3.6.1. Polymer analysis — MDAnalysis.analysis.polymer
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Author: | Richard J. Gowers |
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Year: | 2015 |
Copyright: | GNU Public License v3 |
This module contains various commonly used tools in analysing polymers.
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class
MDAnalysis.analysis.polymer.
PersistenceLength
(atomgroups, start=None, stop=None, step=None)[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: 0
- stop (int, optional) – Last frame of trajectory to analyse, Default: -1
- step (int, optional) – Step between frames to analyse, Default: 1
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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
Requires scipy