END_TEST
/**
* setMathFromFormula() is no longer necessary. LibSBML now keeps formula
* strings and math ASTs synchronized automatically. This (now modified)
* test is kept around to demonstrate the behavioral change.
*/
START_TEST (test_KineticLaw_setMathFromFormula)
{
const char *initial_formula = "k3 / k2";
char* formula;
fail_unless( !KineticLaw_isSetMath (kl) );
fail_unless( !KineticLaw_isSetFormula(kl) );
KineticLaw_setFormula(kl, initial_formula);
fail_unless( KineticLaw_isSetMath (kl) );
fail_unless( KineticLaw_isSetFormula(kl) );
formula = SBML_formulaToString( KineticLaw_getMath(kl) );
fail_unless( !strcmp(formula, initial_formula) );
safe_free(formula);
}
END_TEST
START_TEST (test_KineticLaw_setMath1)
{
ASTNode_t *math = ASTNode_createWithType(AST_TIMES);
ASTNode_t *a = ASTNode_create();
ASTNode_t *b = ASTNode_create();
ASTNode_setName(a, "a");
ASTNode_setName(b, "b");
ASTNode_addChild(math, a);
ASTNode_addChild(math, b);
char *formula;
const ASTNode_t *math1;
int i = KineticLaw_setMath(kl, math);
fail_unless( i == LIBSBML_OPERATION_SUCCESS);
fail_unless( KineticLaw_isSetMath(kl) );
math1 = KineticLaw_getMath(kl);
fail_unless( math1 != NULL );
formula = SBML_formulaToString(math1);
fail_unless( formula != NULL );
fail_unless( !strcmp(formula, "a * b") );
ASTNode_free(math);
}
void prepare_reversible_fast_reaction(Model_t *m, myReaction *re[], mySpecies *sp[], myParameter *param[], myCompartment *comp[], double sim_time, double dt, double *time, myInitialAssignment *initAssign[], char *time_variant_target_id[], unsigned int num_of_time_variant_targets, timeVariantAssignments *timeVarAssign, allocated_memory *mem, copied_AST *cp_AST){
unsigned int i;
unsigned int num_of_reactions = Model_getNumReactions(m);
ASTNode_t *node, *cp_node1, *cp_node2;
myASTNode *myNode = NULL;
myASTNode *copied_myAST[MAX_COPIED_AST];
unsigned int num_of_copied_myAST = 0;
for(i=0; i<num_of_reactions; i++){
if(re[i]->is_fast && re[i]->is_reversible){
node = (ASTNode_t*)KineticLaw_getMath(Reaction_getKineticLaw(re[i]->origin));
node = ASTNode_deepCopy(node);
TRACE(("original math of %s: ", Reaction_getId(re[i]->origin)));
check_AST(node, NULL);
/* alter_tree_structure(m, &node, cp_AST); */
alter_tree_structure(m, &node, NULL, 0, cp_AST);
set_local_para_as_value(node, Reaction_getKineticLaw(re[i]->origin));
TRACE(("alterated math of %s : ", Reaction_getId(re[i]->origin)));
check_AST(node, NULL);
cp_node1 = ASTNode_deepCopy(node);
cp_node2 = ASTNode_deepCopy(node);
/* get products numerator */
myNode = (myASTNode*)malloc(sizeof(myASTNode));
copied_myAST[num_of_copied_myAST++] = myNode;
myNode->origin = cp_node1;
myNode->parent = NULL;
myNode->left = NULL;
myNode->right = NULL;
myASTNode_create(myNode, cp_node1, copied_myAST, &num_of_copied_myAST);
re[i]->products_equili_numerator = (equation*)malloc(sizeof(equation));
TRACE(("target_id is %s\n", Species_getId(re[i]->reactants[0]->mySp->origin)));
check_AST(cp_node1, NULL);
_prepare_reversible_fast_reaction(m, myNode, re[i], sp, param, comp, re, sim_time, dt, time, initAssign, time_variant_target_id, num_of_time_variant_targets, timeVarAssign, (char*)Species_getId(re[i]->reactants[0]->mySp->origin), 0, mem);
/* get reactants numerator */
myNode = (myASTNode*)malloc(sizeof(myASTNode));
copied_myAST[num_of_copied_myAST++] = myNode;
myNode->origin = cp_node2;
myNode->parent = NULL;
myNode->left = NULL;
myNode->right = NULL;
re[i]->reactants_equili_numerator = (equation*)malloc(sizeof(equation));
myASTNode_create(myNode, cp_node2, copied_myAST, &num_of_copied_myAST);
TRACE(("target_id is %s\n", Species_getId(re[i]->products[0]->mySp->origin)));
check_AST(cp_node2, NULL);
_prepare_reversible_fast_reaction(m, myNode, re[i], sp, param, comp, re, sim_time, dt, time, initAssign, time_variant_target_id, num_of_time_variant_targets, timeVarAssign, (char*)Species_getId(re[i]->products[0]->mySp->origin), 1, mem);
myASTNode_free(copied_myAST, num_of_copied_myAST);
}
}
}
int
main (int argc, char *argv[]){
int i, j;
char *model;
double time;
double printstep;
/* libSBML types */
SBMLDocument_t *d;
SBMLReader_t *sr;
Model_t *m;
Reaction_t *r;
KineticLaw_t *kl;
ASTNode_t *nary;
ASTNode_t *diff;
/* SOSlib types */
SBMLResults_t *results;
timeCourse_t *tc;
cvodeSettings_t *set;
/* parsing command-line arguments */
if (argc < 4 ) {
fprintf(stderr,
"usage %s sbml-model-file simulation-time time-steps\n",
argv[0]);
exit(EXIT_FAILURE);
}
model = argv[1];
time = atof(argv[2]);
printstep = atoi(argv[3]);
/* parsing the SBML model with libSBML */
sr = SBMLReader_create();
d = SBMLReader_readSBML(sr, model);
SBMLReader_free(sr);
m = SBMLDocument_getModel(d);
r = Model_getReaction(m,0);
kl = Reaction_getKineticLaw(r);
nary = KineticLaw_getMath(kl);
printf("N-ary formula: %s\n", SBML_formulaToString(nary));
diff = differentiateAST(nary, "Product");
printf("N-ary diff: %s\n", SBML_formulaToString(diff));
ASTNode_free(diff);
return (EXIT_SUCCESS);
}
void
printReactionMath (unsigned int n, Reaction_t *r)
{
char *formula;
KineticLaw_t *kl;
if (Reaction_isSetKineticLaw(r))
{
kl = Reaction_getKineticLaw(r);
if ( KineticLaw_isSetMath(kl) )
{
formula = SBML_formulaToString( KineticLaw_getMath(kl) );
printf("Reaction %d, formula: %s\n", n, formula);
free(formula);
}
}
}
void
printReactionMath (unsigned int n, Reaction_t *r)
{
char *formula;
KineticLaw_t *kl;
if (Reaction_isSetKineticLaw(r))
{
kl = Reaction_getKineticLaw(r);
if ( KineticLaw_isSetMath(kl) )
{
formula = SBML_formulaToDot( KineticLaw_getMath(kl) );
fprintf(fout, "subgraph cluster%u {\n", noClusters);
fprintf(fout, "label=\"Reaction: %s\";\n%s\n", Reaction_getId(r), formula);
free(formula);
noClusters++;
}
}
}
END_TEST
START_TEST (test_KineticLaw_setMath)
{
ASTNode_t *math = SBML_parseFormula("k3 / k2");
char *formula;
const ASTNode_t *math1;
KineticLaw_setMath(kl, math);
math1 = KineticLaw_getMath(kl);
fail_unless( math1 != NULL );
formula = SBML_formulaToString(math1);
fail_unless( formula != NULL );
fail_unless( !strcmp(formula, "k3 / k2") );
fail_unless( KineticLaw_getMath(kl) != math );
fail_unless( KineticLaw_isSetMath(kl) );
safe_free(formula);
/* Reflexive case (pathological) */
KineticLaw_setMath(kl, (ASTNode_t *) KineticLaw_getMath(kl));
math1 = KineticLaw_getMath(kl);
fail_unless( math1 != NULL );
formula = SBML_formulaToString(math1);
fail_unless( formula != NULL );
fail_unless( !strcmp(formula, "k3 / k2") );
fail_unless( KineticLaw_getMath(kl) != math );
safe_free(formula);
KineticLaw_setMath(kl, NULL);
fail_unless( !KineticLaw_isSetMath(kl) );
if (KineticLaw_getMath(kl) != NULL)
{
fail( "KineticLaw_setMath(kl, NULL) did not clear ASTNode." );
}
ASTNode_free(math);
}
static int printXMGReactionTimeCourse ( cvodeData_t *data )
{
int i, j, k, n;
double maxY, minY, result;
Model_t *m;
Reaction_t *r;
KineticLaw_t *kl;
ASTNode_t **kls;
odeModel_t *om = data->model;
cvodeResults_t *results = data->results;
maxY = 0.0;
minY = 0.0;
fprintf(stderr,
"Printing time development of reaction fluxes to XMGrace!\n");
if ( om->m == NULL ) {
fprintf(stderr, "Error: No reaction model availabe\n");
return 1;
}
else m = om->m;
if ( openXMGrace(data) > 0 ) {
fprintf(stderr, "Error: Couldn't open XMGrace\n");
return 1;
}
GracePrintf("yaxis label \"%s\"", "flux [substance/time]");
if ( Model_isSetName(m) )
GracePrintf("subtitle \"%s, %s\"", Model_getName(m),
"reaction flux time courses");
else if ( Model_isSetId(m) )
GracePrintf("subtitle \"%s, %s\"", Model_getId(m),
"reaction flux time courses");
else
GracePrintf("subtitle \"model has no name, %s/id\"",
"reaction flux time courses");
/* print legend */
for ( i=0; i<Model_getNumReactions(m); i++ ) {
r = Model_getReaction(m, i);
if ( Reaction_isSetName(r) )
GracePrintf("g0.s%d legend \"%s: %s \"\n", i+1,
Reaction_getId(r), Reaction_getName(r));
else
GracePrintf("g0.s%d legend \"%s \"\n", i+1, Reaction_getId(r));
}
GracePrintf("legend 1.155, 0.85");
GracePrintf("legend font 8");
GracePrintf("legend char size 0.6");
if(!(kls = (ASTNode_t **)calloc(Model_getNumReactions(m),
sizeof(ASTNode_t *))))
fprintf(stderr, "failed!\n");
for ( i=0; i<Model_getNumReactions(m); i++ ) {
r = Model_getReaction(m, i);
kl = Reaction_getKineticLaw(r);
kls[i] = copyAST(KineticLaw_getMath(kl));
AST_replaceNameByParameters(kls[i], KineticLaw_getListOfParameters(kl));
AST_replaceConstants(m, kls[i]);
}
/* evaluate flux for each time point and print to XMGrace */
for ( i=0; i<=results->nout; i++ ) {
n = 1;
/* set time and variable values to values at time[k] */
data->currenttime = results->time[i];
for ( j=0; j<data->model->neq; j++ )
data->value[j] = results->value[j][i];
/* evaluate kinetic law expressions */
for ( j=0; j<Model_getNumReactions(m); j++ ) {
result = evaluateAST(kls[j], data);
if ( result > maxY ) {
maxY = result;
GracePrintf("world ymax %g", 1.25*maxY);
}
if ( result < minY ) {
minY = result;
GracePrintf("world ymin %g", 1.25*minY);
}
GracePrintf("g0.s%d point %g, %g",
n, results->time[i], result);
n++;
}
}
GracePrintf("yaxis tick major %g", 1.25*(fabs(maxY)+fabs(minY))/10);
GracePrintf("redraw");
closeXMGrace(data, "flux");
/* free temporary ASTNodes */
for ( i=0; i<Model_getNumReactions(m); i++ )
ASTNode_free(kls[i]);
free(kls);
return 0;
}
void printReactionTimeCourse(cvodeData_t *data, Model_t *m, FILE *f)
{
int i, j;
cvodeResults_t *results;
Reaction_t *r;
KineticLaw_t *kl;
ASTNode_t **kls;
if ( data == NULL || data->results == NULL ) {
Warn(stderr, "No results, please integrate first.\n");
return;
}
#if USE_GRACE
if ( Opt.Xmgrace == 1 ) {
printXMGReactionTimeCourse(data);
return;
}
#endif
results = data->results;
if ( Opt.PrintMessage )
fprintf(stderr,
"\nPrinting time course of the reactions (kinetic laws).\n\n");
if(!(kls =
(ASTNode_t **)calloc(Model_getNumReactions(m),
sizeof(ASTNode_t *)))) {
fprintf(stderr, "failed!\n");
}
fprintf(f, "#t ");
for ( i=0; i<Model_getNumReactions(m); i++ ) {
r = Model_getReaction(m, i);
kl = Reaction_getKineticLaw(r);
kls[i] = copyAST(KineticLaw_getMath(kl));
AST_replaceNameByParameters(kls[i], KineticLaw_getListOfParameters(kl));
AST_replaceConstants(m, kls[i]);
fprintf(f, "%s ", Reaction_getId(r));
}
fprintf(f, "\n");
fprintf(f, "##REACTION RATES\n");
for ( i=0; i<=results->nout; ++i ) {
fprintf(f, "%g ", results->time[i]);
data->currenttime = results->time[i];
for ( j=0; j<data->model->neq; j++ ) {
data->value[j] = results->value[j][i];
}
for ( j=0; j<Model_getNumReactions(m); j++ ) {
fprintf(f, "%g ", evaluateAST(kls[j], data));
}
fprintf(f, "\n");
}
fprintf(f, "##REACTION RATES\n");
fprintf(f, "#t ");
for ( i=0; i<Model_getNumReactions(m); i++ ) {
r = Model_getReaction(m, i);
fprintf(f, "%s ", Reaction_getId(r));
ASTNode_free(kls[i]);
}
free(kls);
fprintf(f, "\n");
fflush(f);
#if !USE_GRACE
if ( Opt.Xmgrace == 1 ) {
fprintf(stderr,
"odeSolver has been compiled without XMGRACE functionality.\n");
fprintf(stderr,
"The requested data have been printed to stdout instead.\n");
}
#endif
}
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");
}
}
