class DoubleWellDiscrete¶
- class deeptime.data.DoubleWellDiscrete¶
MCMC process in a symmetric double well potential, spatially discretized to 100 bins.
Encapsulates discrete trajectories and markov state model (see
MarkovStateModel
) with exact transition matrix.Attributes
Returns a
MarkovStateModel
instance with the exact transition matrix.100K frames trajectory at timestep 10, 100 microstates (not all are populated).
100K frames trajectory at timestep 10, bad 2-state discretization (off transition state).
100K frames trajectory at timestep 10, good 2-state discretization (at transition state).
100K frames trajectory at timestep 10, good 6-state discretization.
Exact transition matrix used to generate the data
Methods
dtraj_n
(divides)100K frames trajectory at timestep 10, arbitrary n-state discretization.
dtraj_n2
(divide)100K frames trajectory at timestep 10, arbitrary 2-state discretization.
simulate_trajectories
(n_trajectories, n_steps)Simulates
n_trajectories
discrete trajectories.simulate_trajectory
(n_steps[, start, stop, dt])Generates a discrete trajectory of length less or equal n_steps.
- dtraj_n(divides)¶
100K frames trajectory at timestep 10, arbitrary n-state discretization.
- Parameters:
divides ((n, dtype=int) ndarray) – The state boundaries.
- Returns:
dtraj – Discrete trajectory with
len(divides)
states.- Return type:
(T,) ndarray
- dtraj_n2(divide)¶
100K frames trajectory at timestep 10, arbitrary 2-state discretization.
- simulate_trajectories(n_trajectories: int, n_steps: int, start=None, stop=None, dt=1) List[ndarray] ¶
Simulates
n_trajectories
discrete trajectories. For a more detailed description of the arguments, seesimulate_trajectory()
.
- simulate_trajectory(n_steps, start=None, stop=None, dt=1) ndarray ¶
Generates a discrete trajectory of length less or equal n_steps.
- Parameters:
n_steps (int) – maximum number of steps to simulate
start (int, optional, default=None) – Starting state. If None is given, it is sampled from the stationary distribution.
stop (int, optional, default=None) – Stopping state. If not None and encountered, stops the simulation. This can lead to fewer than n_steps steps.
dt (int, optional, default=1) – Time step to apply when simulating the trajectory.
- Returns:
dtraj – A discrete trajectory.
- Return type:
(T, 1) ndarray
- property analytic_msm¶
Returns a
MarkovStateModel
instance with the exact transition matrix.
- property dtraj¶
100K frames trajectory at timestep 10, 100 microstates (not all are populated).
- property dtraj_n2bad¶
100K frames trajectory at timestep 10, bad 2-state discretization (off transition state).
- property dtraj_n2good¶
100K frames trajectory at timestep 10, good 2-state discretization (at transition state).
- property dtraj_n6good¶
100K frames trajectory at timestep 10, good 6-state discretization.
- property transition_matrix¶
Exact transition matrix used to generate the data