notebooks

Notebooks

figures contains notebooks for loading data and rendering figures the paper.

• See the README.md file in figures for more information

anton2 contains the majority of calculations for the CVs, DGA quantities, and other quantities. It is organized as follows:

• cvs contains notebooks for computing CVs (collective variables, e.g. salt-bridge distances) from the raw trajectories
• dga_calculations contains notebooks for DGA calculation of kinetic statistics. The majority of statistics used for the figures are found in dga_220325.ipynb.
• The remaining notebooks contain various other analyses, some of which are used for the figures.

fitting contains experiments for learning the committor using different methods (of which the LASSO was used in the paper).