mdanalysis

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Read biological assembly information where available.

4

## Is your feature request related to a problem? ## I would like to have access to the different symmetry operations required to build a biological assembly from a file...

BradyAJohnston

Extend Implementation of Unwrap

4

The current implementation of Group.unwrap(PR [#2189](https://github.com/MDAnalysis/mdanalysis/pull/2189)) works for bonded structures. This method should also work for molecules which are part of the same group, e.g., DNA molecules. **Proposed Solution** -...

NinadBhat

Nojump transform using the “hybrid unwrap” scheme

3

## Is your feature request related to a problem? ## MDAnalysis does not have a transformation to create “unwrapped” no-jump trajectories where particles are never put back in the primary...

orbeckst

BLD: install issues on M1 mac

12

`python3 setup.py install --user` on the gcc compile farm M1 machine manages to build MDAnalysis, but then it tries to install deps, and `gsd` cannot be built from source: ```...

tylerjereddy

RDKit Descriptors and fingerprints wrapper

14

Part of the fixes for #2468 Depends on #2775 Changes made in this Pull Request: - RDKit descriptors can be calculated from the `RDKitDescriptors` class, as a subclass of AnalysisBase...

cbouy

Wrap RDKit drawing code for AtomGroups

5

Part of #2468 Depends on #2775 Changes made in this Pull Request: - In notebooks, by importing `from MDAnalysis.visualization.RDKit import RDKitDrawer`, the default representation of the AtomGroup is changed for...

cbouy

retire "master" branch

11

# Background MDAnalysis has existed for a while and so there’s a bit of history built into our development process. One of these pieces of history is that we follow...

orbeckst

## Expected behavior ## Our tests do not use deprecated constructs that will be removed. ## Actual behavior ## Tests trigger `DeprecationWarning` for uses of using the `rmsf` attribute instead...

orbeckst

Follow up from #3685 - in order to fix copying of readers we have a rather cumbersome decorator in place. As @lilyminium mentioned it _might_ be possible to get this...

IAlibay

Restructured WaterOrientationalRelaxation

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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...

PicoCentauri