Open elkhoury opened 7 years ago
This sounds like something we should be able to easily add to the CLI for analysis. We already support --start XXX
and --end YYY
for trajectory analysis, so we'd just have to pass these on to yank.analysis.analyze_directory()
and modify this code to handle that.
Should be easy enough. There is no public API way to do this right now, but you can follow the logic of the analyze_directory
function in the source code @jchodera linked to piece together a temporary solution.
@elkhoury by "convergence plots" do you mean in the Jupyter Notebooks plots from yank analyze report
?
Yes, I mean the convergence plots generated in the Jupyter Notebooks.
Thank you @jchodera, @lnaden
The Analyzer
classes now have a Analyzer.max_n_iterations
property that you can use to limit the number of iterations you want to analyze (implemented in #915). There's still no hook through the CLI for this, but for now, you can add
analyzer_kwargs['max_n_iterations'] = 1000
in the first cell of the Jupyter notebook.
We would like to analyze a subset of the simulation (e.g. 1000 iterations out of 20000 iterations) in order to have the calculated free energies and the convergence plots.
Is there a way to automatically analyze subsets of the data?
Thank you,
Léa El Khoury
(@davidlmobley, @renm1)