# Source code for mdtraj.formats.arc

    ##############################################################################
    # MDTraj: A Python Library for Loading, Saving, and Manipulating
    #         Molecular Dynamics Trajectories.
    # Copyright 2012-2013 Stanford University and the Authors
    #
    # Authors: Lee-Ping Wang
    # Contributors: Robert McGibbon and Jason Swails
    #
    # MDTraj is free software: you can redistribute it and/or modify
    # it under the terms of the GNU Lesser General Public License as
    # published by the Free Software Foundation, either version 2.1
    # of the License, or (at your option) any later version.
    #
    # This library is distributed in the hope that it will be useful,
    # but WITHOUT ANY WARRANTY; without even the implied warranty of
    # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
    # GNU Lesser General Public License for more details.
    #
    # You should have received a copy of the GNU Lesser General Public
    # License along with MDTraj. If not, see <http://www.gnu.org/licenses/>.
    ##############################################################################

    import itertools
    import os

    import numpy as np

    from mdtraj.formats.registry import FormatRegistry
    from mdtraj.utils import cast_indices, in_units_of

    __all__ = ["ArcTrajectoryFile", "load_arc"]

    class _EOF(IOError):
        pass

    @FormatRegistry.register_loader(".arc")
    def load_arc(filename, stride=None, atom_indices=None, frame=None, top=None):
        """Load a TINKER .arc file from disk.

        Parameters
        ----------
        filename : path-like
            Path of TINKER .arc file.
        stride : int, default=None
            Only read every stride-th frame
        atom_indices : array_like, optional
            If not none, then read only a subset of the atoms coordinates from the
            file.
        frame : int, optional
            Use this option to load only a single frame from a trajectory on disk.
            If frame is None, the default, the entire trajectory will be loaded.
            If supplied, ``stride`` will be ignored.
        top : {str, Trajectory, Topology}, optional
            While the ARC format does does contain minimal topology information, it does
            not include residue information. Pass in either a file path
            (e.g. to pdb), a trajectory, or a topology object to supply this information.

        Returns
        -------
        trajectory : md.Trajectory
            The resulting trajectory, as an md.Trajectory object.

        See Also
        --------
        mdtraj.ArcTrajectoryFile :  Low level interface to TINKER .arc files
        """

        if not isinstance(filename, (str, os.PathLike)):
            raise TypeError(
                "filename must be of type path-like for load_arc. you supplied %s" % type(filename),
            )

        # Process topology, if given.
        if top is not None:
            from mdtraj.core.trajectory import _parse_topology

            topology = _parse_topology(top)
        else:
            topology = None

        atom_indices = cast_indices(atom_indices)

        with ArcTrajectoryFile(filename) as f:
            # Set topology. If not given, it's None.
            f.topology = topology

            if frame is not None:
                f.seek(frame)
                n_frames = 1
            else:
                n_frames = None
            return f.read_as_traj(
                n_frames=n_frames,
                stride=stride,
                atom_indices=atom_indices,
            )

    @FormatRegistry.register_fileobject(".arc")
    class ArcTrajectoryFile:
        """Interface for reading and writing to an TINKER archive files.
        (Note that the TINKER .xyz format is identical to this.)  This is
        a file-like object, that both reading or writing depending on the
        `mode` flag. It implements the context manager protocol, so you
        can also use it with the python 'with' statement.

        The conventional units in the arc file is angstrom. The format only
        supports storing the cartesian coordinates and box lengths.

        Attributes
        ----------
        topology : Topology
            A single-chain, single-residue topology generated from the atom and bond
            information found in the TINKER archive/xyz file. It is only generated
            from the first member of the archive

        Parameters
        ----------
        filename : path-like
            The filename to open. A path to a file on disk.
        mode : {'r'}
            The mode in which to open the file, only 'r' for read is supported.
        force_overwrite : bool
            If opened in write mode, and a file by the name of `filename` already
            exists on disk, should we overwrite it?
        """

        distance_unit = "angstroms"

        def __init__(self, filename, mode="r", force_overwrite=True):
            """Open an TINKER.arc file for reading/writing."""
            self._is_open = False
            self._filename = filename
            self._frame_index = 0
            self._mode = mode
            self.topology = None

            if mode == "w":
                raise ValueError("Writing TINKER .arc files is not supported at this time")

            # track which line we're on. this is not essential, but its useful
            # when reporting errors to the user to say what line it occured on.
            self._line_counter = 0

            if mode == "r":
                # if n_atoms is None:
                #     raise ValueError('To open a mdcrd file in mode="r", you must '
                #                      'supply the number of atoms, "n_atoms"')
                if not os.path.exists(filename):
                    raise OSError("The file '%s' doesn't exist" % filename)
                self._fh = open(filename)
                self._is_open = True
            else:
                raise ValueError(
                    'mode must be "r". you supplied "%s"' % mode,
                )

        def seek(self, offset, whence=0):
            """Move to a new file position

            Parameters
            ----------
            offset : int
                A number of frames.
            whence : {0, 1, 2}
                0: offset from start of file, offset should be >=0.
                1: move relative to the current position, positive or negative
                2: move relative to the end of file, offset should be <= 0.
                Seeking beyond the end of a file is not supported
            """
            raise NotImplementedError()

        def tell(self):
            """Current file position

            Returns
            -------
            offset : int
                The current frame in the file.
            """
            raise NotImplementedError()

        def close(self):
            """Close the .arc file"""
            if self._is_open:
                self._fh.close()
                self._is_open = False

        def __del__(self):
            self.close()

        def __enter__(self):
            "Support the context manager protocol"
            return self

        def __exit__(self, *exc_info):
            "Support the context manager protocol"
            self.close()

        def __len__(self):
            "Number of frames in the file"
            raise NotImplementedError()

        def read_as_traj(self, n_frames=None, stride=None, atom_indices=None):
            """Read a trajectory from a ARC file

            Parameters
            ----------
            n_frames : int, optional
                If positive, then read only the next `n_frames` frames. Otherwise read all
                of the frames in the file.
            stride : np.ndarray, optional
                Read only every stride-th frame.
            atom_indices : array_like, optional
                If not none, then read only a subset of the atoms coordinates from the
                file. This may be slightly slower than the standard read because it required
                an extra copy, but will save memory.

            See Also
            --------
            read : Returns the raw data from the file
            """
            from mdtraj.core.trajectory import Trajectory

            if atom_indices is not None:
                topology = self.topology.subset(atom_indices)

            initial = int(self._frame_index)
            xyz, abc, ang = self.read(
                n_frames=n_frames,
                stride=stride,
                atom_indices=atom_indices,
            )
            if len(xyz) == 0:
                return Trajectory(xyz=np.zeros((0, topology.n_atoms, 3)), topology=topology)

            in_units_of(xyz, self.distance_unit, Trajectory._distance_unit, inplace=True)
            in_units_of(abc, self.distance_unit, Trajectory._distance_unit, inplace=True)

            if stride is None:
                stride = 1
            time = (stride * np.arange(len(xyz))) + initial

            return Trajectory(
                xyz=xyz,
                topology=self.topology,
                time=time,
                unitcell_lengths=abc,
                unitcell_angles=ang,
            )

        def read(self, n_frames=None, stride=None, atom_indices=None):
            """Read data from a TINKER .arc file.

            Note that only the
            Cartesian coordinates are read in.  The .arc file also
            contains TINKER-specific numeric atom types and some bonding
            information, which we do not read in.

            Parameters
            ----------
            n_frames : int, None
                The number of frames you would like to read from the file.
                If None, all of the remaining frames will be loaded.
            stride : np.ndarray, optional
                Read only every stride-th frame.
            atom_indices : array_like, optional
                If not none, then read only a subset of the atoms coordinates
                from the file.

            Returns
            -------
            xyz : np.ndarray, shape=(n_frames, n_atoms, 3), dtype=np.float32
                The cartesian coordinates, in angstroms
            """
            if not self._mode == "r":
                raise ValueError(
                    'read() is only available when file is opened in mode="r"',
                )

            if n_frames is None:
                frame_counter = itertools.count()
            else:
                frame_counter = range(n_frames)

            if stride is None:
                stride = 1

            coords = []
            lengths = []
            angles = []
            for i in frame_counter:
                try:
                    coord, length, angle = self._read()
                    if atom_indices is not None:
                        coord = coord[atom_indices, :]
                except _EOF:
                    break

                coords.append(coord)
                lengths.append(length)
                angles.append(angle)

                for j in range(stride - 1):
                    # throw away these frames
                    self._read()

            coords = np.array(coords)
            if any(length is None for length in lengths):
                lengths = angles = None
            else:
                lengths = np.array(lengths)
                angles = np.array(angles)

            return coords, lengths, angles

        def _read(self):
            "Read a single frame"
            from mdtraj.core.element import Element, virtual
            from mdtraj.core.topology import Topology

            # Read in the number of atoms.
            line = self._fh.readline()
            if line == "":
                raise _EOF()

            self._n_atoms = int(line.split()[0])
            self._line_counter += 1

            coords = np.empty((self._n_atoms, 3), dtype=np.float32)
            bond_partners = [[] for i in range(self._n_atoms)]
            atom_names = ["" for i in range(self._n_atoms)]
            line = self._fh.readline()
            s = line.split()
            self._line_counter += 1
            # See if we have box info on this line or not
            cell_lengths = cell_angles = None
            if len(s) == 6:
                try:
                    cell_lengths = np.asarray(
                        [float(s[0]), float(s[1]), float(s[2])],
                    )
                    cell_angles = np.asarray(
                        [float(s[3]), float(s[4]), float(s[5])],
                    )
                    line = self._fh.readline()
                    s = line.split()
                    self._line_counter += 1
                except ValueError:
                    pass
            i = 0
            while i < self._n_atoms - 1:
                atom_names[i] = s[1]
                bond_partners[i] = [int(x) for x in s[6:]]
                coords[i, :] = [float(s[pos]) for pos in [2, 3, 4]]
                i += 1
                line = self._fh.readline()
                s = line.split()
                self._line_counter += 1
            # Now do the last atom
            atom_names[i] = s[1]
            bond_partners[i] = [int(x) for x in s[6:]]
            coords[i, :] = [float(s[pos]) for pos in [2, 3, 4]]
            # Now see if we have to build a topology
            if self.topology is None:
                self.topology = top = Topology()
                chain = top.add_chain()  # only 1 chain
                res = top.add_residue("RES", chain, 1)  # only 1 residue
                for at in atom_names:
                    # First get the element. Try for common 2-letter elements, then
                    # use the first letter only (default to None if I can't find it)
                    if at[:2].upper() in ("NA", "CL", "MG"):
                        elem = Element.getBySymbol(at[:2])
                    else:
                        try:
                            elem = Element.getBySymbol(at[0])
                        except KeyError:
                            elem = virtual
                    top.add_atom(at, elem, res)
                # Now add the bonds
                atoms = list(top.atoms)
                for i, bonds in enumerate(bond_partners):
                    me = atoms[i]
                    for b in bonds:
                        b -= 1
                        if b < i:
                            continue
                        it = atoms[b]
                        top.add_bond(me, it)

            self._frame_index += 1
            return coords, cell_lengths, cell_angles

        def write(self, xyz):
            """The ArcTrajectoryFile does not have a write method,
            because TINKER .arc files have special numerical atom types
            which are not shared by any other trajectory file format.

            Parameters
            ----------
            xyz : np.ndarray, shape=(n_frames, n_atoms, 3)
                The cartesian coordinates of the atoms to write.

            """

            raise RuntimeError("write() is not available for .arc files")