mdtraj.load_hdf5

mdtraj.load_hdf5(filename, stride=None, atom_indices=None, frame=None)

Load an MDTraj hdf5 trajectory file from disk.

Parameters:

filename : str

String filename of HDF Trajectory file.

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.

See also

mdtraj.HDF5TrajectoryFile
Low level interface to HDF5 files

Examples

>>> import mdtraj as md
>>> traj = md.load_hdf5('output.h5')
>>> print traj
<mdtraj.Trajectory with 500 frames, 423 atoms at 0x110740a90>

>>> traj2 = md.load_hdf5('output.h5', stride=2, top='topology.pdb')
>>> print traj2
<mdtraj.Trajectory with 250 frames, 423 atoms at 0x11136e410>
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