END_TEST
START_TEST (test_SBMLConvert_addModifiersToReaction)
{
SBMLDocument_t *d = SBMLDocument_createWithLevelAndVersion(1, 2);
Model_t *m = SBMLDocument_createModel(d);
Reaction_t *r = Model_createReaction(m);
KineticLaw_t *kl = Reaction_createKineticLaw(r);
KineticLaw_setFormula(kl, "k1*S1*S2*S3*S4*S5");
SpeciesReference_t *ssr1;
SpeciesReference_t *ssr2;
Species_t *s1 = Model_createSpecies( m );
Species_setId( s1, "S1" );
Species_t *s2 = Model_createSpecies( m );
Species_setId( s2, "S2");
Species_t *s3 = Model_createSpecies( m );
Species_setId( s3, "S3");
Species_t *s4 = Model_createSpecies( m );
Species_setId( s4, "S4");
Species_t *s5 = Model_createSpecies( m );
Species_setId( s5, "S5");
SpeciesReference_t *sr1 = Reaction_createReactant( r );
SpeciesReference_t *sr2 = Reaction_createReactant( r );
SpeciesReference_t *sr3 = Reaction_createProduct ( r );
SpeciesReference_setSpecies(sr1, "S1");
SpeciesReference_setSpecies(sr2, "S2");
SpeciesReference_setSpecies(sr3, "S5");
fail_unless( Reaction_getNumModifiers(r) == 0, NULL );
fail_unless( SBMLDocument_setLevelAndVersionNonStrict(d, 2, 1) == 1, NULL );
fail_unless( SBMLDocument_getLevel (d) == 2, NULL );
fail_unless( SBMLDocument_getVersion(d) == 1, NULL );
fail_unless( Reaction_getNumModifiers(Model_getReaction(m, 0)) == 2, NULL );
ssr1 = (SpeciesReference_t *) Reaction_getModifier(Model_getReaction(m, 0), 0);
ssr2 = (SpeciesReference_t *) Reaction_getModifier(Model_getReaction(m, 0), 1);
fail_unless( !strcmp(SpeciesReference_getSpecies(ssr1), "S3"), NULL );
fail_unless( !strcmp(SpeciesReference_getSpecies(ssr2), "S4"), NULL );
SBMLDocument_free(d);
}
END_TEST
START_TEST (test_Reaction_removeReactant)
{
SpeciesReference_t *o1, *o2, *o3;
o1 = Reaction_createReactant(R);
o2 = Reaction_createReactant(R);
o3 = Reaction_createReactant(R);
SpeciesReference_setSpecies(o3,"test");
fail_unless( Reaction_removeReactant(R,0) == o1 );
fail_unless( Reaction_getNumReactants(R) == 2 );
fail_unless( Reaction_removeReactant(R,0) == o2 );
fail_unless( Reaction_getNumReactants(R) == 1 );
fail_unless( Reaction_removeReactantBySpecies(R,"test") == o3 );
fail_unless( Reaction_getNumReactants(R) == 0 );
SpeciesReference_free(o1);
SpeciesReference_free(o2);
SpeciesReference_free(o3);
}
END_TEST
START_TEST (test_Reaction_createReactant)
{
Reaction_t *m = Reaction_create(2, 2);
SpeciesReference_t *p = Reaction_createReactant(m);
fail_unless( Reaction_getNumReactants(m) == 1);
fail_unless( SBase_getLevel((SBase_t *) (p)) == 2 );
fail_unless( SBase_getVersion((SBase_t *) (p)) == 2 );
Reaction_free(m);
}
END_TEST
START_TEST (test_SBMLConvert_convertToL3_stoichiometryMath)
{
SBMLDocument_t *d = SBMLDocument_createWithLevelAndVersion(2, 1);
Model_t *m = SBMLDocument_createModel(d);
Compartment_t *c = Model_createCompartment(m);
Compartment_setId ( c, "c" );
Species_t *s = Model_createSpecies(m);
Species_setId(s, "s");
Species_setCompartment(s, "c");
Reaction_t * r = Model_createReaction(m);
SpeciesReference_t *sr = Reaction_createReactant(r);
SpeciesReference_setSpecies(sr, "s");
StoichiometryMath_t *sm = SpeciesReference_createStoichiometryMath(sr);
ASTNode_t * ast = SBML_parseFormula("c*2");
StoichiometryMath_setMath(sm, ast);
fail_unless(Model_getNumRules(m) == 0);
fail_unless(SpeciesReference_isSetId(sr) == 0);
fail_unless( SBMLDocument_setLevelAndVersionNonStrict(d, 3, 1) == 1);
m = SBMLDocument_getModel(d);
r = Model_getReaction(m, 0);
sr = Reaction_getReactant(r, 0);
fail_unless(Model_getNumRules(m) == 1);
fail_unless(SpeciesReference_isSetId(sr) == 1);
Rule_t *rule = Model_getRule(m, 0);
fail_unless( strcmp(SpeciesReference_getId(sr), Rule_getVariable(rule)) == 0 );
SBMLDocument_free(d);
}
END_TEST
START_TEST (test_SBMLConvert_convertToL3_reactant)
{
SBMLDocument_t *d = SBMLDocument_createWithLevelAndVersion(2, 2);
Model_t *m = SBMLDocument_createModel(d);
Reaction_t *r = Model_createReaction(m);
SpeciesReference_t *sr = Reaction_createReactant(r);
SpeciesReference_t *sr1;
SpeciesReference_setSpecies ( sr, "s" );
fail_unless( SBMLDocument_setLevelAndVersionNonStrict(d, 3, 1) == 1, NULL);
sr1 = Reaction_getReactant(Model_getReaction(m, 0), 0);
fail_unless(SpeciesReference_hasRequiredAttributes(sr1) == 1);
SBMLDocument_free(d);
}
END_TEST
START_TEST (test_SBMLConvert_convertToL3_localParameters)
{
SBMLDocument_t *d = SBMLDocument_createWithLevelAndVersion(1, 2);
Model_t *m = SBMLDocument_createModel(d);
Compartment_t *c = Model_createCompartment(m);
Compartment_setId ( c, "c" );
Species_t *s = Model_createSpecies(m);
Species_setId(s, "s");
Species_setCompartment(s, "c");
Reaction_t * r = Model_createReaction(m);
SpeciesReference_t *sr = Reaction_createReactant(r);
SpeciesReference_setSpecies(sr, "s");
KineticLaw_t *kl = Reaction_createKineticLaw(r);
KineticLaw_setFormula(kl, "s*k");
Parameter_t *p = KineticLaw_createParameter(kl);
Parameter_setId(p, "k");
fail_unless(KineticLaw_getNumLocalParameters(kl) == 0);
fail_unless( SBMLDocument_setLevelAndVersionNonStrict(d, 3, 1) == 1 );
m = SBMLDocument_getModel(d);
r = Model_getReaction(m,0);
kl = Reaction_getKineticLaw(r);
fail_unless(KineticLaw_getNumLocalParameters(kl) == 1);
LocalParameter_t *lp = KineticLaw_getLocalParameter(kl, 0);
SBMLDocument_free(d);
}
LIBSBML_CPP_NAMESPACE_USE
int main(int argc,char** argv)
{
int retval = 0;
XMLNamespaces_t * comp;
SBMLNamespaces_t * sbmlns;
SBMLDocument_t * doc;
Compartment_t * c;
Species_t * s1;
Species_t * s2;
Species_t * s3;
Species_t * s4;
Reaction_t * r1;
Reaction_t * r2;
SpeciesReference_t *sr1;
SpeciesReference_t *sr2;
SpeciesReference_t *sr3;
SpeciesReference_t *sr4;
SpeciesReference_t *sr5;
SpeciesReference_t *sr6;
Model_t * model;
CompSBMLDocumentPlugin_t * docPlug;
CompModelPlugin_t *modelPlug;
Submodel_t * sub1;
Submodel_t * sub2;
ModelDefinition_t * modDef;
/* get comp registry entry */
SBMLExtension_t *sbmlext = SBMLExtensionRegistry_getExtension("comp");
/* create the sbml namespaces object with comp */
comp = XMLNamespaces_create();
XMLNamespaces_add(comp, SBMLExtension_getURI(sbmlext, 3, 1, 1), "comp");
sbmlns = SBMLNamespaces_create(3, 1);
SBMLNamespaces_addNamespaces(sbmlns, comp);
/* create the document */
doc = SBMLDocument_createWithSBMLNamespaces(sbmlns);
/* set the comp reqd attribute to true */
docPlug = (CompSBMLDocumentPlugin_t * )(SBase_getPlugin((SBase_t*)(doc), "comp"));
SBMLDocumentPlugin_setRequired((SBMLDocumentPlugin_t*)(docPlug), 1);
/* create the submodel */
modDef = CompSBMLDocumentPlugin_createModelDefinition(docPlug);
Model_setId((Model_t*)(modDef), "enzyme");
Model_setName((Model_t*)(modDef), "enzyme");
c = Model_createCompartment((Model_t*)(modDef));
Compartment_setId(c, "comp");
Compartment_setConstant(c, 1);
Compartment_setSize(c, 1.0);
Compartment_setSpatialDimensions(c, 3);
s1 = Model_createSpecies((Model_t*)(modDef));
Species_setId(s1, "S");
Species_setCompartment(s1, "comp");
Species_setHasOnlySubstanceUnits(s1, 0);
Species_setBoundaryCondition(s1, 0);
Species_setConstant(s1, 0);
s2 = Model_createSpecies((Model_t*)(modDef));
Species_setId(s2, "E");
Species_setCompartment(s2, "comp");
Species_setHasOnlySubstanceUnits(s2, 0);
Species_setBoundaryCondition(s2, 0);
Species_setConstant(s2, 0);
s3 = Model_createSpecies((Model_t*)(modDef));
Species_setId(s3, "D");
Species_setCompartment(s3, "comp");
Species_setHasOnlySubstanceUnits(s3, 0);
Species_setBoundaryCondition(s3, 0);
Species_setConstant(s3, 0);
s4 = Model_createSpecies((Model_t*)(modDef));
Species_setId(s4, "ES");
Species_setCompartment(s4, "comp");
Species_setHasOnlySubstanceUnits(s4, 0);
Species_setBoundaryCondition(s4, 0);
Species_setConstant(s4, 0);
r1 = Model_createReaction((Model_t*)(modDef));
Reaction_setId(r1, "J0");
Reaction_setReversible(r1, 1);
Reaction_setFast(r1, 0);
sr1 = Reaction_createReactant(r1);
SpeciesReference_setSpecies(sr1, "S");
SpeciesReference_setStoichiometry(sr1, 1.0);
SpeciesReference_setConstant(sr1, 1);
sr2 = Reaction_createReactant(r1);
SpeciesReference_setSpecies(sr2, "E");
SpeciesReference_setStoichiometry(sr2, 1.0);
SpeciesReference_setConstant(sr2, 1);
sr3 = Reaction_createProduct(r1);
SpeciesReference_setSpecies(sr3, "ES");
SpeciesReference_setStoichiometry(sr3, 1.0);
SpeciesReference_setConstant(sr3, 1);
r2 = Model_createReaction((Model_t*)(modDef));
Reaction_setId(r2, "J1");
Reaction_setReversible(r2, 1);
Reaction_setFast(r2, 0);
sr4 = Reaction_createProduct(r2);
SpeciesReference_setSpecies(sr4, "E");
SpeciesReference_setStoichiometry(sr4, 1.0);
SpeciesReference_setConstant(sr4, 1);
sr5 = Reaction_createReactant(r2);
SpeciesReference_setSpecies(sr5, "ES");
SpeciesReference_setStoichiometry(sr5, 1.0);
SpeciesReference_setConstant(sr5, 1);
sr6 = Reaction_createProduct(r2);
SpeciesReference_setSpecies(sr6, "D");
SpeciesReference_setStoichiometry(sr6, 1.0);
SpeciesReference_setConstant(sr6, 1);
/* create the model */
model = SBMLDocument_createModel(doc);
Model_setId(model, "aggregate");
/* add the submodels*/
modelPlug = (CompModelPlugin_t*)(SBase_getPlugin((SBase_t *)(model), "comp"));
sub1 = CompModelPlugin_createSubmodel(modelPlug);
Submodel_setId(sub1, "submod1");
Submodel_setModelRef(sub1, "enzyme");
sub2 = CompModelPlugin_createSubmodel(modelPlug);
Submodel_setId(sub2, "submod2");
Submodel_setModelRef(sub2, "enzyme");
/* write the file */
writeSBMLToFile(doc, "enzyme_model.xml");
return retval;
}
LIBSBML_CPP_NAMESPACE_USE
int main(int argc,char** argv)
{
int retval = 0;
XMLNamespaces_t * fbc;
SBMLNamespaces_t * sbmlns;
SBMLDocument_t * doc;
Compartment_t * compartment;
Species_t * species;
Reaction_t * reaction;
SpeciesReference_t *reactant;
SpeciesReference_t *product;
Model_t * model;
SBMLDocumentPlugin_t * docPlug;
SBasePlugin_t * modelPlug;
FluxBound_t * fluxBound;
Objective_t * objective;
FluxObjective_t * fluxObjective;
/* get fbc registry entry */
SBMLExtension_t *sbmlext = SBMLExtensionRegistry_getExtension("fbc");
/* create the sbml namespaces object with fbc */
fbc = XMLNamespaces_create();
XMLNamespaces_add(fbc, SBMLExtension_getURI(sbmlext, 3, 1, 1), "fbc");
sbmlns = SBMLNamespaces_create(3, 1);
SBMLNamespaces_addNamespaces(sbmlns, fbc);
/* create the document */
doc = SBMLDocument_createWithSBMLNamespaces(sbmlns);
/* set the fbc reqd attribute to false */
docPlug = (SBMLDocumentPlugin_t*)(SBase_getPlugin((SBase_t*)(doc), "fbc"));
SBMLDocumentPlugin_setRequired(docPlug, 0);
// create the Model
model = SBMLDocument_createModel(doc);
// create the Compartment
compartment = Model_createCompartment(model);
Compartment_setId(compartment, "compartment");
Compartment_setConstant(compartment, 1);
Compartment_setSize(compartment, 1);
// create the Species
species = Model_createSpecies(model);
Species_setId(species, "Node1");
Species_setCompartment(species, "compartment");
Species_setBoundaryCondition(species, 0);
Species_setConstant(species, 0);
Species_setHasOnlySubstanceUnits(species, 0);
species = Model_createSpecies(model);
Species_setId(species, "Node2");
Species_setCompartment(species, "compartment");
Species_setBoundaryCondition(species, 0);
Species_setConstant(species, 0);
Species_setHasOnlySubstanceUnits(species, 0);
species = Model_createSpecies(model);
Species_setId(species, "Node3");
Species_setCompartment(species, "compartment");
Species_setBoundaryCondition(species, 0);
Species_setConstant(species, 0);
Species_setHasOnlySubstanceUnits(species, 0);
species = Model_createSpecies(model);
Species_setId(species, "Node4");
Species_setCompartment(species, "compartment");
Species_setBoundaryCondition(species, 0);
Species_setConstant(species, 0);
Species_setHasOnlySubstanceUnits(species, 0);
species = Model_createSpecies(model);
Species_setId(species, "Node5");
Species_setCompartment(species, "compartment");
Species_setBoundaryCondition(species, 0);
Species_setConstant(species, 0);
Species_setHasOnlySubstanceUnits(species, 0);
species = Model_createSpecies(model);
Species_setId(species, "Node6");
Species_setCompartment(species, "compartment");
Species_setBoundaryCondition(species, 0);
Species_setConstant(species, 0);
Species_setHasOnlySubstanceUnits(species, 0);
species = Model_createSpecies(model);
Species_setId(species, "Node7");
Species_setCompartment(species, "compartment");
Species_setBoundaryCondition(species, 0);
Species_setConstant(species, 0);
Species_setHasOnlySubstanceUnits(species, 0);
species = Model_createSpecies(model);
Species_setId(species, "Node8");
Species_setCompartment(species, "compartment");
Species_setBoundaryCondition(species, 0);
Species_setConstant(species, 0);
Species_setHasOnlySubstanceUnits(species, 0);
species = Model_createSpecies(model);
Species_setId(species, "Node0");
Species_setCompartment(species, "compartment");
Species_setBoundaryCondition(species, 1);
Species_setConstant(species, 0);
Species_setHasOnlySubstanceUnits(species, 0);
species = Model_createSpecies(model);
Species_setId(species, "Node9");
Species_setCompartment(species, "compartment");
Species_setBoundaryCondition(species, 1);
Species_setConstant(species, 0);
Species_setHasOnlySubstanceUnits(species, 0);
// create the Reactions
reaction = Model_createReaction(model);
Reaction_setId(reaction, "J0");
Reaction_setReversible(reaction, 0);
Reaction_setFast(reaction, 0);
reactant = Reaction_createReactant(reaction);
SpeciesReference_setSpecies(reactant, "Node0");
SpeciesReference_setStoichiometry(reactant, 1);
SpeciesReference_setConstant(reactant, 1);
product = Reaction_createProduct(reaction);
SpeciesReference_setSpecies(product, "Node1");
SpeciesReference_setStoichiometry(product, 1);
SpeciesReference_setConstant(product, 1);
reaction = Model_createReaction(model);
Reaction_setId(reaction, "J1");
Reaction_setReversible(reaction, 0);
Reaction_setFast(reaction, 0);
reactant = Reaction_createReactant(reaction);
SpeciesReference_setSpecies(reactant, "Node1");
SpeciesReference_setStoichiometry(reactant, 1);
SpeciesReference_setConstant(reactant, 1);
product = Reaction_createProduct(reaction);
SpeciesReference_setSpecies(product, "Node2");
SpeciesReference_setStoichiometry(product, 1);
SpeciesReference_setConstant(product, 1);
reaction = Model_createReaction(model);
Reaction_setId(reaction, "J2");
Reaction_setReversible(reaction, 0);
Reaction_setFast(reaction, 0);
reactant = Reaction_createReactant(reaction);
SpeciesReference_setSpecies(reactant, "Node2");
SpeciesReference_setStoichiometry(reactant, 1);
SpeciesReference_setConstant(reactant, 1);
product = Reaction_createProduct(reaction);
SpeciesReference_setSpecies(product, "Node3");
SpeciesReference_setStoichiometry(product, 1);
SpeciesReference_setConstant(product, 1);
reaction = Model_createReaction(model);
Reaction_setId(reaction, "J3");
Reaction_setReversible(reaction, 0);
Reaction_setFast(reaction, 0);
reactant = Reaction_createReactant(reaction);
SpeciesReference_setSpecies(reactant, "Node1");
SpeciesReference_setStoichiometry(reactant, 1);
SpeciesReference_setConstant(reactant, 1);
product = Reaction_createProduct(reaction);
SpeciesReference_setSpecies(product, "Node4");
SpeciesReference_setStoichiometry(product, 1);
SpeciesReference_setConstant(product, 1);
reaction = Model_createReaction(model);
Reaction_setId(reaction, "J4");
Reaction_setReversible(reaction, 0);
Reaction_setFast(reaction, 0);
reactant = Reaction_createReactant(reaction);
SpeciesReference_setSpecies(reactant, "Node4");
SpeciesReference_setStoichiometry(reactant, 1);
SpeciesReference_setConstant(reactant, 1);
product = Reaction_createProduct(reaction);
SpeciesReference_setSpecies(product, "Node3");
SpeciesReference_setStoichiometry(product, 1);
SpeciesReference_setConstant(product, 1);
reaction = Model_createReaction(model);
Reaction_setId(reaction, "J5");
Reaction_setReversible(reaction, 0);
Reaction_setFast(reaction, 0);
reactant = Reaction_createReactant(reaction);
SpeciesReference_setSpecies(reactant, "Node3");
SpeciesReference_setStoichiometry(reactant, 1);
SpeciesReference_setConstant(reactant, 1);
product = Reaction_createProduct(reaction);
SpeciesReference_setSpecies(product, "Node5");
SpeciesReference_setStoichiometry(product, 1);
SpeciesReference_setConstant(product, 1);
reaction = Model_createReaction(model);
Reaction_setId(reaction, "J6");
Reaction_setReversible(reaction, 0);
Reaction_setFast(reaction, 0);
reactant = Reaction_createReactant(reaction);
SpeciesReference_setSpecies(reactant, "Node5");
SpeciesReference_setStoichiometry(reactant, 1);
SpeciesReference_setConstant(reactant, 1);
product = Reaction_createProduct(reaction);
SpeciesReference_setSpecies(product, "Node6");
SpeciesReference_setStoichiometry(product, 1);
SpeciesReference_setConstant(product, 1);
reaction = Model_createReaction(model);
Reaction_setId(reaction, "J7");
Reaction_setReversible(reaction, 0);
Reaction_setFast(reaction, 0);
reactant = Reaction_createReactant(reaction);
SpeciesReference_setSpecies(reactant, "Node6");
SpeciesReference_setStoichiometry(reactant, 1);
SpeciesReference_setConstant(reactant, 1);
product = Reaction_createProduct(reaction);
SpeciesReference_setSpecies(product, "Node7");
SpeciesReference_setStoichiometry(product, 1);
SpeciesReference_setConstant(product, 1);
reaction = Model_createReaction(model);
Reaction_setId(reaction, "J8");
Reaction_setReversible(reaction, 0);
Reaction_setFast(reaction, 0);
reactant = Reaction_createReactant(reaction);
SpeciesReference_setSpecies(reactant, "Node5");
SpeciesReference_setStoichiometry(reactant, 1);
SpeciesReference_setConstant(reactant, 1);
product = Reaction_createProduct(reaction);
SpeciesReference_setSpecies(product, "Node8");
SpeciesReference_setStoichiometry(product, 1);
SpeciesReference_setConstant(product, 1);
reaction = Model_createReaction(model);
Reaction_setId(reaction, "J9");
Reaction_setReversible(reaction, 0);
Reaction_setFast(reaction, 0);
reactant = Reaction_createReactant(reaction);
SpeciesReference_setSpecies(reactant, "Node8");
SpeciesReference_setStoichiometry(reactant, 1);
SpeciesReference_setConstant(reactant, 1);
product = Reaction_createProduct(reaction);
SpeciesReference_setSpecies(product, "Node7");
SpeciesReference_setStoichiometry(product, 1);
SpeciesReference_setConstant(product, 1);
reaction = Model_createReaction(model);
Reaction_setId(reaction, "J10");
Reaction_setReversible(reaction, 0);
Reaction_setFast(reaction, 0);
reactant = Reaction_createReactant(reaction);
SpeciesReference_setSpecies(reactant, "Node7");
SpeciesReference_setStoichiometry(reactant, 1);
SpeciesReference_setConstant(reactant, 1);
product = Reaction_createProduct(reaction);
SpeciesReference_setSpecies(product, "Node9");
SpeciesReference_setStoichiometry(product, 1);
SpeciesReference_setConstant(product, 1);
// Get a SBasePlugin_t object plugged in the model object.
modelPlug = SBase_getPlugin((SBase_t *)(model), "fbc");
// create the fluxBound object and add it to model plugin
fluxBound = FluxBound_create(3, 1, 1);
FluxBound_setId(fluxBound, "bound1");
FluxBound_setReaction(fluxBound, "J0");
FluxBound_setOperation(fluxBound, "equal");
FluxBound_setValue(fluxBound, 10);
FbcModelPlugin_addFluxBound(modelPlug, fluxBound);
// create the objective object and add it to model plugin
objective = Objective_create(3, 1, 1);
Objective_setId(objective, "obj1");
Objective_setType(objective, "maximize");
fluxObjective = Objective_createFluxObjective(objective);
FluxObjective_setReaction(fluxObjective, "J8");
FluxObjective_setCoefficient(fluxObjective, 1);
FbcModelPlugin_addObjective(modelPlug, objective);
// mark obj1 as active objective
FbcModelPlugin_setActiveObjectiveId(modelPlug, "obj1");
/* write the file */
writeSBMLToFile(doc, "fbc_example1.xml");
return retval;
}
