back_jump_prob_discrete

Calculate the back-jump probability resolved with respect to the states in the second discrete trajectory.

Given that a state transition occurred at time \(t_0\), calculate the probability to return back to the initial state as function of the time \(\Delta t\) that has passed since the state transition given that the compound was in a specific state of another discrete trajectory at time \(t_0\).

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 of the file containing the back-jump probabilities.

--norm-out

Output filename of the file containing the normalization factors (optional). Multiplying the back-jump probabilities with the normalization factors yields the total number of back jumps.

-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.

--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 not provided, calculate the probability that a compound returns back to its initial state at time \(t_0 + \Delta t\). This probability might be regarded as the “discontinuous” or “intermittent” back-jump probability.

If provided, calculate the probability that a compound returns back to its initial state at time \(t_0 + \Delta t\) under the condition that it has continuously been in the new state from time \(t_0\) until \(t_0 + \Delta t\), i.e. that the compound does not visit other states before returning back to its initial state. This probability might be regarded as the “continuous” or “true” back-jump probability.

--discard-neg

If provided, discard negative states, i.e. discard back jumps starting from (and consequently ending in) a negative state.

--discard-neg-btw

If provided, discard back jumps when the compound has visited a negative state between \(t_0\) and \(t_0 + \Delta t\).