コード例 #1
0
END_TEST


START_TEST(test_Reaction_reversible)
{
  // defaults
  fail_unless(Reaction_isSetReversible(R) == 1);
  fail_unless(Reaction_getReversible(R) == 1);

  Reaction_setReversible(R, 1);

  fail_unless(Reaction_isSetReversible(R) == 1);
  fail_unless(Reaction_getReversible(R) == 1);

  int ret = Reaction_unsetReversible(R);

  fail_unless(ret == LIBSBML_UNEXPECTED_ATTRIBUTE);
  fail_unless(Reaction_isSetReversible(R) == 1);
  fail_unless(Reaction_getReversible(R) == 1);

  Reaction_setReversible(R, 0);

  fail_unless(Reaction_isSetReversible(R) == 1);
  fail_unless(Reaction_getReversible(R) == 0);

  ret = Reaction_unsetReversible(R);

  fail_unless(ret == LIBSBML_UNEXPECTED_ATTRIBUTE);
  fail_unless(Reaction_isSetReversible(R) == 1);
  fail_unless(Reaction_getReversible(R) == 1);
}
コード例 #2
0
END_TEST


START_TEST (test_Reaction_setReversible1)
{
  int i = Reaction_setReversible(R, 1);

  fail_unless( i == LIBSBML_OPERATION_SUCCESS );
  fail_unless( Reaction_getReversible(R) == 1 );

  i = Reaction_setReversible(R, 0);

  fail_unless( i == LIBSBML_OPERATION_SUCCESS );
  fail_unless( Reaction_getReversible(R) == 0 );
}
コード例 #3
0
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;
}
コード例 #4
0
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;
}