Source code for MDAnalysis.analysis.encore.confdistmatrix
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# Please cite your use of MDAnalysis in published work:
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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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# 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
#
"""
Distance Matrix calculation --- :mod:`MDAnalysis.analysis.ensemble.confdistmatrix`
==================================================================================
The module contains a base class to easily compute, using
parallelization and shared memory, matrices of conformational
distance between the structures stored as frames in a Universe. A
class to compute an RMSD matrix in such a way is also available.
:Author: Matteo Tiberti, Wouter Boomsma, Tone Bengtsen
.. versionadded:: 0.16.0
.. deprecated:: 2.8.0
This module is deprecated in favour of the
MDAKit `mdaencore <https://mdanalysis.org/mdaencore/>`_ and will be removed
in MDAnalysis 3.0.0.
"""
from joblib import Parallel, delayed
import numpy as np
from getpass import getuser
from socket import gethostname
from datetime import datetime
from time import sleep
import logging
import warnings
from ...core.universe import Universe
from ..align import rotation_matrix
from .cutils import PureRMSD
from .utils import TriangularMatrix, trm_indices
[docs]def conformational_distance_matrix(ensemble,
conf_dist_function, select="",
superimposition_select="", n_jobs=1, pairwise_align=True, weights='mass',
metadata=True, verbose=False,
max_nbytes=None):
"""
Run the conformational distance matrix calculation.
args and kwargs are passed to conf_dist_function.
Parameters
----------
ensemble : Universe object
Universe object for which the conformational distance matrix will
be computed.
conf_dist_function : function object
Function that fills the matrix with conformational distance
values. See set_rmsd_matrix_elements for an example.
select : str, optional
use this selection for the calculation of conformational distance
superimposition_select : str, optional
use atoms from this selection for fitting instead of those of
`select`
pairwise_align : bool, optional
Whether to perform pairwise alignment between conformations.
Default is True (do the superimposition)
weights : str/array_like, optional
weights to be used for fit. Can be either 'mass' or an array_like
metadata : bool, optional
Whether to build a metadata dataset for the calculated matrix.
Default is True.
n_jobs : int, optional
Number of cores to be used for parallel calculation
Default is 1. -1 uses all available cores
max_nbytes : str, optional
Threshold on the size of arrays passed to the workers that triggers automated memory mapping in temp_folder (default is None).
See https://joblib.readthedocs.io/en/latest/generated/joblib.Parallel.html for detailed documentation.
verbose : bool, optional
enable verbose output
Returns
-------
conf_dist_matrix : encore.utils.TriangularMatrix object
Conformational distance matrix in triangular representation.
"""
# framesn: number of frames
framesn = len(ensemble.trajectory.timeseries(
ensemble.select_atoms(select), order='fac'))
# Prepare metadata recarray
if metadata:
metadata = np.array([(gethostname(),
getuser(),
str(datetime.now()),
ensemble.filename,
framesn,
pairwise_align,
select,
weights=='mass')],
dtype=[('host', object),
('user', object),
('date', object),
('topology file', object),
('number of frames', int),
('pairwise superimposition', bool),
('superimposition subset', object),
('mass-weighted', bool)])
# Prepare alignment subset coordinates as necessary
rmsd_coordinates = ensemble.trajectory.timeseries(
ensemble.select_atoms(select),
order='fac')
if pairwise_align:
if superimposition_select:
subset_select = superimposition_select
else:
subset_select = select
fitting_coordinates = ensemble.trajectory.timeseries(
ensemble.select_atoms(subset_select),
order='fac')
else:
fitting_coordinates = None
if not isinstance(weights, (list, tuple, np.ndarray)) and weights == 'mass':
weights = ensemble.select_atoms(select).masses.astype(np.float64)
if pairwise_align:
subset_weights = ensemble.select_atoms(subset_select).masses.astype(np.float64)
else:
subset_weights = None
elif weights is None:
weights = np.ones((ensemble.trajectory.timeseries(
ensemble.select_atoms(select))[0].shape[0])).astype(np.float64)
if pairwise_align:
subset_weights = np.ones((fit_coords[0].shape[0])).astype(np.float64)
else:
subset_weights = None
else:
if pairwise_align:
if len(weights) != 2:
raise RuntimeError("used pairwise alignment with custom "
"weights. Please provide 2 tuple with "
"weights for 'select' and "
"'superimposition_select'")
subset_weights = weights[1]
weights = weights[0]
else:
subset_weights = None
# Allocate for output matrix
matsize = framesn * (framesn + 1) // 2
distmat = np.empty(matsize, np.float64)
# Initialize workers. Simple worker doesn't perform fitting,
# fitter worker does.
indices = trm_indices((0, 0), (framesn - 1, framesn - 1))
Parallel(n_jobs=n_jobs, verbose=verbose, require='sharedmem',
max_nbytes=max_nbytes)(delayed(conf_dist_function)(
np.int64(element),
rmsd_coordinates,
distmat,
weights,
fitting_coordinates,
subset_weights) for element in indices)
# When the workers have finished, return a TriangularMatrix object
return TriangularMatrix(distmat, metadata=metadata)
[docs]def set_rmsd_matrix_elements(tasks, coords, rmsdmat, weights, fit_coords=None,
fit_weights=None, *args, **kwargs):
'''
RMSD Matrix calculator
Parameters
----------
tasks : iterator of int of length 2
Given a triangular matrix, this function will calculate RMSD
values from element tasks[0] to tasks[1]. Since the matrix
is triangular, the trm_indices matrix automatically
calculates the corrisponding i,j matrix indices.
The matrix is written as an array in a row-major
order (see the TriangularMatrix class for details).
If fit_coords and fit_weights are specified, the structures
will be superimposed before calculating RMSD, and fit_coords and fit_weights
will be used to place both structures at their center of mass and
compute the rotation matrix. In this case, both fit_coords and fit_weights
must be specified.
coords : numpy.array
Array of the ensemble coordinates
weights : numpy.array
Array of atomic weights, having the same order as the
coordinates array
rmsdmat : encore.utils.TriangularMatrix
Memory-shared triangular matrix object
fit_coords : numpy.array or None, optional
Array of the coordinates used for fitting
fit_weights : numpy.array. optional
Array of atomic weights, having the same order as the
fit_coords array
'''
i, j = tasks
if fit_coords is None and fit_weights is None:
sumweights = np.sum(weights)
rmsdmat[(i + 1) * i // 2 + j] = PureRMSD(coords[i].astype(np.float64),
coords[j].astype(np.float64),
coords[j].shape[0],
weights,
sumweights)
elif fit_coords is not None and fit_weights is not None:
sumweights = np.sum(weights)
subset_weights = np.asarray(fit_weights) / np.mean(fit_weights)
com_i = np.average(fit_coords[i], axis=0,
weights=fit_weights)
translated_i = coords[i] - com_i
subset1_coords = fit_coords[i] - com_i
com_j = np.average(fit_coords[j], axis=0,
weights=fit_weights)
translated_j = coords[j] - com_j
subset2_coords = fit_coords[j] - com_j
rotamat = rotation_matrix(subset1_coords, subset2_coords,
subset_weights)[0]
rotated_i = np.transpose(np.dot(rotamat, np.transpose(translated_i)))
rmsdmat[(i + 1) * i // 2 + j] = PureRMSD(
rotated_i.astype(np.float64), translated_j.astype(np.float64),
coords[j].shape[0], weights, sumweights)
else:
raise TypeError("Both fit_coords and fit_weights must be specified "
"if one of them is given")
[docs]def get_distance_matrix(ensemble,
select="name CA",
load_matrix=None,
save_matrix=None,
superimpose=True,
superimposition_subset="name CA",
weights='mass',
n_jobs=1,
max_nbytes=None,
verbose=False,
*conf_dist_args,
**conf_dist_kwargs):
"""
Retrieves or calculates the conformational distance (RMSD)
matrix. The distance matrix is calculated between all the frames of all
the :class:`~MDAnalysis.core.universe.Universe` objects given as input.
The order of the matrix elements depends on the order of the coordinates
of the ensembles and on the order of the input ensembles themselves,
therefore the order of the input list is significant.
The distance matrix can either be calculated from input ensembles or
loaded from an input numpy binary file.
Please notice that the .npz file does not contain a bi-dimensional array,
but a flattened representation that is meant to represent the elements of
an encore.utils.TriangularMatrix object.
Parameters
----------
ensemble : Universe
select : str
Atom selection string in the MDAnalysis format. Default is "name CA"
load_matrix : str, optional
Load similarity/dissimilarity matrix from numpy binary file instead
of calculating it (default is None). A filename is required.
save_matrix : bool, optional
Save calculated matrix as numpy binary file (default is None). A
filename is required.
superimpose : bool, optional
Whether to superimpose structures before calculating distance
(default is True).
superimposition_subset : str, optional
Group for superimposition using MDAnalysis selection syntax
(default is CA atoms: "name CA")
weights : str/array_like, optional
weights to be used for fit. Can be either 'mass' or an array_like
n_jobs : int, optional
Maximum number of cores to be used (default is 1). If -1 use all cores.
max_nbytes : str, optional
Threshold on the size of arrays passed to the workers that triggers automated memory mapping in temp_folder (default is None).
See https://joblib.readthedocs.io/en/latest/generated/joblib.Parallel.html for detailed documentation.
verbose : bool, optional
print progress
Returns
-------
confdistmatrix : encore.utils.TriangularMatrix
Conformational distance matrix. .
"""
# Load the matrix if required
if load_matrix:
logging.info(
" Loading similarity matrix from: {0}".format(load_matrix))
confdistmatrix = \
TriangularMatrix(
size=ensemble.trajectory.timeseries(
ensemble.select_atoms(select),
order='fac').shape[0],
loadfile=load_matrix)
logging.info(" Done!")
for key in confdistmatrix.metadata.dtype.names:
logging.info(" {0} : {1}".format(
key, str(confdistmatrix.metadata[key][0])))
# Check matrix size for consistency
if not confdistmatrix.size == \
ensemble.trajectory.timeseries(
ensemble.select_atoms(select),
order='fac').shape[0]:
logging.error(
"ERROR: The size of the loaded matrix and of the ensemble"
" do not match")
return None
# Calculate the matrix
else:
# Transfer universe to memory to ensure timeseries() support
ensemble.transfer_to_memory()
if not isinstance(weights, (list, tuple, np.ndarray)) and weights == 'mass':
weight_type = 'Mass'
elif weights is None:
weight_type = 'None'
else:
weight_type = 'Custom'
logging.info(
" Perform pairwise alignment: {0}".format(str(superimpose)))
logging.info(" weighted alignment and RMSD: {0}".format(weight_type))
if superimpose:
logging.info(
" Atoms subset for alignment: {0}"
.format(superimposition_subset))
logging.info(" Calculating similarity matrix . . .")
# Use superimposition subset, if necessary. If the pairwise alignment
# is not required, it will not be performed anyway.
confdistmatrix = conformational_distance_matrix(ensemble,
conf_dist_function=set_rmsd_matrix_elements,
select=select,
pairwise_align=superimpose,
weights=weights,
n_jobs=n_jobs,
max_nbytes=max_nbytes,
verbose=verbose)
logging.info(" Done!")
if save_matrix:
confdistmatrix.savez(save_matrix)
return confdistmatrix