optimModels.utils package

Submodules

optimModels.utils.configurations module

class optimModels.utils.configurations.GeckoConfigurations

Bases: object

SCALE_CONSTANT = 10000
class optimModels.utils.configurations.KineticConfigurations

Bases: object

SOLVER = 'odespy'
SOLVER_METHOD = 1
SOLVER_TIMEOUT = 6000
STEADY_STATE_TIME = 1000000000.0
class optimModels.utils.configurations.SolverConfigurations

Bases: object

ABSOLUTE_TOL = 1e-09
N_STEPS = 10000
RELATIVE_TOL = 1e-06
class optimModels.utils.configurations.StoicConfigurations

Bases: object

DEFAULT_LB = -99999
DEFAULT_UB = 99999
SOLVER = 'cplex'
SOLVER_METHOD = 'FBA'

optimModels.utils.constantes module

class optimModels.utils.constantes.optimType

Bases: object

COMPOSITION = 9
GENE_KO = 3
GENE_UO = 4
MEDIUM = 5
MEDIUM_LEVELS = 6
MEDIUM_REACTION_KO = 7
MEDIUM_REACTION_UO = 8
PROTEIN_KO = 10
PROTEIN_UO = 11
REACTION_KO = 1
REACTION_UO = 2
get_optim_type_name(id)
types = {1: 'Reaction Knockouts', 2: 'Reaction Under/Over expression', 3: 'Gene Knockouts', 4: 'Gene Under/Over expression', 5: 'Medium compositions', 6: 'Medium compositions with levels', 7: 'Medium with Reaction Knockouts', 8: 'Medium with Reaction Under/Over expression', 9: 'Community Composition', 10: 'Protein knockouts', 11: 'Protein Under/Over expression'}
class optimModels.utils.constantes.solverMethod

Bases: object

AdamsBashMoulton2 = 14
AdamsBashforth2 = 13
DORMAN_PRINCE = 7
Dop853 = 10
Dopri5 = 9
EULER = 5
HEUN = 4
LSODA = 1
LSODAR = 2
LSODE = 3
RK4 = 6
RKFehlberg = 8
Radau5 = 12
Vode = 11
get_solver_method_name(id)
methods = {1: 'LSODA', 2: 'LSODAR', 3: 'LSODE', 4: 'HEUN', 5: 'EULER', 6: 'Range Kutta 4', 7: 'DORMAN PRINCE', 8: 'RKFehlberg', 9: 'Dopri5', 10: 'Dop853', 11: 'Vode', 12: 'Radau5', 13: 'AdamsBashforth2', 14: 'AdamsBashMoulton2'}
class optimModels.utils.constantes.solverStatus

Bases: object

Enumeration of possible solution status. (FROM FRAMED

ERROR = 2
INFEASIBLE = -3
INF_OR_UNB = -4
OPTIMAL = 1
SUBOPTIMAL = -1
UNBOUNDED = -2
UNKNOWN = 0
static get_status_str(id)

optimModels.utils.utils module

class optimModels.utils.utils.MyPool(processes=None, initializer=None, initargs=(), maxtasksperchild=None, context=None)

Bases: multiprocessing.pool.Pool

Note : sub-class multiprocessing.pool.Pool instead of multiprocessing.Pool because the latter is only a wrapper function, not a proper class.

Process

alias of NoDaemonProcess

class optimModels.utils.utils.MyTree(name='root', children=None)

Bases: object

Class to implement a generic tree.

add_child(node)
class optimModels.utils.utils.NoDaemonProcess(group=None, target=None, name=None, args=(), kwargs={}, *, daemon=None)

Bases: multiprocessing.context.Process

Extension of class multiprocessing.Process which make ‘daemon’ attribute always return False

daemon
optimModels.utils.utils.fix_exchange_reactions_model(model)

Convert the exchange reactions for the uptake reactions have negative fluxes and excretion reactions have positive fluxes. :param model: Metabolic model

Returns: a new copy of model where all exchange reactions are in the format ” A <—> “

optimModels.utils.utils.get_order_nodes(tree)

Returns the order of nodes

Parameters:tree (instance of MyTree) –
optimModels.utils.utils.merge_two_dicts(x, y)

Module contents