analysis.msd

A package containing classes and functions to handle mean square displacement (MSD) analyses.

Classes

MSD

A class to calculate mean square displacements.

MSDDiffusionFit

A container for the result of a linear diffusion fit.

MSDInputFileReader

A class to read MSD setups from input files.

MSDDataWriter

A class to write MSD data to output files.

MSDLogWriter

A class to write log files.

Functions

msd()

A function to calculate MSDs from an input file.

Submodules

• api
• exceptions
• msd
• msd_input_file_reader
• msd_output_file_writer

Summary

__all__ Exceptions:

MSDError	Exception raised if something goes wrong during the MSD setup or calculation.
MSDWarning	Warning raised if something goes wrong during the MSD setup or calculation.

__all__ Classes:

MSD	A class for calculating the mean square displacement (MSD) of a target selection using multiple simultaneously active time origins.
MSDDataWriter	Class for writing the data of an MSD analysis to a file.
MSDDiffusionFit	A container for the result of a linear diffusion fit of an MSD component.
MSDInputFileReader	A class to read input files to setup the MSD class.
MSDLogWriter	Class for writing the log (setup parameters) of an MSD analysis to a file.

__all__ Functions:

msd	Calculates the mean square displacement (MSD) using a given input file.