BioSimSpace.Trajectory.Trajectory¶

class BioSimSpace.Trajectory.Trajectory(process=None, trajectory=None, topology=None)¶

A class for reading a manipulating biomolecular trajectories.

__init__(process=None, trajectory=None, topology=None)¶

Constructor.

Parameters:	process (`Process`) – A BioSimSpace process object. trajectory (str) – A trajectory file. topology (str) – A topology file.

Methods

`__init__`([process, trajectory, topology])	Constructor.
`getFrames`([indices])	Get trajectory frames as a list of System objects.
`getTrajectory`([format])	Get the current trajectory object.
`nFrames`()	Return the current number of trajectory frames.
`rmsd`([frame, atoms, molecule])	Compute the root mean squared displacement.

getFrames(indices=None)¶

Get trajectory frames as a list of System objects.

Parameters:	indices ([int], [`Time`]) – A list of trajectory frame indices, or time stamps (in ns).
Returns:	frames – The list of System objects.
Return type:	[`System`]

getTrajectory(format='mdtraj')¶

Get the current trajectory object.

Parameters:	format (str) – Whether to return an ‘MDTraj’ or ‘MDAnalysis’ object.
Returns:	trajectory – The trajectory in MDTraj or MDAnalysis format.
Return type:	mdtraj.core.trajectory.Trajectory, MDAnalysis.core.universe.Universe

nFrames()¶

Return the current number of trajectory frames.

Returns:	nFrames – The number of trajectory frames.
Return type:	int

rmsd(frame=None, atoms=None, molecule=None)¶

Compute the root mean squared displacement.

Parameters:	frame (int) – The index of the reference frame. atoms ([int]) – A list of reference atom indices. molecule (int) – The index of the reference molecule.
Returns:	rmsd – A list containing the RMSD value at each time point.
Return type:	[float]