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


.. autoclass:: MMTFReader
.. autofunction:: fetch_mmtf

.. _MMTF:

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)
        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))