/** * \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))); } }
END_TEST START_TEST (test_Reaction_addProductBySpecies) { Species_t *s = Species_create(2, 4); Species_setId(s, "s"); Reaction_addProductBySpecies(R, s, 2.0, "sr", 0); fail_unless( Reaction_getNumReactants(R) == 0 ); fail_unless( Reaction_getNumProducts (R) == 1 ); fail_unless( Reaction_getNumModifiers(R) == 0 ); SpeciesReference_t *sr = Reaction_getProduct(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_addProductBySpecies(R, s, 1.0, "sr", 0) == LIBSBML_DUPLICATE_OBJECT_ID); fail_unless( Reaction_getNumProducts (R) == 1 ); Species_free(s); }
END_TEST START_TEST (test_SpeciesReference_setStoichiometryMath1) { StoichiometryMath_t * sm = StoichiometryMath_create(2, 4); 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); StoichiometryMath_setMath(sm, math); int i = SpeciesReference_setStoichiometryMath(sr, sm); fail_unless( i == LIBSBML_OPERATION_SUCCESS); fail_unless( SpeciesReference_isSetStoichiometryMath(sr) ); fail_unless( SpeciesReference_getStoichiometry(sr) == 1 ); i = SpeciesReference_unsetStoichiometryMath(sr); fail_unless( i == LIBSBML_OPERATION_SUCCESS); fail_unless( !SpeciesReference_isSetStoichiometryMath(sr) ); StoichiometryMath_free(sm); }
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; }
END_TEST START_TEST (test_SpeciesReference_setStoichiometry1) { int i = SpeciesReference_setStoichiometry(sr, 2.0); fail_unless( i == LIBSBML_OPERATION_SUCCESS ); fail_unless( SpeciesReference_getStoichiometry(sr) == 2.0 ); }
END_TEST START_TEST (test_L3_SpeciesReference_stoichiometry) { double stoichiometry = 0.2; fail_unless( !SpeciesReference_isSetStoichiometry(SR)); fail_unless( util_isNaN(SpeciesReference_getStoichiometry(SR))); SpeciesReference_setStoichiometry(SR, stoichiometry); fail_unless( SpeciesReference_getStoichiometry(SR) == stoichiometry ); fail_unless( SpeciesReference_isSetStoichiometry(SR) ); SpeciesReference_unsetStoichiometry(SR); fail_unless( !SpeciesReference_isSetStoichiometry(SR) ); fail_unless( util_isNaN(SpeciesReference_getStoichiometry(SR))); }
END_TEST START_TEST (test_SpeciesReference_setStoichiometry2) { SpeciesReference_t *c = SpeciesReference_create(2, 2); int i = SpeciesReference_setStoichiometry(c, 4); fail_unless( i == LIBSBML_OPERATION_SUCCESS ); fail_unless( SpeciesReference_getStoichiometry(c) == 4.0 ); SpeciesReference_free(c); }
END_TEST START_TEST (test_L3_SpeciesReference_createWithNS ) { XMLNamespaces_t *xmlns = XMLNamespaces_create(); XMLNamespaces_add(xmlns, "http://www.sbml.org", "testsbml"); SBMLNamespaces_t *sbmlns = SBMLNamespaces_create(3,1); SBMLNamespaces_addNamespaces(sbmlns,xmlns); SpeciesReference_t *sr = SpeciesReference_createWithNS (sbmlns); fail_unless( SBase_getTypeCode ((SBase_t *) sr) == SBML_SPECIES_REFERENCE ); fail_unless( SBase_getMetaId ((SBase_t *) sr) == NULL ); fail_unless( SBase_getNotes ((SBase_t *) sr) == NULL ); fail_unless( SBase_getAnnotation((SBase_t *) sr) == NULL ); fail_unless( SBase_getLevel ((SBase_t *) sr) == 3 ); fail_unless( SBase_getVersion ((SBase_t *) sr) == 1 ); fail_unless( SpeciesReference_getNamespaces (sr) != NULL ); fail_unless( XMLNamespaces_getLength(SpeciesReference_getNamespaces(sr)) == 2 ); fail_unless( SpeciesReference_getId (sr) == NULL ); fail_unless( SpeciesReference_getName (sr) == NULL ); fail_unless( SpeciesReference_getSpecies (sr) == NULL ); fail_unless( util_isNaN(SpeciesReference_getStoichiometry (sr)) ); fail_unless( SpeciesReference_getConstant(sr) == 0 ); fail_unless( !SpeciesReference_isSetId (sr) ); fail_unless( !SpeciesReference_isSetName (sr) ); fail_unless( !SpeciesReference_isSetSpecies (sr) ); fail_unless( !SpeciesReference_isSetStoichiometry (sr) ); fail_unless( !SpeciesReference_isSetConstant(sr) ); SpeciesReference_free(sr); XMLNamespaces_free(xmlns); SBMLNamespaces_free(sbmlns); }
END_TEST START_TEST (test_SpeciesReference_setStoichiometryMath4) { StoichiometryMath_t * sm = StoichiometryMath_create(2, 4); ASTNode_t *math = NULL; StoichiometryMath_setMath(sm, math); int i = SpeciesReference_setStoichiometryMath(sr, sm); fail_unless( i == LIBSBML_OPERATION_SUCCESS); fail_unless( SpeciesReference_isSetStoichiometryMath(sr) ); fail_unless( SpeciesReference_getStoichiometry(sr) == 1 ); i = SpeciesReference_unsetStoichiometryMath(sr); fail_unless( i == LIBSBML_OPERATION_SUCCESS); fail_unless( !SpeciesReference_isSetStoichiometryMath(sr) ); StoichiometryMath_free(sm); }
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); }