private void InitializeFromFbcV2(Model model, FbcModelPlugin plugin)
{
if (!plugin.getStrict())
{
Warnings.Add(
"Encountered non-strict model, this software does not support any of the dynamic features of FBC V2, only the static features of the model are imported. ");
}
var numConstraints = plugin.getNumFluxBounds();
for (int i = 0; i < numConstraints; i++)
{
var constraint = plugin.getFluxBound(i);
Constraints.Add(new LPsolveConstraint(constraint.getReaction(), GetOperator(constraint.getOperation()),
constraint.getValue()));
}
var activeObjective = plugin.getActiveObjective();
if (activeObjective == null && plugin.getNumObjectives() > 0)
activeObjective = plugin.getObjective(0);
if (activeObjective == null) return;
var numObjectives = (int)activeObjective.getNumFluxObjectives();
for (int i = 0; i < numObjectives; i++)
{
var objective = activeObjective.getFluxObjective(i);
Objectives.Add(new LPsolveObjective(objective.getReaction(), objective.getCoefficient()));
}
if (activeObjective.getType() == "minimize" || activeObjective.getType() == "minimise") Mode = FBA_Mode.minimize;
else Mode = FBA_Mode.maximize;
ActiveObjective = activeObjective.getId();
for (int i = 0; i < model.getNumReactions(); i++)
{
var reaction = model.getReaction(i);
ReversibilityMap[reaction.getId()] = reaction.getReversible();
var rplug = (FbcReactionPlugin) reaction.getPlugin("fbc");
if (rplug == null) continue;
if (rplug.isSetLowerFluxBound())
{
var param = model.getParameter(rplug.getLowerFluxBound());
if (param != null)
{
Constraints.Add(new LPsolveConstraint(reaction.getId(), lpsolve_constr_types.GE,
param.getValue()));
}
}
if (rplug.isSetUpperFluxBound())
{
var param = model.getParameter(rplug.getUpperFluxBound());
if (param != null)
{
Constraints.Add(new LPsolveConstraint(reaction.getId(), lpsolve_constr_types.LE,
param.getValue()));
}
}
}
}
static void Main(string[] args)
{
SBMLNamespaces sbmlns = new SBMLNamespaces(3, 1, "fbc", 1);
SBMLDocument document = new SBMLDocument(sbmlns);
// create the Model
Model model = document.createModel();
// create the Compartment
Compartment compartment = model.createCompartment();
compartment.setId("compartment");
compartment.setConstant(true);
compartment.setSize(1);
// create the Species
Species species = model.createSpecies();
species.setId("Node1");
species.setCompartment("compartment");
species.setConstant(false);
species.setHasOnlySubstanceUnits(false);
species.setBoundaryCondition(false);
species = model.createSpecies();
species.setId("Node2");
species.setCompartment("compartment");
species.setConstant(false);
species.setHasOnlySubstanceUnits(false);
species.setConstant(false);
species.setHasOnlySubstanceUnits(false);
species.setBoundaryCondition(false);
species = model.createSpecies();
species.setId("Node3");
species.setCompartment("compartment");
species.setConstant(false);
species.setHasOnlySubstanceUnits(false);
species.setBoundaryCondition(false);
species = model.createSpecies();
species.setId("Node4");
species.setCompartment("compartment");
species.setConstant(false);
species.setHasOnlySubstanceUnits(false);
species.setBoundaryCondition(false);
species = model.createSpecies();
species.setId("Node5");
species.setCompartment("compartment");
species.setConstant(false);
species.setHasOnlySubstanceUnits(false);
species.setBoundaryCondition(false);
species = model.createSpecies();
species.setId("Node6");
species.setCompartment("compartment");
species.setConstant(false);
species.setHasOnlySubstanceUnits(false);
species.setBoundaryCondition(false);
species = model.createSpecies();
species.setId("Node7");
species.setCompartment("compartment");
species.setConstant(false);
species.setHasOnlySubstanceUnits(false);
species.setBoundaryCondition(false);
species = model.createSpecies();
species.setId("Node8");
species.setCompartment("compartment");
species.setConstant(false);
species.setHasOnlySubstanceUnits(false);
species.setBoundaryCondition(false);
species = model.createSpecies();
species.setId("Node0");
species.setCompartment("compartment");
species.setConstant(false);
species.setHasOnlySubstanceUnits(false);
species.setBoundaryCondition(true);
species = model.createSpecies();
species.setId("Node9");
species.setCompartment("compartment");
species.setConstant(false);
species.setHasOnlySubstanceUnits(false);
species.setBoundaryCondition(true);
Reaction reaction = model.createReaction();
reaction.setId("J0");
reaction.setReversible(false);
reaction.setFast(false);
SpeciesReference reactant = reaction.createReactant();
reactant.setSpecies("Node0");
reactant.setStoichiometry(1);
reactant.setConstant(true);
SpeciesReference product = reaction.createProduct();
product.setSpecies("Node1");
product.setStoichiometry(1);
product.setConstant(true);
reaction = model.createReaction();
reaction.setId("J1");
reaction.setReversible(false);
reaction.setFast(false);
reactant = reaction.createReactant();
reactant.setSpecies("Node1");
reactant.setStoichiometry(1);
reactant.setConstant(true);
product = reaction.createProduct();
product.setSpecies("Node2");
product.setStoichiometry(1);
product.setConstant(true);
reaction = model.createReaction();
reaction.setId("J2");
reaction.setReversible(false);
reaction.setFast(false);
reactant = reaction.createReactant();
reactant.setSpecies("Node2");
reactant.setStoichiometry(1);
reactant.setConstant(true);
product = reaction.createProduct();
product.setSpecies("Node3");
product.setStoichiometry(1);
product.setConstant(true);
reaction = model.createReaction();
reaction.setId("J3");
reaction.setReversible(false);
reaction.setFast(false);
reactant = reaction.createReactant();
reactant.setSpecies("Node1");
reactant.setStoichiometry(1);
reactant.setConstant(true);
product = reaction.createProduct();
product.setSpecies("Node4");
product.setStoichiometry(1);
product.setConstant(true);
reaction = model.createReaction();
reaction.setId("J4");
reaction.setReversible(false);
reaction.setFast(false);
reactant = reaction.createReactant();
reactant.setSpecies("Node4");
reactant.setStoichiometry(1);
reactant.setConstant(true);
product = reaction.createProduct();
product.setSpecies("Node3");
product.setStoichiometry(1);
product.setConstant(true);
reaction = model.createReaction();
reaction.setId("J5");
reaction.setReversible(false);
reaction.setFast(false);
reactant = reaction.createReactant();
reactant.setSpecies("Node3");
reactant.setStoichiometry(1);
reactant.setConstant(true);
product = reaction.createProduct();
product.setSpecies("Node5");
product.setStoichiometry(1);
product.setConstant(true);
reaction = model.createReaction();
reaction.setId("J6");
reaction.setReversible(false);
reaction.setFast(false);
reactant = reaction.createReactant();
reactant.setSpecies("Node5");
reactant.setStoichiometry(1);
reactant.setConstant(true);
product = reaction.createProduct();
product.setSpecies("Node6");
product.setStoichiometry(1);
product.setConstant(true);
reaction = model.createReaction();
reaction.setId("J7");
reaction.setReversible(false);
reaction.setFast(false);
reactant = reaction.createReactant();
reactant.setSpecies("Node6");
reactant.setStoichiometry(1);
reactant.setConstant(true);
product = reaction.createProduct();
product.setSpecies("Node7");
product.setStoichiometry(1);
product.setConstant(true);
reaction = model.createReaction();
reaction.setId("J8");
reaction.setReversible(false);
reaction.setFast(false);
reactant = reaction.createReactant();
reactant.setSpecies("Node5");
reactant.setStoichiometry(1);
reactant.setConstant(true);
product = reaction.createProduct();
product.setSpecies("Node8");
product.setStoichiometry(1);
product.setConstant(true);
reaction = model.createReaction();
reaction.setId("J9");
reaction.setReversible(false);
reaction.setFast(false);
reactant = reaction.createReactant();
reactant.setSpecies("Node8");
reactant.setStoichiometry(1);
reactant.setConstant(true);
product = reaction.createProduct();
product.setSpecies("Node7");
product.setStoichiometry(1);
product.setConstant(true);
reaction = model.createReaction();
reaction.setId("J10");
reaction.setReversible(false);
reaction.setFast(false);
reactant = reaction.createReactant();
reactant.setSpecies("Node7");
reactant.setStoichiometry(1);
reactant.setConstant(true);
product = reaction.createProduct();
product.setSpecies("Node9");
product.setStoichiometry(1);
product.setConstant(true);
//
// Get a FbcModelPlugin object plugged in the model object.
//
// The type of the returned value of SBase::getPlugin() function is SBasePlugin, and
// thus the value needs to be casted for the corresponding derived class.
//
FbcModelPlugin mplugin = (FbcModelPlugin)(model.getPlugin("fbc"));
FluxBound bound = mplugin.createFluxBound();
bound.setId("bound1");
bound.setReaction("J0");
bound.setOperation("equal");
bound.setValue(10);
Objective objective = mplugin.createObjective();
objective.setId("obj1");
objective.setType("maximize");
// mark obj1 as active objective
mplugin.setActiveObjectiveId("obj1");
FluxObjective fluxObjective = objective.createFluxObjective();
fluxObjective.setReaction("J8");
fluxObjective.setCoefficient(1);
libsbml.writeSBMLToFile(document, "fbc_example1.xml");
}
private void InitializeFromFbcV1(Model model, FbcModelPlugin plugin)
{
var numConstraints = plugin.getNumFluxBounds();
for (int i = 0; i < numConstraints; i++)
{
var constraint = plugin.getFluxBound(i);
Constraints.Add(new LPsolveConstraint(constraint.getReaction(), GetOperator(constraint.getOperation()),
constraint.getValue()));
}
var activeObjective = plugin.getActiveObjective();
if (activeObjective == null && plugin.getNumObjectives() > 0)
activeObjective = plugin.getObjective(0);
if (activeObjective == null) return;
var numObjectives = (int)activeObjective.getNumFluxObjectives();
for (int i = 0; i < numObjectives; i++)
{
var objective = activeObjective.getFluxObjective(i);
Objectives.Add(new LPsolveObjective(objective.getReaction(), objective.getCoefficient()));
}
if (activeObjective.getType() == "minimize" || activeObjective.getType() == "minimise") Mode = FBA_Mode.minimize;
else Mode = FBA_Mode.maximize;
ActiveObjective = activeObjective.getId();
for (int i = 0; i < model.getNumReactions(); i++)
{
var reaction = model.getReaction(i);
ReversibilityMap[reaction.getId()] = reaction.getReversible();
}
}
