mdtraj.load_netcdf¶

mdtraj.load_netcdf(filename, top=None, stride=None, atom_indices=None, frame=None)

Load an AMBER NetCDF file. Since the NetCDF format doesn’t contain information to specify the topology, you need to supply a topology

Parameters
filenamestr

filename of AMBER NetCDF file.

top{str, Trajectory, Topology}

The NetCDF format does not contain topology information. Pass in either the path to a pdb file, a trajectory, or a topology to supply this information.

strideint, default=None

Only read every stride-th frame

atom_indicesarray_like, optional

If not None, then read only a subset of the atoms coordinates from the file. This may be slightly slower than the standard read because it requires an extra copy, but will save memory.

frameint, optional

Use this option to load only a single frame from a trajectory on disk. If frame is None, the default, the entire trajectory will be loaded. If supplied, stride will be ignored.

Returns
trajectorymd.Trajectory

The resulting trajectory, as an md.Trajectory object.

See also

mdtraj.NetCDFTrajectoryFile

Low level interface to NetCDF files