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:

file : str, or NetCDFTrajectoryFile Either an open NetCDFTrajectoryFile object to write to, or a string specifying the filename of a new NetCDF file reportInterval : int The interval (in time steps) at which to write frames. coordinates : bool Whether to write the coordinates to the file. time : bool Whether to write the current time to the file. cell : bool Whether to write the current unitcell dimensions to the file. 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.

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

close()¶

Close the underlying trajectory file

describeNextReport(simulation)¶

Get information about the next report this object will generate.

Parameters:	simulation : simtk.openmm.app.Simulation The Simulation to generate a report for
Returns:	report_description : tuple A five element tuple. The first element is the number of steps until the next report. The remaining elements specify whether that report will require positions, velocities, forces, and energies respectively.

report(simulation, state)¶

Generate a report.

Parameters:	simulation : simtk.openmm.app.Simulation The Simulation to generate a report for state : simtk.openmm.State The current state of the simulation