pyqmmm.md.restraint_plotter

Creates a series of KDE plots based on HYSCORE-guided simulations

Module Contents

Functions

config()	Parses the config file for the users parameters.
combine_inp()	Combines a CPPTRAJ output file with angles and another with distances.
get_xy_data(filename)	Takes a combined file and destructures it into arrays.
collect_xyz_data(filenames)	Retrieves the x and y data from the files.
compare_patch_limits(x_data, y_data, patch_params)	Checks all the data sets and decides what the x and y bounds should be.
get_plot_limits(x_data, y_data, plot_params)
graph_datasets(x_data, y_data, z_data, labels, ...)
restraint_plots()

pyqmmm.md.restraint_plotter.config()

Parses the config file for the users parameters.

Returns:

• labels (dictionary) – Contains labels section where the key is the name and the values is itself

• plot_params (list) – A list of dictionaries where the index is the plot number and the values are the associated floats from the config file

pyqmmm.md.restraint_plotter.combine_inp()

Combines a CPPTRAJ output file with angles and another with distances.

Returns:

• combined (file) – Generates a file with the combined distances and angles for each plot.

• file_array (list) – List of all the files that are generated.

pyqmmm.md.restraint_plotter.get_xy_data(filename)

Takes a combined file and destructures it into arrays.

Parameters:

filename (str) – The name of the file.

Returns:

• x (array) – The x-values, most likely a list of distances.

• y (array) – The y-values, most likely a list of angles.

pyqmmm.md.restraint_plotter.collect_xyz_data(filenames)

Retrieves the x and y data from the files.

Parameters:

filenames (list) – List of the combined file names that were generated.

Returns:

• x_data (array) – A list of values in the x dimension

• y_data (array) – A list of values in the y dimension

• z_data (array) – A list of values in the z dimension

pyqmmm.md.restraint_plotter.compare_patch_limits(x_data, y_data, patch_params)

Checks all the data sets and decides what the x and y bounds should be.

Parameters:

• x_data (list) – A list of lists with the x data for each plot as a list within the list

• y_data (list) – A list of lists with the y data for each plot as a list within the list

• patch_params (list) – The dimensions of the patch as min and max for the height and width

Returns:

• xlim (list) – The lowest and highest values on the x-axis

• ylim (list) – The lowest and highest values on the y-axis

pyqmmm.md.restraint_plotter.get_plot_limits(x_data, y_data, plot_params)

pyqmmm.md.restraint_plotter.graph_datasets(x_data, y_data, z_data, labels, plot_params, show_crosshairs)

pyqmmm.md.restraint_plotter.restraint_plots()