Raj and Yoav session in making multiple protein species

Samo Penic

2021-05-10 6487a03362d35589c286d0660eba123a7ab00535

 src/restore.c

@@ -16,13 +16,14 @@
#include "poly.h"
#include "initial_distribution.h"
#include "io.h"
#include <math.h>

ts_vesicle *parseDump(char *dumpfname) {
   xmlDocPtr doc;
   xmlNodePtr cur, cur1,cur2;
   ts_vesicle *vesicle=NULL;
   doc = xmlParseFile(dumpfname);
	
   int i;
   if (doc == NULL ) {
      fatal("Dump file could not be found or parsed. It is correct file?",1);
   }
@@ -78,15 +79,19 @@
      // END Point Position data & Bonds
   cur = cur->next;
   }
	
   xmlFreeDoc(doc);

//   vesicle->poly_list=init_poly_list(0, 0, vesicle->vlist, vesicle);

   set_vesicle_values_from_tape(vesicle);
   init_normal_vectors(vesicle->tlist);
   mean_curvature_and_energy(vesicle);
   sweep_attraction_bond_energy(vesicle);

   if(vesicle->tape->stretchswitch==1){
      vesicle->tlist->a0=sqrt(3)/4.0*pow((vesicle->tape->dmax+1.0)/2.0,2);  
      for(i=0;i<vesicle->tlist->n;i++){
         stretchenergy(vesicle, vesicle->tlist->tria[i]);
      }
   }
/* TODO: filaments */

//   ts_fprintf(stdout,"Restoration completed\n");
@@ -151,7 +156,8 @@
   //fprintf(stderr,"nvtx=%u\n",atoi((char *)nvtx));
   //TODO: check if nvtx is in agreement with nshell from tape
   ts_vesicle *vesicle=init_vesicle(atoi((char *)nvtx),tape->ncxmax,tape->ncymax,tape->nczmax,tape->stepsize);
   //vesicle->poly_list=init_poly_list(atoi((char *)npoly),atoi((char *)nmono), vesicle->vlist, vesicle);
//   vesicle->poly_list=init_poly_list(atoi((char *)npoly),atoi((char *)nmono), vesicle->vlist, vesicle);
   vesicle->poly_list=init_empty_poly_list(atoi((char *)npoly),atoi((char *)nmono));
   xmlFree(nvtx);
   xmlFree(npoly);
   xmlFree(nmono);
@@ -184,9 +190,8 @@
   child = child->next;
   }


   vesicle->tape=tape;
   set_vesicle_values_from_tape(vesicle);
//   set_vesicle_values_from_tape(vesicle);
   return vesicle;
}

@@ -357,6 +362,29 @@
            }
            xmlFree(values);      
         }
         if(!xmlStrcmp(property_name,(const xmlChar *)"direct_interaction_force")){
            values=xmlNodeListGetString(doc,child->xmlChildrenNode,1);
            vals=(char *)values;
            token=strtok(vals," ");
            idx=0;
            while(token!=NULL){
               if(idx<vesicle->vlist->n){
                  vesicle->vlist->vtx[idx]->direct_interaction_force=atof(token);
               } else if(vesicle->tape->nmono && vesicle->tape->npoly && idx<vesicle->vlist->n+vesicle->tape->nmono*vesicle->tape->npoly) {
                  polyidx=(idx-vesicle->vlist->n)/vesicle->tape->nmono;
                  monoidx=(idx-vesicle->vlist->n)%vesicle->tape->nmono;
                  vesicle->poly_list->poly[polyidx]->vlist->vtx[monoidx]->direct_interaction_force=atof(token);
               } 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]);
                  vesicle->filament_list->poly[filidx]->vlist->vtx[fonoidx]->direct_interaction_force=atof(token);
               }
               idx++;
               token=strtok(NULL," ");
            }
            xmlFree(values);		
         }
         xmlFree(property_name);
      }