mdtraj.load_binpos¶
-
mdtraj.
load_binpos
(filename, top=None, stride=None, atom_indices=None, frame=None)¶ Load an AMBER .binpos file from disk.
The .binpos format is a cross-platform binary trajectory format produced by AMBER software. It stores only the atomic coordinates, and does not store any unit cell informations. Its use is discouraged.
- Parameters
- filenamestr
String filename of AMBER binpos file.
- top{str, Trajectory, Topology}
The BINPOS 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.
See also
mdtraj.BINPOSTrajectoryFile
Low level interface to BINPOS files
Examples
>>> import mdtraj as md >>> traj = md.load_binpos('output.binpos', top='topology.pdb') >>> print traj <mdtraj.Trajectory with 500 frames, 423 atoms at 0x110740a90>
>>> traj2 = md.load_binpos('output.dcd', stride=2, top='topology.pdb') >>> print traj2 <mdtraj.Trajectory with 250 frames, 423 atoms at 0x11136e410>