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check_box and triclinic_vectors don't respect dtype

1

Both of these functions make a lot of assumptions about input dtype, and often "squash" down to float32. These should instead preserve and maintain whatever precision they are given.

richardjgowers

feat: add `RelPropertySelection` to select atoms based on positions relative to a given selection

5

## Is your feature request related to a problem? ## When investigating the solid/liquid interface, I would like to take the outermost solid atoms as the reference and analyse the...

ChiahsinChu

Minimum image convention not working for distances.distance_array

1

I am using mda.analysis.distances.distance_array() to calculate all of the distances between alpha carbons of arginine residue with resid 2 in a cluster and the centroid of the cluster. After identifying...

williambrown3

remove mmtf in 3.0

4

Remove all mmtf-handling code for 3.0. - MMTF is no longer supported by PDB (see #4634 ) - the mmtf-python license is incompatible with our target license LGPLv2.1+ (see https://www.mdanalysis.org/2023/09/22/licensing-update/#why-the-interim-gpl-v3-and-lgpl-v3-package-licenses-the-issue-with-apache-20...

orbeckst

Implement `AnalysisBase` class into `MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel`

1

Currently [`MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel`](https://github.com/MDAnalysis/mdanalysis/blob/develop/package/MDAnalysis/analysis/hydrogenbonds/hbond_autocorrel.py) does lack an implementation of an an `AnalysisBase` class to have a structure similar to `MDAnalysis.analysis.rms`, which would allow an easier implementation of the parallelization mentioned in #4665...

talagayev

Cannot access frames or slice trajectories for large or combined dcds

1

## Expected behavior ## 1. Slice trajectories as described in the [userguide](https://userguide.mdanalysis.org/stable/trajectories/slicing_trajectories.html). Eventual goal is to concatenate / combine a bunch of .dcd trajectories (load all at once) and do...

vishlashkari

LAMMPS DumpReader returns incorrect coordinate transform

6

## Expected behavior ## The coordinate transform of "scaled" LAMMPS trajectory should be imported correctly. ## Actual behavior ## The MDAnalysis calculated incorrectly coordinates from scaled to unscaled. Calculation method...

wjq1228

MAINT: Replace deprecated numpy assertions in coordinates/base.py

8

Contributes to #3743 Changes made in this Pull Request: - Replaced deprecated `assert_almost_equal` and `assert_array_almost_equal` with `assert_allclose` in `testsuite/MDAnalysisTests/coordinates/base.py`. - Converted decimal precision to `atol=10**(-decimal)` and `rtol=0` to maintain original...

Dreamstick9

Use native scipy periodic KDTree for orthorhombic boxes?

10

The MDAnalysos PBC-awared distance calculations normally use a grid-based method with "augmentation" to find minimum image distances. However, as an alternative method a KDTree based method also exists in `lib.pkdtree`....

orbeckst

Enabling of parallelization of `analysis.hydrogenbonds.WaterBridgeAnalysis`

17

Fixes #4666. Changes made in this Pull Request: - Addition of parallelization to `WaterBridgeAnalysis ` class in `analysis.hydrogenbonds.wbridge_analysis`. - Addition of `client_WaterBridgeAnalysis` to `conftest.py`. - Adjustment of tests in `test_wbridge.py`...

talagayev