# Source code for MDAnalysis.topology.TXYZParser

    # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
    # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
    #
    # MDAnalysis --- https://www.mdanalysis.org
    # Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
    # (see the file AUTHORS for the full list of names)
    #
    # Released under the Lesser GNU Public Licence, v2.1 or any higher version
    #
    # Please cite your use of MDAnalysis in published work:
    #
    # R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler,
    # D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein.
    # MDAnalysis: A Python package for the rapid analysis of molecular dynamics
    # simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th
    # Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy.
    # doi: 10.25080/majora-629e541a-00e
    #
    # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein.
    # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations.
    # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
    #
    """TXYZ topology parser
    ====================

    Tinker_ topology parser: reads information from .txyz and .arc files.
    Atom types are read from column 6, while bond connectivity is read from column 7
    onwards.

    .. _Tinker: https://dasher.wustl.edu/tinker/

    See Also
    --------
    MDAnalysis.coordinates.TXYZ : further documentation on the Tinker format

    Classes
    -------

    .. autoclass:: TXYZParser
       :members:
       :inherited-members:

    """

    import itertools
    import numpy as np
    import warnings

    from ..guesser.tables import SYMB2Z
    from ..lib.util import openany
    from .base import TopologyReaderBase
    from ..core.topology import Topology
    from ..guesser.tables import SYMB2Z
    from ..core.topologyattrs import (
        Atomnames,
        Atomids,
        Atomtypes,
        Bonds,
        Resids,
        Resnums,
        Segids,
        Elements,
    )

    class TXYZParser(TopologyReaderBase):
        """Parse a list of atoms from a Tinker XYZ file.

        Creates the following attributes:

        - Atomnames
        - Atomtypes
        - Elements (if all atom names are element symbols)

        .. note::

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

        .. versionadded:: 0.17.0
        .. versionchanged:: 2.4.0
           Adding the `Element` attribute if all names are valid element symbols.
        .. versionchanged:: 2.8.0
           Removed mass guessing (attributes guessing takes place now
           through universe.guess_TopologyAttrs() API).

        """

        format = ["TXYZ", "ARC"]

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

            Returns
            -------
            MDAnalysis Topology object
            """
            with openany(self.filename) as inf:
                # header
                natoms = int(inf.readline().split()[0])

                atomids = np.zeros(natoms, dtype=int)
                names = np.zeros(natoms, dtype=object)
                types = np.zeros(natoms, dtype=object)
                bonds = []

                # Find first atom line, maybe there's box information
                fline = inf.readline()
                try:
                    # If a box second value will be a float
                    # If an atom, second value will be a string
                    float(fline.split()[1])
                except ValueError:
                    # If float conversion failed, we have first atom line
                    pass
                else:
                    # If previous try succeeded it was a box
                    # so read another line to find the first atom line
                    fline = inf.readline()
                # Can't infinitely read as XYZ files can be multiframe
                for i, line in zip(range(natoms), itertools.chain([fline], inf)):
                    line = line.split()
                    atomids[i] = line[0]
                    names[i] = line[1]
                    types[i] = line[5]
                    bonded_atoms = line[6:]
                    for other_atom in bonded_atoms:
                        other_atom = int(other_atom) - 1
                        if i < other_atom:
                            bonds.append((i, other_atom))

            attrs = [
                Atomnames(names),
                Atomids(atomids),
                Atomtypes(types),
                Bonds(tuple(bonds)),
                Resids(np.array([1])),
                Resnums(np.array([1])),
                Segids(np.array(["SYSTEM"], dtype=object)),
            ]
            if all(n.capitalize() in SYMB2Z for n in names):
                attrs.append(Elements(np.array(names, dtype=object)))

            else:
                warnings.warn(
                    "Element information is missing, elements attribute "
                    "will not be populated. If needed these can be "
                    "guessed using universe.guess_TopologyAttrs("
                    "to_guess=['elements'])."
                )

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

            return top