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# MDAnalysis --- https://www.mdanalysis.org
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# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler,
# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein.
# MDAnalysis: A Python package for the rapid analysis of molecular dynamics
# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th
# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy.
# doi: 10.25080/majora-629e541a-00e
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# MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations.
# J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
#
"""
Native contacts analysis --- :mod:`MDAnalysis.analysis.contacts`
================================================================
This module contains classes to analyze native contacts *Q* over a
trajectory. Native contacts of a conformation are contacts that exist
in a reference structure and in the conformation. Contacts in the
reference structure are always defined as being closer then a distance
`radius`. The fraction of native contacts for a conformation can be
calculated in different ways. This module supports 3 different metrics
listed below, as well as custom metrics.
1. *Hard Cut*: To count as a contact the atoms *i* and *j* have to be at least
as close as in the reference structure.
2. *Soft Cut*: The atom pair *i* and *j* is assigned based on a soft potential
that is 1 if the distance is 0, 1/2 if the distance is the same as in
the reference and 0 for large distances. For the exact definition of the
potential and parameters have a look at function :func:`soft_cut_q`.
3. *Radius Cut*: To count as a contact the atoms *i* and *j* cannot be further
apart than some distance `radius`.
The "fraction of native contacts" *Q(t)* is a number between 0 and 1 and
calculated as the total number of native contacts for a given time frame
divided by the total number of contacts in the reference structure.
Examples for contact analysis
-----------------------------
One-dimensional contact analysis
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
As an example we analyze the opening ("unzipping") of salt bridges
when the AdK enzyme opens up; this is one of the example trajectories
in MDAnalysis. ::
import numpy as np
import matplotlib.pyplot as plt
import MDAnalysis as mda
from MDAnalysis.analysis import contacts
from MDAnalysis.tests.datafiles import PSF,DCD
# example trajectory (transition of AdK from closed to open)
u = mda.Universe(PSF,DCD)
# crude definition of salt bridges as contacts between NH/NZ in ARG/LYS and
# OE*/OD* in ASP/GLU. You might want to think a little bit harder about the
# problem before using this for real work.
sel_basic = "(resname ARG LYS) and (name NH* NZ)"
sel_acidic = "(resname ASP GLU) and (name OE* OD*)"
# reference groups (first frame of the trajectory, but you could also use a
# separate PDB, eg crystal structure)
acidic = u.select_atoms(sel_acidic)
basic = u.select_atoms(sel_basic)
# set up analysis of native contacts ("salt bridges"); salt bridges have a
# distance <6 A
ca1 = contacts.Contacts(u, select=(sel_acidic, sel_basic),
refgroup=(acidic, basic), radius=6.0)
# iterate through trajectory and perform analysis of "native contacts" Q
ca1.run()
# print number of averave contacts
average_contacts = np.mean(ca1.timeseries[:, 1])
print('average contacts = {}'.format(average_contacts))
# plot time series q(t)
fig, ax = plt.subplots()
ax.plot(ca1.timeseries[:, 0], ca1.timeseries[:, 1])
ax.set(xlabel='frame', ylabel='fraction of native contacts',
title='Native Contacts, average = {:.2f}'.format(average_contacts))
fig.show()
The first graph shows that when AdK opens, about 20% of the salt
bridges that existed in the closed state disappear when the enzyme
opens. They open in a step-wise fashion (made more clear by the movie
`AdK_zipper_cartoon.avi`_).
.. _`AdK_zipper_cartoon.avi`:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2803350/bin/NIHMS150766-supplement-03.avi
.. rubric:: Notes
Suggested cutoff distances for different simulations
* For all-atom simulations, cutoff = 4.5 Å
* For coarse-grained simulations, cutoff = 6.0 Å
Two-dimensional contact analysis (q1-q2)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Analyze a single DIMS transition of AdK between its closed and open
conformation and plot the trajectory projected on q1-q2 [Franklin2007]_ ::
import MDAnalysis as mda
from MDAnalysis.analysis import contacts
from MDAnalysisTests.datafiles import PSF, DCD
u = mda.Universe(PSF, DCD)
q1q2 = contacts.q1q2(u, 'name CA', radius=8)
q1q2.run()
f, ax = plt.subplots(1, 2, figsize=plt.figaspect(0.5))
ax[0].plot(q1q2.timeseries[:, 0], q1q2.timeseries[:, 1], label='q1')
ax[0].plot(q1q2.timeseries[:, 0], q1q2.timeseries[:, 2], label='q2')
ax[0].legend(loc='best')
ax[1].plot(q1q2.timeseries[:, 1], q1q2.timeseries[:, 2], '.-')
f.show()
Compare the resulting pathway to the `MinActionPath result for AdK`_
[Franklin2007]_.
.. _MinActionPath result for AdK:
http://lorentz.dynstr.pasteur.fr/joel/adenylate.php
Writing your own contact analysis
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
The :class:`Contacts` class has been designed to be extensible for your own
analysis. As an example we will analyze when the acidic and basic groups of AdK
are in contact which each other; this means that at least one of the contacts
formed in the reference is closer than 2.5 Å.
For this we define a new function to determine if any contact is closer than
2.5 Å; this function must implement the API prescribed by :class:`Contacts`::
def is_any_closer(r, r0, dist=2.5):
return np.any(r < dist)
The first two parameters `r` and `r0` are provided by :class:`Contacts` when it
calls :func:`is_any_closer` while the others can be passed as keyword args
using the `kwargs` parameter in :class:`Contacts`.
Next we are creating an instance of the :class:`Contacts` class and use the
:func:`is_any_closer` function as an argument to `method` and run the analysis::
# crude definition of salt bridges as contacts between NH/NZ in ARG/LYS and
# OE*/OD* in ASP/GLU. You might want to think a little bit harder about the
# problem before using this for real work.
sel_basic = "(resname ARG LYS) and (name NH* NZ)"
sel_acidic = "(resname ASP GLU) and (name OE* OD*)"
# reference groups (first frame of the trajectory, but you could also use a
# separate PDB, eg crystal structure)
acidic = u.select_atoms(sel_acidic)
basic = u.select_atoms(sel_basic)
nc = contacts.Contacts(u, select=(sel_acidic, sel_basic),
method=is_any_closer,
refgroup=(acidic, basic), kwargs={'dist': 2.5})
nc.run()
bound = nc.timeseries[:, 1]
frames = nc.timeseries[:, 0]
f, ax = plt.subplots()
ax.plot(frames, bound, '.')
ax.set(xlabel='frame', ylabel='is Bound',
ylim=(-0.1, 1.1))
f.show()
Functions
---------
.. autofunction:: hard_cut_q
.. autofunction:: soft_cut_q
.. autofunction:: radius_cut_q
.. autofunction:: contact_matrix
.. autofunction:: q1q2
Classes
-------
.. autoclass:: Contacts
:members:
"""
from __future__ import division, absolute_import
from six.moves import zip
import os
import errno
import warnings
import bz2
import functools
import numpy as np
import logging
import MDAnalysis
import MDAnalysis.lib.distances
from MDAnalysis.lib.util import openany
from MDAnalysis.analysis.distances import distance_array
from MDAnalysis.core.groups import AtomGroup
from .base import AnalysisBase
logger = logging.getLogger("MDAnalysis.analysis.contacts")
[docs]def soft_cut_q(r, r0, beta=5.0, lambda_constant=1.8):
r"""Calculate fraction of native contacts *Q* for a soft cut off
The native contact function is defined as [Best2013]_
.. math::
Q(r, r_0) = \frac{1}{1 + e^{\beta (r - \lambda r_0)}}
Reasonable values for different simulation types are
- *All Atom*: `lambda_constant = 1.8` (unitless)
- *Coarse Grained*: `lambda_constant = 1.5` (unitless)
Parameters
----------
r: array
Contact distances at time t
r0: array
Contact distances at time t=0, reference distances
beta: float (default 5.0 Angstrom)
Softness of the switching function
lambda_constant: float (default 1.8, unitless)
Reference distance tolerance
Returns
-------
Q : float
fraction of native contacts
References
----------
.. [Best2013] RB Best, G Hummer, and WA Eaton, "Native contacts determine protein
folding mechanisms in atomistic simulations" _PNAS_ **110** (2013),
17874–17879. doi: `10.1073/pnas.1311599110
<http://doi.org/10.1073/pnas.1311599110>`_.
"""
r = np.asarray(r)
r0 = np.asarray(r0)
result = 1/(1 + np.exp(beta*(r - lambda_constant * r0)))
return result.sum() / len(r0)
[docs]def hard_cut_q(r, cutoff):
"""Calculate fraction of native contacts *Q* for a hard cut off.
The cutoff can either be a float or a :class:`~numpy.ndarray` of the same
shape as `r`.
Parameters
----------
r : ndarray
distance matrix
cutoff : ndarray | float
cut off value to count distances. Can either be a float of a ndarray of
the same size as distances
Returns
-------
Q : float
fraction of contacts
"""
r = np.asarray(r)
cutoff = np.asarray(cutoff)
y = r <= cutoff
return y.sum() / r.size
[docs]def radius_cut_q(r, r0, radius):
"""calculate native contacts *Q* based on the single distance radius.
Parameters
----------
r : ndarray
distance array between atoms
r0 : ndarray
unused to fullfill :class:`Contacts` API
radius : float
Distance between atoms at which a contact is formed
Returns
-------
Q : float
fraction of contacts
References
----------
.. [Franklin2007] Franklin, J., Koehl, P., Doniach, S., & Delarue,
M. (2007). MinActionPath: Maximum likelihood trajectory for large-scale
structural transitions in a coarse-grained locally harmonic energy
landscape. Nucleic Acids Research, 35(SUPPL.2), 477–482.
doi: `10.1093/nar/gkm342 <http://doi.org/10.1093/nar/gkm342>`_
"""
return hard_cut_q(r, radius)
def _new_selections(u_orig, selections, frame):
"""create stand alone AGs from selections at frame"""
u = MDAnalysis.Universe(u_orig.filename, u_orig.trajectory.filename)
u.trajectory[frame]
return [u.select_atoms(s) for s in selections]
[docs]def q1q2(u, select='all', radius=4.5):
"""Perform a q1-q2 analysis.
Compares native contacts between the starting structure and final structure
of a trajectory [Franklin2007]_.
Parameters
----------
u : Universe
Universe with a trajectory
select : string, optional
atoms to do analysis on
radius : float, optional
distance at which contact is formed
Returns
-------
contacts : :class:`Contacts`
Contact Analysis that is set up for a q1-q2 analysis
.. versionchanged:: 1.0.0
Changed `selection` keyword to `select`
Support for setting ``start``, ``stop``, and ``step`` has been removed.
These should now be directly passed to :meth:`Contacts.run`.
"""
selection = (select, select)
first_frame_refs = _new_selections(u, selection, 0)
last_frame_refs = _new_selections(u, selection, -1)
return Contacts(u, selection,
(first_frame_refs, last_frame_refs),
radius=radius, method='radius_cut')