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feat: add RelPropertySelection to select atoms based on positions relative to a given selection #4838

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ChiahsinChu opened this issue Dec 16, 2024 · 5 comments · May be fixed by #4841
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feat: add RelPropertySelection to select atoms based on positions relative to a given selection #4838

ChiahsinChu opened this issue Dec 16, 2024 · 5 comments · May be fixed by #4841
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Component-Selections decision needed requires input from developers before moving further enhancement

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@ChiahsinChu
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Is your feature request related to a problem?

When investigating the solid/liquid interface, I would like to take the outermost solid atoms as the reference and analyse the liquid close to the surface (e.g., <= 5 angstroms away from the surface in the direction perpendicular to the surface). However, the reference might shifts during the simulation, and I would like to find a selection updated on-the-fly.

Describe the solution you'd like

I'd like to add a new selection class RelPropertySelection, which can be used in the following way:
relprop [abs] property operator value selection
For example, if I want to choose the water with the z distances to the surface smaller than 3 ang, I can use:
relprop z < 3.0 surface
where surface is the selection of the outermost surface atoms.
@orbeckst
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Sounds like an interesting selection operator.

Do other tools provide similar functionality?

@ChiahsinChu
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As far as I know, no. I have implemented this feature (though in v2.3.0) in my own mda fork. The implementation is simple, and it should not influence the functionality of other modules in the selection.

@orbeckst
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If you already have an implementation then please feel free to put up a PR. It's easier to discuss concrete code than code in the abstract.

@ChiahsinChu ChiahsinChu linked a pull request Dec 18, 2024 that will close this issue
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@orbeckst
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@MDAnalysis/coredevs what do you think about adding a relprop selection operator to the selection language?

You can just 👍 or 👎 this comment (and of course add any comments of your own).

@orbeckst orbeckst linked a pull request Dec 19, 2024 that will close this issue
add relprop for atom selection and corresponding UT #4841
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@RMeli
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RMeli commented Dec 19, 2024

It could be useful, so why not. However, relprop doesn't say anything to me; is this a standard name? If not, can we thing of something more explicit?

@orbeckst orbeckst added the decision needed requires input from developers before moving further label Dec 20, 2024
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add relprop for atom selection and corresponding UT ChiahsinChu/mdanalysis
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@orbeckst @RMeli @ChiahsinChu