Source code for MDAnalysis.transformations.translate

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# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler,
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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




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