# Source code for MDAnalysis.analysis.atomicdistances

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    r"""
    Simple atomic distance analysis --- :mod:`MDAnalysis.analysis.atomicdistances`
    ==============================================================================

    :Author: Xu Hong Chen
    :Year: 2023
    :Copyright: Lesser GNU Public License v2.1+

    This module provides a class to efficiently compute distances between
    two groups of atoms with an equal number of atoms over a trajectory.
    Specifically, for two atom groups ``ag1`` and ``ag2``, it will return
    the distances

    .. math::
        |ag1[i] - ag2[i]|

    for all :math:`i` from :math:`0` to `n_atoms` :math:`- 1`, where
    `n_atoms` is the number of atoms in each atom group. By default,
    this computation is done with periodic boundary conditions, but this
    can be easily turned off. These distances are grouped by time step in
    a NumPy array.

    For more general functions on computing distances between atoms or
    groups of atoms, please see :class:`MDAnalysis.analysis.distances`.

    See Also
    --------
    :mod:`MDAnalysis.analysis.distances`
    :mod:`MDAnalysis.lib.distances`

    Basic usage
    -----------

    This example uses files from the MDAnalysis test suite
    (:data:`~MDAnalysis.tests.datafiles.GRO` and
    :data:`~MDAnalysis.tests.datafiles.XTC`). To get started, execute  ::

       >>> import MDAnalysis as mda
       >>> from MDAnalysis.tests.datafiles import GRO, XTC
       >>> import MDAnalysis.analysis.atomicdistances as ad

    We will calculate the distances between an atom group of atoms 101-105
    and an atom group of atoms 4001-4005 with periodic boundary conditions.
    To select these atoms: ::

       >>> u = mda.Universe(GRO, XTC)
       >>> ag1 = u.atoms[100:105]
       >>> ag2 = u.atoms[4000:4005]

    We can run the calculations using any variable of choice such as
    ``my_dists`` and access our results using ``my_dists.results``: ::

       >>> my_dists = ad.AtomicDistances(ag1, ag2).run()
       >>> my_dists.results
       array([[37.80813681, 33.2594864 , 34.93676414, 34.51183299, 34.96340209],
              [27.11746625, 31.19878079, 31.69439435, 32.63446126, 33.10451345],
              [23.27210749, 30.38714688, 32.48269361, 31.91444505, 31.84583838],
              [18.40607922, 39.21993135, 39.33468192, 41.0133789 , 39.46885946],
              [26.26006981, 37.9966713 , 39.14991106, 38.13423586, 38.95451427],
              [26.83845081, 34.66255735, 35.59335027, 34.8926705 , 34.27175056],
              [37.51994763, 38.12161091, 37.56481743, 36.8488121 , 35.75278065],
              [37.27275501, 37.7831456 , 35.74359073, 34.54893794, 34.76495816],
              [38.76272761, 41.31816555, 38.81588421, 39.82491432, 38.890219  ],
              [39.20012515, 40.00563374, 40.83857688, 38.77886735, 41.45775864]])

    To do the computation without periodic boundary conditions, we can enter
    the keyword argument ``pbc=False`` after ``ag2``. The result is different
    in this case: ::

       >>> my_dists_nopbc = ad.AtomicDistances(ag1, ag2, pbc=False).run()
       >>> my_dists_nopbc.results
       array([[37.80813681, 33.2594864 , 34.93676414, 34.51183299, 34.96340209],
              [27.11746625, 31.19878079, 31.69439435, 32.63446126, 33.10451345],
              [23.27210749, 30.38714688, 32.482695  , 31.91444505, 31.84583838],
              [18.40607922, 39.21992825, 39.33468192, 41.0133757 , 39.46885946],
              [26.26006981, 37.99666906, 39.14990985, 38.13423708, 38.95451311],
              [26.83845081, 34.66255625, 35.59335027, 34.8926705 , 34.27174827],
              [51.86981409, 48.10347964, 48.39570072, 49.14423513, 50.44804292],
              [37.27275501, 37.7831456 , 35.74359073, 34.54893794, 34.76495816],
              [56.39657447, 41.31816555, 38.81588421, 39.82491432, 38.890219  ],
              [39.20012515, 40.00563374, 40.83857688, 38.77886735, 41.45775864]])

    """

    import numpy as np

    from MDAnalysis.lib.distances import calc_bonds

    import logging
    from .base import AnalysisBase

    logger = logging.getLogger("MDAnalysis.analysis.atomicdistances")

    class AtomicDistances(AnalysisBase):
        r"""Class to calculate atomic distances between two AtomGroups over a
        trajectory.

        Parameters
        ----------
        ag1, ag2 : AtomGroup
            :class:`~MDAnalysis.core.groups.AtomGroup` with the
            same number of atoms
        pbc : bool, optional
            If ``True``, calculates atomic distances with periodic boundary
            conditions (PBCs). Setting `pbc` to ``False``, calculates atomic
            distances without considering PBCs. Defaults to ``True``.

        Attributes
        ----------
        results : :class:`numpy.ndarray`
            The distances :math:`|ag1[i] - ag2[i]|` for all :math:`i`
            from :math:`0` to `n_atoms` :math:`- 1` for each frame over
            the trajectory.
        n_frames : int
            Number of frames included in the analysis.
        n_atoms : int
            Number of atoms in each atom group.

        .. versionadded:: 2.5.0
        """

        def __init__(self, ag1, ag2, pbc=True, **kwargs):
            # check ag1 and ag2 have the same number of atoms
            if ag1.atoms.n_atoms != ag2.atoms.n_atoms:
                raise ValueError(
                    "AtomGroups do not " "have the same number of atoms"
                )
            # check ag1 and ag2 are from the same trajectory
            elif ag1.universe.trajectory != ag2.universe.trajectory:
                raise ValueError("AtomGroups are not " "from the same trajectory")

            super(AtomicDistances, self).__init__(
                ag1.universe.trajectory, **kwargs
            )

            self._ag1 = ag1
            self._ag2 = ag2
            self._pbc = pbc

        def _prepare(self):
            # initialize NumPy array of frames x distances for results
            self.results = np.zeros((self.n_frames, self._ag1.atoms.n_atoms))

        def _single_frame(self):
            # if PBCs considered, get box size
            box = self._ag1.dimensions if self._pbc else None
            self.results[self._frame_index] = calc_bonds(
                self._ag1.positions, self._ag2.positions, box
            )