Richard Gowers

Add copy method to AuxReader

4

A copy method needs to be added to `MDAnalysis.auxiliary.base.AuxReader` which should work similarly to the ReaderBase copy method. This should then be extended to include the [XVGReader](https://github.com/MDAnalysis/mdanalysis/blob/develop/package/MDAnalysis/auxiliary/XVG.py).

Setting attributes should have dtype checks

20

Our Topology system is statically typed, each `TopologyAttr` ([found here](https://github.com/MDAnalysis/mdanalysis/blob/develop/package/MDAnalysis/core/topologyattrs.py)) should only accept one data type, e.g. atom names ([here](https://github.com/MDAnalysis/mdanalysis/blob/develop/package/MDAnalysis/core/topologyattrs.py#L769)) should always be strings, resids should always be ints. Currently...

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`

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...

## Description I couldn't see anywhere where the effective length of the data was exposed so I added it. I couldn't see where the other similar properties were tested, so...

started adding ether trappe-ua to forcefield

3

I'm trying to add the parameters from here: https://pubs.acs.org/doi/abs/10.1021/jp049459w couple questions - is this a good idea? or is the idea that people make their own xml files and store...

double bonds

2

So adding double bonds (ie `C=O`) I guess this is low priority because by defining the coordination of atoms this is implicit? If we wanted to add this, from what...

Read secondary structures

5

## Is your feature request related to a problem? ## PDB files have quite a few fields, why not read this data? ## Describe the solution you'd like ## Atom...

AtomMapping distance scoring functions not working with OFF tk 0.11

2

The atom mapping scoring seems to have been broken by off tk 0.11, see here: https://github.com/choderalab/perses/blob/main/perses/rjmc/atom_mapping.py#L1142 gives: ```/usr/share/miniconda3/envs/openfe/lib/python3.9/site-packages/perses/rjmc/atom_mapping.py:1132: in dist return np.linalg.norm(b-a) _ _ _ _ _ _ _ _...

DSLangmuir fitting problems

2

The fitting method for the dual-site Langmuir isotherm doesn't seem to work very well. I've included an example of data where it fails. ```python df = pd.read_csv('./data.csv', sep=' ') T1...