# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# MDAnalysis --- https://www.mdanalysis.org
# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
# Released under the Lesser GNU Public Licence, v2.1 or any higher version
#
# Please cite your use of MDAnalysis in published work:
#
# 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
#
# N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein.
# MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations.
# J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
#
"""
Calculating root mean square quantities --- :mod:`MDAnalysis.analysis.rms`
==========================================================================
:Author: Oliver Beckstein, David L. Dotson, John Detlefs
:Year: 2016
:Copyright: Lesser GNU Public License v2.1+
.. versionadded:: 0.7.7
.. versionchanged:: 0.11.0
Added :class:`RMSF` analysis.
.. versionchanged:: 0.16.0
Refactored RMSD to fit AnalysisBase API
The module contains code to analyze root mean square quantities such
as the coordinat root mean square distance (:class:`RMSD`) or the
per-residue root mean square fluctuations (:class:`RMSF`).
This module uses the fast QCP algorithm [Theobald2005]_ to calculate
the root mean square distance (RMSD) between two coordinate sets (as
implemented in
:func:`MDAnalysis.lib.qcprot.CalcRMSDRotationalMatrix`).
When using this module in published work please cite [Theobald2005]_.
See Also
--------
:mod:`MDAnalysis.analysis.align`
aligning structures based on RMSD
:mod:`MDAnalysis.lib.qcprot`
implements the fast RMSD algorithm.
Example applications
--------------------
Calculating RMSD for multiple domains
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In this example we will globally fit a protein to a reference
structure and investigate the relative movements of domains by
computing the RMSD of the domains to the reference. The example is a
DIMS trajectory of adenylate kinase, which samples a large
closed-to-open transition. The protein consists of the CORE, LID, and
NMP domain.
* superimpose on the closed structure (frame 0 of the trajectory),
using backbone atoms
* calculate the backbone RMSD and RMSD for CORE, LID, NMP (backbone atoms)
The trajectory is included with the test data files. The data in
:attr:`RMSD.results.rmsd` is plotted with :func:`matplotlib.pyplot.plot` (see Figure :ref:`RMSD plot figure <figure-RMSD>`)::
import MDAnalysis
from MDAnalysis.tests.datafiles import PSF,DCD,CRD
u = MDAnalysis.Universe(PSF,DCD)
ref = MDAnalysis.Universe(PSF,DCD) # reference closed AdK (1AKE) (with the default ref_frame=0)
#ref = MDAnalysis.Universe(PSF,CRD) # reference open AdK (4AKE)
import MDAnalysis.analysis.rms
R = MDAnalysis.analysis.rms.RMSD(u, ref,
select="backbone", # superimpose on whole backbone of the whole protein
groupselections=["backbone and (resid 1-29 or resid 60-121 or resid 160-214)", # CORE
"backbone and resid 122-159", # LID
"backbone and resid 30-59"]) # NMP
R.run()
import matplotlib.pyplot as plt
rmsd = R.results.rmsd.T # transpose makes it easier for plotting
time = rmsd[1]
fig = plt.figure(figsize=(4,4))
ax = fig.add_subplot(111)
ax.plot(time, rmsd[2], 'k-', label="all")
ax.plot(time, rmsd[3], 'k--', label="CORE")
ax.plot(time, rmsd[4], 'r--', label="LID")
ax.plot(time, rmsd[5], 'b--', label="NMP")
ax.legend(loc="best")
ax.set_xlabel("time (ps)")
ax.set_ylabel(r"RMSD ($\\AA$)")
fig.savefig("rmsd_all_CORE_LID_NMP_ref1AKE.pdf")
.. _figure-RMSD:
.. figure:: /images/RSMD_plot.png
:scale: 50 %
:alt: RMSD plot
RMSD plot for backbone and CORE, LID, NMP domain of the protein.
Functions
---------
.. autofunction:: rmsd
Analysis classes
----------------
.. autoclass:: RMSD
:members:
:inherited-members:
.. attribute:: results.rmsd
Contains the time series of the RMSD as an N×3 :class:`numpy.ndarray`
array with content ``[[frame, time (ps), RMSD (A)], [...], ...]``.
.. versionadded:: 2.0.0
.. attribute:: rmsd
Alias to the :attr:`results.rmsd` attribute.
.. deprecated:: 2.0.0
Will be removed in MDAnalysis 3.0.0. Please use :attr:`results.rmsd`
instead.
.. autoclass:: RMSF
:members:
:inherited-members:
.. attribute:: results.rmsf
Results are stored in this N-length :class:`numpy.ndarray` array,
giving RMSFs for each of the given atoms.
.. versionadded:: 2.0.0
.. attribute:: rmsf
Alias to the :attr:`results.rmsf` attribute.
.. deprecated:: 2.0.0
Will be removed in MDAnalysis 3.0.0. Please use :attr:`results.rmsf`
instead.
"""
import numpy as np
import logging
import warnings
from ..lib import qcprot as qcp
from ..analysis.base import AnalysisBase, ResultsGroup
from ..exceptions import SelectionError
from ..lib.util import asiterable, iterable, get_weights
logger = logging.getLogger('MDAnalysis.analysis.rmsd')
[docs]def rmsd(a, b, weights=None, center=False, superposition=False):
r"""Returns RMSD between two coordinate sets `a` and `b`.
`a` and `b` are arrays of the coordinates of N atoms of shape
:math:`N times 3` as generated by, e.g.,
:meth:`MDAnalysis.core.groups.AtomGroup.positions`.
Note
----
If you use trajectory data from simulations performed under **periodic
boundary conditions** then you *must make your molecules whole* before
performing RMSD calculations so that the centers of mass of the mobile and
reference structure are properly superimposed.
Parameters
----------
a : array_like
coordinates to align to `b`
b : array_like
coordinates to align to (same shape as `a`)
weights : array_like (optional)
1D array with weights, use to compute weighted average
center : bool (optional)
subtract center of geometry before calculation. With weights given
compute weighted average as center.
superposition : bool (optional)
perform a rotational and translational superposition with the fast QCP
algorithm [Theobald2005]_ before calculating the RMSD; implies
``center=True``.
Returns
-------
rmsd : float
RMSD between `a` and `b`
Notes
-----
The RMSD :math:`\rho(t)` as a function of time is calculated as
.. math::
\rho(t) = \sqrt{\frac{1}{N} \sum_{i=1}^N w_i \left(\mathbf{x}_i(t)
- \mathbf{x}_i^{\text{ref}}\right)^2}
It is the Euclidean distance in configuration space of the current
configuration (possibly after optimal translation and rotation) from a
reference configuration divided by :math:`1/\sqrt{N}` where :math:`N` is
the number of coordinates.
The weights :math:`w_i` are calculated from the input weights
`weights` :math:`w'_i` as relative to the mean:
.. math::
w_i = \frac{w'_i}{\langle w' \rangle}
Example
-------
>>> import MDAnalysis as mda
>>> from MDAnalysis.analysis.rms import rmsd
>>> from MDAnalysis.tests.datafiles import PSF, DCD
>>> u = mda.Universe(PSF, DCD)
>>> bb = u.select_atoms('backbone')
>>> A = bb.positions.copy() # coordinates of first frame
>>> _ = u.trajectory[-1] # forward to last frame
>>> B = bb.positions.copy() # coordinates of last frame
>>> rmsd(A, B, center=True)
6.838544558398293
.. versionchanged:: 0.8.1
*center* keyword added
.. versionchanged:: 0.14.0
*superposition* keyword added
"""
a = np.asarray(a, dtype=np.float64)
b = np.asarray(b, dtype=np.float64)
N = b.shape[0]
if a.shape != b.shape:
raise ValueError('a and b must have same shape')
# superposition only works if structures are centered
if center or superposition:
# make copies (do not change the user data!)
# weights=None is equivalent to all weights 1
a = a - np.average(a, axis=0, weights=weights)
b = b - np.average(b, axis=0, weights=weights)
if weights is not None:
if len(weights) != len(a):
raise ValueError('weights must have same length as a and b')
# weights are constructed as relative to the mean
weights = np.asarray(weights, dtype=np.float64) / np.mean(weights)
if superposition:
return qcp.CalcRMSDRotationalMatrix(a, b, N, None, weights)
else:
if weights is not None:
return np.sqrt(np.sum(weights[:, np.newaxis]
* ((a - b) ** 2)) / N)
else:
return np.sqrt(np.sum((a - b) ** 2) / N)
def process_selection(select):
"""Return a canonical selection dictionary.
Parameters
----------
select : str or tuple or dict
- `str` -> Any valid string selection
- `dict` -> ``{'mobile':sel1, 'reference':sel2}``
- `tuple` -> ``(sel1, sel2)``
Returns
-------
dict
selections for 'reference' and 'mobile'. Values are guarenteed to be
iterable (so that one can provide selections to retain order)
Notes
-----
The dictionary input for `select` can be generated by
:func:`fasta2select` based on a ClustalW_ or STAMP_ sequence alignment.
"""
if isinstance(select, str):
select = {'reference': str(select), 'mobile': str(select)}
elif type(select) is tuple:
try:
select = {'mobile': select[0], 'reference': select[1]}
except IndexError:
raise IndexError(
"select must contain two selection strings "
"(reference, mobile)") from None
elif type(select) is dict:
# compatability hack to use new nomenclature
try:
select['mobile']
select['reference']
except KeyError:
raise KeyError(
"select dictionary must contain entries for keys "
"'mobile' and 'reference'."
) from None
else:
raise TypeError("'select' must be either a string, 2-tuple, or dict")
select['mobile'] = asiterable(select['mobile'])
select['reference'] = asiterable(select['reference'])
return select
[docs]class RMSD(AnalysisBase):
r"""Class to perform RMSD analysis on a trajectory.
The RMSD will be computed for two groups of atoms and all frames in the
trajectory belonging to `atomgroup`. The groups of atoms are obtained by
applying the selection selection `select` to the changing `atomgroup` and
the fixed `reference`.
Note
----
If you use trajectory data from simulations performed under **periodic
boundary conditions** then you *must make your molecules whole* before
performing RMSD calculations so that the centers of mass of the selected
and reference structure are properly superimposed.
Run the analysis with :meth:`RMSD.run`, which stores the results
in the array :attr:`RMSD.results.rmsd`.
.. versionchanged:: 1.0.0
``save()`` method was removed, use ``np.savetxt()`` on
:attr:`RMSD.results.rmsd` instead.
.. versionchanged:: 2.0.0
:attr:`rmsd` results are now stored in a
:class:`MDAnalysis.analysis.base.Results` instance.
.. versionchanged:: 2.8.0
introduced :meth:`get_supported_backends` allowing for parallel
execution on ``multiprocessing`` and ``dask`` backends.
"""
_analysis_algorithm_is_parallelizable = True
[docs] @classmethod
def get_supported_backends(cls):
return ('serial', 'multiprocessing', 'dask',)
def __init__(self, atomgroup, reference=None, select='all',
groupselections=None, weights=None, weights_groupselections=False,
tol_mass=0.1, ref_frame=0, **kwargs):
r"""Parameters
----------
atomgroup : AtomGroup or Universe
Group of atoms for which the RMSD is calculated. If a trajectory is
associated with the atoms then the computation iterates over the
trajectory.
reference : AtomGroup or Universe (optional)
Group of reference atoms; if ``None`` then the current frame of
`atomgroup` is used.
select : str or dict or tuple (optional)
The selection to operate on; can be one of:
1. any valid selection string for
:meth:`~MDAnalysis.core.groups.AtomGroup.select_atoms` that
produces identical selections in `atomgroup` and `reference`; or
2. a dictionary ``{'mobile': sel1, 'reference': sel2}`` where *sel1*
and *sel2* are valid selection strings that are applied to
`atomgroup` and `reference` respectively (the
:func:`MDAnalysis.analysis.align.fasta2select` function returns such
a dictionary based on a ClustalW_ or STAMP_ sequence alignment); or
3. a tuple ``(sel1, sel2)``
When using 2. or 3. with *sel1* and *sel2* then these selection strings
are applied to `atomgroup` and `reference` respectively and should
generate *groups of equivalent atoms*. *sel1* and *sel2* can each also
be a *list of selection strings* to generate a
:class:`~MDAnalysis.core.groups.AtomGroup` with defined atom order as
described under :ref:`ordered-selections-label`).
groupselections : list (optional)
A list of selections as described for `select`, with the difference
that these selections are *always applied to the full universes*,
i.e., ``atomgroup.universe.select_atoms(sel1)`` and
``reference.universe.select_atoms(sel2)``. Each selection describes
additional RMSDs to be computed *after the structures have been
superimposed* according to `select`. No additional fitting is
performed.The output contains one additional column for each
selection.
.. Note:: Experimental feature. Only limited error checking
implemented.
weights : {"mass", ``None``} or array_like (optional)
1. "mass" will use masses as weights for both `select` and `groupselections`.
2. ``None`` will weigh each atom equally for both `select` and `groupselections`.
3. If 1D float array of the same length as `atomgroup` is provided,
use each element of the `array_like` as a weight for the
corresponding atom in `select`, and assumes ``None`` for `groupselections`.
weights_groupselections : False or list of {"mass", ``None`` or array_like} (optional)
1. ``False`` will apply imposed weights to `groupselections` from
``weights`` option if ``weights`` is either ``"mass"`` or ``None``.
Otherwise will assume a list of length equal to length of
`groupselections` filled with ``None`` values.
2. A list of {"mass", ``None`` or array_like} with the length of `groupselections`
will apply the weights to `groupselections` correspondingly.
tol_mass : float (optional)
Reject match if the atomic masses for matched atoms differ by more
than `tol_mass`.
ref_frame : int (optional)
frame index to select frame from `reference`
verbose : bool (optional)
Show detailed progress of the calculation if set to ``True``; the
default is ``False``.
Raises
------
SelectionError
If the selections from `atomgroup` and `reference` do not match.
TypeError
If `weights` or `weights_groupselections` is not of the appropriate type;
see also :func:`MDAnalysis.lib.util.get_weights`
ValueError
If `weights` are not compatible with `atomgroup` (not the same
length) or if it is not a 1D array (see
:func:`MDAnalysis.lib.util.get_weights`).
A :exc:`ValueError` is also raised if the length of `weights_groupselections`
are not compatible with `groupselections`.
Notes
-----
The root mean square deviation :math:`\rho(t)` of a group of :math:`N`
atoms relative to a reference structure as a function of time is
calculated as
.. math::
\rho(t) = \sqrt{\frac{1}{N} \sum_{i=1}^N w_i \left(\mathbf{x}_i(t)
- \mathbf{x}_i^{\text{ref}}\right)^2}
The weights :math:`w_i` are calculated from the input weights `weights`
:math:`w'_i` as relative to the mean of the input weights:
.. math::
w_i = \frac{w'_i}{\langle w' \rangle}
The selected coordinates from `atomgroup` are optimally superimposed
(translation and rotation) on the `reference` coordinates at each time step
as to minimize the RMSD. Douglas Theobald's fast QCP algorithm
[Theobald2005]_ is used for the rotational superposition and to calculate
the RMSD (see :mod:`MDAnalysis.lib.qcprot` for implementation details).
The class runs various checks on the input to ensure that the two atom
groups can be compared. This includes a comparison of atom masses (i.e.,
only the positions of atoms of the same mass will be considered to be
correct for comparison). If masses should not be checked, just set
`tol_mass` to a large value such as 1000.
.. _ClustalW: http://www.clustal.org/
.. _STAMP: http://www.compbio.dundee.ac.uk/manuals/stamp.4.2/
See Also
--------
rmsd
.. versionadded:: 0.7.7
.. versionchanged:: 0.8
`groupselections` added
.. versionchanged:: 0.16.0
Flexible weighting scheme with new `weights` keyword.
.. deprecated:: 0.16.0
Instead of ``mass_weighted=True`` (removal in 0.17.0) use new
``weights='mass'``; refactored to fit with AnalysisBase API
.. versionchanged:: 0.17.0
removed deprecated `mass_weighted` keyword; `groupselections`
are *not* rotationally superimposed any more.
.. versionchanged:: 1.0.0
`filename` keyword was removed.
"""
super(RMSD, self).__init__(atomgroup.universe.trajectory,
**kwargs)
self.atomgroup = atomgroup
self.reference = reference if reference is not None else self.atomgroup
select = process_selection(select)
self.groupselections = ([process_selection(s) for s in groupselections]
if groupselections is not None else [])
self.weights = weights
self.tol_mass = tol_mass
self.ref_frame = ref_frame
self.weights_groupselections = weights_groupselections
self.ref_atoms = self.reference.select_atoms(*select['reference'])
self.mobile_atoms = self.atomgroup.select_atoms(*select['mobile'])
if len(self.ref_atoms) != len(self.mobile_atoms):
err = ("Reference and trajectory atom selections do "
"not contain the same number of atoms: "
"N_ref={0:d}, N_traj={1:d}".format(self.ref_atoms.n_atoms,
self.mobile_atoms.n_atoms))
logger.exception(err)
raise SelectionError(err)
logger.info("RMS calculation "
"for {0:d} atoms.".format(len(self.ref_atoms)))
mass_mismatches = (np.absolute((self.ref_atoms.masses -
self.mobile_atoms.masses)) >
self.tol_mass)
if np.any(mass_mismatches):
# diagnostic output:
logger.error("Atoms: reference | mobile")
for ar, at in zip(self.ref_atoms, self.mobile_atoms):
if ar.name != at.name:
logger.error("{0!s:>4} {1:3d} {2!s:>3} {3!s:>3} {4:6.3f}"
"| {5!s:>4} {6:3d} {7!s:>3} {8!s:>3}"
"{9:6.3f}".format(ar.segid, ar.resid,
ar.resname, ar.name,
ar.mass, at.segid, at.resid,
at.resname, at.name,
at.mass))
errmsg = ("Inconsistent selections, masses differ by more than"
"{0:f}; mis-matching atoms"
"are shown above.".format(self.tol_mass))
logger.error(errmsg)
raise SelectionError(errmsg)
del mass_mismatches
# TODO:
# - make a group comparison a class that contains the checks above
# - use this class for the *select* group and the additional
# *groupselections* groups each a dict with reference/mobile
self._groupselections_atoms = [
{
'reference': self.reference.universe.select_atoms(*s['reference']),
'mobile': self.atomgroup.universe.select_atoms(*s['mobile']),
}
for s in self.groupselections]
# sanity check
for igroup, (sel, atoms) in enumerate(zip(self.groupselections,
self._groupselections_atoms)):
if len(atoms['mobile']) != len(atoms['reference']):
logger.exception('SelectionError: Group Selection')
raise SelectionError(
"Group selection {0}: {1} | {2}: Reference and trajectory "
"atom selections do not contain the same number of atoms: "
"N_ref={3}, N_traj={4}".format(
igroup, sel['reference'], sel['mobile'],
len(atoms['reference']), len(atoms['mobile'])))
# check weights type
acceptable_dtypes = (np.dtype('float64'), np.dtype('int64'))
msg = ("weights should only be 'mass', None or 1D float array."
"For weights on groupselections, "
"use **weight_groupselections**")
if iterable(self.weights):
element_lens = []
for element in self.weights:
if iterable(element):
element_lens.append(len(element))
else:
element_lens.append(1)
if np.unique(element_lens).size > 1:
# jagged data structure
raise TypeError(msg)
if np.array(element).dtype not in acceptable_dtypes:
raise TypeError(msg)
if iterable(self.weights) or self.weights != "mass":
get_weights(self.mobile_atoms, self.weights)
if self.weights_groupselections:
if len(self.weights_groupselections) != len(self.groupselections):
raise ValueError("Length of weights_groupselections is not equal to "
"length of groupselections ")
for weights, atoms, selection in zip(self.weights_groupselections,
self._groupselections_atoms,
self.groupselections):
try:
if iterable(weights) or weights != "mass":
get_weights(atoms['mobile'], weights)
except Exception as e:
raise type(e)(str(e) + ' happens in selection %s' % selection['mobile'])
def _prepare(self):
self._n_atoms = self.mobile_atoms.n_atoms
if not self.weights_groupselections:
if not iterable(self.weights): # apply 'mass' or 'None' to groupselections
self.weights_groupselections = [self.weights] * len(self.groupselections)
else:
self.weights_groupselections = [None] * len(self.groupselections)
for igroup, (weights, atoms) in enumerate(zip(self.weights_groupselections,
self._groupselections_atoms)):
if str(weights) == 'mass':
self.weights_groupselections[igroup] = atoms['mobile'].masses
if weights is not None:
self.weights_groupselections[igroup] = np.asarray(self.weights_groupselections[igroup],
dtype=np.float64) / \
np.mean(self.weights_groupselections[igroup])
# add the array of weights to weights_select
self.weights_select = get_weights(self.mobile_atoms, self.weights)
self.weights_ref = get_weights(self.ref_atoms, self.weights)
if self.weights_select is not None:
self.weights_select = np.asarray(self.weights_select, dtype=np.float64) / \
np.mean(self.weights_select)
self.weights_ref = np.asarray(self.weights_ref, dtype=np.float64) / \
np.mean(self.weights_ref)
current_frame = self.reference.universe.trajectory.ts.frame
try:
# Move to the ref_frame
# (coordinates MUST be stored in case the ref traj is advanced
# elsewhere or if ref == mobile universe)
self.reference.universe.trajectory[self.ref_frame]
self._ref_com = self.ref_atoms.center(self.weights_ref)
# makes a copy
self._ref_coordinates = self.ref_atoms.positions - self._ref_com
if self._groupselections_atoms:
self._groupselections_ref_coords64 = [(self.reference.
select_atoms(*s['reference']).
positions.astype(np.float64)) for s in
self.groupselections]
finally:
# Move back to the original frame
self.reference.universe.trajectory[current_frame]
self._ref_coordinates64 = self._ref_coordinates.astype(np.float64)
if self._groupselections_atoms:
# Only carry out a rotation if we want to calculate secondary
# RMSDs.
# R: rotation matrix that aligns r-r_com, x~-x~com
# (x~: selected coordinates, x: all coordinates)
# Final transformed traj coordinates: x' = (x-x~_com)*R + ref_com
self._rot = np.zeros(9, dtype=np.float64) # allocate space
self._R = self._rot.reshape(3, 3)
else:
self._rot = None
self.results.rmsd = np.zeros((self.n_frames,
3 + len(self._groupselections_atoms)))
self._mobile_coordinates64 = self.mobile_atoms.positions.copy().astype(np.float64)
def _get_aggregator(self):
return ResultsGroup(lookup={'rmsd': ResultsGroup.ndarray_vstack})
def _single_frame(self):
mobile_com = self.mobile_atoms.center(self.weights_select).astype(np.float64)
self._mobile_coordinates64[:] = self.mobile_atoms.positions
self._mobile_coordinates64 -= mobile_com
self.results.rmsd[self._frame_index, :2] = self._ts.frame, self._trajectory.time
if self._groupselections_atoms:
# superimpose structures: MDAnalysis qcprot needs Nx3 coordinate
# array with float64 datatype (float32 leads to errors up to 1e-3 in
# RMSD). Note that R is defined in such a way that it acts **to the
# left** so that we can easily use broadcasting and save one
# expensive numpy transposition.
self.results.rmsd[self._frame_index, 2] = qcp.CalcRMSDRotationalMatrix(
self._ref_coordinates64, self._mobile_coordinates64,
self._n_atoms, self._rot, self.weights_select)
self._R[:, :] = self._rot.reshape(3, 3)
# Transform each atom in the trajectory (use inplace ops to
# avoid copying arrays) (Marginally (~3%) faster than
# "ts.positions[:] = (ts.positions - x_com) * R + ref_com".)
self._ts.positions[:] -= mobile_com
# R acts to the left & is broadcasted N times.
self._ts.positions[:] = np.dot(self._ts.positions, self._R)
self._ts.positions += self._ref_com
# 2) calculate secondary RMSDs (without any further
# superposition)
for igroup, (refpos, atoms) in enumerate(
zip(self._groupselections_ref_coords64,
self._groupselections_atoms), 3):
self.results.rmsd[self._frame_index, igroup] = rmsd(
refpos, atoms['mobile'].positions,
weights=self.weights_groupselections[igroup-3],
center=False, superposition=False)
else:
# only calculate RMSD by setting the Rmatrix to None (no need
# to carry out the rotation as we already get the optimum RMSD)
self.results.rmsd[self._frame_index, 2] = qcp.CalcRMSDRotationalMatrix(
self._ref_coordinates64, self._mobile_coordinates64,
self._n_atoms, None, self.weights_select)
@property
def rmsd(self):
wmsg = ("The `rmsd` attribute was deprecated in MDAnalysis 2.0.0 and "
"will be removed in MDAnalysis 3.0.0. Please use "
"`results.rmsd` instead.")
warnings.warn(wmsg, DeprecationWarning)
return self.results.rmsd
[docs]class RMSF(AnalysisBase):
r"""Calculate RMSF of given atoms across a trajectory.
Note
----
No RMSD-superposition is performed; it is assumed that the user is
providing a trajectory where the protein of interest has been structurally
aligned to a reference structure (see the Examples section below). The
protein also has be whole because periodic boundaries are not taken into
account.
Run the analysis with :meth:`RMSF.run`, which stores the results
in the array :attr:`RMSF.results.rmsf`.
"""
[docs] @classmethod
def get_supported_backends(cls):
return ('serial',)
def __init__(self, atomgroup, **kwargs):
r"""Parameters
----------
atomgroup : AtomGroup
Atoms for which RMSF is calculated
verbose : bool (optional)
Show detailed progress of the calculation if set to ``True``; the
default is ``False``.
Raises
------
ValueError
raised if negative values are calculated, which indicates that a
numerical overflow or underflow occured
Notes
-----
The root mean square fluctuation of an atom :math:`i` is computed as the
time average
.. math::
\rho_i = \sqrt{\left\langle (\mathbf{x}_i - \langle\mathbf{x}_i\rangle)^2 \right\rangle}
No mass weighting is performed.
This method implements an algorithm for computing sums of squares while
avoiding overflows and underflows :footcite:p:`Welford1962`.
Examples
--------
In this example we calculate the residue RMSF fluctuations by analyzing
the :math:`\text{C}_\alpha` atoms. First we need to fit the trajectory
to the average structure as a reference. That requires calculating the
average structure first. Because we need to analyze and manipulate the
same trajectory multiple times, we are going to load it into memory
using the :mod:`~MDAnalysis.coordinates.MemoryReader`. (If your
trajectory does not fit into memory, you will need to :ref:`write out
intermediate trajectories <writing-trajectories>` to disk or
:ref:`generate an in-memory universe
<creating-in-memory-trajectory-label>` that only contains, say, the
protein)::
import MDAnalysis as mda
from MDAnalysis.analysis import align
from MDAnalysis.tests.datafiles import TPR, XTC
u = mda.Universe(TPR, XTC, in_memory=True)
protein = u.select_atoms("protein")
# 1) the current trajectory contains a protein split across
# periodic boundaries, so we first make the protein whole and
# center it in the box using on-the-fly transformations
import MDAnalysis.transformations as trans
not_protein = u.select_atoms('not protein')
transforms = [trans.unwrap(protein),
trans.center_in_box(protein, wrap=True),
trans.wrap(not_protein)]
u.trajectory.add_transformations(*transforms)
# 2) fit to the initial frame to get a better average structure
# (the trajectory is changed in memory)
prealigner = align.AlignTraj(u, u, select="protein and name CA",
in_memory=True).run()
# 3) reference = average structure
ref_coordinates = u.trajectory.timeseries(asel=protein).mean(axis=1)
# make a reference structure (need to reshape into a 1-frame
# "trajectory")
reference = mda.Merge(protein).load_new(ref_coordinates[:, None, :],
order="afc")
We created a new universe ``reference`` that contains a single frame
with the averaged coordinates of the protein. Now we need to fit the
whole trajectory to the reference by minimizing the RMSD. We use
:class:`MDAnalysis.analysis.align.AlignTraj`::
aligner = align.AlignTraj(u, reference,
select="protein and name CA",
in_memory=True).run()
The trajectory is now fitted to the reference (the RMSD is stored as
`aligner.results.rmsd` for further inspection). Now we can calculate
the RMSF::
from MDAnalysis.analysis.rms import RMSF
calphas = protein.select_atoms("name CA")
rmsfer = RMSF(calphas, verbose=True).run()
and plot::
import matplotlib.pyplot as plt
plt.plot(calphas.resnums, rmsfer.results.rmsf)
References
----------
.. footbibliography::
.. versionadded:: 0.11.0
.. versionchanged:: 0.16.0
refactored to fit with AnalysisBase API
.. deprecated:: 0.16.0
the keyword argument `quiet` is deprecated in favor of `verbose`.
.. versionchanged:: 0.17.0
removed unused keyword `weights`
.. versionchanged:: 1.0.0
Support for the ``start``, ``stop``, and ``step`` keywords has been
removed. These should instead be passed to :meth:`RMSF.run`.
"""
super(RMSF, self).__init__(atomgroup.universe.trajectory, **kwargs)
self.atomgroup = atomgroup
def _prepare(self):
self.sumsquares = np.zeros((self.atomgroup.n_atoms, 3))
self.mean = self.sumsquares.copy()
def _single_frame(self):
k = self._frame_index
self.sumsquares += (k / (k+1.0)) * (self.atomgroup.positions - self.mean) ** 2
self.mean = (k * self.mean + self.atomgroup.positions) / (k + 1)
def _conclude(self):
k = self._frame_index
self.results.rmsf = np.sqrt(self.sumsquares.sum(axis=1) / (k + 1))
if not (self.results.rmsf >= 0).all():
raise ValueError("Some RMSF values negative; overflow " +
"or underflow occurred")
@property
def rmsf(self):
wmsg = ("The `rmsf` attribute was deprecated in MDAnalysis 2.0.0 and "
"will be removed in MDAnalysis 3.0.0. Please use "
"`results.rmsd` instead.")
warnings.warn(wmsg, DeprecationWarning)
return self.results.rmsf