4.6.1. Polymer analysis — MDAnalysis.analysis.polymer

Author:Richard J. Gowers
Year:2015
Copyright:GNU Public License v3

This module contains various commonly used tools in analysing polymers.

class MDAnalysis.analysis.polymer.PersistenceLength(atomgroups, **kwargs)[source]

Calculate the persistence length for polymer chains

The persistence length is the length at which two points on the polymer chain become decorrelated.

Notes

This analysis requires that the trajectory supports indexing.

New in version 0.13.0.

Calculate the persistence length for polymer chains

Parameters:
  • atomgroups (list) – List of atomgroups. Each atomgroup should represent a single polymer chain, ordered in the correct order.
  • start (int, optional) – First frame of trajectory to analyse, Default: None becomes 0.
  • stop (int, optional) – Last frame of trajectory to analyse, Default: None becomes n_frames.
  • step (int, optional) – Frame index to stop analysis. Default: None becomes n_frames. Iteration stops before this frame number.
  • verbose (bool (optional)) – Show detailed progress of the calculation if set to True; the default is False.
perform_fit()[source]

Fit the results to an exponential decay

plot(ax=None)[source]

Oooh fancy

MDAnalysis.analysis.polymer.fit_exponential_decay(x, y)[source]

Fit a function to an exponential decay

\[y = \exp(-x/a)\]
Parameters:y (x,) – The two arrays of data
Returns:a – The coefficient a for this decay
Return type:float

Notes

This function assumes that data starts at 1.0 and decays to 0.0