Vis progress

args = parser.parse_args() module-attribute

parser = argparse.ArgumentParser(description='Script that will read the h5 file and create plots to visualize the progress of the simulation.') module-attribute

settings = check_input_settings_file(args.settings) module-attribute

west = h5py.File(args.h5file, 'r') module-attribute

get_pcoords_for_plotting(westfile, settings)

Gets the pcoord and auxdata from the west.h5 file.

PARAMETER	DESCRIPTION
westfile	path to the west.h5 file. TYPE: str
settings	dictionary containing the settings for the analysis. TYPE: dict

RETURNS	DESCRIPTION
results	dictionary containing the pcoord and auxdata. TYPE: dict

obtain_paths_highest_rmsd_jd_weight(max_rmsd, max_jd, max_weight, reverse_iterations)

Determines the paths with highest RMSD, JD, and weight.

PARAMETER	DESCRIPTION
max_rmsd	list containing the maximum RMSD. TYPE: list
max_jd	list containing the maximum Jaccard distance. TYPE: list
max_weight	list containing the maximum weight. TYPE: list
reverse_iterations	list containing the iterations in reverse order. (?) TYPE: list

RETURNS	DESCRIPTION
dict	dictionary containing the highest rmsd, jd, and weight paths. TYPE: dict

plot(jd, rmsd, title, outdir, filename)

Plots the Jaccard distance and the RMSD of the pocket heavy atoms. The plot will be saved to the specified directory.

PARAMETER	DESCRIPTION
jd	list containing the Jaccard distance. TYPE: list
rmsd	list containing the RMSD of the pocket heavy atoms. TYPE: list
title	title of the plot. TYPE: str
outdir	path to outdir. TYPE: str
filename	name of the file. TYPE: str

plot_histogram(results, key, title, directory=None)

Plots the histogram of the specified key. The plot will be saved to the specified directory.

PARAMETER	DESCRIPTION
results	dictionary containing the results of the analysis. TYPE: dict
key	key to plot. TYPE: str
title	title of the plot. TYPE: str
directory	path to outdir. TYPE: str DEFAULT: None

plot_num_walkers(west, outdir)

Plots the number of walkers per iteration. The plot will be saved to the specified directory.

PARAMETER	DESCRIPTION
west	h5 file containing all the info for the simulation. TYPE: h5file
outdir	path to outdir. TYPE: str

plot_stuff(jd, min_md_jd, max_md_jd, average_jd, jd_max, jd_min, jd_sd)

Plots the Jaccard distance against iteration. The plot will be saved to the specified directory.

PARAMETER	DESCRIPTION
jd	list containing the Jaccard distance. TYPE: list
min_md_jd	minimum Jaccard distance of the MD simulations. TYPE: float
max_md_jd	maximum Jaccard distance of the MD simulations. TYPE: float
average_jd	average Jaccard distance of the MD simulations. TYPE: float
jd_max	list containing the maximum Jaccard distance. TYPE: list
jd_min	list containing the minimum Jaccard distance. TYPE: list
jd_sd	list containing the standard deviation of the Jaccard distance. TYPE: list

rolling_average(data, window)

Gets the rolling average. The end of the list will only make the window smaller.

PARAMETER	DESCRIPTION
data	list of the data to obtain the rolling average. TYPE: List[float]
window	size of the window to use. TYPE: int

RETURNS	DESCRIPTION
average	list containing the rolling average. TYPE: list