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Benchmarks for more lib.distances methods required

9

We need benchmarks for the following functions: - `lib.distances.calc_bonds` - `lib.distances.calc_angles` - `lib.distances.calc_dihedrals`

richardjgowers

Type Hints for Analysis Classes

7

## Is your feature request related to a problem? ## With the first version of the CLI released, we now would like to support more Analysis classes. This is especially...

PicoCentauri

## Is your feature request related to a problem? ## #3511(after merging) will add `daltons` as a dependency to the `OpenMMTopologyParser` for which `openmm` library needs to be installed. But...

Atharva7K

Cleaning up analysis.__ini__ and hole2 docs

3

As discussed in this thread: https://github.com/MDAnalysis/mdanalysis/pull/2778#discussion_r443195698 the `analysis.__init__` docstring doesn't seem to be used anywhere and is somewhat superseded by `analysis_modules.rst`, thoughts on what to do with this text? Furthermore,...

IAlibay

Implements compact wrapping and nojump, and updates associated transforms.

11

Implemented function `distances.apply_compact_PBC`. With it I could easily adapt `AtomGroup.wrap()` to also do compact wrapping, depending on a keyword. Backward compatibility is maintained. Also optimized the way `compound_indices` are handled...

mnmelo

Clarify differences between waterdynamics MSD and Einstein MSD

1

We should clarify what the differences are between the `EinsteinMSD` code and the `waterdynamics` MSD code. AFAIK the primary difference is that currently the waterdynamics MSD code accepts updating atom...

hmacdope

Feature: AtomGroupGroup

19

So this is kind of inspired by https://groups.google.com/forum/#!topic/mdnalysis-discussion/eqegNLWvHAY and also some other work I did on coarse-graining before. Wouldn't it be cool if we could do something like: ```python from...

richardjgowers

An example for loading a LAMMPS data (topology) and dump (trajectory) pair in MDAnalysis documentation

5

## Problem ## There is no example in the documentation that shows how a pair of LAMMPS data (topology) and dump (trajectory) can be loaded with the *format="LAMMPSDUMP"* option of...

amirhs1

Add contexts to guess attributes better (especially elements and masses)

10

I started writing this as a comment in #2553 but it got, wow, *really* long. Let me know if I should move it there to carry on the discussion, or...

lilyminium

WIP: Lammpsdump velocities (and other fields)

4

Following #3360 (thanks for the great work!) I was implementing a first draft of a parser for the velocities. Before adding tests I quickly wanted to hear if the way...

schlaicha