END_TEST
START_TEST (test_RDFAnnotation_C_parseCVTerms)
{
SBase_t * obj = (SBase_t *) (Model_getCompartment(m, 0));
XMLNode_t* node = RDFAnnotationParser_parseCVTerms(obj);
fail_unless(XMLNode_getNumChildren(node) == 1);
const XMLNode_t* rdf = XMLNode_getChild(node, 0);
fail_unless(!strcmp(XMLNode_getName(rdf), "RDF"));
fail_unless(!strcmp(XMLNode_getPrefix(rdf), "rdf"));
fail_unless(!strcmp(XMLNode_getURI(rdf), "http://www.w3.org/1999/02/22-rdf-syntax-ns#"));
fail_unless(XMLNode_getNumChildren(rdf) == 1);
const XMLNode_t* desc = XMLNode_getChild(rdf, 0);
fail_unless(!strcmp(XMLNode_getName(desc), "Description"));
fail_unless(!strcmp(XMLNode_getPrefix(desc), "rdf"));
fail_unless(!strcmp(XMLNode_getURI(desc), "http://www.w3.org/1999/02/22-rdf-syntax-ns#"));
fail_unless(XMLNode_getNumChildren(desc) == 1);
const XMLNode_t * is1 = XMLNode_getChild(desc, 0);
fail_unless(!strcmp(XMLNode_getName(is1), "is"));
fail_unless(!strcmp(XMLNode_getPrefix(is1), "bqbiol"));
fail_unless(XMLNode_getNumChildren(is1) == 1);
const XMLNode_t * Bag = XMLNode_getChild(is1, 0);
fail_unless(!strcmp(XMLNode_getName(Bag), "Bag"));
fail_unless(!strcmp(XMLNode_getPrefix(Bag), "rdf"));
fail_unless(!strcmp(XMLNode_getURI(Bag), "http://www.w3.org/1999/02/22-rdf-syntax-ns#"));
fail_unless(XMLNode_getNumChildren(Bag) == 4);
const XMLNode_t * li = XMLNode_getChild(Bag, 0);
fail_unless(!strcmp(XMLNode_getName(li), "li"));
fail_unless(!strcmp(XMLNode_getPrefix(li), "rdf"));
fail_unless(!strcmp(XMLNode_getURI(li), "http://www.w3.org/1999/02/22-rdf-syntax-ns#"));
fail_unless(XMLNode_getNumChildren(li) == 0);
const XMLNode_t * li1 = XMLNode_getChild(Bag, 1);
fail_unless(!strcmp(XMLNode_getName(li1), "li"));
fail_unless(!strcmp(XMLNode_getPrefix(li1), "rdf"));
fail_unless(!strcmp(XMLNode_getURI(li1), "http://www.w3.org/1999/02/22-rdf-syntax-ns#"));
fail_unless(XMLNode_getNumChildren(li1) == 0);
const XMLNode_t * li2 = XMLNode_getChild(Bag, 2);
fail_unless(!strcmp(XMLNode_getName(li2), "li"));
fail_unless(!strcmp(XMLNode_getPrefix(li2), "rdf"));
fail_unless(!strcmp(XMLNode_getURI(li2), "http://www.w3.org/1999/02/22-rdf-syntax-ns#"));
fail_unless(XMLNode_getNumChildren(li2) == 0);
const XMLNode_t * li3 = XMLNode_getChild(Bag, 3);
fail_unless(!strcmp(XMLNode_getName(li3), "li"));
fail_unless(!strcmp(XMLNode_getPrefix(li3), "rdf"));
fail_unless(!strcmp(XMLNode_getURI(li3), "http://www.w3.org/1999/02/22-rdf-syntax-ns#"));
fail_unless(XMLNode_getNumChildren(li3) == 0);
XMLNode_free(node);
}
END_TEST
START_TEST (test_SBMLConvertStrict_convertSBO)
{
SBMLDocument_t *d = SBMLDocument_createWithLevelAndVersion(2, 4);
Model_t * m = SBMLDocument_createModel(d);
/* create a compartment with SBO */
Compartment_t * c = Model_createCompartment(m);
Compartment_setId(c, "c");
SBase_setSBOTerm((SBase_t *) (c), 240);
fail_unless( SBMLDocument_setLevelAndVersionStrict(d, 2, 3) == 1 );
fail_unless( SBMLDocument_getLevel (d) == 2, NULL );
fail_unless( SBMLDocument_getVersion(d) == 3, NULL );
fail_unless( SBMLDocument_setLevelAndVersionStrict(d, 2, 2) == 1 );
fail_unless( SBMLDocument_getLevel (d) == 2, NULL );
fail_unless( SBMLDocument_getVersion(d) == 2, NULL );
/* check that sbo term has been removed */
Compartment_t *c1 = Model_getCompartment(SBMLDocument_getModel(d), 0);
fail_unless (SBase_getSBOTerm((SBase_t *) (c1)) == -1, NULL );
SBMLDocument_free(d);
}
END_TEST
START_TEST (test_SBMLConvertStrict_convertNonStrictSBO)
{
SBMLDocument_t *d = SBMLDocument_createWithLevelAndVersion(2, 4);
Model_t * m = SBMLDocument_createModel(d);
/* create a compartment with SBO */
Compartment_t * c = Model_createCompartment(m);
Compartment_setId(c, "c");
Compartment_setConstant(c, 0);
SBase_setSBOTerm((SBase_t *) (c), 64);
/* conversion to L2V3 and L2V2 should fail due to bad SBO
* but to L2V1 and L1 should pass as sbo terms not applicable
*/
fail_unless( SBMLDocument_setLevelAndVersionStrict(d, 2, 3) == 0 );
fail_unless( SBMLDocument_getLevel (d) == 2, NULL );
fail_unless( SBMLDocument_getVersion(d) == 4, NULL );
fail_unless( SBMLDocument_setLevelAndVersionStrict(d, 2, 2) == 0 );
fail_unless( SBMLDocument_getLevel (d) == 2, NULL );
fail_unless( SBMLDocument_getVersion(d) == 4, NULL );
fail_unless( SBMLDocument_setLevelAndVersionStrict(d, 2, 1) == 1 );
fail_unless( SBMLDocument_getLevel (d) == 2, NULL );
fail_unless( SBMLDocument_getVersion(d) == 1, NULL );
/* check that sbo term has been removed */
Compartment_t *c1 = Model_getCompartment(SBMLDocument_getModel(d), 0);
fail_unless (SBase_getSBOTerm((SBase_t *) (c1)) == -1, NULL );
fail_unless( SBMLDocument_setLevelAndVersionStrict(d, 1, 2) == 1 );
fail_unless( SBMLDocument_getLevel (d) == 1, NULL );
fail_unless( SBMLDocument_getVersion(d) == 2, NULL );
/* check that sbo term has been removed */
Compartment_t *c2 = Model_getCompartment(SBMLDocument_getModel(d), 0);
fail_unless (SBase_getSBOTerm((SBase_t *) (c2)) == -1, NULL );
SBMLDocument_free(d);
}
void printSpecies(Model_t *m, FILE *f)
{
int i, j;
Species_t *s;
Compartment_t *c;
fprintf(f, "\n");
fprintf(f, "# Initial Conditions for Species and Compartments:\n");
for ( i=0; i<Model_getNumCompartments(m); i++ ) {
if ( i== 0 ) fprintf(f, "# Compartments:\n");
c = Model_getCompartment(m,i);
if(Compartment_isSetId(c))
fprintf(f, "%s ", Compartment_getId(c));
if(Compartment_isSetName(c))
fprintf(f, "(%s) ", Compartment_getName(c));
if ( Compartment_isSetVolume(c) )
fprintf(f, "= %g; ", Compartment_getSize(c));
fprintf(f, "%s", Compartment_getConstant(c) ? "" : "variable; ");
if(Compartment_isSetOutside(c))
fprintf(f, "outside %s; ", Compartment_getOutside(c));
/* fprintf(f, "\n"); */
fprintf(f, "dimensions %d; ", Compartment_getSpatialDimensions(c));
if(Compartment_isSetUnits(c))
fprintf(f, "[%s]; ", Compartment_getUnits(c));
fprintf(f, "\n");
fprintf(f, "# Species concentrations in `compartment' %s\n",
Compartment_getId(c));
for(j=0;j<Model_getNumSpecies(m);j++){
s = Model_getSpecies(m,j);
if(strcmp(Species_getCompartment(s), Compartment_getId(c))==0){
fprintf(f, "%s ", Species_getId(s));
if(Species_isSetName(s))
fprintf(f, "(%s) ", Species_getName(s));
if ( Species_isSetInitialAmount(s) )
fprintf(f, "= %g/%g; ",
Species_getInitialAmount(s),
Compartment_getSize(c));
else if ( Species_isSetInitialConcentration(s) )
fprintf(f, "= %g; ", Species_getInitialConcentration(s));
else
fprintf(f, "# no initial value;");
fprintf(f, "%s", Species_getBoundaryCondition(s) ? "boundary;" : "");
fprintf(f, "%s", Species_getConstant(s) ? "constant;" : "");
if(Species_isSetCharge(s))
fprintf(f, "charge = %d; ", Species_getCharge(s));
fprintf(f, "\n");
}
}
fprintf(f, "\n");
}
}
END_TEST
START_TEST (test_RDFAnnotation_C_delete)
{
SBase_t * obj = (SBase_t *) (Model_getCompartment(m, 0));
XMLNode_t* node = RDFAnnotationParser_parseCVTerms(obj);
XMLNode_t* n1 = RDFAnnotationParser_deleteRDFAnnotation(node);
fail_unless(XMLNode_getNumChildren(n1) == 0);
fail_unless(!strcmp(XMLNode_getName(n1), "annotation"));
XMLNode_free(node);
}
END_TEST
START_TEST (test_SBMLConvertStrict_convertToL1)
{
SBMLDocument_t *d = SBMLDocument_createWithLevelAndVersion(2, 4);
/* create model with metaid */
Model_t * m = SBMLDocument_createModel(d);
SBase_setMetaId((SBase_t *) (m), "_m");
/* create a compartment with sbo*/
Compartment_t * c = Model_createCompartment(m);
Compartment_setId(c, "c");
SBase_setSBOTerm((SBase_t *) (c), 240);
/* create a species with hasOnlySubstanceUnits = true*/
Species_t *s = Model_createSpecies(m);
Species_setId(s, "s");
Species_setCompartment(s, "c");
Species_setHasOnlySubstanceUnits(s, 1);
fail_unless( SBMLDocument_setLevelAndVersionStrict(d, 1, 2) == 1 );
fail_unless( SBMLDocument_getLevel (d) == 1, NULL );
fail_unless( SBMLDocument_getVersion(d) == 2, NULL );
///* check that attributes that are no longer valid have been removed */
Model_t * m1 = SBMLDocument_getModel(d);
fail_unless (SBase_getMetaId((SBase_t *) (m1)) == NULL);
Compartment_t *c1 = Model_getCompartment(m1, 0);
fail_unless (SBase_getSBOTerm((SBase_t *) (c1)) == -1, NULL );
Species_t *s1 = Model_getSpecies(m1, 0);
fail_unless (Species_getHasOnlySubstanceUnits(s1) == 0);
SBMLDocument_free(d);
}
END_TEST
START_TEST (test_SBMLConvert_convertToL3_compartment)
{
SBMLDocument_t *d = SBMLDocument_createWithLevelAndVersion(2, 2);
Model_t *m = SBMLDocument_createModel(d);
const char *sid = "C";
Compartment_t *c = Model_createCompartment(m);
Compartment_t *c1;
Compartment_setId ( c, sid );
fail_unless( SBMLDocument_setLevelAndVersionNonStrict(d, 3, 1) == 1, NULL);
c1 = Model_getCompartment(m, 0);
fail_unless(Compartment_hasRequiredAttributes(c1) == 1);
SBMLDocument_free(d);
}
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;
}
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;
}
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);
}
