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:

filename : str

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.

stride : int, default=None

Only read every stride-th frame

atom_indices : array_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.

frame : int, 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:

trajectory : md.Trajectory

The resulting trajectory, as an md.Trajectory object.