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);
var compdoc = (CompSBMLDocumentPlugin)(document.getPlugin("comp"));
compdoc.setRequired(true);
var mod1 = compdoc.createModelDefinition();
mod1.setId("enzyme");
mod1.setName("enzyme");
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");
mod1.addSpecies(spec);
spec.setId("E");
mod1.addSpecies(spec);
spec.setId("D");
mod1.addSpecies(spec);
spec.setId("ES");
mod1.addSpecies(spec);
var rxn = new Reaction(sbmlns);
rxn.setReversible(true);
rxn.setFast(false);
var rxn2 = new Reaction(sbmlns);
rxn2.setReversible(true);
rxn2.setFast(false);
rxn.setId("J0");
rxn2.setId("J1");
var sr = new SpeciesReference(3, 1);
sr.setConstant(true);
sr.setStoichiometry(1);
sr.setSpecies("S");
rxn.addReactant(sr);
sr.setSpecies("E");
rxn.addReactant(sr);
rxn2.addProduct(sr);
sr.setSpecies("ES");
rxn.addProduct(sr);
rxn2.addReactant(sr);
sr.setSpecies("D");
rxn2.addProduct(sr);
mod1.addReaction(rxn);
mod1.addReaction(rxn2);
var mod1plug = (CompModelPlugin)(mod1.getPlugin("comp"));
var m1port = new Port();
m1port.setIdRef("comp");
m1port.setId("comp_port");
mod1plug.addPort(m1port);
m1port.setIdRef("S");
m1port.setId("S_port");
mod1plug.addPort(m1port);
m1port.setIdRef("E");
m1port.setId("E_port");
mod1plug.addPort(m1port);
m1port.setIdRef("D");
m1port.setId("D_port");
mod1plug.addPort(m1port);
m1port.setIdRef("ES");
m1port.setId("ES_port");
mod1plug.addPort(m1port);
m1port.setIdRef("J0");
m1port.setId("J0_port");
mod1plug.addPort(m1port);
m1port.setIdRef("J1");
m1port.setId("J1_port");
mod1plug.addPort(m1port);
//Define the 'simple' model
var mod2 = compdoc.createModelDefinition();
mod2.setId("simple");
var comp2 = mod2.createCompartment();
comp2.setSpatialDimensions(3);
comp2.setConstant(true);
comp2.setId("comp");
comp2.setSize(1L);
spec.setCompartment("comp");
spec.setHasOnlySubstanceUnits(false);
spec.setConstant(false);
spec.setBoundaryCondition(false);
spec.setId("S");
spec.setInitialConcentration(5);
mod2.addSpecies(spec);
spec.setId("D");
spec.setInitialConcentration(10);
mod2.addSpecies(spec);
var rxn3 = new Reaction(sbmlns);
//We have to construct it this way because we get the comp plugin from it later.
rxn3.setReversible(true);
rxn3.setFast(false);
rxn3.setId("J0");
var sr2 = new SpeciesReference(3, 1); //These will not need plugins.
sr2.setConstant(true);
sr2.setStoichiometry(1);
sr2.setSpecies("S");
rxn3.addReactant(sr2);
sr2.setSpecies("D");
rxn3.addProduct(sr2);
mod2.addReaction(rxn3);
var mod2plug = (CompModelPlugin)(mod2.getPlugin("comp"));
var port = new Port();
port.setId("S_port");
port.setIdRef("S");
mod2plug.addPort(port);
var port2 = mod2plug.createPort();
port2.setId("D_port");
port2.setIdRef("D");
port.setId("comp_port");
port.setIdRef("comp");
mod2plug.addPort(port);
port.setId("J0_port");
port.setIdRef("J0");
mod2plug.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("enzyme");
var submod2 = mplugin.createSubmodel();
submod2.setId("B");
submod2.setModelRef("simple");
var del = submod2.createDeletion();
del.setPortRef("J0_port");
del.setId("oldrxn");
// 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);
spec.setId("E");
spec.unsetInitialConcentration();
sre.unsetIdRef();
sre2.unsetIdRef();
sre.setPortRef("E_port");
sre2.setDeletion("oldrxn");
model.addSpecies(spec);
spec.setId("ES");
spec.unsetInitialConcentration();
sre.setPortRef("ES_port");
sre2.setDeletion("oldrxn");
model.addSpecies(spec);
//Synchronize the reactions
var rxn1plug = (CompSBasePlugin)(rxn.getPlugin("comp"));
var rxn2plug = (CompSBasePlugin)(rxn2.getPlugin("comp"));
var deletion = new ReplacedElement();
deletion.setDeletion("oldrxn");
deletion.setSubmodelRef("B");
rxn1plug.addReplacedElement(deletion);
rxn2plug.addReplacedElement(deletion);
var re2 = new ReplacedElement();
re2.setSubmodelRef("A");
re2.setPortRef("J0_port");
rxn1plug.addReplacedElement(re2);
re2.setPortRef("J1_port");
rxn2plug.addReplacedElement(re2);
model.addReaction(rxn);
model.addReaction(rxn2);
libsbml.writeSBMLToFile(document, "spec_example4.xml");
document = libsbml.readSBMLFromFile("spec_example4.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_example4_rt.xml");
}
return(retval);
}
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);
}
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);
//Create our submodel
var compdoc = (CompSBMLDocumentPlugin)(document.getPlugin("comp"));
compdoc.setRequired(true);
var mod1 = compdoc.createModelDefinition();
mod1.setId("enzyme");
mod1.setName("enzyme");
var comp = mod1.createCompartment();
comp.setSpatialDimensions(3);
comp.setConstant(true);
comp.setId("comp");
comp.setSize(1L);
var spec = new Species(3, 1);
spec.setCompartment("comp");
spec.setHasOnlySubstanceUnits(false);
spec.setConstant(false);
spec.setBoundaryCondition(false);
spec.setId("S");
mod1.addSpecies(spec);
spec.setId("E");
mod1.addSpecies(spec);
spec.setId("D");
mod1.addSpecies(spec);
spec.setId("ES");
mod1.addSpecies(spec);
var rxn = new Reaction(3, 1);
rxn.setReversible(true);
rxn.setFast(false);
var rxn2 = new Reaction(rxn);
rxn.setId("J0");
rxn2.setId("J1");
var sr = new SpeciesReference(3, 1);
sr.setConstant(true);
sr.setStoichiometry(1);
sr.setSpecies("S");
rxn.addReactant(sr);
sr.setSpecies("E");
rxn.addReactant(sr);
rxn2.addProduct(sr);
sr.setSpecies("ES");
rxn.addProduct(sr);
rxn2.addReactant(sr);
sr.setSpecies("D");
rxn2.addProduct(sr);
mod1.addReaction(rxn);
mod1.addReaction(rxn2);
// create the Model
var model = document.createModel();
model.setId("aggregate");
// Create a submodel
var mplugin = (CompModelPlugin)(model.getPlugin("comp"));
var submod1 = mplugin.createSubmodel();
submod1.setId("submod1");
submod1.setModelRef("enzyme");
var submod2 = new Submodel();
submod2.setId("submod2");
submod2.setModelRef("enzyme");
mplugin.addSubmodel(submod2);
libsbml.writeSBMLToFile(document, "enzyme_model.xml");
document = libsbml.readSBMLFromFile("enzyme_model.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, "enzyme_model_rt.xml");
}
return(retval);
}
public static int Main(string[] args)
{
int retval = 0;
SBMLNamespaces sbmlns = new SBMLNamespaces(3, 1, "comp", 1);
// create the document
SBMLDocument document = new SBMLDocument(sbmlns);
// create the Model
Model model = document.createModel();
// create a replacement parameter
Parameter parameter = model.createParameter();
parameter.setId("x");
parameter.setConstant(true);
// create a parameter to be a conversion factor
Parameter param2 = model.createParameter();
param2.setId("x_conv");
param2.setMetaId("_110013");
param2.setConstant(true);
// create a parameter to be a conversion factor
Parameter param3 = model.createParameter();
param3.setId("lcf");
param3.setConstant(true);
// Convert parameter to the plugin version so we can add the new attributes and replacements to it.
CompSBasePlugin splugin = (CompSBasePlugin)(parameter.getPlugin("comp"));
// Add a replaced element.
ReplacedElement rep1 = splugin.createReplacedElement();
int rv = rep1.setSubmodelRef("submod1");
rv = rep1.setConversionFactor("x_conv");
rv = rep1.setIdRef("param1");
// Add a second replaced element in a different way.
ReplacedElement rep2 = new ReplacedElement();
rv = rep2.setSubmodelRef("submod2");
rv = rep2.setDeletion("del1");
rv = splugin.addReplacedElement(rep2);
//Now create a replaced element that points into a submodel.
rep2.unsetDeletion();
rep2.setIdRef("submod2");
SBaseRef sbr5 = rep2.createSBaseRef();
sbr5.setIdRef("submodelG");
SBaseRef sbr6 = sbr5.createSBaseRef();
sbr6.setIdRef("buriedElement");
splugin.addReplacedElement(rep2);
// Create a submodel
CompModelPlugin mplugin = (CompModelPlugin)(model.getPlugin("comp"));
CompSBMLDocumentPlugin compdoc = (CompSBMLDocumentPlugin)(document.getPlugin("comp"));
compdoc.setRequired(true);
ModelDefinition moddef1 = compdoc.createModelDefinition();
moddef1.setId("Mod1");
Parameter m1param1 = moddef1.createParameter();
m1param1.setId("param1");
m1param1.setConstant(true);
Parameter m1param2 = moddef1.createParameter();
m1param2.setId("param2");
m1param2.setConstant(false);
m1param2.setValue(3.2);
ModelDefinition moddef2 = new ModelDefinition();
moddef2.setId("Mod2");
Parameter subparam2 = moddef2.createParameter();
subparam2.setId("subparam2");
subparam2.setConstant(false);
compdoc.addModelDefinition(moddef2);
ExternalModelDefinition extmod1 = compdoc.createExternalModelDefinition();
extmod1.setId("ExtMod1");
extmod1.setSource("urn:miriam:biomodels.db:BIOMD0000000127");
ExternalModelDefinition extmod2 = new ExternalModelDefinition();
extmod2.setId("ExtMod2");
extmod2.setSource("otherfile.xml");
extmod2.setModelRef("modelnamethere");
extmod2.setMd5("406022s908ge74sklj");
compdoc.addExternalModelDefinition(extmod2);
Submodel submod1 = mplugin.createSubmodel();
submod1.setId("submod1");
submod1.setModelRef("Mod1");
Deletion del1 = submod1.createDeletion();
del1.setId("deletionA");
del1.setIdRef("param2");
Submodel submod2 = new Submodel();
submod2.setId("submod2");
submod2.setModelRef("ExtMod1");
submod2.setSubstanceConversionFactor("subcf");
submod2.setTimeConversionFactor("tcf");
submod2.setExtentConversionFactor("xtf");
Deletion del2 = new Deletion();
del2.setId("deletionB");
del2.setMetaIdRef("_0010110");
rv = submod2.addDeletion(del2);
del2.setId("deletionC");
del2.unsetMetaIdRef();
del2.setPortRef("port2");
rv = submod2.addDeletion(del2);
del2.unsetId();
del2.unsetPortRef();
del2.setUnitRef("mph");
rv = submod2.addDeletion(del2);
del2.unsetUnitRef();
del2.setIdRef("submodG");
SBaseRef sbr = del2.createSBaseRef();
sbr.setIdRef("element5");
rv = submod2.addDeletion(del2);
Deletion del3 = new Deletion();
del3.setIdRef("submodG");
SBaseRef sbr2 = new SBaseRef();
sbr2.setIdRef("subsubmodQ");
SBaseRef subsbr = sbr2.createSBaseRef();
subsbr.setPortRef("toBdel");
del3.setSBaseRef(sbr2);
submod2.addDeletion(del3);
mplugin.addSubmodel(submod2);
Port port1 = mplugin.createPort();
port1.setId("port1");
port1.setMetaIdRef("_110013");
Port port2 = new Port();
port2.setId("port2");
port2.setIdRef("x");
mplugin.addPort(port2);
port2.setId("port3");
port2.setIdRef("submod2");
port2.setSBaseRef(sbr2);
mplugin.addPort(port2);
libsbml.writeSBMLToFile(document, "comp_example1.xml");
document = libsbml.readSBMLFromFile("comp_example1.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)
{
OStringStream stream = new OStringStream();
document.printErrors(stream);
Console.WriteLine("Errors encoutered when round-tripping SBML file: \n" +
stream.str());
retval = -1;
}
libsbml.writeSBMLToFile(document, "comp_example1_rt.xml");
}
return(retval);
}
static void Main(string[] args)
{
SBMLNamespaces sbmlns = new SBMLNamespaces(3, 1, "multi", 1);
// create the document
SBMLDocument document = new SBMLDocument(sbmlns);
// set the required attribute to true
SBMLDocumentPlugin docPlug =
(SBMLDocumentPlugin)(document.getPlugin("multi"));
docPlug.setRequired(true);
// create the Model
Model model = document.createModel();
// create the compartments
Compartment c = model.createCompartment();
c.setId("membrane");
c.setConstant(true);
// set the multi attribute isType via the compartmentPlugin
MultiCompartmentPlugin compPlug =
(MultiCompartmentPlugin)(c.getPlugin("multi"));
compPlug.setIsType(true);
// create the speciesTypes
MultiModelPlugin modelPlug =
(MultiModelPlugin)(model.getPlugin("multi"));
MultiSpeciesType st = modelPlug.createMultiSpeciesType();
st.setId("stX");
st.setCompartment("membrane");
// create species
Species s = model.createSpecies();
s.setId("s1");
s.setCompartment("membrane");
s.setBoundaryCondition(false);
s.setHasOnlySubstanceUnits(false);
s.setConstant(false);
// set the multi attribute speciesType via the compartmentPlugin
MultiSpeciesPlugin spPlug =
(MultiSpeciesPlugin)(s.getPlugin("multi"));
spPlug.setSpeciesType("stX");
// create species feature
SpeciesFeature sf = spPlug.createSpeciesFeature();
sf.setSpeciesFeatureType("a");
sf.setOccur(1);
sf.setComponent("b");
SpeciesFeatureValue sfv = sf.createSpeciesFeatureValue();
sfv.setValue("c");
// create a subListOfSpeciesFeatures
SubListOfSpeciesFeatures subloSF = spPlug.createSubListOfSpeciesFeatures();
subloSF.setRelation(libsbml.Relation_fromString("and"));
// add speciesFeatures to the subList
SpeciesFeature sf1 = new SpeciesFeature(3, 1, 1);
sf1.setSpeciesFeatureType("a1");
sf1.setOccur(1);
sf1.setComponent("b1");
SpeciesFeatureValue sfv1 = sf1.createSpeciesFeatureValue();
sfv1.setValue("c1");
subloSF.appendAndOwn(sf1);
sf1 = new SpeciesFeature(3, 1, 1);
sf1.setSpeciesFeatureType("a2");
sf1.setOccur(1);
sf1.setComponent("b2");
sfv1 = sf1.createSpeciesFeatureValue();
sfv1.setValue("c2");
subloSF.appendAndOwn(sf1);
// create a second subListOfSpeciesfeatures
subloSF = spPlug.createSubListOfSpeciesFeatures();
subloSF.setRelation(libsbml.Relation_fromString("or"));
sf1 = new SpeciesFeature(3, 1, 1);
sf1.setSpeciesFeatureType("a3");
sf1.setOccur(1);
sf1.setComponent("b3");
sfv1 = sf1.createSpeciesFeatureValue();
sfv1.setValue("c3");
subloSF.appendAndOwn(sf1);
sf1 = new SpeciesFeature(3, 1, 1);
sf1.setSpeciesFeatureType("a4");
sf1.setOccur(1);
sf1.setComponent("b4");
sfv1 = sf1.createSpeciesFeatureValue();
sfv1.setValue("c4");
subloSF.appendAndOwn(sf1);
libsbml.writeSBML(document, "multi_example3.xml");
}
public static void Main(string[] args)
{
//
// Creates an SBMLNamespaces object with the given SBML level, version
// package name, package version.
//
// (NOTE) By defualt, the name of package (i.e. "groups") will be used
// if the arugment for the prefix is missing or empty. Thus the argument
// for the prefix can be added as follows:
//
// SBMLNamespaces sbmlns(3,1,"groups",1,"GROUP");
//
SBMLNamespaces sbmlns = new SBMLNamespaces(3, 1, "groups", 1);
//
// (NOTES) The above code creating an SBMLNamespaces object can be replaced
// with one of the following other styles.
//
// (1) Creates an SBMLNamespace object with a SBML core namespace and then
// adds a groups package namespace to the object.
//
// SBMLNamespaces sbmlns(3,1);
// sbmlns.addPkgNamespace("groups",1);
//
// OR
//
// SBMLNamespaces sbmlns(3,1);
// sbmlns.addNamespace(GroupsExtension::XmlnsL3V1V1,"groups");
//
// (2) Creates a GroupsPkgNamespaces object (SBMLNamespace derived class for
// groups package. The class is basically used for createing an SBase derived
// objects defined in the groups package) with the given SBML level, version,
// and package version
//
// GroupsPkgNamespaces sbmlns(3,1,1);
//
// create the document
SBMLDocument document = new SBMLDocument(sbmlns);
// create the Model
Model model = document.createModel();
// create the Compartment
Compartment compartment = model.createCompartment();
compartment.setId("cytosol");
compartment.setConstant(true);
compartment = model.createCompartment();
compartment.setId("mitochon");
compartment.setConstant(true);
// create the Species
Species species = model.createSpecies();
species.setId("ATPc");
species.setCompartment("cytosol");
species.setInitialConcentration(1);
species.setHasOnlySubstanceUnits(false);
species.setBoundaryCondition(false);
species.setConstant(false);
species = model.createSpecies();
species.setId("ATPm");
species.setCompartment("mitochon");
species.setInitialConcentration(2);
species.setHasOnlySubstanceUnits(false);
species.setBoundaryCondition(false);
species.setConstant(false);
// create the Groups
//
// Get a GroupsModelPlugin 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.
//
GroupsModelPlugin mplugin = (GroupsModelPlugin)(model.getPlugin("groups"));
//
// Creates a Group object via GroupsModelPlugin object.
//
Group group = mplugin.createGroup();
group.setId("ATP");
group.setKind(libsbml.GROUP_KIND_CLASSIFICATION);
group.setSBOTerm("SBO:0000252");
Member member = group.createMember();
member.setIdRef("ATPc");
member = group.createMember();
member.setIdRef("ATPm");
libsbml.writeSBML(document, "groups_example1-cs.xml");
}
public static void Main(string[] args)
{
ArraysPkgNamespaces arraysNs = new ArraysPkgNamespaces();
SBMLDocument doc = new SBMLDocument(arraysNs);
doc.setPackageRequired("arrays", true);
Model model = doc.createModel();
// create compartment
Compartment comp = model.createCompartment();
comp.setMetaId("dd");
comp.setId("s");
comp.setConstant(true);
// set dimensions
ArraysSBasePlugin compPlugin = (ArraysSBasePlugin)comp.getPlugin("arrays");
Dimension dim = compPlugin.createDimension();
dim.setId("i");
dim.setSize("n");
// create species
Species species = model.createSpecies();
species.setId("A");
species.setCompartment("s");
species.setHasOnlySubstanceUnits(false);
species.setBoundaryCondition(false);
species.setConstant(false);
ArraysSBasePlugin splugin = (ArraysSBasePlugin)species.getPlugin("arrays");
dim = splugin.createDimension();
dim.setId("i");
dim.setSize("n");
species = model.createSpecies();
species.setId("B");
species.setCompartment("s");
species.setHasOnlySubstanceUnits(false);
species.setBoundaryCondition(false);
species.setConstant(false);
splugin = (ArraysSBasePlugin)species.getPlugin("arrays");
dim = splugin.createDimension();
dim.setId("i");
dim.setSize("n");
species = model.createSpecies();
species.setId("C");
species.setCompartment("s");
species.setHasOnlySubstanceUnits(false);
species.setBoundaryCondition(false);
species.setConstant(false);
splugin = (ArraysSBasePlugin)species.getPlugin("arrays");
dim = splugin.createDimension();
dim.setId("i");
dim.setSize("n");
// create parameter
Parameter param = model.createParameter();
param.setId("n");
param.setValue(100);
param.setConstant(true);
// create reaction
Reaction reaction = model.createReaction();
reaction.setId("reaction1");
reaction.setReversible(false);
reaction.setFast(false);
ArraysSBasePlugin reactionPlugin = (ArraysSBasePlugin)reaction.getPlugin("arrays");
dim = reactionPlugin.createDimension();
dim.setId("i");
dim.setSize("n");
SpeciesReference speciesRef = reaction.createReactant();
speciesRef.setSpecies("A");
speciesRef.setConstant(false);
ArraysSBasePlugin refPlugin = (ArraysSBasePlugin)speciesRef.getPlugin("arrays");
Index index = refPlugin.createIndex();
ASTNode ast = new ASTNode(libsbml.AST_LINEAR_ALGEBRA_SELECTOR);
ASTNode ci = new ASTNode(libsbml.AST_NAME);
ci.setName("A");
ast.addChild(ci);
ci = new ASTNode(libsbml.AST_NAME);
ci.setName("i");
ast.addChild(ci);
index.setMath(ast);
speciesRef = reaction.createProduct();
speciesRef.setSpecies("C");
speciesRef.setConstant(false);
refPlugin = (ArraysSBasePlugin)speciesRef.getPlugin("arrays");
index = refPlugin.createIndex();
ast = new ASTNode(libsbml.AST_LINEAR_ALGEBRA_SELECTOR);
ci = new ASTNode(libsbml.AST_NAME);
ci.setName("C");
ast.addChild(ci);
ci = new ASTNode(libsbml.AST_NAME);
ci.setName("i");
ast.addChild(ci);
index.setMath(ast);
libsbml.writeSBMLToFile(doc, "arrays1.xml");
}
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);
}
}