END_TEST


START_TEST (test_Reaction_addProductBySpecies)
{
  Species_t *s = Species_create(2, 4);
  Species_setId(s, "s");
  Reaction_addProductBySpecies(R, s, 2.0, "sr", 0);

  fail_unless( Reaction_getNumReactants(R) == 0 );
  fail_unless( Reaction_getNumProducts (R) == 1 );
  fail_unless( Reaction_getNumModifiers(R) == 0 );

  SpeciesReference_t *sr = Reaction_getProduct(R, 0);

  fail_unless(!strcmp(SpeciesReference_getSpecies(sr), "s"));
  fail_unless(util_isEqual(SpeciesReference_getStoichiometry(sr), 2.0) == 1);
  fail_unless(!strcmp(SpeciesReference_getId(sr), "sr"));
  fail_unless(SpeciesReference_getConstant(sr) == 0);

  fail_unless(Reaction_addProductBySpecies(R, s, 1.0, "sr", 0) == LIBSBML_DUPLICATE_OBJECT_ID);
  fail_unless( Reaction_getNumProducts (R) == 1 );

  Species_free(s);
}
END_TEST



START_TEST (test_Reaction_addProduct1)
{
  Reaction_t *m = Reaction_create(2, 2);
  SpeciesReference_t *p 
    = SpeciesReference_create(2, 2);
  SpeciesReference_t *p1 
    = SpeciesReference_create(2, 2);
  SpeciesReference_setSpecies(p1, "k");
  SpeciesReference_setId(p1, "k1");

  int i = Reaction_addProduct(m, p);

  fail_unless( i == LIBSBML_INVALID_OBJECT);
  
  SpeciesReference_setSpecies(p, "k");
  SpeciesReference_setId(p, "k1");
  i = Reaction_addProduct(m, p);

  fail_unless( i == LIBSBML_OPERATION_SUCCESS);
  fail_unless( Reaction_getNumProducts(m) == 1);

  i = Reaction_addProduct(m, p1);

  fail_unless( i == LIBSBML_DUPLICATE_OBJECT_ID);
  fail_unless( Reaction_getNumProducts(m) == 1);

  SpeciesReference_free(p);
  SpeciesReference_free(p1);
  Reaction_free(m);
}
Example #3
0
/**
 * \fn void SBML_reaction(Model_t *mod, pEspeces molecules, Reaction_t *react, int nbEspeces)
 * \author Amine Ghozlane
 * \brief  Simulation of a discrete transision
 * \param  mod Model of the SBML file
 * \param  molecules Struct Especes
 * \param  react Reaction id
 * \param  nbEspeces Number of molecules
 */
void SBML_reaction(Model_t *mod, pEspeces molecules, Reaction_t *react, int nbEspeces)
{
  /* Simulation d'une transision discrete */
  SpeciesReference_t *reactif;
  Species_t *especeId;
  int i, ref = 0;

  /*boucle pour retirer des reactifs*/
  for (i = 0; i < (int)Reaction_getNumReactants(react); i++) {
      /* Indentification du reactif */
      reactif = Reaction_getReactant(react, i);
      especeId = Model_getSpeciesById(mod, SpeciesReference_getSpecies(reactif));
      ref = Especes_find(molecules, Species_getId(especeId), nbEspeces);
      /* Modification de sa quantite */
      Especes_setQuantite(molecules, ref, (Especes_getQuantite(molecules, ref)- SpeciesReference_getStoichiometry(reactif)));
  }

  /*boucle pour ajouter des produits */
  for (i = 0; i < (int)Reaction_getNumProducts(react); i++) {
      /* Indentification du reactif */
      reactif = Reaction_getProduct(react, i);
      especeId = Model_getSpeciesById(mod, SpeciesReference_getSpecies(reactif));
      ref = Especes_find(molecules, Species_getId(especeId), nbEspeces);
      /* Modification de sa quantite */
      Especes_setQuantite(molecules, ref, (Especes_getQuantite(molecules, ref)+ SpeciesReference_getStoichiometry(reactif)));
  }
}
END_TEST


START_TEST (test_Reaction_getProduct)
{
  SpeciesReference_t *sr1 = SpeciesReference_create(2, 4);
  SpeciesReference_t *sr2 = SpeciesReference_create(2, 4);


  SpeciesReference_setSpecies(sr1, "P1");
  SpeciesReference_setSpecies(sr2, "P2");

  Reaction_addProduct(R, sr1);
  Reaction_addProduct(R, sr2);

  SpeciesReference_free(sr1);
  SpeciesReference_free(sr2);

  fail_unless( Reaction_getNumReactants(R) == 0 );
  fail_unless( Reaction_getNumProducts (R) == 2 );
  fail_unless( Reaction_getNumModifiers(R) == 0 );

  sr1 = Reaction_getProduct(R, 0);
  sr2 = Reaction_getProduct(R, 1);

  fail_unless( !strcmp(SpeciesReference_getSpecies(sr1), "P1") );
  fail_unless( !strcmp(SpeciesReference_getSpecies(sr2), "P2") );

}
END_TEST


START_TEST (test_Reaction_getModifierById)
{
  SpeciesReference_t *msr1 = SpeciesReference_createModifier(2, 4);
  SpeciesReference_t *msr2 = SpeciesReference_createModifier(2, 4);


  SpeciesReference_setSpecies(msr1, "M1");
  SpeciesReference_setSpecies(msr2, "M2");


  Reaction_addModifier(R, msr1);
  Reaction_addModifier(R, msr2);

  fail_unless( Reaction_getNumReactants(R) == 0 );
  fail_unless( Reaction_getNumProducts (R) == 0 );
  fail_unless( Reaction_getNumModifiers(R) == 2 );

  fail_unless( Reaction_getModifierBySpecies(R, "M1") != msr1 );
  fail_unless( Reaction_getModifierBySpecies(R, "M2") != msr2 );
  fail_unless( Reaction_getModifierBySpecies(R, "M3") == NULL );
  
  SpeciesReference_free(msr1);
  SpeciesReference_free(msr2);
}
END_TEST


START_TEST (test_Reaction_getProductById)
{
  SpeciesReference_t *sr1 = SpeciesReference_create(2, 4);
  SpeciesReference_setSpecies(sr1, "P1");
  SpeciesReference_t *sr2 = SpeciesReference_create(2, 4);
  SpeciesReference_setSpecies(sr2, "P1");


  Reaction_addProduct(R, sr1);
  Reaction_addProduct(R, sr2);

  fail_unless( Reaction_getNumReactants(R) == 0 );
  fail_unless( Reaction_getNumProducts (R) == 2 );
  fail_unless( Reaction_getNumModifiers(R) == 0 );

  fail_unless( Reaction_getProductBySpecies(R, "P1") != sr1  );
  fail_unless( Reaction_getProductBySpecies(R, "P2") != sr2  );
  fail_unless( Reaction_getProductBySpecies(R, "P3") == NULL );

  SpeciesReference_free(sr1);
  SpeciesReference_free(sr2);
}
END_TEST


START_TEST (test_Reaction_getModifier)
{
  SpeciesReference_t *msr1 = SpeciesReference_createModifier(2, 4);
  SpeciesReference_t *msr2 = SpeciesReference_createModifier(2, 4);


  SpeciesReference_setSpecies(msr1, "M1");
  SpeciesReference_setSpecies(msr2, "M2");

  Reaction_addModifier(R, msr1);
  Reaction_addModifier(R, msr2);

  SpeciesReference_free(msr1);
  SpeciesReference_free(msr2);

  fail_unless( Reaction_getNumReactants(R) == 0 );
  fail_unless( Reaction_getNumProducts (R) == 0 );
  fail_unless( Reaction_getNumModifiers(R) == 2 );

  msr1 = Reaction_getModifier(R, 0);
  msr2 = Reaction_getModifier(R, 1);

  fail_unless(!strcmp(SpeciesReference_getSpecies(msr1), "M1"));
  fail_unless(!strcmp(SpeciesReference_getSpecies(msr2), "M2"));
}
END_TEST


START_TEST (test_Reaction_removeProduct)
{
  SpeciesReference_t *o1, *o2, *o3;

  o1 = Reaction_createProduct(R);
  o2 = Reaction_createProduct(R);
  o3 = Reaction_createProduct(R);
  SpeciesReference_setSpecies(o3,"test");

  fail_unless( Reaction_removeProduct(R,0) == o1 );
  fail_unless( Reaction_getNumProducts(R)  == 2  );
  fail_unless( Reaction_removeProduct(R,0) == o2 );
  fail_unless( Reaction_getNumProducts(R)  == 1  );
  fail_unless( Reaction_removeProductBySpecies(R,"test") == o3 );
  fail_unless( Reaction_getNumProducts(R)  == 0  );

  SpeciesReference_free(o1);
  SpeciesReference_free(o2);
  SpeciesReference_free(o3);
}
END_TEST


START_TEST (test_Reaction_addModifier)
{
  SpeciesReference_t * msr = SpeciesReference_createModifier(2, 4);
  SpeciesReference_setSpecies(msr, "s");
  Reaction_addModifier(R, msr);

  fail_unless( Reaction_getNumReactants(R) == 0 );
  fail_unless( Reaction_getNumProducts (R) == 0 );
  fail_unless( Reaction_getNumModifiers(R) == 1 );

  SpeciesReference_free(msr);
}
END_TEST


START_TEST (test_Reaction_addProduct4)
{
  Reaction_t *m = Reaction_create(2, 2);
  SpeciesReference_t *p = NULL; 

  int i = Reaction_addProduct(m, p);

  fail_unless( i == LIBSBML_OPERATION_FAILED);
  fail_unless( Reaction_getNumProducts(m) == 0);

  Reaction_free(m);
}
END_TEST


START_TEST (test_Reaction_createProduct)
{
  Reaction_t *m = Reaction_create(2, 2);
  
  SpeciesReference_t *p = Reaction_createProduct(m);

  fail_unless( Reaction_getNumProducts(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_Reaction_addProduct3)
{
  Reaction_t *m = Reaction_create(2, 2);
  SpeciesReference_t *p 
    = SpeciesReference_create(1, 2);
  SpeciesReference_setSpecies(p, "k");

  int i = Reaction_addProduct(m, p);

  fail_unless( i == LIBSBML_LEVEL_MISMATCH);
  fail_unless( Reaction_getNumProducts(m) == 0);

  SpeciesReference_free(p);
  Reaction_free(m);
}
Example #13
0
END_TEST


START_TEST (test_Reaction_addModifierBySpecies)
{
  Species_t *s = Species_create(2, 4);
  Species_setId(s, "s");
  Reaction_addModifierBySpecies(R, s, "sr");

  fail_unless( Reaction_getNumReactants(R) == 0 );
  fail_unless( Reaction_getNumProducts (R) == 0 );
  fail_unless( Reaction_getNumModifiers(R) == 1 );

  SpeciesReference_t *sr = Reaction_getModifier(R, 0);

  fail_unless(!strcmp(SpeciesReference_getSpecies(sr), "s"));
  fail_unless(!strcmp(SpeciesReference_getId(sr), "sr"));

  fail_unless(Reaction_addModifierBySpecies(R, s, "sr") == LIBSBML_DUPLICATE_OBJECT_ID);
  fail_unless( Reaction_getNumModifiers (R) == 1 );

  Species_free(s);
}
Example #14
0
int
main (int argc, char* argv[])
{
  unsigned int i,j,errors;
  const char* filename   = argv[1];
  SBMLDocument_t* document;
  Model_t* m;

  if (argc != 3)
  {
    printf("\nUsage: unsetNotes <input-filename> <output-filename>\n");
    return 1;
  }

  filename = argv[1];  
  document = readSBML(filename);

  errors =  SBMLDocument_getNumErrors(document);

  if(errors > 0)
  {
    SBMLDocument_printErrors(document, stderr);
    SBMLDocument_free(document);
    return errors;
  }

  m = SBMLDocument_getModel( document );
  SBase_unsetNotes((SBase_t*)m);

  for(i=0; i < Model_getNumReactions(m); i++)
  {
    Reaction_t* re = Model_getReaction(m, i);
    SBase_unsetNotes((SBase_t*)re);

    for(j=0; j < Reaction_getNumReactants(re); j++)
    {
      SpeciesReference_t* rt = Reaction_getReactant(re,j);
      SBase_unsetNotes((SBase_t*)rt);
    }

    for(j=0; j < Reaction_getNumProducts(re); j++)
    {
      SpeciesReference_t* rt = Reaction_getProduct(re,j);
      SBase_unsetNotes((SBase_t*)rt);
    }

    for(j=0; j < Reaction_getNumModifiers(re); j++)
    {
      SpeciesReference_t* md = Reaction_getModifier(re,j);
      SBase_unsetNotes((SBase_t*)md);
    }

    if(Reaction_isSetKineticLaw(re))
    {
      KineticLaw_t* kl =  Reaction_getKineticLaw(re);
      SBase_unsetNotes((SBase_t*)kl);

      for(j=0; j < KineticLaw_getNumParameters(kl); j++)
      {
        Parameter_t* pa = KineticLaw_getParameter(kl, j);
        SBase_unsetNotes((SBase_t*)pa);
      }
    }

  }

  for(i=0; i < Model_getNumSpecies(m); i++)
  {
    Species_t* sp = Model_getSpecies(m, i);
    SBase_unsetNotes((SBase_t*)sp);
  }

  for(i=0; i < Model_getNumCompartments(m); i++)
  {
    Compartment_t* sp = Model_getCompartment(m,i);
    SBase_unsetNotes((SBase_t*)sp);
  }

  for(i=0; i < Model_getNumFunctionDefinitions(m); i++)
  {
    FunctionDefinition_t* sp = Model_getFunctionDefinition(m,i);
    SBase_unsetNotes((SBase_t*)sp);
  }

  for(i=0; i < Model_getNumUnitDefinitions(m); i++)
  {
    UnitDefinition_t* sp = Model_getUnitDefinition(m, i);
    SBase_unsetNotes((SBase_t*)sp);
  }

  for(i=0; i < Model_getNumParameters(m); i++)
  {
    Parameter_t* sp = Model_getParameter(m, i);
    SBase_unsetNotes((SBase_t*)sp);
  }

  for(i=0; i < Model_getNumRules(m); i++)
  {
    Rule_t* sp = Model_getRule(m, i);
    SBase_unsetNotes((SBase_t*)sp);
  }

  for(i=0; i < Model_getNumInitialAssignments(m); i++)
  {
    InitialAssignment_t* sp = Model_getInitialAssignment(m, i);
    SBase_unsetNotes((SBase_t*)sp);
  }

  for(i=0; i < Model_getNumEvents(m); i++)
  {
    Event_t* sp = Model_getEvent(m, i);
    SBase_unsetNotes((SBase_t*)sp);

    for(j=0; j < Event_getNumEventAssignments(sp); j++)
    {
      EventAssignment_t* ea = Event_getEventAssignment(sp, j);
      SBase_unsetNotes((SBase_t*)ea);
    }
  }

  for(i=0; i < Model_getNumSpeciesTypes(m); i++)
  {
    SpeciesType_t* sp = Model_getSpeciesType(m, i);
    SBase_unsetNotes((SBase_t*)sp);
  }

  for(i=0; i < Model_getNumConstraints(m); i++)
  {
    Constraint_t* sp = Model_getConstraint(m, i);
    SBase_unsetNotes((SBase_t*)sp);
  }

  writeSBML(document, argv[2]);

  SBMLDocument_free(document);
  return errors;
}
Example #15
0
int
main (int argc, char* argv[])
{
  unsigned int i,j,errors;
  const char* filename;
  SBMLDocument_t* document;
  Model_t* m;

  if (argc != 2)
  {
    printf("\nUsage: printNotes filename\n\n");
    return 1;
  }

  filename  = argv[1];
  document  = readSBML(filename);

  errors = SBMLDocument_getNumErrors( document);

  printf("\n%s\n\n", filename);

  if(errors > 0)
  {
    SBMLDocument_printErrors(document, stderr);
    SBMLDocument_free(document);
    return errors;
  }


  /* Model */

  m = SBMLDocument_getModel(document);
  printNotes((SBase_t*)m, Model_getId(m));

  for(i=0; i < Model_getNumReactions(m); i++)
  {
    Reaction_t* re = Model_getReaction( m, i);
    printNotes((SBase_t*)re, Reaction_getId(re));

    /* SpeciesReference (Reactant) */

    for(j=0; j < Reaction_getNumReactants( re); j++)
    {
      SpeciesReference_t* rt =  Reaction_getReactant(re, j);
      if (SBase_isSetNotes((SBase_t*) rt)) printf("   ");
      printNotes((SBase_t*)rt, SpeciesReference_getSpecies( rt ) );
    }

    /* SpeciesReference (Product) */

    for(j=0; j < Reaction_getNumProducts( re ); j++)
    {
      SpeciesReference_t* rt = Reaction_getProduct( re, j);
      if (SBase_isSetNotes((SBase_t*) rt)) printf("   ");
      printNotes((SBase_t*)rt, SpeciesReference_getSpecies( rt ) );
    }

    /* ModifierSpeciesReference (Modifiers) */

    for(j=0; j < Reaction_getNumModifiers( re ); j++)
    {
      SpeciesReference_t* md = Reaction_getModifier(re, j);
      if (SBase_isSetNotes((SBase_t*) md)) printf("   ");
      printNotes((SBase_t*)md, SpeciesReference_getSpecies( md ) );
    }

    /* KineticLaw */

    if(Reaction_isSetKineticLaw( re ))
    {
      KineticLaw_t* kl = Reaction_getKineticLaw( re );
      if (SBase_isSetNotes((SBase_t*) kl)) printf("   ");
      printNotes((SBase_t*)kl, "");

      /* Parameter */

      for(j=0; j < KineticLaw_getNumParameters( kl ); j++)
      {
        Parameter_t* pa = KineticLaw_getParameter( kl, j);
        if (SBase_isSetNotes((SBase_t*) pa)) printf("   ");
        printNotes((SBase_t*)pa, Parameter_getId(pa));
      }
    }

  }

  /* Species */

  for(i=0; i < Model_getNumSpecies(m); i++)
  {
    Species_t* sp = Model_getSpecies(m, i);
    printNotes((SBase_t*)sp, Species_getId(sp));
  }

  /* Compartments */

  for(i=0; i < Model_getNumCompartments( m ); i++)
  {
    Compartment_t* sp = Model_getCompartment(m, i);
    printNotes((SBase_t*)sp, Compartment_getId(sp));
  }

  /* FunctionDefinition */

  for(i=0; i < Model_getNumFunctionDefinitions(m); i++)
  {
    FunctionDefinition_t* sp = Model_getFunctionDefinition(m, i);
    printNotes((SBase_t*)sp, FunctionDefinition_getId(sp));
  }

  /* UnitDefinition */

  for(i=0; i < Model_getNumUnitDefinitions(m); i++)
  {
    UnitDefinition_t* sp = Model_getUnitDefinition( m, i);
    printNotes((SBase_t*)sp, UnitDefinition_getId(sp));
  }

  /* Parameter */

  for(i=0; i < Model_getNumParameters( m ); i++)
  {
    Parameter_t* sp = Model_getParameter( m, i);
    printNotes((SBase_t*)sp, Parameter_getId(sp));
  }

  /* Rule */

  for(i=0; i < Model_getNumReactions( m ); i++)
  {
    Rule_t* sp = Model_getRule(m, i);
    printNotes((SBase_t*)sp, "");
  }

  /* InitialAssignment */

  for(i=0; i < Model_getNumInitialAssignments(m); i++)
  {
    InitialAssignment_t* sp = Model_getInitialAssignment(m, i);
    printNotes((SBase_t*)sp, "");
  }

  /* Event */

  for(i=0; i < Model_getNumEvents(m); i++)
  {
    Event_t* sp = Model_getEvent(m, i);
    printNotes((SBase_t*)sp, Event_getId(sp));

    /* Trigger */

    if(Event_isSetTrigger( sp ))
    {
      Trigger_t* tg = Event_getTrigger(sp);
      if (SBase_isSetNotes( (SBase_t*) tg)) printf( "   " );
      printNotes((SBase_t*)tg, "");
    }

    /* Delay */

    if(Event_isSetDelay(sp))
    {
      Delay_t* dl = Event_getDelay(sp);
      if (SBase_isSetNotes( (SBase_t*) dl)) printf( "   " );
      printNotes((SBase_t*) dl, "");
    }

    /* EventAssignment */

    for(j=0; j < Event_getNumEventAssignments(sp); j++)
    {
      EventAssignment_t* ea = Event_getEventAssignment(sp, j);
      if (SBase_isSetNotes( (SBase_t*) ea)) printf( "   " );      
      printNotes((SBase_t*)ea, "");
    }
  }

  /* SpeciesType */

  for(i=0; i < Model_getNumSpeciesTypes(m); i++)
  {
    SpeciesType_t* sp = Model_getSpeciesType(m, i);
    printNotes((SBase_t*)sp, SpeciesType_getId(sp));
  }

  /* Constraints */

  for(i=0; i < Model_getNumConstraints(m); i++)
  {
    Constraint_t* sp = Model_getConstraint(m, i);
    printNotes((SBase_t*)sp, "");
  }

  SBMLDocument_free( document );
  return errors;
}
static int
drawModelTxt(Model_t *m, char *file) {

  Species_t *s;
  Reaction_t *re;
  const ASTNode_t *math;
  SpeciesReference_t *sref;
  ModifierSpeciesReference_t *mref;
  int i,j;
  int reversible;
  char filename[WORDSIZE];
  FILE *f;
  
  sprintf(filename, "%s.dot", file);
  f = fopen(filename, "w");

  fprintf(f ,"digraph reactionnetwork {\n");
  fprintf(f ,"label=\"%s\";\n",
	  Model_isSetName(m) ?
	  Model_getName(m) : (Model_isSetId(m) ? Model_getId(m) : "noId") );
  fprintf(f ,"overlap=scale;\n");
 
  for ( i=0; i<Model_getNumReactions(m); i++ ) {
    
    re = Model_getReaction(m,i);
    reversible = Reaction_getReversible(re);
    
    for ( j=0; j<Reaction_getNumModifiers(re); j++ ) {
      mref = Reaction_getModifier(re,j);
      fprintf(f ,"%s->%s [style=dashed arrowhead=odot];\n",
	      ModifierSpeciesReference_getSpecies(mref), Reaction_getId(re));
    }
    for ( j=0; j<Reaction_getNumReactants(re); j++ ) {
      sref = Reaction_getReactant(re,j);
      fprintf(f ,"%s->%s [label=\"",
	      SpeciesReference_getSpecies(sref), Reaction_getId(re));
      
      if ( (SpeciesReference_isSetStoichiometryMath(sref)) ) {
	math = SpeciesReference_getStoichiometryMath(sref);
	if ( (strcmp(SBML_formulaToString(math),"1") !=
	      0) ) {
	  fprintf(f ,"%s", SBML_formulaToString(math));
	}	
      }
      else {
	if ( SpeciesReference_getStoichiometry(sref) != 1) {
	  fprintf(f ,"%g",SpeciesReference_getStoichiometry(sref));
	}
      }
      if ( reversible == 1 ) {
	fprintf(f ,"\" arrowtail=onormal];\n");
      }
      else {
	fprintf(f ,"\" ];\n");
      }
    }
    for ( j=0; j<Reaction_getNumProducts(re); j++ ) {
      sref = Reaction_getProduct(re,j);
      fprintf(f ,"%s->%s [label=\"",
	      Reaction_getId(re), SpeciesReference_getSpecies(sref));
      if ( (SpeciesReference_isSetStoichiometryMath(sref)) ) {
	math = SpeciesReference_getStoichiometryMath(sref);
	if ( (strcmp(SBML_formulaToString(math),"1") !=
	      0) ) {
	  fprintf(f ,"%s ", SBML_formulaToString(math));
	}
      }
      else {
	if ( SpeciesReference_getStoichiometry(sref) != 1) {
	  fprintf(f ,"%g ",SpeciesReference_getStoichiometry(sref));
	}
      }
      if ( reversible == 1 ) {
	fprintf(f ,"\" arrowtail=onormal];\n");
      }
      else {
	fprintf(f ,"\" ];\n");
      }    

    }
    
  }
  for ( i=0; i<Model_getNumReactions(m); i++ ) {
    re = Model_getReaction(m,i);
    fprintf(f ,"%s [label=\"%s\" shape=box];\n",
	    Reaction_getId(re),
	    Reaction_isSetName(re) ?
	    Reaction_getName(re) : Reaction_getId(re));
  }

  for ( i=0; i<Model_getNumSpecies(m); i++) {
    s = Model_getSpecies(m, i);
    fprintf(f ,"%s [label=\"%s\"];",
	    Species_getId(s),
	    Species_isSetName(s) ? Species_getName(s) : Species_getId(s));
  }  
  fprintf(f ,"}\n");
  return 1;
}
SBML_ODESOLVER_API int drawModel(Model_t *m, char* file, char *format) {
  
#if !USE_GRAPHVIZ

  SolverError_error(
		    WARNING_ERROR_TYPE,
		    SOLVER_ERROR_NO_GRAPHVIZ,
		    "odeSolver has been compiled without GRAPHIZ functionality. ",
		    "Graphs are printed to stdout in the graphviz' .dot format.");
  drawModelTxt(m, file);
  
#else

  GVC_t *gvc;
  Agraph_t *g;
  Agnode_t *r;
  Agnode_t *s;  
  Agedge_t *e;
  Agsym_t *a;
  Species_t *sp;
  Reaction_t *re;
  const ASTNode_t *math;  
  SpeciesReference_t *sref;
  ModifierSpeciesReference_t *mref;
  char *output[4];
  char *command = "dot";
  char *formatopt;
  char *outfile;
  int i,j;
  int reversible;
  char name[WORDSIZE];
  char label[WORDSIZE];

  /* setting name of outfile */
  ASSIGN_NEW_MEMORY_BLOCK(outfile, strlen(file)+ strlen(format)+7, char, 0);
  sprintf(outfile, "-o%s_rn.%s", file, format);

  /* setting output format */
  ASSIGN_NEW_MEMORY_BLOCK(formatopt, strlen(format)+3, char, 0);
  sprintf(formatopt, "-T%s", format);

  /* construct command-line */
  output[0] = command;
  output[1] = formatopt;
  output[2] = outfile;
  output[3] = NULL;

  /* set up renderer context */
  gvc = (GVC_t *) gvContext();
#if GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION < 4
  dotneato_initialize(gvc, 3, output);
#elif GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION == 4
  parse_args(gvc, 3, output);
#elif GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION >= 6 || GRAPHVIZ_MAJOR_VERSION >= 3
  gvParseArgs(gvc, 3, output);  
#endif  

  g = agopen("G", AGDIGRAPH);
  
  /* avoid overlapping nodes, for graph embedding by neato */ 
  a = agraphattr(g, "overlap", "");
  agxset(g, a->index, "scale");

  for ( i=0; i<Model_getNumReactions(m); i++ ) {

    re = Model_getReaction(m,i);
    reversible = Reaction_getReversible(re);
    sprintf(name, "%s", Reaction_getId(re));
    r = agnode(g,name);
    a = agnodeattr(g, "shape", "ellipse");    
    agxset(r, a->index, "box");
    
    sprintf(label, "%s", Reaction_isSetName(re) ?
	    Reaction_getName(re) : Reaction_getId(re));
    agset(r, "label", label);
    
    sprintf(label, "%s.htm", Reaction_getId(re));
    a = agnodeattr(g, "URL", "");
    agxset(r, a->index, label);
    
    for ( j=0; j<Reaction_getNumModifiers(re); j++ ) {

      mref = Reaction_getModifier(re,j);
      sp = Model_getSpeciesById(m, ModifierSpeciesReference_getSpecies(mref));
      
      sprintf(name,"%s", Species_getId(sp));
      s = agnode(g,name);
      sprintf(label, "%s", Species_isSetName(sp) ? 
	      Species_getName(sp) : Species_getId(sp));
      agset(s, "label", label);

      if ( Species_getBoundaryCondition(sp) ) {
	a = agnodeattr(g, "color", "");
	agxset(s, a->index, "blue");
      }
      if ( Species_getConstant(sp) ) {
	a = agnodeattr(g, "color", "");
	agxset(s, a->index, "green4");
      }

      sprintf(label, "%s.htm", Species_getId(sp));
      a = agnodeattr(g, "URL", "");
      agxset(s, a->index, label);
	
      e = agedge(g,s,r);
      a = agedgeattr(g, "style", "");
      agxset(e, a->index, "dashed");
      a = agedgeattr(g, "arrowhead", "");
      agxset(e, a->index, "odot");
    }

    for ( j=0; j<Reaction_getNumReactants(re); j++ ) {

      sref = Reaction_getReactant(re,j);
      sp = Model_getSpeciesById(m, SpeciesReference_getSpecies(sref));
      
      sprintf(name,"%s", Species_getId(sp));
      s = agnode(g, name);
      sprintf(label, "%s", Species_isSetName(sp) ? 
	      Species_getName(sp) : Species_getId(sp));
      agset(s, "label", label);

      if ( Species_getBoundaryCondition(sp) ) {
	a = agnodeattr(g, "color", "");
	agxset(s, a->index, "blue");
      }
      if ( Species_getConstant(sp) ) {
	a = agnodeattr(g, "color", "");
	agxset(s, a->index, "green4");
      }

      sprintf(label, "%s.htm", Species_getId(sp));
      a = agnodeattr(g, "URL", "");
      agxset(s, a->index, label);
      
      e = agedge(g,s,r);
      a = agedgeattr(g, "label", "");
      
      if ( (SpeciesReference_isSetStoichiometryMath(sref)) ) {
	math = SpeciesReference_getStoichiometryMath(sref);
	if ( (strcmp(SBML_formulaToString(math),"1") !=
	      0) ) {
	  agxset (e, a->index, SBML_formulaToString(math));
	}
      }
      else {
	if ( SpeciesReference_getStoichiometry(sref) != 1 ) {
	  sprintf(name, "%g", SpeciesReference_getStoichiometry(sref));
	  agxset (e, a->index, name);
	}
      }
      if ( reversible == 1 ) {
	a = agedgeattr(g, "arrowtail", "");
	agxset(e, a->index, "onormal");
      }      
    }
    
    for ( j=0; j<Reaction_getNumProducts(re); j++ ) {
      sref = Reaction_getProduct(re,j);
      sp = Model_getSpeciesById(m, SpeciesReference_getSpecies(sref));
      sprintf(name,"%s", Species_getId(sp));
      s = agnode(g,name);
      sprintf(label, "%s", Species_isSetName(sp) ? 
	      Species_getName(sp) : Species_getId(sp));
      agset(s, "label", label);

      if ( Species_getBoundaryCondition(sp) ) {
	a = agnodeattr(g, "color", "");
	agxset(s, a->index, "blue");
      }
      if ( Species_getConstant(sp) ) {
	a = agnodeattr(g, "color", "");
	agxset(s, a->index, "green4");
      }

      sprintf(label, "%s.htm", Species_getId(sp));
      a = agnodeattr(g, "URL", "");
      agxset(s, a->index, label);
            
      e = agedge(g,r,s);
      a = agedgeattr(g, "label", "");
      if ( SpeciesReference_isSetStoichiometryMath(sref) ) {
	math = SpeciesReference_getStoichiometryMath(sref);
	if ( (strcmp(SBML_formulaToString(math),"1") !=
	      0) ) {
	  agxset (e, a->index, SBML_formulaToString(math));
	}
      }
      else {
	if ( SpeciesReference_getStoichiometry(sref) != 1 ) {
	  sprintf(name, "%g",SpeciesReference_getStoichiometry(sref));
	  agxset (e, a->index,name);
	}
      }
      if ( reversible == 1 ) {
	a = agedgeattr(g, "arrowtail", "");
	agxset(e, a->index, "onormal");
      }      
    }   
  }

  /* Compute a layout */
#if GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION <= 2
  gvBindContext(gvc, g);
  dot_layout(g);
#elif GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION == 4
  gvlayout_layout(gvc, g);
#elif GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION >= 6 || GRAPHVIZ_MAJOR_VERSION >= 3
  gvLayoutJobs(gvc, g);
#endif

  /* Write the graph according to -T and -o options */
#if GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION <= 2
  dotneato_write(gvc);
#elif GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION == 4
  emit_jobs(gvc, g);
#elif GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION >= 6 || GRAPHVIZ_MAJOR_VERSION >= 3
  gvRenderJobs(gvc, g);
#endif
  
  /* Clean out layout data */
#if GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION <= 2
  dot_cleanup(g);
#elif GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION == 4
  gvlayout_cleanup(gvc, g);
#elif GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION >= 6 || GRAPHVIZ_MAJOR_VERSION >= 3
  gvFreeLayout(gvc, g);
#endif
  
  /* Free graph structures */
#if GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION <= 2
  dot_cleanup(g);
#else
  agclose(g);
#endif

  /* Clean up output file and errors */
#if GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION <= 2
  gvFREEcontext(gvc);
  dotneato_eof(gvc);
#elif GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION == 4
  dotneato_terminate(gvc);
#elif GRAPHVIZ_MAJOR_VERSION == 2 && GRAPHVIZ_MINOR_VERSION >= 6 || GRAPHVIZ_MAJOR_VERSION >= 3
  gvFreeContext(gvc); 
#endif  

  xfree(formatopt);  
  xfree(outfile);
  
#endif
  
  return 1;

}
void printReactions(Model_t *m, FILE *f)
{
  
  int i,j,k;
  Reaction_t *r;
  SpeciesReference_t *sref;
  KineticLaw_t *kl;
  Rule_t *rl;
  AssignmentRule_t *asr;
  AlgebraicRule_t *alr;
  RateRule_t *rr;
  Event_t *e;
  EventAssignment_t *ea;
  Parameter_t *p;
  FunctionDefinition_t *fd;
  SBMLTypeCode_t type;
  const ASTNode_t *math;

  math = NULL;
  
  fprintf(f, "\n");
  for(i=0;i<Model_getNumParameters(m);i++){
    if(i==0)
      fprintf(f, "# Global parameters:\n");
    p = Model_getParameter(m,i);
    if(Parameter_isSetId(p))
      fprintf(f, "%s ",  Parameter_getId(p));
    if(Parameter_isSetName(p))
      fprintf(f, "(%s) ", Parameter_getName(p));
    if(Parameter_isSetValue(p))
      fprintf(f, "= %g; ", Parameter_getValue(p));
    if(Parameter_isSetUnits(p))
      fprintf(f, "[%s]; ", Parameter_getUnits(p));
    if(!Parameter_getConstant(p))
      fprintf(f, "(variable);");
    fprintf(f, "\n");
    
    if ( i==Model_getNumParameters(m)-1 )
      fprintf(f, "\n");
  }

  fprintf(f, "# Reactions:\n");
  for ( i=0; i<Model_getNumReactions(m); i++ ) {    
    r = Model_getReaction(m,i);
  
    fprintf(f, "%s: %s",
	   Reaction_isSetName(r) ? Reaction_getName(r) : Reaction_getId(r),
	   Reaction_getFast(r) ? "(fast)" : "");
    for ( k=0; k<Reaction_getNumReactants(r); k++ ) {
      sref = Reaction_getReactant(r,k);

      if ( SpeciesReference_isSetStoichiometryMath(sref) )	
	fprintf(f, "%s ",
		SBML_formulaToString(\
		SpeciesReference_getStoichiometryMath(sref)));
      else 
	if ( SpeciesReference_getStoichiometry(sref) != 1. )
	  fprintf(f, "%g ",  SpeciesReference_getStoichiometry(sref));
	
      fprintf(f, "%s", SpeciesReference_getSpecies(sref));
      if(k+1<Reaction_getNumReactants(r))
	fprintf(f, "%s", " + ");
    }
    
    fprintf(f, "%s", Reaction_getReversible(r) ? " <-> " : " -> ");
    for ( k=0; k<Reaction_getNumProducts(r); k++ ) {
      sref = Reaction_getProduct(r,k);
      if ( SpeciesReference_isSetStoichiometryMath(sref) )
	fprintf(f, "%s ",
	       SBML_formulaToString(\
		   SpeciesReference_getStoichiometryMath(sref)));
      else
	if ( SpeciesReference_getStoichiometry(sref) != 1. )
	  fprintf(f, "%g ", SpeciesReference_getStoichiometry(sref));
      
      fprintf(f, "%s", SpeciesReference_getSpecies(sref));
      if(k+1<Reaction_getNumProducts(r))
	fprintf(f, "%s", " + ");
    }
    fprintf(f, ";  ");
    if(Reaction_isSetKineticLaw(r)){
      kl = Reaction_getKineticLaw(r);
      math = KineticLaw_getMath(kl);
      fprintf(f, "%s;", SBML_formulaToString(math));
      for(k=0;k<KineticLaw_getNumParameters(kl);k++){
	
	p = KineticLaw_getParameter(kl,k);
	fprintf(f, " %s",  Parameter_getId(p));
	if(Parameter_isSetName(p))
	  fprintf(f, " (%s)", Parameter_getName(p));
	if(Parameter_isSetValue(p))
	  fprintf(f, " = %g", Parameter_getValue(p));
	if(Parameter_isSetUnits(p))
	  fprintf(f, " [%s]", Parameter_getUnits(p));
	if ( !Parameter_getConstant(p) )
	  fprintf(f, " (variable)");
	fprintf(f, ";");
      }
     /*  fprintf(f, "\n"); */
    }else
      fprintf(f, "#   no rate law is set for this reaction.");
    fprintf(f, "\n");
  }
    
  for(i=0;i<Model_getNumRules(m);i++){
    rl = Model_getRule(m,i);
    if ( i == 0 ) {
      fprintf(f, "# Rules:\n");
    }
    type = SBase_getTypeCode((SBase_t *)rl);
     
     
    if ( type == SBML_RATE_RULE ) {
      rr =  (RateRule_t *) rl;
      fprintf(f, " rateRule:       d%s/dt = ", RateRule_getVariable(rr));
    }
    if ( type == SBML_ALGEBRAIC_RULE ) {
      alr = (AlgebraicRule_t *) rl;
      fprintf(f, " algebraicRule:       0 = ");
    }
    if ( type == SBML_ASSIGNMENT_RULE ) {
      asr = (AssignmentRule_t *) rl;
      fprintf(f, " assignmentRule (%s): %s = ",
	     RuleType_toString(AssignmentRule_getType(asr)),
	     AssignmentRule_getVariable(asr));
    }
    if(!Rule_isSetMath(rl)){
      if(Rule_isSetFormula(rl)){
	Rule_setMathFromFormula(rl);
	
      }
    }
    if(Rule_isSetMath(rl))
      fprintf(f, "%s\n", SBML_formulaToString(Rule_getMath(rl)));
	     
  }
  fprintf(f, "\n");

  for(i=0;i<Model_getNumEvents(m);i++){
    if(i==0)
      fprintf(f, "# Events:\n");
    e = Model_getEvent(m,i);
    if(Event_isSetId(e))
      fprintf(f, "%s: ", Event_getId(e));
    if(Event_isSetName(e))
      fprintf(f, "(%s) ", Event_getName(e));   
    if(Event_isSetTrigger(e)) {
      math = Event_getTrigger(e);
      fprintf(f, "trigger: %s\n", SBML_formulaToString(math));
    }
    if(Event_isSetDelay(e))
      fprintf(f, "delay: %s;\n", SBML_formulaToString(Event_getDelay(e)));
    if(Event_isSetTimeUnits(e))
      fprintf(f, "time Units: %s;\n", Event_getTimeUnits(e));
    for(k=0;k<Event_getNumEventAssignments(e);k++){      
      ea = Event_getEventAssignment(e,k);
      if(EventAssignment_isSetVariable(ea))
	fprintf(f, "  event:  %s = %s;\n",
	       EventAssignment_getVariable(ea),
	       EventAssignment_isSetMath(ea) ?
	       SBML_formulaToString(EventAssignment_getMath(ea)) :
	       "# no math set;\n");
    }

    if(i==Model_getNumEvents(m)-1)
       fprintf(f, "\n"); 
  }  


  for ( i=0; i<Model_getNumFunctionDefinitions(m); i++ ) {

    if ( i==0 ) fprintf(f, "# Functions:\n");

    fd = Model_getFunctionDefinition(m,i);
    if ( FunctionDefinition_isSetName(fd) )
      fprintf(f, "%s: ", FunctionDefinition_getName(fd));
    if(FunctionDefinition_isSetId(fd) && FunctionDefinition_isSetMath(fd)){
      fprintf(f, "%s( ", FunctionDefinition_getId(fd));
      math = FunctionDefinition_getMath(fd);
	for(j=0;j<ASTNode_getNumChildren(math)-1;j++){
	  fprintf(f, "%s", SBML_formulaToString(ASTNode_getChild(math, j)));
	  if(j<ASTNode_getNumChildren(math)-2)
	    fprintf(f, ", ");
	  if(j==ASTNode_getNumChildren(math)-2)
	    fprintf(f, ") = ");
	}
      fprintf(f, "%s;", SBML_formulaToString(ASTNode_getRightChild(math)));
    }
    fprintf(f, "\n");
  } 
  
}
Example #19
0
int main(int argc, char** argv)
{
    myspecies_t* species;	//pinakas ximikon stoixeion
    reaction_t *reaction;	//20 ximikes antidraseis
    int i,j,k,num_species, num_reactions;
    double V;
    FILE *pf1, *pf2, *pf3, *pf4, *pf5, *pf6, *fsize;

    SBMLDocument_t *d;
    Model_t        *m;
    ListOf_t    *lo;
    Species_t   *sp;
    Reaction_t  *re;
    Parameter_t *p;
    KineticLaw_t *kin;
    SpeciesReference_t *sr;
    Compartment_t *c;

	//an den exei 2 argument
	if(argc != 2)
    {
        printf("Ektelesi: %s <SBML xml>\n", argv[0]);
        exit(-1);
    }

    //arxeia results
    if((pf1 = fopen("RT_reactant.txt", "w")) == NULL)
    {
        printf("Error create file %s\n","RT_reactant.txt");
        exit(-1);
    }
    
    if((pf2 = fopen("RT_product.txt", "w")) == NULL)
    {
        printf("Error create file %s\n","RT_product.txt");
        fclose(pf1);
        exit(-1);
    }
    
    if((pf3 = fopen("VT_reactant.txt", "w")) == NULL)
    {
        printf("Error create file %s\n","VT_reactant.txt");
        fclose(pf1);
        fclose(pf2);
        exit(-1);
    }
    
    if((pf4 = fopen("VT_product.txt", "w")) == NULL)
    {
        printf("Error create file %s\n","VT_product.txt");
        fclose(pf1);
        fclose(pf2);
        fclose(pf3);
        exit(-1);
    }
    
    if((pf5 = fopen("ST.txt", "w")) == NULL)
    {
        printf("Error create file %s\n","ST.txt");
        fclose(pf1);
        fclose(pf2);
        fclose(pf3);
        fclose(pf4);
        exit(-1);
    }
    
    if((pf6 = fopen("k_parameter.txt", "w")) == NULL)
    {
        printf("Error create file %s\n","k_parameter.txt");
        fclose(pf1);
        fclose(pf2);
        fclose(pf3);
        fclose(pf4);
        fclose(pf5);
        exit(-1);
    }

    fsize = fopen("fsize.txt", "w");

    //anoigo to SBML arxeio
    d = readSBML(argv[1]);
    //d=readSBML("C:/home/orsalia/BIOMD0000000001");
    m = SBMLDocument_getModel(d);
    num_species = Model_getNumSpecies(m);
    num_reactions = Model_getNumReactions(m);

    fprintf(fsize,"%d\n",num_species);
    fprintf(fsize,"%d\n",num_reactions);
    
    //Pairnoume ton ogko
    c = Model_getCompartment(m,0);
    V = Compartment_getVolume(c);


    //Desmeysi pinakon domon gia stoixeia kai reaction
    species =  (myspecies_t*) malloc(num_species*sizeof(myspecies_t));
    reaction = (reaction_t*) malloc(num_reactions*sizeof(reaction_t));

    //gemizo ton pinaka me tis arxikes sigkentroseis ton stoixeion
    for(i=0;i<num_species;i++)
    {
        sp = Model_getSpecies(m,i);
        species[i].conc = Species_getInitialConcentration(sp)?Species_getInitialConcentration(sp):Species_getInitialAmount(sp);
        species[i].name = malloc(50*sizeof(char));
        strcpy(species[i].name,Species_getId(sp));
        strcpy(species[i].name2,Species_getName(sp));
    }

    ///gemizo ton pinaka domon ton reaction
    for(i=0;i<num_reactions;i++)
    {
        re = Model_getReaction(m,i);
        kin = Reaction_getKineticLaw(re);
        p = KineticLaw_getParameter(kin,0);

        reaction[i].react_num = Reaction_getNumReactants(re);
        reaction[i].product_num = Reaction_getNumProducts(re);
        reaction[i].react = (x_vector_t*) malloc(reaction[i].react_num*sizeof(x_vector_t));
        reaction[i].product = (x_vector_t*) malloc(reaction[i].product_num*sizeof(x_vector_t));

		for(j=0;j<reaction[i].react_num;j++)
        {
            sr = Reaction_getReactant(re,j);

            for(k=0;k<num_species;k++)
            {
                //an vrei to stoixeio ston megalo pinaka krata ti thesi tou
                if (strcmp(SpeciesReference_getSpecies(sr),species[k].name) == 0)
                {
                    reaction[i].react[j].x = k;		//ithesi ston pinaka species
                    reaction[i].react[j].v = (-1) * SpeciesReference_getStoichiometry(sr);
                    break;
                }
            }
        }
        
        for(j=0;j<reaction[i].product_num;j++)
        {
            sr = Reaction_getProduct(re,j);

            for(k=0;k<num_species;k++)
            {
                //an vrei to stoixeio ston megalo pinaka krata ti thesi tou
                if (strcmp(SpeciesReference_getSpecies(sr),species[k].name) == 0)
                {
                    reaction[i].product[j].x = k;	//ithesi ston pinaka species
                    reaction[i].product[j].v = SpeciesReference_getStoichiometry(sr);
                    break;
                }
            }
        }
        
        reaction[i].k = Parameter_getValue(p);

        //vlepo tin eidos antidraseis einai kai vazo to c tis kathe antidrasis
        if(reaction[i].react_num == 3)
        {
        	reaction[i].type = 7;
            reaction[i].c = Parameter_getValue(p)/(V*V);	//mallon
        }
        else if(reaction[i].react_num == 2)
        {	
          	sr = Reaction_getReactant(re,0);
          	
          	if (SpeciesReference_getStoichiometry(sr) == 2 )
        	{
        		reaction[i].type = 5;
            	reaction[i].c = 2*Parameter_getValue(p)/(V*V);	//oute kan
        	}
        	else
        	{
        		sr = Reaction_getReactant(re,1);
        	
        		if (SpeciesReference_getStoichiometry(sr) == 2 )
		    	{
		    		reaction[i].type = 6;
		        	reaction[i].c = 2*Parameter_getValue(p)/(V*V);	//oute kan
		    	}
		    	else
		    	{
		    		reaction[i].type = 2;
		        	reaction[i].c = Parameter_getValue(p)/V;	
		    	}
		    }
            
        }
        else //if(reaction[i].react_num == 1)
        {	
        	sr = Reaction_getReactant(re,0);
        	
            if (SpeciesReference_getStoichiometry(sr) == 2 )		//an einai bimolecular me to idio stoixeio
            {
                reaction[i].type = 3;
                reaction[i].c = 2*Parameter_getValue(p)/V;
            }
            else if(SpeciesReference_getStoichiometry(sr) == 3 )
            {
            	reaction[i].type = 4;
                reaction[i].c = 3*Parameter_getValue(p)/(V*V);	//mallon
            }
            else 
            {
                reaction[i].type = 1;
            	reaction[i].c = Parameter_getValue(p);
            }
        }
    }

	for(i=0;i<num_species;i++)
	{
		//fprintf(pf5,"%d\t%s\n",(int)species[i].conc,species[i].name2);
		fprintf(pf5,"%d\t\n",(int)species[i].conc);
	}

	for(i=0;i<num_reactions;i++)
	{
		for(k=0;k<reaction[i].react_num;k++)
		{
			fprintf(pf1,"%d\t",reaction[i].react[k].x+1);
			fprintf(pf3,"%d\t",reaction[i].react[k].v);
		}
		
		for(k=0;k<reaction[i].product_num;k++)
		{
			fprintf(pf2,"%d\t",reaction[i].product[k].x+1);
			fprintf(pf4,"%d\t",reaction[i].product[k].v);
		}

		fprintf(pf1,"\n");
		fprintf(pf3,"\n");
		fprintf(pf2,"\n");
		fprintf(pf4,"\n");
		
		fprintf(pf6,"%f\n",reaction[i].k);
		
		
		
	}
	
	
    fclose(pf1);
    fclose(pf2);
    fclose(pf3);
    fclose(pf4);
    fclose(pf5);
    fclose(pf6);
    fclose(fsize);

}