# Source code for MDAnalysis.transformations.wrap

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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