Source code for MDAnalysis.coordinates.MMTF

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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:
.. autofunction:: fetch_mmtf

.. _MMTF: https://mmtf.rcsb.org/

"""
import mmtf

from . import base
from ..core.universe import Universe
from ..due import due, Doi


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



[docs]
class MMTFReader(base.SingleFrameReaderBase):
    """Coordinate reader for the Macromolecular Transmission Format format (MMTF_)."""
    format = 'MMTF'

    @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




[docs]
def fetch_mmtf(pdb_id):
    """Create a Universe from the RCSB Protein Data Bank using mmtf format

    Parameters
    ----------
    pdb_id : string
        PDB code of the desired data, eg '4UCP'


    Returns
    -------
    Universe
        MDAnalysis Universe of the corresponding PDB system


    See Also
    --------
    mmtf.fetch : Function for fetching raw mmtf data


    .. versionadded:: 0.16.0
    """
    return Universe(mmtf.fetch(pdb_id))