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]