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