Page on trajectories and on-the-fly transformations #40
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orbeckst
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orbeckst
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Covers the essentials very nicely, see comments for possible changes.
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@orbeckst @richardjgowers I'll merge this tomorrow unless there are objections? |
| On-the-fly transformations | ||
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| An on-the-fly transformation is a function that modifies the data contained in a trajectory :class:`~MDAnalysis.coordinates.base.Timestep`. It is called for each current time step as it is loaded into memory. A transformation function must also return the current :class:`~MDAnalysis.coordinates.base.Timestep`, as transformations are often chained together. |
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Maybe clarify that the point is so that the transformations are applied automatically/silently as filters (though maybe this word in ambiguous) to provide the desired representation of your system.
One example of x+2 below is good for custom plugin demonstration, but the residue one is (as far as I can tell) useless? Maybe better is to show how to unwrap every frame to rectify a simulation output for visualisation?
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I took that out and added in an example unwrapping, entering a protein in a box, and wrapping water around it. Unfortunately normal reStructuredText files don't let me embed NGLView widgets, but I'll be able to link to related notebooks on transformations when #38 is merged.
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@lilyminium this needs to get merged right? I didn't understand the merge conflict :( |
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Yes! Fixed the merge conflicts. This will be more informative than the current stub. |
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@orbeckst @richardjgowers if you're happy with the little addition of "how to set boxes for every frame" to the OTF transformations page, this PR can set the user guide to 1.0 |
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The box setting example is good in principle. I would just use more realistic numbers such as 10,20,30 instead of an almost pathological box.
I don’t know if you have an example for wrap/unwrap (sorry no time to check) but if not, one could pretty much take the blog post with its animated gifs. Anyway, can come later, just remembered.
Oliver
… Am 11.06.2020 um 03:03 schrieb Lily Wang ***@***.***>:
@orbeckst @richardjgowers if you're happy with the little addition of "how to set boxes for every frame" to the OTF transformations page, this PR can set the user guide to 1.0
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Thanks @orbeckst, that's a good idea and we could just link it instead of replicating it; I'll look into it tomorrow :-) |
orbeckst
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orbeckst
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lgtm (just in case more green approval marks make you feel good about work that's already outstanding)
Closes MDAnalysis/mdanalysis#2269
This PR fleshes out the Trajectories page to explain roughly how it works and why you have to iterate over it. It also has a brief intro to on-the-fly transformations.
Are there any other trajectory-related concepts that are important to cover?