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Issue 3659 fixed loading for MOL2 and PDB edge cases

11

Fixes #3659 Changes made in this Pull Request: - New squash function `squash_by_attributes` that uses unique combinations of attributes to determine residues - `MOL2Parser` and `PDBParser` now use this function...

zwsmith200

## Expected behavior ## Either creating a universe via `in_memory=True` or using :meth:`transfer_to_memory` should allow me to pass optional kwargs through to the `MemoryReader` creation (they aren't super useful, but...

IAlibay

HydrogenBondAnalysis log warn test fails with more than 4 workers

6

## Expected behavior ## All tests pass on all supported platforms. ## Actual behavior ## The CI cron job for the ARM platform fails with the following error: ``` ____________...

jbarnoud

Github pages is leaving behind quite a lot of artifacts (31 since April) For full list see: ``` curl \ -H "Accept: application/vnd.github.v3+json" \ https://api.github.com/repos/MDAnalysis/mdanalysis/actions/artifacts ``` They have a retention...

IAlibay

Docs specify incorrect memory order for Timestep

2

## Expected behavior ## The docs specify the memory order of `timestep._pos' correctly to be "C". ## Actual behavior ## The docs [here](https://docs.mdanalysis.org/stable/documentation_pages/coordinates/base.html?highlight=_pos#MDAnalysis.coordinates.base.Timestep._pos) specifies ``` _pos of dtype float32 of...

hmacdope

cmaps are not correctly merged with Merge()

3

## Is your feature request related to a problem? ## I don't think cmaps is properly considered as TopologyObjects. ``` u1 = mda.Universe('xxx.pdb') u2 = mda.Universe('xxx.pdb') u1.add_TopologyAttr('cmaps', [[0,1,2,3,4]]) u2.add_TopologyAttr('cmaps', [[4,5,6,7,8]])...

ksy141

RDF along axis

3

## Is your feature request related to a problem? ## I would like to be able to compute RDFs along a specific axis, which may or may not vary along...

dpadula85

compile Cython extensions with Cython >= 3.0

9

Fixes #2988 Changes made in this Pull Request: - Do not any longer use deprecated NumPy API. - requires Cython >= 3.0 (tested locally with 3.0a6) - fixed direct ndarray.base...

orbeckst

Collective analysis of different analysis classes on the same trajectory

6

_Disclaimer: I thought there was an issue in the past with this idea but I was not able to find it. Sorry if the following idea is a duplication_ ##...

PicoCentauri

PDBx/mmCIF Reader/Topology Reader

22

Hi all, I've been using OpenMM to run simulations for the past couple of years. Unlike other tools, OpenMM does not write a 'topology' file (e.g. `.gro`, `.prmtop`) but instead...

JoaoRodrigues