Source code for mdtraj.reporters.dcdreporter

##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
#         Molecular Dynamics Trajectories.
# Copyright 2012-2013 Stanford University and the Authors
#
# Authors: Robert McGibbon
# Contributors:
#
# MDTraj is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as
# published by the Free Software Foundation, either version 2.1
# of the License, or (at your option) any later version.
#
# This library is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with MDTraj. If not, see <http://www.gnu.org/licenses/>.
##############################################################################

"""OpenMM Reporter for saving the state of a molecular dynamics simulation
through time in the AMBER NetCDF format
"""

from ..formats.dcd import DCDTrajectoryFile
from .basereporter import _BaseReporter


[docs] class DCDReporter(_BaseReporter): """DCDReporter stores a molecular dynamics trajectory in the CHARMM / NAMD DCD Format Parameters ---------- file : str, or DCDTrajectoryFile Either an open DCDTrajectoryFile object to write to, or a string specifying the filename of a new DCD file to save the trajectory to. reportInterval : int The interval (in time steps) at which to write frames. atomSubset : array_like, default=None Only write a subset of the atoms, with these (zero based) indices to the file. If None, *all* of the atoms will be written to disk. Examples -------- >>> simulation = Simulation(topology, system, integrator) >>> dcd_reporter = DCDReporter('traj.dcd', 100) >>> simulation.reporters.append(dcd_reporter) >>> simulation.step(10000) >>> traj = mdtraj.trajectory.load('traj.dcd') """ @property def backend(self): return DCDTrajectoryFile
[docs] def __init__(self, file, reportInterval, atomSubset=None): super().__init__( file, reportInterval, coordinates=True, time=False, cell=True, potentialEnergy=False, kineticEnergy=False, temperature=False, velocities=False, atomSubset=atomSubset, )