dexom_python.enum_functions subpackage

Submodules

diversity-based enumeration

param model
type model: cobrapy Model
param reaction_weights: keys = reactions and values = weights
type reaction_weights: dict
param prev_sol: a previous imat solution
type prev_sol: Solution instance
param threshold: detection threshold of activated reactions
type threshold: float
param obj_tol: variance allowed in the objective_values of the solutions
type obj_tol: float
param maxiter: maximum number of solutions to search for
type maxiter: foat
param dist_anneal: parameter which influences the probability of selecting reactions
type dist_anneal: float
param out_path: path to which the solutions are saved if save==True
type out_path: str
param icut: if True, icut constraints are applied
type icut: bool
param full: if True, the full-DEXOM implementation is used
type full: bool
param save: if True, every individual solution is saved in the iMAT solution format
type save: bool
returns: solution
rtype: an EnumSolution object

class dexom_python.enum_functions.enumeration.EnumSolution(solutions, binary, objective_value)[source]

Bases: object

class for solutions of enumeration methods

Parameters

solutions (list) – list of pandas dataframes containing flux values with reaction ids as index
binary (list) – list containing binary arrays of reaction activity (0 for inactive, 1 for active)
objective_value (float) – objective value returned by the solver at the end of the optimization

dexom_python.enum_functions.enumeration.analyze_div_enum_results(result_path, solution_path, out_path)[source]

This function calculates the average pairwise hamming distance and average next neighbour distance for each iteration - it’s very slow

Parameters

dexom_python.enum_functions.enumeration.create_enum_variables(model, reaction_weights, eps=0.01, thr=1e-05, full=False)[source]

dexom_python.enum_functions.enumeration.get_recent_solution_and_iteration(dirpath, startsol_num)[source]

dexom_python.enum_functions.enumeration.write_batch_script1(directory, username, modelfile, weightfile, reactionlist, imatsol, objtol, filenums=100, iters=100)[source]

dexom_python.enum_functions.enumeration.write_batch_script2(filenums)[source]: Warning: this function has not been updated with recent changes to DEXOM

dexom_python.enum_functions.enumeration.write_batch_script_divenum(directory, username, modelfile, weightfile, rxnsols, objtol, eps=0.0001, thr=1e-05, tol=1e-08, filenums=100, iters=100, t=6000)[source]

dexom_python.enum_functions.enumeration.write_rxn_enum_script(directory, modelfile, weightfile, reactionlist, imatsol, username, eps=0.0001, thr=1e-05, tol=1e-08, iters=100, maxiters=10000000000.0)[source]

integer-cut method

param model
type model: cobrapy Model
param prev_sol: an imat solution used as a starting point
type prev_sol: imat Solution object
param reaction_weights: keys = reactions and values = weights
type reaction_weights: dict
param eps: activation threshold in imat
type eps: float
param thr: detection threshold of activated reactions
type thr: float
param tlim: time limit for imat
type tlim: int
param tol: tolerance for imat
type tol: float
param obj_tol: variance allowed in the objective_values of the solutions
type obj_tol: float
param maxiter: maximum number of solutions to check for
type maxiter: foat
param full: if True, carries out integer-cut on all reactions; if False, only on reactions with non-zero weights
type full: bool
returns: solution – In the case of integer-cut, all_solutions and unique_solutions are identical
rtype: EnumSolution object

param model
type model: cobrapy Model
param prev_sol: an imat solution used as a starting point
type prev_sol: imat Solution object
param reaction_weights: keys = reactions and values = weights
type reaction_weights: dict
param eps: activation threshold in imat
type eps: float
param thr: detection threshold of activated reactions
type thr: float
param tlim: time limit for imat
type tlim: int
param tol: tolerance for imat
type tol: float
param obj_tol: variance allowed in the objective_values of the solutions
type obj_tol: float
param maxiter: maximum number of solutions to check for
type maxiter: foat
param icut: if True, icut constraints are applied
type icut: bool
param full: if True, carries out integer-cut on all reactions; if False, only on reactions with non-zero weights
type full: bool
param only_ones: if True, only the ones in the binary solution are used for distance calculation (as in dexom matlab)
type only_ones: bool

Reaction enumeration method