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

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.

mdtraj.BINPOSTrajectoryFile

Low level interface to BINPOS files

Examples

>>> import mdtraj as md

>>> traj2 = md.load_binpos('output.dcd', stride=2, top='topology.pdb')