# Source code for mdtraj.formats.gro

    """gro.py: Used for loading Gromacs GRO files."""

    ##############################################################################
    # MDTraj: A Python Library for Loading, Saving, and Manipulating
    #         Molecular Dynamics Trajectories.
    # Copyright 2012-2015 Stanford University and the Authors
    #
    # Authors: Robert McGibbon, Lee-Ping Wang, Peter Eastman
    # Contributors: 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/>.
    #
    # Portions of this code originate from the OpenMM molecular simulation
    # toolkit, copyright (c) 2012 Stanford University and the Authors. Those
    # portions are distributed under the following terms:
    #
    # Permission is hereby granted, free of charge, to any person obtaining a
    # copy of this software and associated documentation files (the "Software"),
    # to deal in the Software without restriction, including without limitation
    # the rights to use, copy, modify, merge, publish, distribute, sublicense,
    # and/or sell copies of the Software, and to permit persons to whom the
    # Software is furnished to do so, subject to the following conditions:
    #
    # The above copyright notice and this permission notice shall be included in
    # all copies or substantial portions of the Software.
    #
    # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
    # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
    # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
    # THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,
    # DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
    # OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE
    # USE OR OTHER DEALINGS IN THE SOFTWARE.
    ##############################################################################

    import itertools
    import os
    import warnings
    from re import findall, match, sub

    import numpy as np

    import mdtraj as md
    from mdtraj.core import element as elem
    from mdtraj.formats import pdb
    from mdtraj.formats.registry import FormatRegistry
    from mdtraj.utils import cast_indices, ensure_type, in_units_of

    @FormatRegistry.register_loader(".gro")
    def load_gro(filename, stride=None, atom_indices=None, frame=None, top=None):
        """Load a GROMACS GRO file.

        Parameters
        ----------
        filename : path-like
            Path to the GRO file on disk.
        stride : int, default=None
            Only read every stride-th model from the file
        atom_indices : array_like, optional
            If not none, then read only a subset of the atoms coordinates from the
            file. These indices are zero-based.
        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 : mdtraj.core.Topology, default=None
            if you give a topology as input the topology won't be parsed from the gro file
            it saves time if you have to parse a big number of files
        """

        with GroTrajectoryFile(filename, "r", top=top) as f:
            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(".gro")
    class GroTrajectoryFile:
        """Interface for reading and writing to GROMACS GRO files.

        Parameters
        ----------
        filename : path-like
            The filename to open. A path to a file on disk.
        mode : {'r', 'w'}
            The mode in which to open the file, either 'r' for read or 'w' for write.
        force_overwrite : bool
            If opened in write mode, and a file by the name of `filename` already
            exists on disk, should we overwrite it?
        top : mdtraj.core.Topology, default=None
            if you give a topology as input the topology won't be parsed from the gro file
            it saves time if you have to parse a big number of files

        Attributes
        ----------
        n_atoms : int
            The number of atoms in the file
        topology : md.Topology
            The topology. TODO(rmcgibbo) note about chain

        See Also
        --------
        load_gro : High-level wrapper that returns a ``md.Trajectory``
        """

        distance_unit = "nanometers"

        def __init__(self, filename, mode="r", force_overwrite=True, top=None):
            self._open = False
            self._file = None
            self._mode = mode

            self.topology = top

            if mode == "r":
                self._open = True
                self._frame_index = 0
                self._file = open(filename)
                try:
                    if self.topology is None:
                        self.n_atoms, self.topology = self._read_topology()
                    else:
                        self.n_atoms = self.topology.n_atoms
                finally:
                    self._file.seek(0)
            elif mode == "w":
                self._open = True
                if os.path.exists(filename) and not force_overwrite:
                    raise OSError('"%s" already exists' % filename)
                self._frame_index = 0
                self._file = open(filename, "w")
            else:
                raise ValueError("invalid mode: %s" % mode)

        def write(
            self,
            coordinates,
            topology,
            time=None,
            unitcell_vectors=None,
            precision=3,
        ):
            """Write one or more frames of a molecular dynamics trajectory to disk
            in the GROMACS GRO format.

            Parameters
            ----------
            coordinates : np.ndarray, dtype=np.float32, shape=(n_frames, n_atoms, 3)
                The cartesian coordinates of each atom, in units of nanometers.
            topology : mdtraj.Topology
                The Topology defining the model to write.
            time : np.ndarray, dtype=float32, shape=(n_frames), optional
                The simulation time corresponding to each frame, in picoseconds.
                If not supplied, the numbers 0..n_frames will be written.
            unitcell_vectors : np.ndarray, dtype=float32, shape=(n_frames, 3, 3), optional
                The periodic box vectors of the simulation in each frame, in nanometers.
            precision : int, optional
                The number of decimal places to print for coordinates. Default is 3
            """
            if not self._open:
                raise ValueError("I/O operation on closed file")
            if not self._mode == "w":
                raise ValueError("file not opened for writing")

            coordinates = ensure_type(
                coordinates,
                dtype=np.float32,
                ndim=3,
                name="coordinates",
                can_be_none=False,
                warn_on_cast=False,
            )
            time = ensure_type(
                time,
                dtype=float,
                ndim=1,
                name="time",
                can_be_none=True,
                shape=(len(coordinates),),
                warn_on_cast=False,
            )
            unitcell_vectors = ensure_type(
                unitcell_vectors,
                dtype=float,
                ndim=3,
                name="unitcell_vectors",
                can_be_none=True,
                shape=(len(coordinates), 3, 3),
                warn_on_cast=False,
            )

            for i in range(coordinates.shape[0]):
                frame_time = None if time is None else time[i]
                frame_box = None if unitcell_vectors is None else unitcell_vectors[i]
                self._write_frame(
                    coordinates[i],
                    topology,
                    frame_time,
                    frame_box,
                    precision,
                )

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

            Returns
            -------
            trajectory : Trajectory
                A trajectory object containing the loaded portion of the file.
            """
            from mdtraj.core.trajectory import Trajectory

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

            coordinates, time, unitcell_vectors = self.read(
                stride=stride,
                atom_indices=atom_indices,
            )
            if len(coordinates) == 0:
                return Trajectory(xyz=np.zeros((0, topology.n_atoms, 3)), topology=topology)

            coordinates = in_units_of(
                coordinates,
                self.distance_unit,
                Trajectory._distance_unit,
                inplace=True,
            )
            unitcell_vectors = in_units_of(
                unitcell_vectors,
                self.distance_unit,
                Trajectory._distance_unit,
                inplace=True,
            )

            traj = Trajectory(xyz=coordinates, topology=topology, time=time)
            traj.unitcell_vectors = unitcell_vectors
            return traj

        def read(self, n_frames=None, stride=None, atom_indices=None):
            """Read data from a molecular dynamics trajectory in the GROMACS GRO
            format.

            Parameters
            ----------
            n_frames : int, optional
                If n_frames is not None, the next n_frames of data from the file
                will be read. Otherwise, all of the frames in the file will be read.
            stride : int, optional
                If stride is not None, read only every stride-th frame from disk.
            atom_indices : np.ndarray, dtype=int, optional
                The specific indices of the atoms you'd like to retrieve. If not
                supplied, all of the atoms will be retrieved.

            Returns
            -------
            coordinates : np.ndarray, shape=(n_frames, n_atoms, 3)
                The cartesian coordinates of the atoms, in units of nanometers.
            time : np.ndarray, None
                The time corresponding to each frame, in units of picoseconds, or
                None if no time information is present in the trajectory.
            unitcell_vectors : np.ndarray, shape=(n_frames, 3, 3)
                The box vectors in each frame, in units of nanometers
            """
            if not self._open:
                raise ValueError("I/O operation on closed file")
            if not self._mode == "r":
                raise ValueError("file not opened for reading")

            coordinates = []
            unitcell_vectors = []
            time = []
            contains_time = True

            atom_indices = cast_indices(atom_indices)
            atom_slice = slice(None) if atom_indices is None else atom_indices

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

            for i in frameiter:
                try:
                    frame_xyz, frame_box, frame_time = self._read_frame()
                    contains_time = contains_time and (frame_time is not None)
                    coordinates.append(frame_xyz[atom_slice])
                    unitcell_vectors.append(frame_box)
                    time.append(frame_time)
                except StopIteration:
                    break

            coordinates, unitcell_vectors, time = map(
                np.array,
                (coordinates, unitcell_vectors, time),
            )

            if not contains_time:
                time = None
            else:
                time = time[::stride]

            return coordinates[::stride], time, unitcell_vectors[::stride]

        def _read_topology(self):
            if not self._open:
                raise ValueError("I/O operation on closed file")
            if not self._mode == "r":
                raise ValueError("file not opened for reading")
            pdb.PDBTrajectoryFile._loadNameReplacementTables()

            n_atoms = None
            topology = md.Topology()
            chain = topology.add_chain()
            residue = None
            atomReplacements = {}

            # This is needed because sometimes
            # residue names get replaced and this
            # brings to wrong residue parsing
            old_resname = None
            for ln, line in enumerate(self._file):
                if ln == 1:
                    n_atoms = int(line.strip())
                elif ln > 1 and ln < n_atoms + 2:
                    (thisresnum, thisresname, thisatomname, thisatomnum) = (
                        line[i * 5 : i * 5 + 5].strip() for i in range(4)
                    )
                    thisresnum, thisatomnum = map(int, (thisresnum, thisatomnum))
                    if residue is None or residue.resSeq != thisresnum or old_resname != thisresname:
                        if residue is not None and thisresnum == residue.resSeq:
                            warnings.warn(
                                f"WARNING: two consecutive residues with same number ({thisresname}, {old_resname})",
                            )
                        old_resname = thisresname
                        if thisresname in pdb.PDBTrajectoryFile._residueNameReplacements:
                            thisresname = pdb.PDBTrajectoryFile._residueNameReplacements[thisresname]
                        residue = topology.add_residue(
                            thisresname,
                            chain,
                            resSeq=thisresnum,
                        )
                        if thisresname in pdb.PDBTrajectoryFile._atomNameReplacements:
                            atomReplacements = pdb.PDBTrajectoryFile._atomNameReplacements[thisresname]
                        else:
                            atomReplacements = {}

                    thiselem = thisatomname
                    if len(thiselem) > 1:
                        thiselem = thiselem[0] + sub("[A-Z0-9]", "", thiselem[1:])
                    try:
                        element = elem.get_by_symbol(thiselem)
                    except KeyError:
                        element = elem.virtual
                    if thisatomname in atomReplacements:
                        thisatomname = atomReplacements[thisatomname]

                    topology.add_atom(
                        thisatomname,
                        element=element,
                        residue=residue,
                        serial=thisatomnum,
                    )
            topology.create_standard_bonds()
            return n_atoms, topology

        def _read_frame(self):
            if not self._open:
                raise ValueError("I/O operation on closed file")
            if not self._mode == "r":
                raise ValueError("file not opened for reading")

            atomcounter = itertools.count()
            comment = None
            boxvectors = None

            xyz = np.zeros((self.n_atoms, 3), dtype=np.float32)

            got_line = False
            firstDecimalPos = None
            atomindex = -1
            for ln, line in enumerate(self._file):
                got_line = True
                if ln == 0:
                    comment = line.strip()
                    continue
                elif ln == 1:
                    assert self.n_atoms == int(line.strip())
                    continue
                if firstDecimalPos is None:
                    try:
                        firstDecimalPos = line.index(".", 20)
                        secondDecimalPos = line.index(".", firstDecimalPos + 1)
                    except ValueError:
                        firstDecimalPos = secondDecimalPos = None
                crd = _parse_gro_coord(line, firstDecimalPos, secondDecimalPos)
                if crd is not None and atomindex < self.n_atoms - 1:
                    atomindex = next(atomcounter)
                    xyz[atomindex, :] = (crd[0], crd[1], crd[2])
                elif _is_gro_box(line) and ln == self.n_atoms + 2:
                    sline = line.split()
                    boxvectors = tuple([float(i) for i in sline])
                    # the gro_box line comes at the end of the record
                    break
                else:
                    raise Exception("Unexpected line in .gro file: " + line)

            if not got_line:
                raise StopIteration()

            time = None
            if "t=" in comment:
                # title string (free format string, optional time in ps after 't=')
                time = float(findall(r"t= *(\d+\.\d+)", comment)[-1])

            # box vectors (free format, space separated reals), values: v1(x) v2(y)
            # v3(z) v1(y) v1(z) v2(x) v2(z) v3(x) v3(y), the last 6 values may be
            # omitted (they will be set to zero).
            box = [boxvectors[i] if i < len(boxvectors) else 0 for i in range(9)]
            unitcell_vectors = np.array(
                [
                    [box[0], box[3], box[4]],
                    [box[5], box[1], box[6]],
                    [box[7], box[8], box[2]],
                ],
            )

            return xyz, unitcell_vectors, time

        def _write_frame(self, coordinates, topology, time, box, precision):
            comment = "Generated with MDTraj"
            if time is not None:
                comment += ", t= %s" % time

            varwidth = precision + 5
            fmt = "%%5d%%-5s%%5s%%5d%%%d.%df%%%d.%df%%%d.%df" % (
                varwidth,
                precision,
                varwidth,
                precision,
                varwidth,
                precision,
            )
            assert topology.n_atoms == coordinates.shape[0]
            lines = [comment, " %d" % topology.n_atoms]
            if box is None:
                box = np.zeros((3, 3))

            for i in range(topology.n_atoms):
                atom = topology.atom(i)
                residue = atom.residue
                serial = atom.serial
                if serial is None:
                    serial = atom.index
                if serial >= 100000:
                    serial %= 100000
                lines.append(
                    fmt
                    % (
                        residue.resSeq,
                        residue.name,
                        atom.name,
                        serial,
                        coordinates[i, 0],
                        coordinates[i, 1],
                        coordinates[i, 2],
                    ),
                )

            lines.append(
                f"{box[0, 0]:10.5f}{box[1, 1]:10.5f}{box[2, 2]:10.5f}"
                f"{box[0, 1]:10.5f}{box[0, 2]:10.5f}{box[1, 0]:10.5f}"
                f"{box[1, 2]:10.5f}{box[2, 0]:10.5f}{box[2, 1]:10.5f}",
            )

            self._file.write("\n".join(lines))
            self._file.write("\n")

        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.
            """
            return self._frame_index

        def close(self):
            "Close the file"
            if self._open:
                self._file.close()
                self._open = False

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

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

    def _isint(word):
        """ONLY matches integers! If you have a decimal point? None shall pass!

        @param[in] word String (for instance, '123', '153.0', '2.', '-354')
        @return answer Boolean which specifies whether the string is an integer (only +/- sign followed by digits)

        """
        return match("^[-+]?[0-9]+$", word)

    def _isfloat(word):
        """Matches ANY number; it can be a decimal, scientific notation, what have you
        CAUTION - this will also match an integer.

        @param[in] word String (for instance, '123', '153.0', '2.', '-354')
        @return answer Boolean which specifies whether the string is any number

        """
        return match(r"^[-+]?[0-9]*\.?[0-9]*([eEdD][-+]?[0-9]+)?$", word)

    def _parse_gro_coord(line, firstDecimal, secondDecimal):
        """Determines whether a line contains GROMACS data or not

        @param[in] line The line to be tested

        """
        if firstDecimal is None or secondDecimal is None:
            return None
        digits = secondDecimal - firstDecimal
        try:
            return tuple(float(line[20 + i * digits : 20 + (i + 1) * digits]) for i in range(3))
        except ValueError:
            return None

    def _is_gro_box(line):
        """Determines whether a line contains a GROMACS box vector or not

        @param[in] line The line to be tested

        """
        sline = line.split()
        if len(sline) == 9 and all([_isfloat(i) for i in sline]):
            return 1
        elif len(sline) == 3 and all([_isfloat(i) for i in sline]):
            return 1
        else:
            return 0