ENH: support reading box vectors from TPR files - #5466
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August 18, 2026 16:23
Add a new 'subselection' keyword argument to AlignTraj.__init__ that accepts a selection string or AtomGroup. When provided, only those atoms are written to the output trajectory (enabling a performance/memory trade-off), while the superposition/RMSD fit is still computed using the atoms defined by 'select'. Also add a module-level guide in MDAnalysis.analysis.align documenting three usage patterns for aligning sub-systems with different memory characteristics. Changes: - package/MDAnalysis/analysis/align.py: add subselection param + docs - testsuite/MDAnalysisTests/analysis/test_align.py: 4 new unit tests - package/CHANGELOG: Enhancements + Documentation entries - package/AUTHORS: add Akshit Boora Closes MDAnalysis#5380
Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## develop #5466 +/- ##
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- Coverage 93.87% 93.86% -0.02%
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Files 182 182
Lines 22522 22534 +12
Branches 3206 3209 +3
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- Misses 917 920 +3
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Fixes #5375
Changes made in this Pull Request:
TPRReader._read_first_frame()inpackage/MDAnalysis/coordinates/TPR.pyto capture theBoxtuple fromextract_box_info()and setts.dimensions = triclinic_box(*box_info.size).convert_units=Trueconverts nm to Å;convert_units=Falsepreserves nm) following MDAnalysis coordinate reader standards.testsuite/MDAnalysisTests/coordinates/test_tpr.pyfor single (mda.Universe(tpr)) and double (mda.Universe(tpr, tpr)) TPR universes across different GROMACS TPR versions.package/CHANGELOG.LLM / AI generated code disclosure
LLMs or other AI-powered tools (beyond simple IDE use cases) were used in this contribution: No
PR Checklist
package/CHANGELOGfile updated?package/AUTHORS? (If it is not, add it!)Developers Certificate of Origin
I certify that I can submit this code contribution as described in the Developer Certificate of Origin, under the MDAnalysis LICENSE.