Comments (6)
@wenchangzhou-qtx we're working on a programmatic way of constructing the object (#84), it shouldn't be too long, but for now I'd recommend the file format.
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I think there are ways to use the API in a python script that doesn't involve passing through that [ugly] csv file. You might want to check the docstring of the FEMap object for this purpose https://github.com/OpenFreeEnergy/cinnabar/blob/main/cinnabar/femap.py#L54
That said, I agree in that we probably need to update the examples we have and add one that uses the API instead of the CSV file.
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Hmm, I think what's happening here is the MLE method gives DG estimates from the computed DDG values, but these are centered around 0. There's then a choice of rescaling these up to the experimental values, or as is happening here the experimental results are brought back down to the 0-centered MLE values
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@richardjgowers yeah, confirmed. I switched off centralizing
(True
by default), now I can get reasonable plot at least from what is shown in the x and y axis. But all the data points are off the diagonal, I guess these data points are dummies right?
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In order to use this tool, do I need to prepare my own results following the exact format of example.csv
?
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Hey @richardjgowers, just check with you whether this new feature is now available, I might miss the announcement somewhere.
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Related Issues (20)
- not catching node name mismatch HOT 3
- Update readme and examples
- Add plot_bar to plotly example notebook
- Seaborn calls in WhyNotToUseR2ForDDG notebook fail
- Versioneer causing failures on conda-forge builds HOT 1
- add controllable guidelines on plots
- make FEMap a gufe tokenizable HOT 4
- base class for MLE estimation-like methods
- FEMap add to/from networkx method
- add option for get_absolute_dataframe to shift values HOT 1
- Update API docs
- Add userguide docs
- Update changelog docs
- MLE ddG errors != calculated ddG errors for open cycle
- [Question] Allow arbitrary xy tick frequency when plotting
- Refactor stats into base and derived class so we can drop in different MLE solvers? HOT 1
- readthedocs is deeply unhappy
- Error of exactly zero will trigger SVD failure when generating absolute values
- refactoring bootstrap stats HOT 2
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