mdtraj.load_dcd

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

Load an DCD file from disk.

The .dcd format is a cross-platform compressed binary trajectory format produced by many software packages, including CHARMM, NAMD, and OpenMM. It stores atomic coordinates, box vectors, and time information.

Parameters

filenamepath-like

Path of DCD file.

top{path-like, Trajectory, Topology}

DCD XTC 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.DCDTrajectoryFile

Low level interface to DCD files

Examples

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

>>> traj2 = md.load_dcd('output.dcd', stride=2, top='topology.pdb')
>>> print traj2
<mdtraj.Trajectory with 250 frames, 423 atoms at 0x11136e410>