add relprop for atom selection and corresponding UT
#4841
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## develop #4841 +/- ##
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Files 177 189 +12
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Looks sensible at first glance.
In addition to the inline comments, could you please also add documentation to core.groups.AtomGroup.select_atoms() after prop
mdanalysis/package/MDAnalysis/core/groups.py
Line 2995 in ac145ec
prop 's docs) so that we can see how users would use it.
UPDATE: I added a few more comments after submitting my review. Please look at these, too. In particular, can you please explain the rationale for comparing to the COM of the reference group instead of calculating all distances and then comparing the min?
Additionally, the comparison needs to be able to take into account PBC (periodic=True).
package/MDAnalysis/core/selection.py
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| values = values[:, col] | ||
| sel = self.sel.apply(group) | ||
| rel_value = ( | ||
| sel.center_of_geometry().reshape(3).astype(np.float32)[col] |
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Your docs should make clear that the COM of the second group is used.
Is this what this selection should do? Or should it calculate all-vs-all distances and then compute the min over all distances and then compare this minimal distance to the value?
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When using center_of_geometry you also need to think carefully to what value wrap and unwrap needs to be set, especially if the user does not get a choice in setting it.
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Yes. COG (not COM) is what I want to implement. In my cases, the planar surfaces are used, and taking the average positions of the surfaces is better than the minimal distances as reference. But I can see the case when the minimal distance would be a better choice, for example, for the curved surfaces. I suggest to have a new selecton class. What is your opinion?
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Hello @ChiahsinChu! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found: There are currently no PEP 8 issues detected in this Pull Request. Cheers! 🍻 Comment last updated at 2025-01-07 05:28:06 UTC |
Implementaton of #4838
Changes made in this Pull Request:
relpropkeyword for atom selectionI will update the User Guide once this implementation (especially the interface to users) is accepted.
PR Checklist
Developers certificate of origin
📚 Documentation preview 📚: https://mdanalysis--4841.org.readthedocs.build/en/4841/