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

__delattr__	Implement delattr(self, name).
__dir__	Default dir() implementation.
__eq__	Return self==value.
__format__	Default object formatter.
__ge__	Return self>=value.
__getattribute__	Return getattr(self, name).
__gt__	Return self>value.
__hash__	Return hash(self).
__init__([process, trajectory, topology])	Constructor.
__init_subclass__	This method is called when a class is subclassed.
__le__	Return self<=value.
__lt__	Return self<value.
__ne__	Return self!=value.
__new__	Create and return a new object.
__reduce__	Helper for pickle.
__reduce_ex__	Helper for pickle.
__repr__()	Return a string showing how to instantiate the object.
__setattr__	Implement setattr(self, name, value).
__sizeof__	Size of object in memory, in bytes.
__str__()	Return a human readable string representation of the object.
__subclasshook__	Abstract classes can override this to customize issubclass().
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.

Attributes

__dict__
__doc__
__module__
__weakref__	list of weak references to the object (if defined)

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)

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]