Source code for MDAnalysis.coordinates.TRR

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"""
TRR trajectory files --- :mod:`MDAnalysis.coordinates.TRR`
==========================================================

Read and write GROMACS TRR trajectories.

See Also
--------
MDAnalysis.coordinates.XTC: Read and write GROMACS XTC trajectory files.
MDAnalysis.coordinates.XDR: BaseReader/Writer for XDR based formats
"""
from __future__ import absolute_import

from . import base
from .XDR import XDRBaseReader, XDRBaseWriter
from ..lib.formats.libmdaxdr import TRRFile
from ..lib.mdamath import triclinic_vectors, triclinic_box


[docs]class TRRWriter(XDRBaseWriter): """Writer for the Gromacs TRR format. The Gromacs TRR trajectory format is a lossless format. The TRR format can store *velocoties* and *forces* in addition to the coordinates. It is also used by other Gromacs tools to store and process other data such as modes from a principal component analysis. If the data dictionary of a :class:`Timestep` contains the key 'lambda' the corresponding value will be used as the lambda value for written TRR file. If ``None`` is found the lambda is set to 0. """ format = 'TRR' multiframe = True units = {'time': 'ps', 'length': 'nm', 'velocity': 'nm/ps', 'force': 'kJ/(mol*nm)'} _file = TRRFile def _write_next_frame(self, ag): """Write information associated with ``ag`` at current frame into trajectory Parameters ---------- ag : AtomGroup or Universe See Also -------- <FormatWriter>.write(AtomGroup/Universe/TimeStep) The normal write() method takes a more general input .. versionchanged:: 1.0.0 Renamed from `write_next_timestep` to `_write_next_frame`. .. deprecated:: 1.0.0 Deprecated the use of Timestep as arguments to write. Use either an AtomGroup or Universe. To be removed in version 2.0. """ if isinstance(ag, base.Timestep): ts = ag else: try: ts = ag.ts except AttributeError: try: # special case: can supply a Universe, too... ts = ag.trajectory.ts except AttributeError: raise TypeError("No Timestep found in ag argument") xyz = None if ts.has_positions: xyz = ts.positions.copy() if self._convert_units: self.convert_pos_to_native(xyz) velo = None if ts.has_velocities: velo = ts.velocities.copy() if self._convert_units: self.convert_velocities_to_native(velo) forces = None if ts.has_forces: forces = ts.forces.copy() if self._convert_units: self.convert_forces_to_native(forces) time = ts.time step = ts.frame if self._convert_units: dimensions = self.convert_dimensions_to_unitcell(ts, inplace=False) box = triclinic_vectors(dimensions) lmbda = 0 if 'lambda' in ts.data: lmbda = ts.data['lambda'] self._xdr.write(xyz, velo, forces, box, step, time, lmbda, self.n_atoms)
[docs]class TRRReader(XDRBaseReader): """Reader for the Gromacs TRR format. The Gromacs TRR trajectory format is a lossless format. The TRR format can store *velocoties* and *forces* in addition to the coordinates. It is also used by other Gromacs tools to store and process other data such as modes from a principal component analysis. The lambda value is written in the data dictionary of the returned :class:`Timestep` Notes ----- See :ref:`Notes on offsets <offsets-label>` for more information about offsets. """ format = 'TRR' units = {'time': 'ps', 'length': 'nm', 'velocity': 'nm/ps', 'force': 'kJ/(mol*nm)'} _writer = TRRWriter _file = TRRFile def _frame_to_ts(self, frame, ts): """convert a trr-frame to a mda TimeStep""" ts.time = frame.time ts.frame = self._frame ts.data['step'] = frame.step ts.has_positions = frame.hasx ts.has_velocities = frame.hasv ts.has_forces = frame.hasf ts.dimensions = triclinic_box(*frame.box) if self.convert_units: self.convert_pos_from_native(ts.dimensions[:3]) if ts.has_positions: if self._sub is not None: ts.positions = frame.x[self._sub] else: ts.positions = frame.x if self.convert_units: self.convert_pos_from_native(ts.positions) if ts.has_velocities: if self._sub is not None: ts.velocities = frame.v[self._sub] else: ts.velocities = frame.v if self.convert_units: self.convert_velocities_from_native(ts.velocities) if ts.has_forces: if self._sub is not None: ts.forces = frame.f[self._sub] else: ts.forces = frame.f if self.convert_units: self.convert_forces_from_native(ts.forces) ts.data['lambda'] = frame.lmbda return ts