Forward Flux Sampling¶

str(object='') -> str str(bytes_or_buffer[, encoding[, errors]]) -> str

Create a new string object from the given object. If encoding or errors is specified, then the object must expose a data buffer that will be decoded using the given encoding and error handler. Otherwise, returns the result of object.str() (if defined) or repr(object). encoding defaults to sys.getdefaultencoding(). errors defaults to 'strict'.

str(object='') -> str str(bytes_or_buffer[, encoding[, errors]]) -> str

Create a new string object from the given object. If encoding or errors is specified, then the object must expose a data buffer that will be decoded using the given encoding and error handler. Otherwise, returns the result of object.str() (if defined) or repr(object). encoding defaults to sys.getdefaultencoding(). errors defaults to 'strict'.

Canvas dimensions (width, height) for the simulation.

Defines the size of the 2D lattice on which tile assembly occurs. Must be large enough to accommodate the largest expected structures.

Type of boundary conditions for the simulation canvas.

Determines how the edges of the canvas are handled: - Periodic: opposite edges are connected (torus topology) - Square: finite canvas with hard boundaries - Tube: periodic in one dimension, finite in the other

Use constant-variance, variable-configurations-per-surface method.

When true, the number of configurations generated at each surface is determined dynamically to achieve a target variance of the forward probablity relative to the mean squared (var_per_mean2). When false, exactly max_configs configurations are generated at each surface.

Number of consecutive high-probability surfaces required for early cutoff.

FFS terminates early only after this many consecutive surfaces exceed cutoff_probability. Prevents premature termination due to statistical fluctuations. Only used when early_cutoff is true.

Success probability threshold for early cutoff.

If early_cutoff is true and the success probability exceeds this value for cutoff_number consecutive surfaces, FFS terminates early.

Enable early termination when success probabilities become very high.

When true, FFS will terminate early if the success probability exceeds cutoff_probability for cutoff_number consecutive surfaces, provided the structure size is at least min_cutoff_size.

Evolution bounds for the initial dimer-to-n-mer surface, to avoid infinite simulations.

Configuration data retention mode for each surface.

Controls what data is retained during FFS simulation: - ConfigRetentionMode.None: No configuration data retained (minimal memory) - ConfigRetentionMode.DataFrameOnly: Only dataframe-compatible data retained (default) - ConfigRetentionMode.Full: Full state objects retained (maximum memory, allows full access)

For backward compatibility, bool values are also accepted: - False -> ConfigRetentionMode.None - True -> ConfigRetentionMode.Full

Maximum number of configurations to generate at each surface level.

When constant_variance is false, exactly this many configurations are generated. When constant_variance is true, this serves as an upper limit to prevent excessive computation when success probabilities are very low.

Minimum number of configurations to generate at each surface level.

Ensures a minimum sample size even when constant_variance is true and the target variance is achieved with fewer configurations.

Minimum structure size required before early cutoff can occur.

Prevents early termination when structures are still small, even if success probabilities are high. Ensures the simulation reaches a meaningful size before terminating. Only used when early_cutoff is true.

Minimum nucleation rate threshold for early termination.

If specified, FFS terminates early when the calculated nucleation rate falls below this threshold. Useful for avoiding excessive computation when nucleation rates become negligibly small. Units: M/s.

Size increment between consecutive FFS surfaces.

The number of tiles by which the target size increases between consecutive surfaces.

Initial cluster size for the first FFS surface.

The size (number of tiles) that defines the first surface. Must be >=2.

Whether to store the FFS configuration in the result.

When true, the complete FFSRunConfig is saved with the results.

Whether to store the tile system in the result.

Evolution bounds for subsequent surface-to-surface transitions, to avoid infinite simulations.

Target structure size for FFS termination.

Type of additional data tracking during simulation.

Controls what extra information is recorded during evolution: - None: no additional tracking (fastest, default) - Order: track attachment order of tiles - LastAttachTime: track when the tile at each location last attached - PrintEvent: print events as they occur (debugging) - Movie: record all events

Target variance per mean squared for the constant-variance method.

Controls the statistical precision when constant_variance is true. Lower values require more configurations but provide better statistics. Typical values are 0.01 (1% variance) to 0.1 (10% variance). Only used when constant_variance is true.

str(object='') -> str str(bytes_or_buffer[, encoding[, errors]]) -> str

Create a new string object from the given object. If encoding or errors is specified, then the object must expose a data buffer that will be decoded using the given encoding and error handler. Otherwise, returns the result of object.str() (if defined) or repr(object). encoding defaults to sys.getdefaultencoding(). errors defaults to 'strict'.

float: Dimerization rate, in M/s.

list[float]: Forward probability vector.

float: Nucleation rate, in M/s. Calculated from the forward probability vector, and dimerization rate.

list[FFSLevelRef]: list of surfaces.

str(object='') -> str str(bytes_or_buffer[, encoding[, errors]]) -> str

Create a new string object from the given object. If encoding or errors is specified, then the object must expose a data buffer that will be decoded using the given encoding and error handler. Otherwise, returns the result of object.str() (if defined) or repr(object). encoding defaults to sys.getdefaultencoding(). errors defaults to 'strict'.

str(object='') -> str str(bytes_or_buffer[, encoding[, errors]]) -> str

Create a new string object from the given object. If encoding or errors is specified, then the object must expose a data buffer that will be decoded using the given encoding and error handler. Otherwise, returns the result of object.str() (if defined) or repr(object). encoding defaults to sys.getdefaultencoding(). errors defaults to 'strict'.

NDArray[np.uint]: a direct, mutable view of the state's canvas. This is potentially unsafe.

int: the number of tiles in the state.

float: the total time the state has simulated, in seconds.

int: the total number of events that have occurred in the state.

float: the total rate of possible next events for the state.