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

.. autofunction:: translate

.. autofunction:: center_in_box

from __future__ import absolute_import, division
from six import raise_from

import numpy as np
from functools import partial

from ..lib.mdamath import triclinic_vectors

[docs]def translate(vector): """ Translates the coordinates of a given :class:`~MDAnalysis.coordinates.base.Timestep` instance by a given vector. Example ------- 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.base.Timestep` object """ if len(vector)>2: vector = np.float32(vector) else: raise ValueError("{} vector is too short".format(vector)) def wrapped(ts): ts.positions += vector return ts return wrapped
[docs]def center_in_box(ag, center='geometry', point=None, wrap=False): """ Translates the coordinates of a given :class:`~MDAnalysis.coordinates.base.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 =,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.base.Timestep` object """ pbc_arg = wrap if point: point = np.asarray(point, np.float32) if point.shape != (3, ) and point.shape != (1, 3): raise ValueError('{} is not a valid point'.format(point)) try: if center == 'geometry': center_method = partial(ag.center_of_geometry, pbc=pbc_arg) elif center == 'mass': center_method = partial(ag.center_of_mass, pbc=pbc_arg) else: raise ValueError('{} is not a valid argument for center'.format(center)) except AttributeError: if center == 'mass': raise_from( AttributeError('{} is not an AtomGroup object with masses'.format(ag)), None) else: raise_from(ValueError('{} is not an AtomGroup object'.format(ag)), None) def wrapped(ts): if point is None: boxcenter = np.sum(ts.triclinic_dimensions, axis=0) / 2 else: boxcenter = point ag_center = center_method() vector = boxcenter - ag_center ts.positions += vector return ts return wrapped