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"); } }