# Source code for MDAnalysis.coordinates.TXYZ

    # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
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    # 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)
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    #
    # Please cite your use of MDAnalysis in published work:
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    # 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.
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    # 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 file format --- :mod:`MDAnalysis.coordinates.TXYZ`
    =======================================================

    Coordinate reader for Tinker_ xyz files .txyz and trajectory .arc files.
    Differences between Tinker format_ and normal xyz files:

    - there is only one header line containing both the number of atoms and a comment
    - column 1 contains atom numbers (starting from 1)
    - column 6 contains atoms types
    - the following columns indicate connectivity (atoms to which that particular atom is
      bonded, according to numbering in column 1)

    .. _format: http://chembytes.wikidot.com/tnk-tut00#toc2
    .. _Tinker: https://dasher.wustl.edu/tinker/

    Classes
    -------

    .. autoclass:: TXYZReader
       :members:
       :inherited-members:

    """
    import numpy as np
    import os
    import errno

    from ..lib import util
    from . import base
    from ..lib.util import openany, cached, store_init_arguments
    from .timestep import Timestep

    class TXYZReader(base.ReaderBase):
        """Reads from a TXYZ file"""

        format = ["TXYZ", "ARC"]
        # these are assumed!
        units = {"time": "ps", "length": "Angstrom"}
        _Timestep = Timestep

        @store_init_arguments
        def __init__(self, filename, **kwargs):
            super(TXYZReader, self).__init__(filename, **kwargs)

            # the filename has been parsed to be either be foo.xyz or foo.xyz.bz2 by
            # coordinates::core.py so the last file extension will tell us if it is
            # bzipped or not
            root, ext = os.path.splitext(self.filename)
            self.xyzfile = util.anyopen(self.filename)
            self._cache = dict()
            # Check if file has box information saved
            with util.openany(self.filename) as inp:
                inp.readline()
                line = inp.readline()
                # If second line has float at second position, we have box info
                try:
                    float(line.split()[1])
                except ValueError:
                    self.periodic = False
                else:
                    self.periodic = True
            self.ts = self._Timestep(self.n_atoms, **self._ts_kwargs)

            self._read_next_timestep()

        @property
        @cached("n_atoms")
        def n_atoms(self):
            """number of atoms in a frame"""
            with util.anyopen(self.filename) as f:
                n = f.readline().split()[0]
            # need to check type of n
            return int(n)

        @property
        @cached("n_frames")
        def n_frames(self):
            try:
                return self._read_xyz_n_frames()
            except IOError:
                return 0

        def _read_xyz_n_frames(self):
            # the number of lines in the XYZ file will be 1 greater than the
            # number of atoms
            linesPerFrame = self.n_atoms + 1
            if self.periodic:
                linesPerFrame += 1
            counter = 0
            offsets = []

            with util.anyopen(self.filename) as f:
                line = True
                while line:
                    if not counter % linesPerFrame:
                        offsets.append(f.tell())
                    line = f.readline()
                    counter += 1

            # need to check this is an integer!
            n_frames = int(counter / linesPerFrame)
            self._offsets = offsets
            return n_frames

        def _read_frame(self, frame):
            self.xyzfile.seek(self._offsets[frame])
            self.ts.frame = frame - 1  # gets +1'd in next
            return self._read_next_timestep()

        def _read_next_timestep(self, ts=None):
            # check that the timestep object exists
            if ts is None:
                ts = self.ts

            f = self.xyzfile

            try:
                # we assume that there is only one header line per frame
                f.readline()
                if self.periodic:
                    ts.dimensions = f.readline().split()
                # convert all entries at the end once for optimal speed
                tmp_buf = []
                for i in range(self.n_atoms):
                    tmp_buf.append(f.readline().split()[2:5])
                ts.positions = tmp_buf
                ts.frame += 1
                return ts
            except (ValueError, IndexError) as err:
                raise EOFError(err) from None

        def _reopen(self):
            self.close()
            self.open_trajectory()

        def open_trajectory(self):
            if self.xyzfile is not None:
                raise IOError(
                    errno.EALREADY, "TXYZ file already opened", self.filename
                )

            self.xyzfile = util.anyopen(self.filename)

            # reset ts
            ts = self.ts
            ts.frame = -1

            return self.xyzfile

        def close(self):
            """Close arc trajectory file if it was open."""
            if self.xyzfile is None:
                return
            self.xyzfile.close()
            self.xyzfile = None