From 6487a03362d35589c286d0660eba123a7ab00535 Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@gmail.com>
Date: Mon, 10 May 2021 11:14:04 +0000
Subject: [PATCH] Raj and Yoav session in making multiple protein species
---
src/restore.c | 49 +++++++++++++++++++++++++++++++++++++++++--------
1 files changed, 41 insertions(+), 8 deletions(-)
diff --git a/src/restore.c b/src/restore.c
index a490d53..9ee9c45 100644
--- a/src/restore.c
+++ b/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);
}
@@ -417,6 +445,7 @@
char *b;
int idx, polyidx;
char *token[2];
+ int temp_cnt=0;
while (child != NULL) {
conname=xmlGetProp(child, (xmlChar *)"Name");
if ((!xmlStrcmp(child->name, (const xmlChar *)"DataArray")) && !xmlStrcmp(conname, (const xmlChar *)"connectivity") ){
@@ -428,11 +457,15 @@
while(token[0]!=NULL){
if(idx<3*(vesicle->vlist->n-2)){
bond_add(vesicle->blist, vesicle->vlist->vtx[atoi(token[0])], vesicle->vlist->vtx[atoi(token[1])]);
+ //fprintf(stderr,"Bonds in vesicle count idx=%d\n",idx);
}
else {
//find grafted vtx
if(vesicle->tape->npoly && vesicle->tape->nmono && (vesicle->tape->nmono-1)==(idx-3*(vesicle->vlist->n-2))%(vesicle->tape->nmono)
- && idx<(3*vesicle->vlist->n-2+vesicle->tape->nmono*vesicle->tape->npoly+vesicle->tape->npoly)){
+ && idx<(3*vesicle->vlist->n-2+vesicle->tape->nmono*vesicle->tape->npoly)){
+ temp_cnt++;
+ //fprintf(stderr,"%d: Bonds in poly count idx=%d, t1=%s t2=%s\n",temp_cnt,idx, token[0], token[1]);
+
polyidx=(idx-3*(vesicle->vlist->n-2))/(vesicle->tape->nmono);
//fprintf(stderr,"poly=%d, vertex=%d\n",polyidx,atoi(token[0]));
vesicle->poly_list->poly[polyidx]->grafted_vtx=vesicle->vlist->vtx[atoi(token[0])];
--
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