/**
* \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)));
}
}
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;
}
SBML_ODESOLVER_API int IntegratorInstance_updateModel(integratorInstance_t *engine)
{
int i;
Species_t *s;
Compartment_t *c;
Parameter_t *p;
odeModel_t *om = engine->om;
cvodeData_t *data = engine->data;
cvodeResults_t *results = engine->results;
int nout = results->nout;
int nvalues = data->nvalues;
Model_t *m = om->m;
for ( i=0; i<nvalues; i++ ) {
if ( (s = Model_getSpeciesById(m, om->names[i]))
!= NULL ) {
Species_setInitialConcentration(s, results->value[i][nout]);
}
else if ( (c = Model_getCompartmentById(m, om->names[i])) != NULL ) {
Compartment_setSize(c, results->value[i][nout]);
}
else if ( (p = Model_getParameterById(m, om->names[i])) != NULL ) {
Parameter_setValue(p, results->value[i][nout]);
}
else
return 0;
}
return 1;
}
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;
}
static int printXMGLegend(cvodeData_t *data, int nvalues)
{
int i, found;
odeModel_t *om = data->model;
Model_t *m = om->simple;
Species_t *s;
Parameter_t *p;
Compartment_t *c;
for ( i=0; i<nvalues; i++ ) {
found = 0;
if ( (s = Model_getSpeciesById(m, om->names[i])) != NULL ) {
if ( Species_isSetName(s) ) {
GracePrintf("g0.s%d legend \"%s: %s\"\n", i+1,
om->names[i], Species_getName(s));
found++;
}
}
else if ( (c = Model_getCompartmentById(m, om->names[i])) ) {
if ( Compartment_isSetName(c) ) {
GracePrintf("g0.s%d legend \"%s: %s\"\n", i+1,
om->names[i], Compartment_getName(c));
found++;
}
}
else if ( (p = Model_getParameterById(m, om->names[i])) ) {
if ( Parameter_isSetName(p) ) {
GracePrintf("g0.s%d legend \"%s: %s\"\n", i+1,
om->names[i], Parameter_getName(p));
found++;
}
}
if ( found == 0 )
GracePrintf("g0.s%d legend \"%s\"\n", i+1, om->names[i]);
}
GracePrintf("legend 1.155, 0.85");
GracePrintf("legend font 8");
GracePrintf("legend char size 0.6");
return 0;
}
/**
* \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);*/
}
}
}
}
/*
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);
}
}
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;
}
