mdanalysis

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mda.fetch_alphafold()

4

## Is your feature request related to a problem? ## Can we have `mda.fetch_alphafold()` to get a model from https://www.alphafold.ebi.ac.uk/ ? ## Describe the solution you'd like ## ```python u...

orbeckst

Fast cythonized inverse array of unsorted, unique indice

9

Fixes #3387 Changes made in this Pull Request: - Added cython implementation of inverse of unsorted, unqiue array - Replaced python code in groups.py with new cython function - Added...

mdaviesNCL

Replace custom lib.util.which with shutil.which

4

Given the newest version of MDAnalysis support Python 3.6+, is it reasonable to replace `lib.util.which` with [`shutil.which`](https://docs.python.org/3/library/shutil.html)? They seems to have identical intended uses and functionality. Using the standard library...

Seanny123

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...

PicoCentauri

Applying Transformation to Chain of Traj doesn't Apply to First Frame of 2nd, 3rd... trajectories

9

## Expected behavior ## After creating a universe with multiple trajectory files, and a series of transformations are applied following the protein example. Those transformations are expected to be applied...

jaclark5

Inconsistent resnames when loading pdb and mol2 with repeat resnums

1

## Expected behavior ## I am using a PDB file that appears to be prepared incorrectly and includes residue number 200 for both the ligand and a protein residue. When...

zwsmith200

Code formatting, style guide enforcement and static checks

25

I recently started using code formatting (with [black](https://black.readthedocs.io/en/stable/)), style guide enforcement (with [flake8](http://flake8.pycqa.org/en/latest/index.html#)) and static code checks (with [mypy](http://mypy-lang.org/)). I tried to apply them to MDAnalysis for fun and came...

RMeli

Have LinearDensity support updating AtomGroups, more intuitive names, save bins

7

**Is your feature request related to a problem? Please describe.** 1. [This mailing list issue](https://groups.google.com/forum/#!searchin/mdnalysis-discussion/density%7Csort:date/mdnalysis-discussion/hTcPz8jaE_A/gUa5arH8AgAJ) is a good use case of Linear Density but is foiled by the class not...

lilyminium

Allow LammpsDumpParser Topology reader more flexibility in coordinate column data.

21

## Is your feature request related to a problem? ## The LAMMPS DumpParser topology creator is somewhat inflexible in the column format it expects. Now that we support other coordinate...

hmacdope

Update align.alignto method

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Fixes #1825 Changes made in this Pull Request: - The value of parameter "subselection" of method align.alignto was set to "all" if the mobile and reference `AtomGroup`s came from the...

JoseAntonioSiguenza