Building model

There is two ways to create models. Shorthand notation is useful for quickly prototyping models. It takes less space and syntax is designed to resemble original BioOpt format. However for people unfamiliar with shorthand notation it might prove difficult to understand your code. On the other hand explicit notation is unambiguous but longer. It is also faster if you are trying to improve code performance for big models. The choice is yours but in long-term using explicit notation is advised.

Explicit notation

First let’s try to create a model using explicit notation

from bioopt.model import *

# Create left-hand-side of reaction
reactants = ReactionMemberList()
reactants.append(ReactionMember(Metabolite("Na"), coefficient=2))
reactants.append(ReactionMember(Metabolite("H2O"), coefficient=2))

# Create right-hand-side of reaction
products = ReactionMemberList()
products.append(ReactionMember(Metabolite("NaOH"), coefficient=2))
products.append(ReactionMember(Metabolite("H2"), coefficient=1))

# Combine previously created objects into complete reaction definition.Note that direction and constraints are not
# required. By default reaction would be unconstrained and allow to flow both directions. However if direction is
# specified default constraints will reflect reaction directionality.
r1 = Reaction("Burn", reactants, products, Direction.forward(), Bounds(-1, Bounds.inf())) # Lower bound will be reset to 0 because reaction is not reversible
r2 = Reaction("Break", products, reactants)

# Let's now create model with this reaction
m = Model()
m.reactions = [r1, r2]
print(m)

-REACTIONS
Burn[0, inf]     : 2 Na + 2 H2O   -> 2 NaOH + 1 H2
Break[-inf, inf] : 2 NaOH + 1 H2 <-> 2 Na + 2 H2O

-CONSTRAINTS
Burn    [0, inf]
Break   [-inf, inf]

Short-hand notation

Now let’s create same model using short-hand notation. Notice how more convenient is notation for reactants and products

reactants = 2*Metabolite("Na") + 2*Metabolite("H2O")
products = 2*Metabolite("NaOH") + 2*Metabolite("H2")
r1 = Reaction("Burn", reactants, products, Direction.forward(), Bounds(0, Bounds.inf()))
r2 = Reaction("Break", products, reactants)
m = Model()
m.reactions = [r1, r2]

Write BioOpt file

Once you have a created BioOpt model it can be saved on disc by calling save() member function.

m.save("export.bioopt")