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

filenamepath-like: 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.