mdtraj.reporters.NetCDFReporter

class mdtraj.reporters.NetCDFReporter(file, reportInterval, coordinates=True, time=True, cell=True, atomSubset=None)

NetCDFReporter stores a molecular dynamics trajectory in the AMBER NetCDF format.

Parameters

filestr, or NetCDFTrajectoryFile

Either an open NetCDFTrajectoryFile object to write to, or a string specifying the filename of a new NetCDF file

reportIntervalint

The interval (in time steps) at which to write frames.

coordinatesbool

Whether to write the coordinates to the file.

timebool

Whether to write the current time to the file.

cellbool

Whether to write the current unitcell dimensions to the file.

atomSubsetarray_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.

Examples

>>> simulation = Simulation(topology, system, integrator)
>>> nc_reporter = NetCDFReporter('traj.h5', 100)
>>> simulation.reporters.append(nc_reporter)
>>> simulation.step(10000)

>>> traj = mdtraj.trajectory.load('traj.nc')

Attributes

backend

Methods

close()	Close the underlying trajectory file
describeNextReport(simulation)	Get information about the next report this object will generate.
report(simulation, state)	Generate a report.

__init__(file, reportInterval, coordinates=True, time=True, cell=True, atomSubset=None)

Create a NetCDFReporter.

Methods

__init__(file, reportInterval[, …])	Create a NetCDFReporter.
close()	Close the underlying trajectory file
describeNextReport(simulation)	Get information about the next report this object will generate.
report(simulation, state)	Generate a report.

Attributes

backend