dtrj

Functions dealing with discrete trajectories.

Discrete trajectories must be stored in arrays. Arrays that serve as discrete trajectory must meet the requirements listed in mdtools.check.dtrj().

Functions

back_jump_prob	Calculate the back-jump probability averaged over all states.
back_jump_prob_discrete	Calculate the back-jump probability resolved with respect to the states in a second discrete trajectory.
get_ax	Return the frame/compound axis for a discrete trajectory given its compound/frame axis.
kaplan_meier	Estimate the state survival function using the Kaplan-Meier estimator.
kaplan_meier_discrete	Estimate the state survival function using the Kaplan-Meier estimator resolved with respect to the states in a second discrete trajectory.
leave_prob	Calculate the probability that a compound leaves its state after a lag time \(\Delta t\) given that it has entered the state at time \(t_0\).
leave_prob_discrete	Calculate the probability that a compound leaves its state after a lag time \(\Delta t\) given that it has entered the state at time \(t_0\) resolved with respect to the states in a second discrete trajectory.
lifetimes	Calculate the state lifetimes for each compound.
lifetimes_per_state	Calculate the state lifetimes for each state.
locate_trans	Locate the frames of state transitions inside a discrete trajectory.
n_leaves_vs_time	Calculate the number of compounds that leave their state after a lag time \(\Delta t\) given that they have entered the state at time \(t_0\).
n_leaves_vs_time_discrete	Calculate the number of compounds that leave their state after a lag time \(\Delta t\) resolved with respect to the states in a second discrete trajectory.
remain_prob	Calculate the probability that a compound is still (or again) in the same state as at time \(t_0\) after a lag time \(\Delta t\).
remain_prob_discrete	Calculate the probability that a compound is still (or again) in the same state as at time \(t_0\) after a lag time \(\Delta t\) resolved with respect to the states in a second discrete trajectory.
trans_ix	Get the frame indices of state transitions in a discrete trajectory.
trans_per_state	Count the number of transitions leading into or out of a state.
trans_per_state_vs_time	Count the number of transitions leading into or out of a state for each frame in a discrete trajectory.
trans_rate	Calculate the transition rate for each compound averaged over all states.
trans_rate_per_state	Calculate the transition rate for each state averaged over all compounds.
trans_rate_tot	Calculate the transition rate averaged over all compounds and over all states.