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
- filenamestr
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.
- 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.
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>