Source code for MDAnalysis.transformations.translate

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"""\
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


[docs] 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
[docs] 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