mdtraj.load_xtc

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

Load a Gromacs XTC file from disk.

The .xtc format is a cross-platform compressed binary trajectory format produced by the gromacs software that stores atomic coordinates, box vectors, and time information. It is lossy (storing coordinates to about 1e-3 A) and extremely space-efficient.

Parameters:

filename : str

Filename (string) of xtc trajectory.

top : {str, Trajectory, Topology}

The XTC format does not contain topology information. Pass in either the path to a RCSB 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.

See also

mdtraj.XTCTrajectoryFile
Low level interface to XTC files

Examples

>>> import mdtraj as md
>>> traj = md.load_xtc('output.xtc', top='topology.pdb')
>>> print traj
<mdtraj.Trajectory with 500 frames, 423 atoms at 0x110740a90>
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