Release 2.11.0 of MDAnalysis and MDAnalysisTests

Overview

This is a minor release of MDAnalysis.

This release supports NumPy 2.0+ and offers backwards compatibility through to NumPy 1.26.0.

Supported Python versions:

• 3.11, 3.12, 3.13, 3.14

Major features & changes

See the CHANGELOG for more details.

Analysis methods

• Paralllelization supporrt for; DiffusionMap (PR #4745), AtomicDistances (PR #4822),
• DSSP improvements
  • Inclusion of PRO in secondary structure assessment (PR #5065).
  • Improved performance of distance calculations and correctly handles periodic boundaries in hydrogen bond detection (PR #5182).
• Fixed issue where Analysis classes would not work with GSD trajectories (Issue #5224, PR #5260).
• AtomicDistances now uses the results dictionary for its outputs, in line with other analysis classes (PR #5347).
• Fix to mean aggregation of InterRDF bins when running in parallel (PR #5344).
• Fix to issue where numpy boolean arrays passed to run() would incorrectly select frame indices (PPR #5476).
• Fix to incorrect reduction of eigenvectors in the GNMAnalysis class when running analysis with multiprocessing (PR #5495).
• Fix incorrect aggreggation in InterRDF_s when running in parallel (PR #5497).

File formats

• TPR reader improvements
  • Support for GROMACS 2026 TPR files (PR #5219).
  • Fix issue with reading old TPR files (TPX version < 103) (PR #5146).
  • Fix to position & velocity parsing to properly convert to MDAnalysis base units rather than using Gromacs' native units (PR #5374).
  • Support for reading linear angle potentials (PR #5372).
  • Box vectors can now be read from TPR files (PR #5466).
• Implementation of a mda.fetch_pdb() convenience which allows for creation of Universes by directly pulling from the Protein DataBank (PR #4943).
• Added support for reading unit cell dimensions from CRYSIN records in MOL2 files (PR #5187).
• Implementation of an MMCIF file reader using the gemmi library (PR #4712).

Library internals

• Significant AtomGroup.wrap() performance improvement. wrap() now scales close to O(N) instead of O(N^2) at large compound counts.
• Bond guessing now words with mixed case atomtypes (PR #5343).
• Velocities and forces are now also rotated when applying trajectory rotation transformations (PR #5421).
• Fix inccorrect capped_distance in some triclinic boxes (where both b_x and c_y are non-zero), leading to atom pairs within the cutoff distance being missed (PR #5481).

New Contributors

• @spyke7 made their first contribution in #5153
• @Pranay096 made their first contribution in #5158
• @PardhavMaradani made their first contribution in #5185
• @tani-dubey made their first contribution in #5173
• @BradyAJohnston made their first contribution in #5202
• @IAyaanHere made their first contribution in #5205
• @khushi-phougat made their first contribution in #5212
• @Dreamstick9 made their first contribution in #5156
• @jeremyleung521 made their first contribution in #5237
• @harshitgajjela-droid made their first contribution in #5265
• @kunjsinha made their first contribution in #5260
• @aygarwal made their first contribution in #5277
• @ParthUppal523 made their first contribution in #5294
• @ollyfutur made their first contribution in #5296
• @Amarendra22 made their first contribution in #5291
• @shubhammittal2241 made their first contribution in #5178
• @charity-g made their first contribution in #5347
• @saiudayagiri made their first contribution in #5401
• @apoorva-01 made their first contribution in #5415
• @Aryaman-Chaudhri made their first contribution in #5139
• @sici17 made their first contribution in #5439
• @AkshitBoora made their first contribution in #5466

Full Changelog: package-2.10.0...package-2.11.0