END_TEST
START_TEST (test_Reaction_getReactant)
{
SpeciesReference_t *sr1 = SpeciesReference_create(2, 4);
SpeciesReference_t *sr2 = SpeciesReference_create(2, 4);
SpeciesReference_setSpecies(sr1, "R1");
SpeciesReference_setSpecies(sr2, "R2");
Reaction_addReactant(R, sr1);
Reaction_addReactant(R, sr2);
SpeciesReference_free(sr1);
SpeciesReference_free(sr2);
fail_unless( Reaction_getNumReactants(R) == 2 );
fail_unless( Reaction_getNumProducts (R) == 0 );
fail_unless( Reaction_getNumModifiers(R) == 0 );
sr1 = Reaction_getReactant(R, 0);
sr2 = Reaction_getReactant(R, 1);
fail_unless( !strcmp(SpeciesReference_getSpecies(sr1), "R1") );
fail_unless( !strcmp(SpeciesReference_getSpecies(sr2), "R2") );
}
/**
* \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)));
}
}
int SBML_checkQuantite(Model_t *mod, Reaction_t *react, int nbEspeces, pEspeces molecules)
{
/* Determine le nombre de reaction possible a partir de la quantite des reactifs */
int ref = 0, i;
double quantite = 0.0, minStep = 0.0, temp = 0.0;
SpeciesReference_t *reactif;
Species_t *especeId;
/*TODO Il est possible de reprogrammer ca plus proprement */
/* Recupere la quantite de la premiere molecule */
reactif = Reaction_getReactant(react, 0);
especeId = Model_getSpeciesById(mod, SpeciesReference_getSpecies(reactif));
ref = Especes_find(molecules, Species_getId(especeId), nbEspeces);
/* Cas ou la quantite de la molecule est egale a zero */
if ((quantite = Especes_getQuantite(molecules, ref)) <= 0.0) return END;
/* Calcul du nombre de pas minimum qu'il sera possible d'effectuer */
/* C'est le nombre minimum d'etat de tous les reactifs qui determine le nombre de pas */
minStep = floor(quantite / SpeciesReference_getStoichiometry(reactif));
/*fprintf(stderr,"round species %s minstep %f quantite %f stochiometry %f\n",Species_getId(especeId),round(quantite / SpeciesReference_getStoichiometry(reactif)),quantite,SpeciesReference_getStoichiometry(reactif));
fprintf(stderr,"ceil species %s minstep %f quantite %f stochiometry %f\n",Species_getId(especeId),ceil(quantite / SpeciesReference_getStoichiometry(reactif)),quantite,SpeciesReference_getStoichiometry(reactif));
fprintf(stderr,"floor species %s minstep %f quantite %f stochiometry %f\n",Species_getId(especeId),floor(quantite / SpeciesReference_getStoichiometry(reactif)),quantite,SpeciesReference_getStoichiometry(reactif));*/
/* Cas ou le nombre de pas est egal a 0 */
if(minStep==0.0) return END;
/* On calcule pour les autres reactifs */
for (i = 1; i < (int)Reaction_getNumReactants(react); i++) {
/* Recupere la quantite d'une molecule */
reactif = Reaction_getReactant(react, i);
especeId = Model_getSpeciesById(mod, SpeciesReference_getSpecies(reactif));
ref = Especes_find(molecules, Species_getId(especeId), nbEspeces);
quantite= Especes_getQuantite(molecules, ref);
/* La quantite est egale a 0 */
if(quantite<=0.0) return END;
/* On calcule le nombre de pas minimum qu'il sera possible d'effectuer */
temp = floor(Especes_getQuantite(molecules, ref)/SpeciesReference_getStoichiometry(reactif));
/*fprintf(stderr,"species %s minstep %f temp %f\n",Species_getId(especeId),minStep,temp);*/
/*fprintf(stderr,"round species %s minstep %f quantite %f stochiometry %f\n",Species_getId(especeId),round(quantite / SpeciesReference_getStoichiometry(reactif)),quantite,SpeciesReference_getStoichiometry(reactif));
fprintf(stderr,"ceil species %s minstep %f quantite %f stochiometry %f\n",Species_getId(especeId),ceil(quantite / SpeciesReference_getStoichiometry(reactif)),quantite,SpeciesReference_getStoichiometry(reactif));
fprintf(stderr,"floor species %s minstep %f quantite %f stochiometry %f\n",Species_getId(especeId),floor(quantite / SpeciesReference_getStoichiometry(reactif)),quantite,SpeciesReference_getStoichiometry(reactif));*/
/* Cas ou le nombre de pas est egal a 0 */
if(temp==0.0) return END;
/* Si le nouveau nombre est inferieur au precedent, on change la valeur de minStep */
if (minStep > temp) minStep = temp;
}
/*fprintf(stderr,"minStep returned %d\n",(int)minStep);*/
return (int)minStep;
}
/**
* \fn void SBML_setReactions(Model_t *mod, pEspeces molecules, pScore result, double *reactions_ratio, int nbReactions, int nbEspeces)
* \author Amine Ghozlane
* \brief Alloc memory and initialize the struct Especes
* \param mod Model of the SBML file
* \param molecules Struct Especes
* \param result Struct Score
* \param reactions_ratio List of computed reaction ratio
* \param nbReactions Number of reaction
* \param nbEspeces Number of molecules
*/
void SBML_setReactions(Model_t *mod, pEspeces molecules, pScore result, double *reactions_ratio, int nbReactions, int nbEspeces)
{
/* Initialisation les reactions auquelles participent chaque espece */
int ref = 0, i, j, resultat=OK;
SpeciesReference_t *reactif=NULL;
Species_t *especeId=NULL;
Reaction_t *react=NULL;
const char *kf=NULL;
/*const ASTNode_t *km;*/
KineticLaw_t *kl=NULL;
/* Recherche les reactions ou apparaissent chaque espece */
for (i = 0; i < nbReactions; i++) {
react = Model_getReaction(mod, i);
/* Recherche si la reaction est etudiee */
resultat = SBML_findReaction(result->reaction,Reaction_getId(react), result->nb_reaction);
/* Etude des reactifs */
for (j = 0; j < (int)Reaction_getNumReactants(react); j++) {
/* Recuperation d'un reactif */
reactif = Reaction_getReactant(react, j);
/* Recuperation du nom de l'espece */
especeId = Model_getSpeciesById(mod, SpeciesReference_getSpecies(reactif));
/* Recherche la reference de cette molecule dans la struture molecule */
ref = Especes_find(molecules, Species_getId(especeId), nbEspeces);
/* Recuperation de la loi cinetique sur la */
kl = Reaction_getKineticLaw(react);
/* Reaction dont on recherche le bon ratio */
if(resultat!=OK){
Especes_allocReactions(molecules, ref, react, reactions_ratio[resultat]);
}
/* Si la loi cinetique est au format : formule on recupere le ratio en question */
else if (KineticLaw_isSetFormula(kl)) {
kf = KineticLaw_getFormula(kl);
Especes_allocReactions(molecules, ref, react, SBML_evalExpression(kf));
} else { /* Sinon on n'utilise pas ces informations */
/*km = KineticLaw_getMath(kl);*/
fprintf(stderr,"SBML equation are taken into account, use instead the parameter file\n");
/*exit(EXIT_FAILURE);*/
}
}
}
}
END_TEST
START_TEST (test_SBMLConvert_convertToL3_stoichiometryMath)
{
SBMLDocument_t *d = SBMLDocument_createWithLevelAndVersion(2, 1);
Model_t *m = SBMLDocument_createModel(d);
Compartment_t *c = Model_createCompartment(m);
Compartment_setId ( c, "c" );
Species_t *s = Model_createSpecies(m);
Species_setId(s, "s");
Species_setCompartment(s, "c");
Reaction_t * r = Model_createReaction(m);
SpeciesReference_t *sr = Reaction_createReactant(r);
SpeciesReference_setSpecies(sr, "s");
StoichiometryMath_t *sm = SpeciesReference_createStoichiometryMath(sr);
ASTNode_t * ast = SBML_parseFormula("c*2");
StoichiometryMath_setMath(sm, ast);
fail_unless(Model_getNumRules(m) == 0);
fail_unless(SpeciesReference_isSetId(sr) == 0);
fail_unless( SBMLDocument_setLevelAndVersionNonStrict(d, 3, 1) == 1);
m = SBMLDocument_getModel(d);
r = Model_getReaction(m, 0);
sr = Reaction_getReactant(r, 0);
fail_unless(Model_getNumRules(m) == 1);
fail_unless(SpeciesReference_isSetId(sr) == 1);
Rule_t *rule = Model_getRule(m, 0);
fail_unless( strcmp(SpeciesReference_getId(sr), Rule_getVariable(rule)) == 0 );
SBMLDocument_free(d);
}
END_TEST
START_TEST (test_SBMLConvert_convertToL3_reactant)
{
SBMLDocument_t *d = SBMLDocument_createWithLevelAndVersion(2, 2);
Model_t *m = SBMLDocument_createModel(d);
Reaction_t *r = Model_createReaction(m);
SpeciesReference_t *sr = Reaction_createReactant(r);
SpeciesReference_t *sr1;
SpeciesReference_setSpecies ( sr, "s" );
fail_unless( SBMLDocument_setLevelAndVersionNonStrict(d, 3, 1) == 1, NULL);
sr1 = Reaction_getReactant(Model_getReaction(m, 0), 0);
fail_unless(SpeciesReference_hasRequiredAttributes(sr1) == 1);
SBMLDocument_free(d);
}
END_TEST
START_TEST (test_Reaction_addReactantBySpecies)
{
Species_t *s = Species_create(2, 4);
Species_setId(s, "s");
Reaction_addReactantBySpecies(R, s, 2.0, "sr", 0);
fail_unless( Reaction_getNumReactants(R) == 1 );
fail_unless( Reaction_getNumProducts (R) == 0 );
fail_unless( Reaction_getNumModifiers(R) == 0 );
SpeciesReference_t *sr = Reaction_getReactant(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_addReactantBySpecies(R, s, 1.0, "sr", 0) == LIBSBML_DUPLICATE_OBJECT_ID);
Species_free(s);
}
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;
}
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");
}
}
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);
}