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MDAnalysis / mdanalysis

MDAnalysis is a Python library to analyze molecular dynamics simulations.
https://mdanalysis.org
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Ensemble of Universes #2663

Open lilyminium opened 4 years ago

lilyminium commented 4 years ago

Is your feature request related to a problem?

I think a lot of people simulate in replicate and need to account for that, calculating PCA for a shared subspace or clustering over an ensemble, etc. It's always a bit tedious tracking which frame is from where. Also, analyses like the encore library operate on ensembles. Encore deals with this by merging them into a new Universe and pulling all the frames into memory, sometimes multiple times. This gets prohibitively large quite quickly, especially when you only care about a small selection of atoms (e.g. alpha-carbons) in your full solvated universe.

Describe the solution you'd like

Have a Universe container that holds Universes and has convenience methods for iterating over selected frames and selecting atoms from each Universe, allowing for different atom indices from each.

Describe alternatives you've considered

Additional context

@orbeckst once noted that analysis functions can't use FrameIterators so I overengineered a container that could be used in place of a Universe.trajectory in AnalysisBase classes.

orbeckst commented 4 years ago

That’s a neat idea. It’s also fairly localized so could even be labelled “experimental” for a start until we figure out under which circumstances it breaks.

I also like it because with ChainReader and Ensemble we would be supplying functionality to aggregate existing data in a way that makes analysis simpler.

orbeckst commented 2 years ago

@alescoulie did you want to share your thoughts on ensemble analysis here?

ALescoulie commented 2 years ago

I've been experimenting with ensemble analysis and was able to make a decorator that creates a wrapper of analysis base classes to accept an ensemble group I created around just storing a dictionary of universes, and extending some of the universe functionality to that group. It's a relatively simple solution compared to what @lilyminium has been working on. I've started working on a PR based on this for MDAnalysis.