LibSBML fbc_example1.java

// 
// @file    fbc_example1.java
// @brief   SBML FBC example
// @author  Frank Bergmann 
//
// 

import org.sbml.libsbml.*;

public class fbc_example1
{

  public static void main(String[] args)
  {
    System.loadLibrary("sbmlj");

    SBMLNamespaces sbmlns = new SBMLNamespaces(3,1,"fbc",1);
                
    // create the document
                
    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);
                
                
    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");

  }

}

LibSBML, an application programming interface (API) library for SBML.

SBML Team http://www.sbml.org/ sbml-team@googlegroups.com