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#!/usr/bin/env python
# -*- coding: utf-8 -*-
# MDAnalysis example: native contact analysis (q1-q2)
"""
Example: Calculating the percentage of native contacts
======================================================
The percentag of native contacts, q, is the number of observed contacts
relative to the number of contacts in a reference state (typically, the
native state). The number of *contacts* is the total number of unique CA atoms
within in a fixed radius of all CA atoms.
This example script takes a trajectory of AdK in which the enzyme transitions
from the closed to the open state. Two sets of native contacts are computed:
*q1*
contacts relative to the initial (closed) state, pdb 1AKE
*q2*
contacts relative to the final (open) state, pdb 4AKE
The trajectory was generated with the dynamic importance sampling method (DIMS)
and taken from [Beckstein2009].
The final result is stored in a bzipped data file `adk_dims_q1q2.dat.bz2` and
the q1-q2 graph is also written to `figures/nativecontacts.pdf`
(requires :mod:`matplotlib`).
[Beckstein2009] O. Beckstein, E.J. Denning, J.R. Perilla and T.B. Woolf,
Zipping and Unzipping of Adenylate Kinase: Atomistic Insights
into the Ensemble of Open ↔ Closed Transitions. J Mol Biol 394
(2009), 160–176, doi:10.1016/j.jmb.2009.09.009
.. SeeAlso:: :mod:`MDAnalysis.analysis.contacts`
"""
import MDAnalysis.analysis.contacts
from MDAnalysis.tests.datafiles import PSF, DCD # AdK example trajectory
try:
import matplotlib
matplotlib.use('agg') # no interactive plotting, only save figures
from pylab import savefig, clf
have_matplotlib = True
except ImportError:
have_matplotlib = False
C = MDAnalysis.analysis.contacts.ContactAnalysis(PSF, DCD, targetdir="./output")
C.run()
print "Data file was written to {0!r}".format(C.output_bz2)
if have_matplotlib:
matplotlib.rc('font', size=14)
matplotlib.rc('figure', figsize=(3.4, 3.8))
clf()
C.plot(linewidth=3)
savefig("./figures/nativecontacts.pdf")
savefig("./figures/nativecontacts.png")
print "Wrote figures to ./figures/nativecontacts.{pdf,png}"