pestifer.tasks.mdplot module

Definition of the MDPlotTask class for making plots of energy-like quantities from NAMD runs. This class is a descendant of the BaseTask class and is used to extract energy-like data from NAMD log files, pressure profiles, and XST files, and to generate plots based on this data. It handles the collection of energy data from multiple NAMD runs, creates CSV files for energy and pressure profile data, and generates plots for specified traces and profiles. The plots can include energy traces, pressure profiles, and histograms, with options for units, legends, and grid lines. It also supports the extraction of data from existing NAMD log files and XST files, allowing for flexible data visualization.

Usage as a task in a build workflow is described in the mdplot documentation. This module is also used in standalone form by the mdplot command.

class pestifer.tasks.mdplot.MDPlotTask(specs: dict = None, **kwargs)

Bases: BaseTask

A class for making plots of energy-like quantities from a series of one or more NAMD runs. Since NAMD runs are always invoked using a log-parser, a csv file is created that contains all energy-like data from the run.

do()

This a stub method that should be overridden by subclasses. It is intended to be the main method that performs the task’s operations. Subclasses should implement this method to define the specific behavior of the task. This method is called when the task is executed.