{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# Q1 vs Q2 contact analysis\n", "\n", "Here we calculate a Q1 vs Q2 plot, where Q1 refers to fraction of native contacts along a trajectory with reference to the first frame, and Q2 represents the fraction of native contacts with reference to the last.\n", "\n", "**Last executed:** Sep 25, 2020 with MDAnalysis 1.0.0\n", "\n", "**Last updated:** June 29, 2020 with MDAnalysis 1.0.0\n", "\n", "**Minimum version of MDAnalysis:** 0.17.0\n", "\n", "**Packages required:**\n", " \n", "* MDAnalysis (Michaud-Agrawal *et al.*, 2011, Gowers *et al.*, 2016)\n", "* MDAnalysisTests\n", "* [matplotlib](https://matplotlib.org)\n", "* [pandas](https://pandas.pydata.org)\n", "\n", "**See also**\n", "\n", "* [Fraction of native contacts over a trajectory](contacts_native_fraction.ipynb)\n", "* [Write your own contacts analysis method](contacts_custom.ipynb)\n", "* [Contact analysis: number of contacts within a cutoff](contacts_within_cutoff.ipynb)\n", "\n", "
\n", " | Frame | \n", "Q1 | \n", "Q2 | \n", "
---|---|---|---|
0 | \n", "0.0 | \n", "1.000000 | \n", "0.946494 | \n", "
1 | \n", "1.0 | \n", "0.980926 | \n", "0.949262 | \n", "
2 | \n", "2.0 | \n", "0.973660 | \n", "0.952952 | \n", "
3 | \n", "3.0 | \n", "0.972752 | \n", "0.951107 | \n", "
4 | \n", "4.0 | \n", "0.970027 | \n", "0.948339 | \n", "