END_TEST
START_TEST (test_L3_Species_initDefaults)
{
Species_t *s = Species_create(3,1);
fail_unless( Species_getId (s) == NULL );
fail_unless( Species_getName (s) == NULL );
fail_unless( Species_getCompartment (s) == NULL );
fail_unless( util_isNaN(Species_getInitialAmount (s)) );
fail_unless( util_isNaN(Species_getInitialConcentration (s)) );
fail_unless( Species_getSubstanceUnits (s) == NULL );
fail_unless( Species_getHasOnlySubstanceUnits(s) == 0 );
fail_unless( Species_getBoundaryCondition(s) == 0 );
fail_unless( Species_getConstant(s) == 0 );
fail_unless( Species_getConversionFactor (s) == NULL );
fail_unless( !Species_isSetId (s) );
fail_unless( !Species_isSetName (s) );
fail_unless( !Species_isSetCompartment (s) );
fail_unless( !Species_isSetInitialAmount (s) );
fail_unless( !Species_isSetInitialConcentration (s) );
fail_unless( !Species_isSetSubstanceUnits (s) );
fail_unless( !Species_isSetHasOnlySubstanceUnits(s) );
fail_unless( !Species_isSetBoundaryCondition(s) );
fail_unless( !Species_isSetConstant(s) );
fail_unless( !Species_isSetConversionFactor (s) );
Species_initDefaults(s);
fail_unless( Species_getId (s) == NULL );
fail_unless( Species_getName (s) == NULL );
fail_unless( Species_getCompartment (s) == NULL );
fail_unless( util_isNaN(Species_getInitialAmount (s)) );
fail_unless( util_isNaN(Species_getInitialConcentration (s)) );
fail_unless( !strcmp(Species_getSubstanceUnits (s),"mole" ));
fail_unless( Species_getHasOnlySubstanceUnits(s) == 0 );
fail_unless( Species_getBoundaryCondition(s) == 0 );
fail_unless( Species_getConstant(s) == 0 );
fail_unless( Species_getConversionFactor (s) == NULL );
fail_unless( !Species_isSetId (s) );
fail_unless( !Species_isSetName (s) );
fail_unless( !Species_isSetCompartment (s) );
fail_unless( !Species_isSetInitialAmount (s) );
fail_unless( !Species_isSetInitialConcentration (s) );
fail_unless( Species_isSetSubstanceUnits (s) );
fail_unless( Species_isSetHasOnlySubstanceUnits(s) );
fail_unless( Species_isSetBoundaryCondition(s) );
fail_unless( Species_isSetConstant(s) );
fail_unless( !Species_isSetConversionFactor (s) );
Species_free(s);
}
SBML_ODESOLVER_API void CvodeData_initializeValues(cvodeData_t *data)
{
int i;
Parameter_t *p;
Species_t *s;
Compartment_t *c;
odeModel_t *om = data->model;
Model_t *ode = om->simple;
/* First, fill cvodeData_t structure with data from
the derived SBML model */
for ( i=0; i<data->nvalues; i++ ) {
if ( (s = Model_getSpeciesById(ode, om->names[i])) )
data->value[i] = Species_getInitialConcentration(s);
else if ( (c = Model_getCompartmentById(ode, om->names[i])) )
data->value[i] = Compartment_getSize(c);
else if ((p = Model_getParameterById(ode, om->names[i])) )
data->value[i] = Parameter_getValue(p);
}
/* initialize assigned parameters */
for ( i=0; i<om->nass; i++ )
data->value[om->neq+i] = evaluateAST(om->assignment[i],data);
/* set current time to 0 */
data->currenttime = 0.0;
}
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_L3_Species_initialConcentration)
{
double initialConcentration = 0.2;
fail_unless( !Species_isSetInitialConcentration(S));
fail_unless( util_isNaN(Species_getInitialConcentration(S)));
Species_setInitialConcentration(S, initialConcentration);
fail_unless( Species_getInitialConcentration(S) == initialConcentration );
fail_unless( Species_isSetInitialConcentration(S) );
Species_unsetInitialConcentration(S);
fail_unless( !Species_isSetInitialConcentration(S) );
fail_unless( util_isNaN(Species_getInitialConcentration(S)));
}
END_TEST
START_TEST (test_L3_Species_createWithNS )
{
XMLNamespaces_t *xmlns = XMLNamespaces_create();
XMLNamespaces_add(xmlns, "http://www.sbml.org", "testsbml");
SBMLNamespaces_t *sbmlns = SBMLNamespaces_create(3,1);
SBMLNamespaces_addNamespaces(sbmlns,xmlns);
Species_t *s =
Species_createWithNS (sbmlns);
fail_unless( SBase_getTypeCode ((SBase_t *) s) == SBML_SPECIES );
fail_unless( SBase_getMetaId ((SBase_t *) s) == NULL );
fail_unless( SBase_getNotes ((SBase_t *) s) == NULL );
fail_unless( SBase_getAnnotation((SBase_t *) s) == NULL );
fail_unless( SBase_getLevel ((SBase_t *) s) == 3 );
fail_unless( SBase_getVersion ((SBase_t *) s) == 1 );
fail_unless( Species_getNamespaces (s) != NULL );
fail_unless( XMLNamespaces_getLength(Species_getNamespaces(s)) == 2 );
fail_unless( Species_getId (s) == NULL );
fail_unless( Species_getName (s) == NULL );
fail_unless( Species_getCompartment (s) == NULL );
fail_unless( util_isNaN(Species_getInitialAmount (s)) );
fail_unless( util_isNaN(Species_getInitialConcentration (s)) );
fail_unless( Species_getSubstanceUnits (s) == NULL );
fail_unless( Species_getHasOnlySubstanceUnits(s) == 0 );
fail_unless( Species_getBoundaryCondition(s) == 0 );
fail_unless( Species_getConstant(s) == 0 );
fail_unless( Species_getConversionFactor (s) == NULL );
fail_unless( !Species_isSetId (s) );
fail_unless( !Species_isSetName (s) );
fail_unless( !Species_isSetCompartment (s) );
fail_unless( !Species_isSetInitialAmount (s) );
fail_unless( !Species_isSetInitialConcentration (s) );
fail_unless( !Species_isSetSubstanceUnits (s) );
fail_unless( !Species_isSetHasOnlySubstanceUnits(s) );
fail_unless( !Species_isSetBoundaryCondition(s) );
fail_unless( !Species_isSetConstant(s) );
fail_unless( !Species_isSetConversionFactor (s) );
Species_free(s);
XMLNamespaces_free(xmlns);
SBMLNamespaces_free(sbmlns);
}
END_TEST
START_TEST (test_Species_setInitialConcentration)
{
fail_unless( !Species_isSetInitialAmount (S) );
fail_unless( !Species_isSetInitialConcentration(S) );
Species_setInitialConcentration(S, 3.4);
fail_unless( !Species_isSetInitialAmount (S) );
fail_unless( Species_isSetInitialConcentration(S) );
fail_unless( Species_getInitialConcentration(S) == 3.4 );
}
END_TEST
START_TEST (test_SBMLConvert_convertToL1_Species_Concentration)
{
SBMLDocument_t *d = SBMLDocument_createWithLevelAndVersion(2, 1);
Model_t *m = SBMLDocument_createModel(d);
const char *sid = "C";
Compartment_t *c =
Compartment_create(2, 1);
Species_t *s =
Species_create(2, 1);
Compartment_setId ( c, sid );
Compartment_setSize ( c, 1.2 );
Model_addCompartment( m, c );
Species_setId ( s, "s" );
Species_setCompartment ( s, sid );
Species_setInitialConcentration( s, 2.34 );
Model_addSpecies ( m, s );
fail_unless( SBMLDocument_setLevelAndVersion(d, 1, 2) == 1, NULL);
/**
* These tests will fail under Cygwin because of a minimal
* setlocale() implementation (see setlocale manpage).
*/
#ifndef CYGWIN
fail_unless( Species_getInitialAmount(Model_getSpecies(m, 0)) == 2.808, NULL );
#endif
Species_t * s1 = Model_getSpecies(m, 0);
fail_unless (s1 != NULL);
fail_unless (!strcmp(Species_getCompartment(s1), "C"));
fail_unless(Compartment_getSize(Model_getCompartmentById(m, "C")) == 1.2);
fail_unless(Species_getInitialConcentration(s1) == 2.34);
fail_unless(Species_isSetInitialConcentration(s1) == 1);
SBMLDocument_free(d);
}
END_TEST
START_TEST (test_Species_setInitialConcentration2)
{
Species_t *c =
Species_create(2, 2);
int i = Species_setInitialConcentration(c, 4);
fail_unless( i == LIBSBML_OPERATION_SUCCESS );
fail_unless( Species_getInitialConcentration(c) == 4 );
fail_unless( Species_isSetInitialConcentration(c));
i = Species_unsetInitialConcentration(c);
fail_unless( i == LIBSBML_OPERATION_SUCCESS );
fail_unless( !Species_isSetInitialConcentration(c));
Species_free(c);
}
/*
setValues: the user can enter a species name and
change its initial condition (amount or concentration)
*/
static void setValues(Model_t *m) {
char *species;
char *newIA;
char *newIC;
Species_t *s;
printf("Please enter the id of the species to change: ");
species = get_line(stdin);
species = util_trim(species);
if ( (s = Model_getSpeciesById(m,species) ) ) {
printf("\n");
printf("Id: %s\n", Species_getId(s));
if ( Species_isSetName(s) ) {
printf("Name: %s\n", Species_getName(s));
}
if ( Species_isSetInitialAmount(s) ) {
printf("Initial Amount: %g", Species_getInitialAmount(s));
}
else if (Species_isSetInitialConcentration(s) ) {
printf("Initial Concentration: %g", Species_getInitialConcentration(s));
}
if ( Species_getHasOnlySubstanceUnits(s) ) {
if ( Species_isSetSubstanceUnits(s) ) {
printf("%s ", Species_getSubstanceUnits(s));
}
} else {
if ( Species_isSetSubstanceUnits(s) ) {
printf("%s ", Species_getSubstanceUnits(s));
}
if ( Species_isSetSpatialSizeUnits(s) ) {
printf("%s%s", "/", Species_getSpatialSizeUnits(s));
}
}
if ( Species_getHasOnlySubstanceUnits(s) ) {
printf(" (has only substance units)");
}
printf("\n");
if ( Species_isSetCharge(s) ) {
printf("Charge: %-10d", Species_getCharge(s));
}
printf("\n");
printf("%s ", Species_getBoundaryCondition(s) ?
"Species is a Boundary\n" : "\n");
printf("%s ", Species_getConstant(s) ?
"Species is set constant" : "\n");
printf("\n");
if ( Species_isSetInitialAmount(s) ) {
printf("Please enter new initial Amount: ");
newIA = get_line(stdin);
newIA = util_trim(newIA);
Species_setInitialAmount(s, (float) atof(newIA));
}
else if ( Species_isSetInitialConcentration(s) ) {
printf("Please enter new initial Concentration: ");
newIC = get_line(stdin);
newIC = util_trim(newIC);
Species_setInitialConcentration(s, (float) atof(newIC));
}
}
else {
printf("%s not found.\n", species);
}
}
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);
}
