corneto.methods.metabolism package#

Submodules#

corneto.methods.metabolism.fba module#

class corneto.methods.metabolism.fba.FBAProblem(graph, create_reaction_indicators=False, reaction_objective=None, backend=<corneto.DeprecatedBackend object>)#

Bases: ProblemDef

Parameters:

  • graph (BaseGraph)

  • create_reaction_indicators (bool)

  • reaction_objective (int | str | None)

  • backend (Backend | None)

get_fluxes()#
Return type:

ndarray

get_fluxes_dict()#
Return type:

Dict

corneto.methods.metabolism.fba.fba_problem(G, create_reaction_indicators=False, num_fluxes=1, eps=0.0001, backend=<corneto.DeprecatedBackend object>)#
corneto.methods.metabolism.fba.multicondition_imat(model, w, alpha=0.001, eps=0.01, use_unblocked_flux_indicators=False, scale=False, backend=<corneto.DeprecatedBackend object>)#

Module contents#

corneto.methods.metabolism.evaluate_gpr_rules(gpr_expressions, symbol_values_list, func_and=<function _and>, func_or=<function _or>, default_value=0, pattern='\\\\b(?!and\\\\b|or\\\\b)[A-Za-z0-9_]+\\\\b', n_processes=None)#
Parameters:
corneto.methods.metabolism.get_unique_genes(G, gpr_field='GPR', startswith=None, regex='\\b(?!and\\b|or\\b)[A-Za-z0-9_]+\\b')#
corneto.methods.metabolism.get_genes_from_gpr(gpr_expression, regex='\\b(?!and\\b|or\\b)[A-Za-z0-9_]+\\b')#
corneto.methods.metabolism.evaluate_gpr_expression(gpr_expressions, symbol_values, func_and=<function _and>, func_or=<function _or>, default_value=0, pattern='\\\\b(?!and\\\\b|or\\\\b)[A-Za-z0-9_]+\\\\b')#
Parameters:

  • gpr_expressions (list)

  • symbol_values (dict)