OptlangHelper 0.0.3

Named Tuples

There are several NamedTuples that are defined in OptlangHelper and assist with defining variables, constraints, and the objective.

Bounds object has attributes of

• lb, the lower bound of the entity associated with this bound: default is 0.

• up, the upper bound of the associated entity: default is 1000.

tupVariable object has attributes of

• name, the name of the variable represented by this tuple

• bounds, the lower and upper limit bounds associated with the tuple: (0,1000) is the default

• type, the variable type: “integer”; “binary”; “continuous” is the default.

tupConstraint object has attributes of

• name, the name of the variable represented by this tuple

• bounds, the lower and upper limit bounds associated with the tuple: (0,0) is the default

• expr, the constraint expression: None is the default.

tupObjective object has attributes of

• name, the name of the variable represented by this tuple

• expr, the objective expression: None is the default.

• direction, the optimization direction: “max” is the default.

All of the above objects are fed into the define_model function

• model_name, the name of the model

• variables, the tupVariable objects for the model.

• constraints, the tupConstraint objects for the model.

• objective, the tupObjective object for the model.

• optlang, specifies whether an optlang model is returned (True), or the raw dictionary (False) by default.

This function calls all of the class functions and returns either the GLPK model as as dictionary or an optlang object.

Example

The following blocks define the intended usage of the GLPK class.

from optlanghelper import tupVariable, tupConstraint, tupObjective, define_model

# define the variables
variables = {}
for var in vars:
    variables[var.name] = tupVariable(var.name, Bounds(0, 5), "continuous")
    variables[var.name+"_bin"] = tupVariable(var.name+"_bin", Bounds(0, 1), "binary")

# define the constraints
constraints = {}
for name, content in constraint_info.items():
   lb, ub = content["low_bound"], content["high_bound"]
   consExpr = {}
   ## define the constraint expression
   for varName, coef in var_info.items():
       if varName not in consCoefs:  continue
       coef2 = consCoefs[varName]
       consExpr[varName].update({"elements": [varName, coef2], "operation": "Mul"})
   ## create the constraint tuple
   constraints[nutrient] = tupConstraint(name=nutrient, bounds=Bounds(lb, ub), expr={"elements": list(consExpr.values()), "operation": "Add"})

for varName in var_info.keys():
   constraints[varName+"_bin"] = tupConstraint(varName+"_bin", bounds=Bounds(0,None),
                                            expr={
                                                "elements": [
                                                    variables[varName].bounds.ub,
                                                    {"elements": [-1, variables[varName].name,], "operation": "Mul"},
                                                    {"elements": [-variables[varName].bounds.ub, variables[varName+"_bin"].name], "operation": "Mul"}],
                                               "operation": "Add"})

# define the objective
objective = tupObjective("< optimization name>", [], "min")
for varName, coef in var_info.items():
    objective.expr.append({
        "elements": [
            {"elements": [variables[varName].name, coef],
            "operation": "Mul"}],
        "operation": "Add"
    })

# create an optlang model from all of the variables, constraints, and objective defined above
model = define_model("< model name>", list(variables.values()), list(constraints.values()), objective, True)

from optlanghelper import define_model_auto

model = define_model_auto("community_fba", variables, constraints, objective)
model.optimize()