Jonathan Barnoud

run mypy and pyright in CI

4

## Is your feature request related to a problem? ## Type hinting is an addition to modern python that helps detect errors before runtime. Type analysis must be run on...

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: ``` ____________...

Support for Gromacs's TNG format

10

Gromacs is slowly moving toward the new TNG trajectory format. The format got introduced in the late releases of the 4 serie, and should become the default format eventually. TNG...

Unpacking errors in x3dna

3

At least 2 lines in the legacy x3dna module use unpacking with too many values to unpack. https://github.com/MDAnalysis/mdanalysis/blob/97ec6df207fa934095ffb093daadf319ca2bfb38/package/MDAnalysis/analysis/legacy/x3dna.py#L204 https://github.com/MDAnalysis/mdanalysis/blob/97ec6df207fa934095ffb093daadf319ca2bfb38/package/MDAnalysis/analysis/legacy/x3dna.py#L213-L216 In both occurrences, the left side expects 6 values, but 12...

Lazy index building for XTC and TRR tajectories

4

## Is your feature request related to a problem? ## Reading an XTC or TRR trajectory for the first time can be very slow, especially for large files. This is...

Provide flexibility to define what is a protein

10

The selector used to select what is a protein is very limited and uses a hardcoded list of protein residues. I encountered limitations due to that while using specific names...

Add "how to contribute" to the README

1

Instruction on how to contribute would make contributors welcome.

martinize2 always writes the itp files in the working directory

1

The command line lets you choose where the output PDB and TOP will be written, though the ITP files are always written in the working directory. This causes 2 issues:...

For the 4th biounit of 1zmx, the top file contains ``` #include "martini.itp" #include "molecule_0.itp" #include "molecule_1.itp" #include "molecule_0.itp" #include "molecule_2.itp" #include "molecule_3.itp" ``` This leads to grompp complaining: ```...

``` WARNING - unknown-residue - Can't add bonds based on atom names for residue D-HYP13 because 'Residue HYP is not known to force field universal'. Falling back to distance criteria....