extract_renewal_events

extract_renewal_events.extract_renewal_events(universe, ref, sel, cms, compound='atoms', begin=0, every=1, coord_traj=False, verbose=False, debug=False)[source]

Extract renewal events from an trajectory.

A renewal event occurs when the selection compound that was continuously bound the longest to a reference compound dissociates from it.[1] Such an event is called “trackable”, if its start time \(t_0\) and its renewal time \(\tau_{renew}\) are exactly known. This means, the first and last event of each reference compound must be discarded, because \(t_0\) of the first event and \(\tau_{renew}\) of the last event are unknown due to the limited trajectory length.

Parameters:

  • universe (MDAnalysis.core.universe.Universe) – The MDAnalysis Universe which holds the unwrapped and whole reference compounds.

  • ref, sel (MDAnalysis.core.groups.AtomGroup) – The reference and selection AtomGroup.

  • cms (array_like) – List of boolean contact matrices as e.g. generated with mdtools.structure.contact_matrix(), one for each frame. The contact matrices must be given as SciPy sparse matrices. The rows must stand for the reference compounds, the columns for the selection compounds.

  • compound ({'atoms', 'segments', 'residues', 'fragments'}, optional) – For which type of components the contact matrices in cms were calculated. Refer to the MDAnalysis’ user guide for an explanation of these terms.

  • begin (int, optional) – The frame number of the trajectory to which the first contact matrix in cms corresponds to.

  • every (int, optional) – To how many frames of the trajectory one frame in cms corresponds to.

  • coord_traj (bool, optional) – Generate a trajectory containing for each single reference compound for each frame the index of the selection compound that is continuously bound the longest to the reference compound. See also discrete_coord() from discrete_coord.py

  • verbose (bool, optional) – If True, print progress information to standard output.

  • debug (bool, optional) – If True, check the input arguments.

Returns:

  • refix_t0 (numpy.ndarray) – The indices of the reference compounds which underwent trackable renewal events. Indexing starts at zero.

  • selix_t0 (numpy.ndarray) – The corresponding indices of the selection compounds that were continuously bound the longest to the reference compounds. Indexing starts at zero.

  • t0 (numpy.ndarray) – The corresponding times when the selection compounds started coordinating to the reference compounds.

  • trenew (numpy.ndarray) – The corresponding renewal times needed till dissociation of the selection compounds.

  • refpos_t0 (numpy.ndarray) – The corresponding center of mass positions of the reference compounds at time t0.

  • selpos_t0 (numpy.ndarray) – The corresponding center of mass positions of the selection compounds at time t0.

  • refdispl (numpy.ndarray) – The corresponding displacements of the reference compounds during trenew.

  • seldispl (numpy.ndarray) – The corresponding displacements of the selection compounds during trenew.

  • traj (numpy.ndarray) – Only returned if coord_traj is True. Array of shape (n, len(cms)), where n is the number of reference compounds. The elements of the array are the indices of the selection compounds that are continuously bound the longest to the given reference compound. Indexing starts at zero. An index of -1 indicates that in the given frame no selection compound was bound to the given reference compound.

Notes

The output is sorted by refix_t0 as primary sort order, t0 as secondary sort order, trenew as tertiary sort order and selix_t0 as quaternary sort order.

References