Oliver Beckstein

mda.fetch_pdb() to generate Universe from Protein Databank structures

8

## Is your feature request related to a problem? ## We used to have `mda.fetch_mmtf()` to get a structure from the PDB but with the demise of MMTF, this was...

Remove encore (following its deprecation #4274 in favor of the [mdaencore](https://github.com/MDAnalysis/mdaencore) MDAKit) Remove analysis.encore - [ ] code - [ ] tests - [ ] CI - [ ] add...

`analysis.atomicdistances.AtomicDistances` does not use Results

9

## Expected behavior ## All analysis classes [based on AnalysisBase](https://docs.mdanalysis.org/stable/documentation_pages/analysis/base.html) store results in an instance of [MDAnalysis.analysis.results.Results](https://docs.mdanalysis.org/stable/documentation_pages/analysis/results.html#MDAnalysis.analysis.results.Results) > Results are always stored in the attribute [AnalysisBase.results](https://docs.mdanalysis.org/stable/documentation_pages/analysis/base.html#MDAnalysis.analysis.base.AnalysisBase.results), which is an instance...

asv: remove distances.DistancesBench.time_contact_matrix_sparse 10,000 benchmark

1

## Expected behavior ## All ASV benchmarks for the latest develop run (see [benchmarks.benchmarks](https://github.com/MDAnalysis/mdanalysis/tree/develop/benchmarks/benchmarks) for the code and the [MDAnalysis/benchmarks](https://github.com/MDAnalysis/benchmarks) repo + the [benchmarks wiki](https://github.com/MDAnalysis/benchmarks/wiki) for more details.) ## Actual...

asv: fix GeoSelectionBench.time_geometric_selections

5

## Expected behavior ## All ASV benchmarks for the latest develop run (see [benchmarks.benchmarks](https://github.com/MDAnalysis/mdanalysis/tree/develop/benchmarks/benchmarks) for the code and the [MDAnalysis/benchmarks](https://github.com/MDAnalysis/benchmarks) repo + the [benchmarks wiki](https://github.com/MDAnalysis/benchmarks/wiki) for more details.) ## Actual...

## Expected behavior ## All ASV benchmarks for the latest develop run (see [benchmarks.benchmarks](https://github.com/MDAnalysis/mdanalysis/tree/develop/benchmarks/benchmarks) for the code and the [MDAnalysis/benchmarks](https://github.com/MDAnalysis/benchmarks) repo + the [benchmarks wiki](https://github.com/MDAnalysis/benchmarks/wiki) for more details.) ## Actual...

Follow-up on PR #1695, which included initial tests for distance based calculations. The comments noted a few issues * use of core.flags https://github.com/MDAnalysis/mdanalysis/pull/1695#discussion_r148338963 * clear separation of tests with and...

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...

As part of running MDAKit tests https://github.com/MDAnalysis/MDAKits/actions/runs/16355349978/job/46212233563#step:10:169 the following error came up: ``` ==================================== ERRORS ==================================== _____________________ ERROR collecting test_rdf_parser.py ______________________ ../../../miniconda3/envs/test/lib/python3.12/site-packages/solvation_analysis/tests/test_rdf_parser.py:88: in ("fec_F", np.NaN), ^^^^^^ ../../../miniconda3/envs/test/lib/python3.12/site-packages/numpy/__init__.py:781: in __getattr__ raise...