Source code for MDAnalysis.transformations.wrap

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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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"""\
Wrap/unwrap transformations --- :mod:`MDAnalysis.transformations.wrap`
======================================================================

Wrap/unwrap the atoms of a given AtomGroup in the unit cell. :func:`wrap` 
translates the atoms back in the unit cell. :func:`unwrap` translates the
atoms of each molecule so that bons don't split over images.

.. autoclass:: wrap

.. autoclass:: unwrap

"""

from ..lib._cutil import make_whole

from .base import TransformationBase


class wrap(TransformationBase):
    """
    Shift the contents of a given AtomGroup back into the unit cell. ::
    
       +-----------+          +-----------+
       |           |          |           |
       |         3 | 6        | 6       3 |
       |         ! | !        | !       ! |
       |       1-2-|-5-8  ->  |-5-8   1-2-|
       |         ! | !        | !       ! |
       |         4 | 7        | 7       4 |
       |           |          |           |
       +-----------+          +-----------+
    
    Example
    -------
    
    .. code-block:: python
        
        ag = u.atoms 
        transform = mda.transformations.wrap(ag)
        u.trajectory.add_transformations(transform)
        
    Parameters
    ----------
    
    ag: Atomgroup
        Atomgroup to be wrapped in the unit cell
    compound : {'atoms', 'group', 'residues', 'segments', 'fragments'}, optional
        The group which will be kept together through the shifting process.
    
    Notes
    -----
    When specifying a `compound`, the translation is calculated based on
    each compound. The same translation is applied to all atoms
    within this compound, meaning it will not be broken by the shift.
    This might however mean that not all atoms from the compound are
    inside the unit cell, but rather the center of the compound is.
    
    Returns
    -------
    MDAnalysis.coordinates.timestep.Timestep


    .. 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, compound='atoms',
                 max_threads=None, parallelizable=True):
        super().__init__(max_threads=max_threads,
                         parallelizable=parallelizable)

        self.ag = ag
        self.compound = compound

    def _transform(self, ts):
        self.ag.wrap(compound=self.compound)
        return ts


class unwrap(TransformationBase):
    """
    Move all atoms in an AtomGroup so that bonds don't split over images

    Atom positions are modified in place.

    This function is most useful when atoms have been packed into the primary
    unit cell, causing breaks mid molecule, with the molecule then appearing
    on either side of the unit cell. This is problematic for operations
    such as calculating the center of mass of the molecule. ::
    
       +-----------+     +-----------+
       |           |     |           |
       | 6       3 |     |         3 | 6
       | !       ! |     |         ! | !
       |-5-8   1-2-| ->  |       1-2-|-5-8
       | !       ! |     |         ! | !
       | 7       4 |     |         4 | 7
       |           |     |           |
       +-----------+     +-----------+
    
    Example
    -------
    
    .. code-block:: python
        
        ag = u.atoms 
        transform = mda.transformations.unwrap(ag)
        u.trajectory.add_transformations(transform)
    
    Parameters
    ----------
    atomgroup : AtomGroup
        The :class:`MDAnalysis.core.groups.AtomGroup` to work with.
        The positions of this are modified in place.
    
    Returns
    -------
    MDAnalysis.coordinates.timestep.Timestep


    .. 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, max_threads=None, parallelizable=True):
        super().__init__(max_threads=max_threads,
                         parallelizable=parallelizable)

        self.ag = ag

        try:
            self.ag.fragments
        except AttributeError:
            raise AttributeError("{} has no fragments".format(self.ag))

    def _transform(self, ts):
        for frag in self.ag.fragments:
            make_whole(frag)
        return ts