webng.analysis package
Submodules
webng.analysis.analysis module
webng.analysis.average module
- class webng.analysis.average.weAverage(opts)[source]
Bases:
weAnalysis
Class for the averaging analysis.
This tool creates a N by N matrix-like plot where N is the number of observables in the BNGL tool (unless overridden by the dimensions option). The diagonal will contain 1D probability distributions and off diagonals will contain 2D probability heatmaps of each dimension vs each other dimension.
This tool uses w_pdist WESTPA tool to calculate probabilty distributions hence it needs w_pdist to be accessible directly from the commandline.
webng.analysis.cluster module
- class webng.analysis.cluster.weCluster(opts)[source]
Bases:
weAnalysis
webng.analysis.evolution module
- class webng.analysis.evolution.weEvolution(opts)[source]
Bases:
weAnalysis
Class for the evolution analysis.
This tool creates N plots where N is the number of observables (unless overridden by the dimensions option). Each plot contains the evolution of the 1D probability distirubion over WE iterations.
This tool uses w_pdist WESTPA tool to calculate probabilty distributions hence it needs w_pdist to be accessible directly from the commandline.
webng.analysis.network module
webng.analysis.utils module
- webng.analysis.utils.circumcircle(P1, P2, P3)[source]
Used for plotting voronoi center in average analysis.
Adapted from: http://local.wasp.uwa.edu.au/~pbourke/geometry/circlefrom3/Circle.cpp
- webng.analysis.utils.pull_all_data(n_iter, iter_group)[source]
This function reshapes the progress coordinate and auxiliary data for each iteration and retuns it to the tool.
- webng.analysis.utils.pull_data(n_iter, iter_group)[source]
This function reshapes the progress coordinate and auxiliary data for each iteration and retuns it to the tool.
- webng.analysis.utils.pull_weight(n_iter, iter_group)[source]
Custom weight puller for a custom version of w_pdist. This will probably eventually make it into the main repo