Seems that the bugs are fixed. Pegs are self avoidant now

Samo Penic

2016-07-13 82a8abcddd62838bfcd06b6081042caf4d385a88

 src/restore.c

@@ -57,6 +57,7 @@
                  if ((!xmlStrcmp(cur2->name, (const xmlChar *)"Points"))){
                     //fprintf(stderr,"Found point data\n");
                     if(vesicle!=NULL)
                        //fprintf(stderr,"Fils: %ld, Nfono: %ld\n", vesicle->tape->nfil, vesicle->tape->nfono);
                        parseXMLVertexPosition(vesicle, doc, cur2);
                  }
                  if ((!xmlStrcmp(cur2->name, (const xmlChar *)"Cells"))){
@@ -164,6 +165,16 @@
       if ((!xmlStrcmp(child->name, (const xmlChar *)"tristar"))){
         parseTrisurfTristar(vesicle, doc, child);
      }
       if ((!xmlStrcmp(child->name, (const xmlChar *)"nucleus"))){
         parseTrisurfNucleus(vesicle, doc, child);
      }
        if ((!xmlStrcmp(child->name, (const xmlChar *)"constant_volume"))){
         parseTrisurfConstantVolume(doc, child);
      }
        if ((!xmlStrcmp(child->name, (const xmlChar *)"constant_area"))){
         parseTrisurfConstantArea(doc, child);
      }


   child = child->next;
   }
@@ -178,6 +189,33 @@


/* Low level tags parsers */
ts_bool parseTrisurfConstantVolume(xmlDocPtr doc, xmlNodePtr cur){
   xmlChar *cvol = xmlNodeListGetString(doc, cur->xmlChildrenNode, 1);
   char *n=(char *)cvol;
   V0=atof(n);
   xmlFree(cvol);
   return TS_SUCCESS;
}
ts_bool parseTrisurfConstantArea(xmlDocPtr doc, xmlNodePtr cur){
   xmlChar *carea = xmlNodeListGetString(doc, cur->xmlChildrenNode, 1);
   char *n=(char *)carea;
   A0=atof(n);
   xmlFree(carea);
   return TS_SUCCESS;
}

ts_bool parseTrisurfNucleus(ts_vesicle *vesicle, xmlDocPtr doc, xmlNodePtr cur){
   xmlChar *coords = xmlNodeListGetString(doc, cur->xmlChildrenNode, 1);
   char *n=(char *)coords;
   char *token=strtok(n," ");
   ts_uint i;
   for(i=0;i<3;i++){
      vesicle->nucleus_center[i]=atof(token);
      token=strtok(NULL," ");
   }
   xmlFree(coords);
   return TS_SUCCESS;
}

ts_bool parseTrisurfVtxn(ts_vertex_list *vlist, xmlDocPtr doc, xmlNodePtr cur){

@@ -310,7 +348,7 @@
            } else {
               filidx=(idx-vesicle->vlist->n-vesicle->tape->nmono*vesicle->tape->npoly)/vesicle->tape->nfono;
               fonoidx=(idx-vesicle->vlist->n-vesicle->tape->nmono*vesicle->tape->npoly)%vesicle->tape->nfono;
               fprintf(stderr,"filidx=%d, fonoidx=%d, coord=%s,%s,%s\n",filidx,fonoidx,token[0],token[1],token[2]);
               //fprintf(stderr,"filidx=%d, fonoidx=%d, coord=%s,%s,%s\n",filidx,fonoidx,token[0],token[1],token[2]);
               vesicle->filament_list->poly[filidx]->vlist->vtx[fonoidx]->x=atof(token[0]);
               vesicle->filament_list->poly[filidx]->vlist->vtx[fonoidx]->y=atof(token[1]);
               vesicle->filament_list->poly[filidx]->vlist->vtx[fonoidx]->z=atof(token[2]);
@@ -323,7 +361,7 @@
      }
      child=child->next;
   }
   fprintf(stderr,"Came here\n");
   //fprintf(stderr,"Came here\n");
   //fprintf(stderr,"Vertices position j=%d\n",idx);   

   return TS_SUCCESS;