adding additional "simple" analysis tools?

[Oliver Beckstein]

Hi Devs,

In the discussion on the nuclear acid analysis module rewrite, it came also up that we don’t have analysis classes to do very basic things such as “compute the distances between each pair of atoms, dist(a[i] - b[i])  in two groups a and b” (or angles for that matter). Other packages provide such functionality.  

I opened https://github.com/MDAnalysis/mdanalysis/issues/3654 to propose to add a simple distances.DistanceAnalysis. For any seasoned MDAnalysis developer this will be trivial and I am sure that anyone who knows about calc_bonds() has written an efficient implementation already. However, especially people new to MDA might not know all the tricks and might not know the fastest way to calculate distances under PBC, so having such “trivial” tools might still help. 

My reasons for proposing are:

+ convenience for users, especially new ones

+ improve reproducibility (using well tested building block code)

+ reduce code duplication

+ make basic analysis available in mdacli

+ serves as simple “best practice” examples

There are downsides:

- more code to maintain

- potentially overkill for a simple problem

- need more documentation (especially in the User Guide)

Implementing such tools would be good “first issues” (especially for GSOC/Outreachy applicants).

Do you think that we should add “trivial” analysis tools like the above? If yes, what other tools should we add? 

Oliver

--

Oliver Beckstein (he/his/him)

email: orbe...@mdanalysis.org
twitter: @orbeckst

GitHub: @orbeckst

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