Utils

Input/Output

Helper functions for loading dataframes (incl. PLUMED files) and directly creating datasets from them.

load_dataframe(file_names[, folder, start, ...])	Load dataframe(s) from file(s).
create_dataset_from_files(file_names[, ...])	Initialize a dataset from (a list of) files.

Time-lagged datasets

Create a dataset of pairs of time-lagged configurations.

create_timelagged_dataset(X[, t, lag_time, ...])

Create a DictDataset of time-lagged configurations.

FES

Trainer

Functions used in conjunction with the lightning Trainer (e.g. logging, metrics…).

MetricsCallback()

Lightning callback which saves logged metrics into a dictionary.

Compute (and plot) the free energy surface along the CVs.

compute_fes(X[, temp, fes_units, kbt, ...])

Compute the Free Energy Surface using a kernel density estimation (KDE) along the given variables.

Plotting utils

plot_metrics(metrics[, keys, x, labels, ...])	Plot logged metrics.
plot_features_distribution(dataset, features)	Plot distribution of the given features.