cobra.flux_analysis.geometric

cobra.flux_analysis.geometric#

Provide an implementation of geometric FBA.

Attributes#

logger

Functions#

geometric_fba(→ cobra.Solution)

Perform geometric FBA to obtain a unique, centered flux distribution.

Module Contents#

cobra.flux_analysis.geometric.logger#
cobra.flux_analysis.geometric.geometric_fba(model: cobra.Model, epsilon: float = 1e-06, max_tries: int = 200, processes: int | None = None) → cobra.Solution[source]#

Perform geometric FBA to obtain a unique, centered flux distribution.

Geometric FBA [1] formulates the problem as a polyhedron and then solves it by bounding the convex hull of the polyhedron. The bounding forms a box around the convex hull which reduces with every iteration and extracts a unique solution in this way.

Parameters:

  • model (cobra.Model) – The model to perform geometric FBA on.

  • epsilon (float, optional) – The convergence tolerance of the model (default 1E-06).

  • max_tries (int, optional) – Maximum number of iterations (default 200).

  • processes (int, optional) – The number of parallel processes to run. If not explicitly passed, will be set from the global configuration singleton (default None).

Returns:

The solution object containing all the constraints required for geometric FBA.

Return type:

cobra.Solution

Raises:

RuntimeError – If iteration count becomes equal to max_tries.

References