##############################################################################
# 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,
)