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sstrajectory

SSTrajectory Class

Reading in trajectories starts with the SSTrajectory class. Upon reading, SOURSOP extracts out individual protein chains which can then be subsequently analyzed.

By way of a quickstart example:

from soursop.sstrajectory import SSTrajectory
import numpy as np

# read in a trajectory
TrajOb = SSTrajectory('traj.xtc', 'start.pdb')

# get the first protein chain (this is an SSProtein object)
ProtObj = TrajOb.proteinTrajectoryList[0]

# print the mean radius of gyration
print(np.mean(ProtObj.get_radius_of_gyration()))

The set of possible SSProtein functions can be found in the ssprotein documentation page (quick-link to the left in the navigation bar). The remainder of these documents walk through trajectory initialization, SSTrajectory class variables, SSTrajectory properties, and SSTrajectory functions.

.. autoclass:: soursop.sstrajectory.SSTrajectory

        .. automethod:: __init__

SSTrajectory Properties

Properties are class variables that are dynamically calculated. They do not require parentheses at the end. For example:

from soursop.sstrajectory import SSTrajectory

# read in a trajectory
TrajOb = SSTrajectory('traj.xtc', 'start.pdb')

print(TrajOb.n_frames)

Will print the number of frames associated with this trajectory.

Properties

.. automethod:: soursop.sstrajectory.SSTrajectory.n_frames

.. automethod:: soursop.sstrajectory.SSTrajectory.n_proteins

.. automethod:: soursop.sstrajectory.SSTrajectory.length

In addition to these three functions, the Python builtin len() returns the number of frames in a trajectory.

SSTrajectory Functions

Functions enable operations to be performed on the entire system. Note if you wish to obtain information about a specific protein in isolation, you should use the SSProtein objects, but for information where multiple proteins are considered all operations should be performed at the level of the SSTrajectory object.

Functions

.. automethod:: soursop.sstrajectory.SSTrajectory.get_overall_radius_of_gyration

.. automethod:: soursop.sstrajectory.SSTrajectory.get_overall_hydrodynamic_radius

.. automethod:: soursop.sstrajectory.SSTrajectory.get_overall_asphericity

.. automethod:: soursop.sstrajectory.SSTrajectory.get_interchain_distance_map

.. automethod:: soursop.sstrajectory.SSTrajectory.get_interchain_contact_map

.. automethod:: soursop.sstrajectory.SSTrajectory.get_interchain_distance