MDAnalysis 2.0 is here

22 Aug 2021

We are happy to release version 2.0.0 of MDAnalysis!

This is a new major version, and includes major API breaking changes in addition to a large number of updates and enhancements. This release concludes our current roadmap, an updated roadmap detailing our future steps will shortly be published.

This version supports Python 3.6 through to 3.9 on Windows (32- and 64-bit), MacOS, and Linux. It also offers preliminary support for ppc64le and ARM64, but does not currently support Apple M1 processors.

Support for legacy version of Python (e.g. 2.7 and 3.5) is only available in MDAnalysis 1.x releases.

Upgrading to MDAnalysis version 2.0.0

To install with conda from the conda-forge channel run

conda update -c conda-forge mdanalysis

To install from PyPi with pip run

pip install --upgrade MDAnalysis

For more help with installation see the installation instructions in the User Guide.

Notable new additions

There were many awesome contributions to MDAnalysis for version 2.0.0. Here we list a few notable example of these. For more information please see the CHANGELOG.

RDKit converter

Google Summer of Code student @cbouy implemented a new RDKit converter which allows for seamless conversions from RDKit to MDAnalysis structures. See @cbouy’s GSoC RDKit report for more information.

It currently accurately converts 90% of chemical space (based on ChEMBL27), but future changes will improve this.

OpenMM converter

@ahy3nz implemented an OpenMM converter which can read OpenMM objects directly into MDAnalysis.

Universe serialization

Google Summer of Code student @yuxuanzhuang implemented a means to serialize MDAnalysis.Universe objects, paving the way for parallel analysis. See @yuxuanzhuang’s GSoC Universe serialization report for more information.

Mean Square Displacement

@hmacdope implemented a new Mean Square Displacement analysis class.

Results class

@PicoCentauri implemented a Results class to store results from analysis classes. This change streamlines the API for analysis classe and paves the way for a soon-to-be released command line interface for MDAnalysis.

H5MD support

NSF REU student @edisj implemented both a reader and writer for the H5MD format.

Bond-Angle-Torsion coordinates

@daveminh implemented a means to translate from Cartesian to Bond-Angle-Torsion coordinates.

Important fixes

For a full list of bugfixes see the CHANGELOG. The following are selected fixes that may have lead to wrong results depending on your use case.

Core

Fixes an issue where select_atom, AtomGroup.unique, ResidueGroup.unique, and SegmentGroup.unique did not sort the output atoms (Issues #3364 #2977)
Fixes the sometimes wrong sorting of atoms into fragments when unwrapping (Issue #3352)
AtomGroup.center now works correctly for compounds + unwrapping (Issue #2984)

File formats

Fixes support for DL_POLY HISTORY files that contain cell information even if there are no periodic boundary conditions (Issue #3314)
PDBWriter will use chainID instead of segID (Issue #3144)
PDBParser and PDBWriter now assign and use the element attribute (Issues #2422 #2423)

Analyses

Fixes issue when attempting to use/pass mean positions to PCA analysis (Issue #2728)
Fixes issue with WaterBridgeAnalysis double counting waters (Issue #3119)
Documents and fixes the density keyword for rdf.InterRDF_s (Issue #2811)
Fixed Janin analysis residue filtering, including CYSH (Issue #2898)

Changes to functionality

Deprecated hbonds.hbond_analysis has been removed in favour of hydrogenbonds.hbond_analysis (Issues #2739, #2746)
TPRParser now loads TPR files with tpr_resid_from_one=True by default, 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)
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

Author statistics

Altogether, this represents the work of 35 authors, 17 of which were new contributors:

MDAnalysis thanks NumFOCUS’s continued support as the organisation’s fiscal sponsor.

The MDAnalysis Team

MDAnalysis