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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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"""
XYZ Topology Parser
===================

.. versionadded:: 0.9.1

Reads an xyz file and pulls the atom information from it.  Because
xyz only has atom name information, all information about residues
and segments won't be populated.

Classes
-------

.. autoclass:: XYZParser
   :members:

"""
import numpy as np

from ..lib.util import openany
from .base import TopologyReaderBase
from ..core.topology import Topology
from ..core.topologyattrs import (
    Atomnames,
    Atomids,
    Resids,
    Resnums,
    Segids,
    Elements,
)


class XYZParser(TopologyReaderBase):
    """Parse a list of atoms from an XYZ file.

    Creates the following attributes:
     - Atomnames

    .. note::

        By default, atomtypes and masses will be guessed on Universe creation.
        This may change in release 3.0.
        See :ref:`Guessers` for more information.


    .. versionadded:: 0.9.1

    .. versionchanged: 1.0.0
       Store elements attribute, based on XYZ atom names
     .. versionchanged:: 2.8.0
        Removed type and mass guessing (attributes guessing takes place now
        through universe.guess_TopologyAttrs() API).

    """

    format = "XYZ"

    def parse(self, **kwargs):
        """Read the file and return the structure.

        Returns
        -------
        MDAnalysis Topology object
        """
        with openany(self.filename) as inf:
            natoms = int(inf.readline().strip())
            inf.readline()

            names = np.zeros(natoms, dtype=object)

            # Can't infinitely read as XYZ files can be multiframe
            for i in range(natoms):
                name = inf.readline().split()[0]
                names[i] = name

        attrs = [
            Atomnames(names),
            Atomids(np.arange(natoms) + 1),
            Resids(np.array([1])),
            Resnums(np.array([1])),
            Segids(np.array(["SYSTEM"], dtype=object)),
            Elements(names),
        ]

        top = Topology(natoms, 1, 1, attrs=attrs)

        return top