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msmbuilder / msmexplorer

Data visualizations for biomolecular dynamics
http://msmbuilder.org/msmexplorer/
MIT License
17 stars 17 forks source link

add implied timescales plot vs lag time #89

Closed jeiros closed 7 years ago

jeiros commented 7 years ago

I'd be interested in having an implied timescales plot API. Do you have in mind adding it? I could give it a go.

cxhernandez commented 7 years ago

What did you have in mind for the command arguments? A list of msmbuilder.msm.MarkovStateModel objects perhaps?

jeiros commented 7 years ago

Yes, that's what I thought. A list of msm objects each calculated at a different lag time.

Another option would be passing a list of lag times, with an extra argument for a clustered trajectories list (a list of np.arrays). But that would mean that the actual computation of the msms is done inside the function (which I don't know if it's consistent with the rest of your API, from the looks of it it's all basically plotting functions without too much computation, so you leave the actual computation of msms to the user and msmbuilder).

cxhernandez commented 7 years ago

done in #90