extract_renewal_events

Extract renewal events from a molecular dynamics trajectory.

A renewal event occurs when the selection compound that was continuously bound the longest to a reference compound dissociates from it.[1]

A new trajectory is generated containing only these renewal events for all reference compounds undergoing such events. The new trajectory contains the indices of the reference and selection compound, the time \(t_0\) when the selection compound started coordinating to the reference compound, the renewal time \(\tau\) needed till dissociation of the selection compound, the center of mass positions of the reference and selection compound at \(t_0\) and the displacements of the reference and selection compound during \(\tau\).

Options

-f

Trajectory file. See supported coordinate formats of MDAnalysis. Important: This scripts requires an unwrapped trajectory! At least the reference and selection compounds must be unwrapped in order to get the correct displacements. If you want to calculate center-of-mass displacements, the reference and selection compounds need to be whole, too. You can use e.g. scripts.trajectory.unwrap_trj to unwrap a wrapped trajectory and make broken molecules whole.

-s

Topology file. See supported topology formats of MDAnalysis.

-o

Output filename.

--dtrj

Output filename for the discrete coordination trajectory (optional). If provided, generate a discrete 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. Indexing starts at zero. An index of -1 indicates that in the given frame no selection compound was bound to the given reference compound. The discrete trajectory is stored as numpy.ndarray of dtype numpy.int32 and shape (n, f), where n is the number of reference compounds and f is the number of frames. The generated discrete trajectory is the same as the one created by scripts.discretization.discrete_coord.

-b

First frame to read from the trajectory. Frame numbering starts at zero. Default: 0.

-e

Last frame to read from the trajectory. This is exclusive, i.e. the last frame read is actually END - 1. A value of -1 means to read the very last frame. Default: -1.

--every

Read every n-th frame from the trajectory. Default: 1.

--ref

Selection string for the reference AtomGroup. See MDAnalysis’ selection syntax for possible choices.

--sel

Selection string for the selection AtomGroup. See MDAnalysis’ selection syntax for possible choices.

-c

Contact cutoff distance in Angstrom. A reference and selection atom are considered to be in contact, if their distance is less than or equal to the given cutoff.

--compound

{‘atoms’, ‘segments’, ‘residues’, ‘fragments’}

The compounds of the reference and selection group to use for the analysis. Contacts between the reference and selection group can be computed either for individual ‘atoms’, ‘segments’, ‘residues’, or ‘fragments’. Refer to the MDAnalysis’ user guide for an explanation of these terms. This option also affects how displacements are calculated. If not set to ‘atoms’, the center of mass of the compound is used to calculate its displacement. Note that in any case, even if CMP is e.g. ‘residues’, only the atoms belonging to the reference/selection group are taken into account, even if the compound might comprise additional atoms that are not contained in the reference/selection group. Default: 'atoms'.

--min-contacts

Compounds of the reference and selection group are only considered to be in contact, if there are at least MINCONTACTS contacts between the atoms of the compounds. --min-contacts is ignored if --compound is set to 'atoms'. Default: 1.

--intermittency

Maximum number of frames a selection atom is allowed to leave the cutoff range of a reference atom whilst still being considered to be bound to the reference atom, provided that it is indeed bound again to the reference atom after this unbound period. The other way round, a selection atom is only considered to be bound to a reference atom, if it has been bound to it for at least this number of consecutive frames. Default: 0.

--debug

Run in debug mode.