of temporary files when using HOLE2 (see: https://github.com/MDAnalysis/mdanalysis/issues/3556).

Release 2.1.0 of MDAnalysis

In line with ongoing attempts to align with NEP29, this version of MDAnalysis drops support for Python 3.6 and raises the minimum NumPy version to 1.18.0.

Please note that at time of release whilst all the MDAnalysis core functionality supports Python 3.10, some optional modules do not due to a lack of support by dependencies which they require. We hope that this support will gradually be added as more of these dependencies release new versions compatible with Python 3.10.

Supported python versions:

  • 3.7, 3.8, 3.9, 3.10

Major changes:

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

Enhancements:

  • Addition of a new dielectric analysis module (PR #2118)

  • The TPR parser now supports reading files from GROMACS 2022 (PR #3514)

  • The H5MDReader can now load trajectories without a topology (PR #3466)

  • Custom compiler flags can be used when building MDAnalysis from source (PR #3429)

  • The RDKit reader now supports parsing R/S chirality (PR #3445)

  • A new method to apply the minimum image convention to a collection of vectors, minimize_vectors, has been introduced (PR #3472)

Fixes:

  • Fixed various integer overflow issues in the distance calculation backend of MDAnalysis which would prevent calculations on large systems (Issues #3183, #3512).

  • Fixed issues with the creation of VMD surfaces in HOLE2 when using a non-contiguous start/stop/step.

  • Fixes reading of charges with the ITPParser (Issue #3419).

  • Fixed issue with the creation of a Universe from a custom object which only provides a topology (Issue #3443).

  • Fixed issue with accessing newly created values added via add_Segment or add_Residue (Issue #3437).

Changes:

  • packaging is now a core dependency of MDAnalysis.

  • Indexing a Group (AtomGroup, ResidueGroup, SegmentGroup) with None now raises a TypeError. Prior to this indexing by None would incorrectly return the whole Group but claim to have a length of 1 atom (Issue #3092).

  • The TRZReader now defaults to a dt value of 1.0 ps instead of the previous 0.0 ps (Issue #3257).

Deprecations:

  • The pbc keyword argument for various Group methods has been deprecated in favor of wrap. The deprecated keyword will be removed in version 3.0.0 (Issue #1760).

Known test failures:

  • pytest-xdist and more than 4 workers

    • Under these conditions a test related to logging for HydrogenBondAnalysis can fail. This is not thought to impact the validity of MDAnalysis. See here for more details: https://github.com/MDAnalysis/mdanalysis/issues/3543

  • Windows builds

    • In some cases users may get permission errors with tests involving symlinks. This should not impact the behaviour of MDAnalysis but may impact the creation of temporary files when using HOLE2 (see: https://github.com/MDAnalysis/mdanalysis/issues/3556).

Release 2.0.0 of MDAnalysis

This is the first version of MDAnalysis to solely support python 3.6+

Supported python versions:

  • 3.6, 3.7, 3.8, 3.9

Please note that starting with the next minor version, MDAnalysis will be following NEP29.

Notes:

  • This is a major release and introduces major advertised API breaks. Caution is advised when upgrading to 2.0.0.

Major changes:

Enhancements:

  • LAMMPSDumpReader can now read coordinates in all different LAMMPS coordinate conventions (Issue #3358)

  • New Results class for storing analysis results (Issue #3115)

  • New OpenMM coordinate and topology converters (Issue #2863, PR #2917)

  • New intra_bonds,intra_angles, intra_dihedrals, etc… methods to return connections involve atoms within AtomGroups instead of including atoms outside of it (Issue #1264, #2821, PR #3200)

  • Support for Groamcs 2021 TPR files (Issue #3180)

  • Adds preliminary support for ppc64le and aarch64 [ARM] (Issue #3127, PR #2956 #3149)

  • New selection operators (Issue #3054, PR #2927)

  • New refactor of helix analysis class as analysis.helix_analysis (Issue #2452)

  • New converter between RDKit molecules and MDAnalysis AtomGroup objects (Issue #2468). Also includes from_smiles Universe generator method, and the aromatic and smarts selection.

  • New analysis method for calculating Mean Squared Dsiplacements (Issue #2438)

  • New converter between Cartesian and Bond-Angle-Torsion coordinates (PR #2668)

  • Universes and readers can now be pickled paving the way to easier parallel analyses (Issue #2723)

  • New H5MDReader and H5MDWriter (Issue #762, #2866)

Fixes:

  • Fixes an issue where select_atom, AtomGroup.unique, ResidueGroup.unique, and SegmentGroup.unique did not sort the output atoms (Issues #3364 #2977)

  • GRO files now only support unit cells defined with 3 or 9 entries (Issue #3305)

  • Fixes the sometimes wrong sorting of atoms into fragments when unwrapping (Issue #3352)

  • Fixes issue when atttempting to use/pass mean positions to PCA analysis (Issue #2728)

  • Fixes support for DL_POLY HISTORY files that contain cell information even if there are no periodic boundary conditions (Issue #3314)

  • Fixes issue with WaterBridgeAnalysis double counting waters (Issue #3119)

  • PDBWriter will use chainID instead of segID (Issue #3144)

  • PDBParser and PDBWriter now assign and use the element attribute (Issues #3030 #2422)

  • AtomGroup.center now works correctly for compounds + unwrapping (Issue #2984)

  • Documents and fixes the density keyword for rdf.InterRDF_s (Isuse #2811)

  • Fixed Janin analysis residue filtering, including CYSH (Issue #2898)

Changes:

  • New converter API for all MDAnalysis converters under MDAnalysis.converters

  • Timestep now stores information in ‘C’ memory layout instead of the previous ‘F’ default (PR #1738)

  • hbonds.hbond_analysis has been remove din favour of hydrogenbonds.hbond_analysis (Issues #2739, #2746)

  • TPRParser now loads TPR files with tpr_resid_from_one=True by deafult, which starts TPR resid indexing from 1 (instead of 0 as in previous MDAnalysis versions) (Issue #2364, PR #3152)

  • analysis.hole has now been removed in favour of analysis.hole2.hole (Issue #2739)

  • Writer.write(Timestep) and Writer.write_next_timestep have been removed. Please use write() instead (Issue #2739)

  • Removes deprecated density_from_Universe, density_from_PDB, Bfactor2RMSF, and notwithin_coordinates_factory from MDAnalysis.analysis.density (Issue #2739)

  • Changes the minimum numpy supported version to 1.16.0 (Issue #2827)

  • Removes deprecated waterdynamics.HydrogenBondLifetimes (PR #2842)

  • hbonds.WaterBridgeAnalysis has been moved to hydrogenbonds.WaterBridgeAnalysis (Issue #2739 PR #2913)

Deprecations:

  • The bfactors attribute is now aliased to tempfactors and will be removed in 3.0.0 (Issue #1901)

  • WaterBridgeAnalysis.generate_table() now returns table information, with the table attribute being deprecated

  • Various analysis result attributes which are now stored in Results will be deprecated in 3.0.0 (Issue #3261)

  • In 3.0.0 the ParmEd classes will only be accessible from the MDAnalysis.converters module

  • In 2.1.0 the TRZReader will default to a dt of 1.0 ps when failing to read it from the input TRZ trajectory

See the CHANGELOG for more changes and details.

Known issues:

  • Windows builds

    • For some compilers (seen on MVC v.19xx), differences in floating point precision leads to PBC wrapping differing from expected outcomes. This leads to failures in the MDAnalysisTests.lib.test_augment tests. To our knowledge this does not significantly affect results (as all other tests pass). We will aim to fix this in version 2.1.0.