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# -*- 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
#
"""\
Trajectory translation --- :mod:`MDAnalysis.transformations.translate`
======================================================================
Translate the coordinates of a given trajectory by a given vector.
The vector can either be user defined, using the function :func:`translate`
or defined by centering an AtomGroup in the unit cell using the function
:func:`center_in_box`
.. autoclass:: translate
.. autoclass:: center_in_box
"""
import numpy as np
from functools import partial
from .base import TransformationBase
class translate(TransformationBase):
"""
Translates the coordinates of a given :class:`~MDAnalysis.coordinates.timestep.Timestep`
instance by a given vector.
Example
-------
.. code-block:: python
ts = MDAnalysis.transformations.translate([1,2,3])(ts)
Parameters
----------
vector: array-like
coordinates of the vector to which the coordinates will be translated
Returns
-------
:class:`~MDAnalysis.coordinates.timestep.Timestep` object
.. versionchanged:: 2.0.0
The transformation was changed from a function/closure to a class
with ``__call__``.
.. versionchanged:: 2.0.0
The transformation was changed to inherit from the base class for
limiting threads and checking if it can be used in parallel analysis.
"""
def __init__(self, vector, max_threads=None, parallelizable=True):
super().__init__(
max_threads=max_threads, parallelizable=parallelizable
)
self.vector = vector
if len(self.vector) > 2:
self.vector = np.float32(self.vector)
else:
raise ValueError("{} vector is too short".format(self.vector))
def _transform(self, ts):
ts.positions += self.vector
return ts
class center_in_box(TransformationBase):
"""
Translates the coordinates of a given :class:`~MDAnalysis.coordinates.timestep.Timestep`
instance so that the center of geometry/mass of the given :class:`~MDAnalysis.core.groups.AtomGroup`
is centered on the unit cell. The unit cell dimensions are taken from the input Timestep object.
If a point is given, the center of the atomgroup will be translated to this point instead.
Example
-------
.. code-block:: python
ag = u.residues[1].atoms
ts = MDAnalysis.transformations.center(ag,center='mass')(ts)
Parameters
----------
ag: AtomGroup
atom group to be centered on the unit cell.
center: str, optional
used to choose the method of centering on the given atom group. Can be 'geometry'
or 'mass'
point: array-like, optional
overrides the unit cell center - the coordinates of the Timestep are translated so
that the center of mass/geometry of the given AtomGroup is aligned to this position
instead. Defined as an array of size 3.
wrap: bool, optional
If `True`, all the atoms from the given AtomGroup will be moved to the unit cell
before calculating the center of mass or geometry. Default is `False`, no changes
to the atom coordinates are done before calculating the center of the AtomGroup.
Returns
-------
:class:`~MDAnalysis.coordinates.timestep.Timestep` object
.. versionchanged:: 2.0.0
The transformation was changed from a function/closure to a class
with ``__call__``.
.. versionchanged:: 2.0.0
The transformation was changed to inherit from the base class for
limiting threads and checking if it can be used in parallel analysis.
"""
def __init__(
self,
ag,
center="geometry",
point=None,
wrap=False,
max_threads=None,
parallelizable=True,
):
super().__init__(
max_threads=max_threads, parallelizable=parallelizable
)
self.ag = ag
self.center = center
self.point = point
self.wrap = wrap
pbc_arg = self.wrap
if self.point:
self.point = np.asarray(self.point, np.float32)
if self.point.shape != (3,) and self.point.shape != (1, 3):
raise ValueError("{} is not a valid point".format(self.point))
try:
if self.center == "geometry":
self.center_method = partial(
self.ag.center_of_geometry, wrap=pbc_arg
)
elif self.center == "mass":
self.center_method = partial(
self.ag.center_of_mass, wrap=pbc_arg
)
else:
raise ValueError(f"{self.center} is valid for center")
except AttributeError:
if self.center == "mass":
errmsg = f"{self.ag} is not an AtomGroup object with masses"
raise AttributeError(errmsg) from None
else:
raise ValueError(
f"{self.ag} is not an AtomGroup object"
) from None
def _transform(self, ts):
if self.point is None:
if ts.dimensions is None:
raise ValueError("Box is None")
boxcenter = np.sum(ts.triclinic_dimensions, axis=0) / 2
else:
boxcenter = self.point
ag_center = self.center_method()
vector = boxcenter - ag_center
ts.positions += vector
return ts
|
