psamm.fastgapfill – FastGapFill algorithm

Implementation of fastGapFill.

Described in [Thiele14].

psamm.fastgapfill.fastgapfill(model_extended, core, solver, weights={}, epsilon=1e-05)

Run FastGapFill gap-filling algorithm by calling psamm.fastcore.fastcore().

FastGapFill will try to find a minimum subset of reactions that includes the core reactions and it also has no blocked reactions. Return the set of reactions in the minimum subset. An extended model that includes artificial transport and exchange reactions can be generated by calling create_extended_model().

Parameters:
  • model – psamm.metabolicmodel.MetabolicModel.
  • core – reactions in the original metabolic model.
  • weights – a weight dictionary for reactions in the model.
  • solver – linear programming library to use.
  • epsilon – float number, threshold for Fastcore algorithm.