Philip Loche

`center` attribute does not take cell dimensions into account

14

## Expected behavior ## Calculating center positions like the center of mass in a periodic cell should take the periodicity into account. An edge case to test are two particles...

Inconsistency between LAMMPS cell origin and coordinates

3

## Is your feature request related to a problem? ## Simulation cells in MDAnalysis (MDA) are defined via the `dimensions` attribute defining the cell via 3 lengths and 3 angles....

Restructured WaterOrientationalRelaxation

11

Partly Fixes MDAnalysis/waterdynamics#22 Changes made in this Pull Request: The `WaterOrientationalRelaxation` was restructured to follow the `start`, `stop` and `step` attributes of the `AnalysisBase`. The documentation was also improved and...

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_ ##...

Long-term solution for import sorting

7

## Is your feature request related to a problem? ## As [discussed](https://github.com/MDAnalysis/mdanalysis/pull/3644#issuecomment-1100836585) in #3644 I am always frustrated when I see unsorted imports 🙃. Especially, for a new import, it...

Cleanup and restructure of AnalysisBase classes docstrings

21

Fixes #919 Fixes #3651 Changes made in this Pull Request: * Deprecate `verbose` parameter in `AnalysisBase.__init__` (follows issue #3651) * Moved all docstrings from `__init__` function to class docstring (follows...

Deprecate `verbose` option in initialization of `AnalysisBase`

9

## Is your feature request related to a problem? ## The verbose option for Analysis classes appears in the `init` function and as well in the `run` method. The first...

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...

Improve error message when calling `AtmGroup.unwrap()` without bonds

2

When calling the `unwrap()` method of an `AtomGroup` the method correctly checks for existing bonds and raises an error if this is not the case. https://github.com/MDAnalysis/mdanalysis/blob/24abb160788ef87a48ed6eb196c1704d68fbc2da/package/MDAnalysis/core/groups.py#L1827-L1829 Even though the error...

Add an `AnalysisCollection` class

18

Fixes #3569 The `AnalysisCollection ` follows the discussion of #3569 resetting the timestep object for each analysis by default. If requested the user can set the `reset_timestep` variable to `False`...