private static int Main(string[] args)
{
var retval = 0;
var sbmlns = new SBMLNamespaces(3, 1, "comp", 1);
// create the document
var document = new SBMLDocument(sbmlns);
//Define the external model definition
var compdoc = (CompSBMLDocumentPlugin)(document.getPlugin("comp"));
compdoc.setRequired(true);
var extmod = compdoc.createExternalModelDefinition();
extmod.setId("ExtMod1");
extmod.setSource("enzyme_model.xml");
extmod.setModelRef("enzyme");
//Define the 'simple' model
var mod1 = compdoc.createModelDefinition();
mod1.setId("simple");
var comp = mod1.createCompartment();
comp.setSpatialDimensions(3);
comp.setConstant(true);
comp.setId("comp");
comp.setSize(1L);
var spec = new Species(sbmlns);
//We have to construct it this way because we get the comp plugin from it later.
spec.setCompartment("comp");
spec.setHasOnlySubstanceUnits(false);
spec.setConstant(false);
spec.setBoundaryCondition(false);
spec.setId("S");
spec.setInitialConcentration(5);
mod1.addSpecies(spec);
spec.setId("D");
spec.setInitialConcentration(10);
mod1.addSpecies(spec);
var rxn = new Reaction(3, 1);
rxn.setReversible(true);
rxn.setFast(false);
rxn.setId("J0");
var sr = new SpeciesReference(3, 1);
sr.setConstant(true);
sr.setStoichiometry(1);
sr.setSpecies("S");
rxn.addReactant(sr);
sr.setSpecies("D");
rxn.addProduct(sr);
mod1.addReaction(rxn);
var mod1plug = (CompModelPlugin)(mod1.getPlugin("comp"));
var port = new Port();
port.setId("S_port");
port.setIdRef("S");
mod1plug.addPort(port);
var port2 = mod1plug.createPort();
port2.setId("D_port");
port2.setIdRef("D");
port.setId("comp_port");
port.setIdRef("comp");
mod1plug.addPort(port);
port.setId("J0_port");
port.setIdRef("J0");
mod1plug.addPort(port);
// create the Model
var model = document.createModel();
model.setId("complexified");
// Set the submodels
var mplugin = (CompModelPlugin)(model.getPlugin("comp"));
var submod1 = mplugin.createSubmodel();
submod1.setId("A");
submod1.setModelRef("ExtMod1");
var submod2 = mplugin.createSubmodel();
submod2.setId("B");
submod2.setModelRef("simple");
var del = submod2.createDeletion();
del.setPortRef("J0_port");
// Synchronize the compartments
var mcomp = model.createCompartment();
mcomp.setSpatialDimensions(3);
mcomp.setConstant(true);
mcomp.setId("comp");
mcomp.setSize(1L);
var compartplug = (CompSBasePlugin)(mcomp.getPlugin("comp"));
var re = new ReplacedElement();
re.setIdRef("comp");
re.setSubmodelRef("A");
compartplug.addReplacedElement(re);
re.setSubmodelRef("B");
re.unsetIdRef();
re.setPortRef("comp_port");
compartplug.addReplacedElement(re);
//Synchronize the species
spec.setId("S");
spec.setInitialConcentration(5);
var specplug = (CompSBasePlugin)(spec.getPlugin("comp"));
var sre = specplug.createReplacedElement();
sre.setSubmodelRef("A");
sre.setIdRef("S");
var sre2 = specplug.createReplacedElement();
sre2.setSubmodelRef("B");
sre2.setPortRef("S_port");
model.addSpecies(spec);
spec.setId("D");
spec.setInitialConcentration(10);
sre.setIdRef("D");
sre2.setPortRef("D_port");
model.addSpecies(spec);
libsbml.writeSBMLToFile(document, "spec_example3.xml");
document = libsbml.readSBMLFromFile("spec_example3.xml");
if (document == null)
{
Console.WriteLine("Error reading back in file.");
retval = -1;
}
else
{
document.setConsistencyChecks(libsbml.LIBSBML_CAT_UNITS_CONSISTENCY, false);
document.checkConsistency();
if (document.getErrorLog().getNumFailsWithSeverity(2) > 0 ||
document.getErrorLog().getNumFailsWithSeverity(3) > 0)
{
var stream = new OStringStream();
document.printErrors(stream);
Console.WriteLine("Errors encoutered when round-tripping SBML file: \n" +
stream.str());
retval = -1;
}
libsbml.writeSBMLToFile(document, "spec_example3_rt.xml");
}
return(retval);
}
public static int Main(string[] args)
{
// Creates an SBMLNamespaces object with the given SBML level, version
// package name, package version.
SBMLNamespaces sbmlns = new SBMLNamespaces(3, 1, "qual", 1);
// create the document
SBMLDocument document = new SBMLDocument(sbmlns);
// mark qual as required
document.setPackageRequired("qual", true);
// create the Model
Model model = document.createModel();
// create the Compartment
Compartment compartment = model.createCompartment();
compartment.setId("c");
compartment.setConstant(true);
// Get a QualModelPlugin object plugged in the model object.
QualModelPlugin mplugin = (QualModelPlugin)(model.getPlugin("qual"));
// create the QualitativeSpecies
QualitativeSpecies qs = mplugin.createQualitativeSpecies();
qs.setId("s1");
qs.setCompartment("c");
qs.setConstant(false);
qs.setInitialLevel(1);
qs.setMaxLevel(4);
qs.setName("sss");
// create the Transition
Transition t = mplugin.createTransition();
t.setId("d");
t.setSBOTerm(1);
Input i = t.createInput();
i.setId("RD");
i.setQualitativeSpecies("s1");
i.setTransitionEffect(libsbml.INPUT_TRANSITION_EFFECT_NONE);
i.setSign(libsbml.INPUT_SIGN_NEGATIVE);
i.setThresholdLevel(2);
i.setName("aa");
Output o = t.createOutput();
o.setId("wd");
o.setQualitativeSpecies("s1");
o.setTransitionEffect(libsbml.OUTPUT_TRANSITION_EFFECT_PRODUCTION);
o.setOutputLevel(2);
o.setName("aa");
FunctionTerm ft = t.createFunctionTerm();
ASTNode math = libsbml.parseL3Formula("geq(s1, 2)");
ft.setResultLevel(1);
ft.setMath(math);
DefaultTerm dt = t.createDefaultTerm();
dt.setResultLevel(2);
int result = libsbml.writeSBML(document, "qual_example1.xml");
if (result == 1)
{
Console.WriteLine("Wrote file");
return(0);
}
else
{
Console.WriteLine("Failed to write");
return(1);
}
}
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 static int Main(string[] args)
{
var sbmlns = new SBMLNamespaces(3, 1, "comp", 1);
// create the document
var document = new SBMLDocument(sbmlns);
//Define the external model definitions
var compdoc = (CompSBMLDocumentPlugin)(document.getPlugin("comp"));
compdoc.setRequired(true);
var extmod = compdoc.createExternalModelDefinition();
extmod.setId("ExtMod1");
extmod.setSource("enzyme_model.xml");
extmod.setModelRef("enzyme");
// create the main Model
var model = document.createModel();
// Set the submodels
var mplugin = (CompModelPlugin)(model.getPlugin("comp"));
var submod1 = mplugin.createSubmodel();
submod1.setId("A");
submod1.setModelRef("ExtMod1");
var submod2 = mplugin.createSubmodel();
submod2.setId("B");
submod2.setModelRef("ExtMod1");
// create a replacement compartment
var comp = model.createCompartment();
comp.setSpatialDimensions(3);
comp.setConstant(true);
comp.setId("comp");
comp.setSize(1L);
//Tell the model that this compartment replaces both of the inside ones.
var compartplug = (CompSBasePlugin)(comp.getPlugin("comp"));
var re = new ReplacedElement();
re.setIdRef("comp");
re.setSubmodelRef("A");
compartplug.addReplacedElement(re);
re.setSubmodelRef("B");
compartplug.addReplacedElement(re);
// create a replacement species
var spec = model.createSpecies();
spec.setCompartment("comp");
spec.setHasOnlySubstanceUnits(false);
spec.setConstant(false);
spec.setBoundaryCondition(false);
spec.setId("S");
//Tell the model that this species replaces both of the inside ones.
var spp = (CompSBasePlugin)(spec.getPlugin("comp"));
re.setIdRef("S");
re.setSubmodelRef("A");
spp.addReplacedElement(re);
re.setSubmodelRef("B");
spp.addReplacedElement(re);
libsbml.writeSBMLToFile(document, "spec_example2.xml");
document = libsbml.readSBMLFromFile("spec_example2.xml");
if (document == null)
{
Console.WriteLine("Error reading back in file.");
return(-1);
}
else
{
document.setConsistencyChecks(libsbml.LIBSBML_CAT_UNITS_CONSISTENCY, false);
document.checkConsistency();
if (document.getErrorLog().getNumFailsWithSeverity(2) > 0 ||
document.getErrorLog().getNumFailsWithSeverity(3) > 0)
{
var stream = new OStringStream();
document.printErrors(stream);
Console.WriteLine("Errors encoutered when round-tripping SBML file: \n" +
stream.str());
return(-1);
}
libsbml.writeSBMLToFile(document, "spec_example2_rt.xml");
}
return(0);
}
