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
"""
import errno
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 *velocities* 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. If the data dictionary of a :class:`Timestep` contains the key 'step' the corresponding value will be used as the step value for the written TRR file. If the dictionary does not contain 'step', then the step is set to the :class:`Timestep` frame attribute. """ 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`. .. versionchanged:: 2.0.0 Deprecated support for Timestep argument has now been removed. Use AtomGroup or Universe as an input instead. .. versionchanged:: 2.1.0 When possible, TRRWriter assigns `ts.data['step']` to `step` rather than `ts.frame`. """ try: ts = ag.ts except AttributeError: try: # special case: can supply a Universe, too... ts = ag.trajectory.ts except AttributeError: errmsg = "Input obj is neither an AtomGroup or Universe" raise TypeError(errmsg) from None 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.data.get('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 *velocities* 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 _read_next_timestep(self, ts=None): """copy next frame into timestep versionadded:: 2.4.0 TRRReader implements this method so that it can use read_direct_xvf to read the data directly into the timestep rather than copying it from a temporary array. """ if self._frame == self.n_frames - 1: raise IOError(errno.EIO, 'trying to go over trajectory limit') if ts is None: ts = self.ts # allocate arrays to read into, will set to proper values # in _frame_to_ts ts.has_positions = True ts.has_velocities = True ts.has_forces = True frame = self._xdr.read_direct_xvf(ts.positions, ts.velocities, ts.forces) self._frame += 1 self._frame_to_ts(frame, ts) return ts 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: if ts.dimensions is not None: 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