SepTop analysis notebook #225
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Line #15. dg_0 = json_0["estimate"].magnitude
Would need to guard this with some try/excepts here, in case:
- You picked up a file that isn't a results JSON.
- The estimate is None for any of the repeats.
- There is not file for some repeats.
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The code is now filtering for result json files, raises a ValueError if the estimate is None, and when only a single repeat is provided, uses the MBAR error as uncertainty and uses the standard deviation if results from more results are provided. We may want to change this in the future.
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We'd probably want to give them a few flavours of this:
- What if they want to look at the individual legs of the cycle (i.e. look if things are going wrong with the solvent or complex leg)?
- What if they want to get a dG (here we can just refer to the cinnabar cookbook).
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Line #12. # Use standard deviation as error when more than 1 repeat
Maybe this is a more general problem with the error estimation but you would want to switch all edges to use the MBAR error if any edge has a single repeat; otherwise, the errors might have very different magnitudes due to how the MBAR estimator works and you would bias the MLE predictions to the edges with errors from MBAR.
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@jthorton , I agree, that would be better! I won't have time to do this before my vacation, would you maybe be able to change this?
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No problem I can add that in!
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