# Source code for MDAnalysis.coordinates.MMTF

    # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
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    """MMTF trajectory reader --- :mod:`MDAnalysis.coordinates.MMTF`
    ================================================================

    Reads coordinates data from the Macromolecular Transmission Format format
    (MMTF_). This should generally be a quicker alternative to PDB.

    .. versionadded:: 0.16.0
    .. versionchanged:: 0.20.0
       Unit cell is now properly treated as optional

    Classes
    -------

    .. autoclass:: MMTFReader
       :members:

    .. _MMTF: https://www.rcsb.org/news/feature/65a1af31c76ca3abcc925d0c

    """
    import warnings
    import mmtf

    from . import base
    from ..core.universe import Universe
    from ..lib.util import cached, store_init_arguments
    from ..due import due, Doi

    def _parse_mmtf(fn):
        if fn.endswith("gz"):
            return mmtf.parse_gzip(fn)
        else:
            return mmtf.parse(fn)

    class MMTFReader(base.SingleFrameReaderBase):
        """Coordinate reader for the Macromolecular Transmission Format format (MMTF_).

        .. deprecated:: 2.8.0
           The MMTF format is no longer supported / serviced by the
           Protein Data Bank. The Reader will be removed in version 3.0.
           Users are encouraged to instead use alternative PDB formats.
        """

        format = "MMTF"

        @store_init_arguments
        def __init__(self, filename, convert_units=True, n_atoms=None, **kwargs):
            wmsg = (
                "The MMTF Reader is deprecated and will be removed in "
                "MDAnalysis version 3.0.0"
            )
            warnings.warn(wmsg, DeprecationWarning)

            super(MMTFReader, self).__init__(
                filename, convert_units, n_atoms, **kwargs
            )

        @staticmethod
        def _format_hint(thing):
            """Can this Reader read *thing*?

            .. versionadded:: 1.0.0
            """
            return isinstance(thing, mmtf.MMTFDecoder)

        @due.dcite(
            Doi("10.1371/journal.pcbi.1005575"),
            description="MMTF Reader",
            path="MDAnalysis.coordinates.MMTF",
        )
        def _read_first_frame(self):
            # TOOD: Check units?
            if isinstance(self.filename, mmtf.MMTFDecoder):
                top = self.filename
            else:
                top = _parse_mmtf(self.filename)
            self.n_atoms = top.num_atoms

            self.ts = ts = self._Timestep(self.n_atoms, **self._ts_kwargs)
            ts._pos[:, 0] = top.x_coord_list
            ts._pos[:, 1] = top.y_coord_list
            ts._pos[:, 2] = top.z_coord_list
            if not top.unit_cell is None:
                # optional field
                ts.dimensions = top.unit_cell

            return ts