void printMath (Model_t *m) { unsigned int n; for (n = 0; n < Model_getNumFunctionDefinitions(m); ++n) { printFunctionDefinition(n + 1, Model_getFunctionDefinition(m, n)); } for (n = 0; n < Model_getNumRules(m); ++n) { printRuleMath(n + 1, Model_getRule(m, n)); } printf("\n"); for (n = 0; n < Model_getNumReactions(m); ++n) { printReactionMath(n + 1, Model_getReaction(m, n)); } printf("\n"); for (n = 0; n < Model_getNumEvents(m); ++n) { printEventMath(n + 1, Model_getEvent(m, n)); } }
void printMath (Model_t *m) { unsigned int n; /* a digraph must have a name thus * need to check that Model_getId does not return NULL * and provide a name if it does */ if (Model_getId(m) != NULL) { fprintf(fout, "digraph %s {\n", Model_getId(m)); } else { fprintf(fout, "digraph example {\n"); } fprintf(fout, "compound=true;\n"); for (n = 0; n < Model_getNumFunctionDefinitions(m); ++n) { printFunctionDefinition(n + 1, Model_getFunctionDefinition(m, n)); } for (n = 0; n < Model_getNumRules(m); ++n) { printRuleMath(n + 1, Model_getRule(m, n)); } printf("\n"); for (n = 0; n < Model_getNumReactions(m); ++n) { printReactionMath(n + 1, Model_getReaction(m, n)); } printf("\n"); for (n = 0; n < Model_getNumEvents(m); ++n) { printEventMath(n + 1, Model_getEvent(m, n)); } fprintf(fout, "}\n"); }
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_SBMLConvertStrict_convertL1ParamRule) { SBMLDocument_t *d = SBMLDocument_createWithLevelAndVersion(1, 2); Model_t * m = SBMLDocument_createModel(d); /* create a compartment */ Compartment_t * c = Model_createCompartment(m); Compartment_setId(c, "c"); /* create a parameter */ Parameter_t * p = Model_createParameter(m); Parameter_setId(p, "p"); Parameter_t * p1 = Model_createParameter(m); Parameter_setId(p1, "p1"); /* create a math element */ ASTNode_t *math = SBML_parseFormula("p"); /* create an assignment rule */ Rule_t *ar = Model_createAssignmentRule(m); Rule_setVariable(ar, "p1"); Rule_setMath(ar, math); Rule_setUnits(ar, "mole"); fail_unless( SBMLDocument_setLevelAndVersionStrict(d, 2, 1) == 1 ); fail_unless( SBMLDocument_getLevel (d) == 2, NULL ); fail_unless( SBMLDocument_getVersion(d) == 1, NULL ); Rule_t * r1 = Model_getRule(SBMLDocument_getModel(d), 0); fail_unless (Rule_getUnits(r1) == NULL ); 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; }
/* allocates memory for substructures of a new odeModel, writes variable and parameter names and returns a pointer to the the newly created odeModel. */ static odeModel_t * ODEModel_fillStructures(Model_t *ode) { int i, j, found, neq, nalg, nconst, nass, nevents, nvalues; Compartment_t *c; Parameter_t *p; Species_t *s; Rule_t *rl; AssignmentRule_t *ar; AlgebraicRule_t *alr; RateRule_t *rr; SBMLTypeCode_t type; ASTNode_t *math; odeModel_t *om; neq = 0; nalg = 0; nconst = 0; nass = 0; nvalues = 0; found = 0; /* counting number of equations (ODEs/rateRules and assignment Rules) to initialize CvodeData structure. Any other occuring values are stored as parameters. */ for ( j=0; j<Model_getNumRules(ode); j++ ) { rl = Model_getRule(ode,j); type = SBase_getTypeCode((SBase_t *)rl); if ( type == SBML_RATE_RULE ) neq++; if ( type == SBML_ASSIGNMENT_RULE ) nass++; if ( type == SBML_ALGEBRAIC_RULE ) { nalg++; } } nvalues = Model_getNumCompartments(ode) + Model_getNumSpecies(ode) + Model_getNumParameters(ode); nconst = nvalues - nass - neq - nalg; nevents = Model_getNumEvents(ode); om = ODEModel_allocate(neq, nconst, nass, nevents, nalg); RETURN_ON_FATALS_WITH(NULL); om->neq = neq; om->nalg = nalg; /* this causes crash at the moment, because ODEs have been constructed for that should be defined by alg. rules */ om->nconst = nconst; om->nass = nass; om->nsens = 0; /* sensitivity parameters can be chosen later */ /* filling the Ids of all rate rules (ODEs) and assignment rules the ODE model */ neq = 0; nass = 0; nalg = 0; for ( j=0; j<Model_getNumRules(ode); j++ ) { rl = Model_getRule(ode,j); type = SBase_getTypeCode((SBase_t *)rl); if ( type == SBML_RATE_RULE ) { rr = (RateRule_t *)rl; ASSIGN_NEW_MEMORY_BLOCK(om->names[neq], strlen(RateRule_getVariable(rr))+1, char, NULL) sprintf(om->names[neq],RateRule_getVariable(rr)); neq++; } else if ( type == SBML_ASSIGNMENT_RULE ) {
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; }
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"); } }