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Raised meaningful error for short peptide stretch

10

Fixes #5046 Changes made in this Pull Request: - Added a block for raising value error inside __init__ in dssp.py - Checked the length of `ag.residues`, and just raised a...

spyke7

Added NoJump on-the-fly example to MSD documentation (Issue #4169)

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This PR updates the MSD documentation inside `MDAnalysis.analysis.msd` to show users how to correctly apply the NoJump transformation using on-the-fly trajectory transformations. Issue #4169 noted that although NoJump exists, there...

tani-dubey

Improve msd_type parsing: add whitespace handling, type validation, and missing tests

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### Summary `EinsteinMSD` currently lowercases the `msd_type` string but does not handle leading/trailing whitespace or non-string inputs. This leads to errors such as: - msd_type=" xy " → ValueError instead...

tani-dubey

Add RMSFResidue analysis class for per-residue RMSF computation

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This PR adds a new analysis module `RMSFResidue` that computes Root Mean Square Fluctuations (RMSF) on a per-residue basis. ### Motivation MDAnalysis currently provides atom-level RMSF via `RMSF`. This PR...

Nitin-Prata

tests: modernize deprecated numpy assertions in test_gnm.py (ref #3743)

2

Contributes to issue #3743. This PR updates deprecated NumPy testing functions in test_gnm.py: - Replaces assert_almost_equal and assert_array_almost_equal with numpy.testing.assert_allclose - Uses pytest.approx for scalar floating point comparisons - Preserves...

shubhammittal2241

Fixes #5170: Improve msd_type parsing

1

This PR implements enhancement proposed in issue #5170 ## Summary EinsteinMSD currently lowercases the msd_type string but does not: - strip whitespace - validate the type - handle mixed-case safely...

tani-dubey

Fixes #3743: Modernize test assertions in test_msd.py

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### Summary of Changes- This PR Modernize test assertions in testsuite\MDAnalysisTests\analysis\test_msd.py ### Changes made- 1. Replaced deprecated `assert_almost_equal `with` assert_allclose` using tolerances equivalent to the previous decimal keyword. 2. Replaced...

tani-dubey

CI: mypy hangs

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## Expected behavior ## All CI completes. ## Actual behavior ## The mypy job has been hanging on multiple PRs. ## Code to reproduce the behavior ## See eg *...

orbeckst

Incorrect unwrapping for LAMMPS trajectories due to unused image flags for periodic boundary condition

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## Is your feature request related to a problem? ## MDAnalysis universe currently ignores `LAMMPS image flags (ix, iy and iz)` to properly unwrap wrapped coordinates according to `periodic boundary...

gitsirsha

Update azure windows runners to use 'windows-latest'

1

Fixes # Changes made in this Pull Request: - ## PR Checklist - [ ] Issue raised/referenced? - [ ] Tests updated/added? - [ ] Documentation updated/added? - [ ]...

IAlibay