state_lifetime_discrete

Calculate the average lifetime of the states in a discrete trajectory resolved with respect to the states in a second discrete trajectory.

Calculate the average residence time for how long a compound resides in a specific state before it changes states given that it was in a specific state of a second discrete trajectory at time \(t_0\). This is done by computing the probability to be in the same state as at time \(t_0\) after a lag time \(\Delta t\) as function of the states in the second discrete trajectory. Afterwards, these probabilities are fitted by stretched exponential functions, whose integrals from zero to infinity are the average lifetimes of the states in the first discrete trajectory. See also mdtools.dtrj.remain_prob_discrete().

Options

--f1: Name of the file containing the first discrete trajectory. The discrete trajectory must be stored as numpy.ndarray either in a binary NumPy .npy file or in a (compressed) NumPy .npz archive. See mdtools.file_handler.load_dtrj() for more information about the requirements for the input file.
--f2: Name of the file containing the second discrete trajectory. The second discrete trajectory must have the same shape as the first discrete trajectory.
-o: Output filename.
-b: First frame to read from the discrete trajectory. Frame numbering starts at zero. Default: 0.
-e: Last frame to read from the discrete 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 discrete trajectory. Default: 1.
--restart: Number of frames between restarting points for calculating the remain probability. Must be an integer multiple of --every. Default: 100.
--intermittency1: Allowed intermittency for the first discrete trajectory: Maximum number of frames a compound is allowed to leave its state whilst still being considered to be in this state provided that it returns to this state after the given number of frames. In other words, a compound is only considered to have left its state if it has left it for at least the given number of frames.
--intermittency2: Allowed intermittency for the second discrete trajectory.
--continuous: If given, compounds must continuously be in the same state without interruption in order to be counted (see notes section of mdtools.dtrj.remain_prob()).
--discard-neg-start: Discard all transitions starting from a negative state (see notes section of mdtools.dtrj.remain_prob()). Must not be used together with --discard-all-neg.
--discard-all-neg: Discard all negative states (see notes section of mdtools.dtrj.remain_prob()). Must not be used together with --discard-neg-start.
--end-fit: End time for fitting the remain probability (in trajectory steps). This is inclusive, i.e. the time given here is still included in the fit. If None, the fit ends at 90% of the lag times. Default: None.
--stop-fit: Stop fitting the remain probability as soon as it falls below the given value. The fitting is stopped by whatever happens earlier: --end-fit or --stop-fit. Default: 0.01.