mdtraj.iterload

mdtraj.iterload(filename, chunk=100, **kwargs)

An iterator over a trajectory from one or more files on disk, in fragments

This may be more memory efficient than loading an entire trajectory at once

Parameters

filenamepath-like

Path to the trajectory file on disk

chunkint

Number of frames to load at once from disk per iteration. If 0, load all.

Other Parameters

top{str, Trajectory, Topology}

Most trajectory formats do not contain topology information. Pass in either the path to a RCSB PDB file, a trajectory, or a topology to supply this information. This option is not required for the .h5, .lh5, and .pdb formats, which already contain topology 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.

skipint, default=0

Skip first n frames.

See also

load, load_frame

Examples

>>> import mdtraj as md
>>> for chunk in md.iterload('output.xtc', top='topology.pdb')
...    print chunk
<mdtraj.Trajectory with 100 frames, 423 atoms at 0x110740a90>
<mdtraj.Trajectory with 100 frames, 423 atoms at 0x110740a90>
<mdtraj.Trajectory with 100 frames, 423 atoms at 0x110740a90>
<mdtraj.Trajectory with 100 frames, 423 atoms at 0x110740a90>
<mdtraj.Trajectory with 100 frames, 423 atoms at 0x110740a90>