BioSimSpace.Trajectory.Trajectory¶
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class
BioSimSpace.Trajectory.
Trajectory
(process=None, trajectory=None, topology=None)¶ A class for reading a manipulating biomolecular trajectories.
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__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])Compute the root mean squared displacement.
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getFrames
(indices=None)¶ Get trajectory frames as a list of System objects.
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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
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nFrames
()¶ Return the current number of trajectory frames.
- Returns
nFrames – The number of trajectory frames.
- Return type
int
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rmsd
(frame=None, atoms=None)¶ Compute the root mean squared displacement.
- Parameters
frame (int) – The index of the reference frame.
atoms ([int]) – A list of reference atom indices.
- Returns
rmsd – A list containing the RMSD value at each time point.
- Return type
[float]
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