mdtraj.formats.AmberNetCDFRestartFile

class mdtraj.formats.AmberNetCDFRestartFile(filename, mode='r', force_overwrite=False)

Interface for reading and writing AMBER NetCDF files. This is a file-like object, that supports both reading and writing depending on the mode flag. It implements the context manager protocol, so you can also use it with the python ‘with’ statement.

Parameters

filenamepath-like

The name of the file to open

mode{‘r’, ‘w’}, default=’r’

The mode in which to open the file. Valid options are ‘r’ or ‘w’ for ‘read’ or ‘write’

force_overwritebool, default=False

In write mode, if a file named filename already exists, clobber it and overwrite it

Attributes

n_atoms

n_frames

Methods

read([atom_indices])	Read data from an AMBER NetCDF restart file
read_as_traj(topology[, atom_indices])	Read an AMBER ASCII restart file as a trajectory.
write(coordinates[, time, cell_lengths, …])	Write one frame of a MD trajectory to disk in the AMBER NetCDF restart file format.

close
flush

__init__(filename, mode='r', force_overwrite=False)

Initialize self. See help(type(self)) for accurate signature.

Methods

__init__(filename[, mode, force_overwrite])	Initialize self.
close()
flush()
read([atom_indices])	Read data from an AMBER NetCDF restart file
read_as_traj(topology[, atom_indices])	Read an AMBER ASCII restart file as a trajectory.
write(coordinates[, time, cell_lengths, …])	Write one frame of a MD trajectory to disk in the AMBER NetCDF restart file format.

Attributes

distance_unit
n_atoms
n_frames