/* vim: set ts=4 sts=4 sw=4 noet : */
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#include <stdio.h>
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#include <string.h>
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#include <stdlib.h>
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#include <libxml/xmlmemory.h>
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#include <libxml/parser.h>
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#include <general.h>
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#include <restore.h>
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#include <snapshot.h>
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#include <zlib.h>
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#include "vesicle.h"
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#include "vertex.h"
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#include "triangle.h"
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#include "bond.h"
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#include "energy.h"
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#include "poly.h"
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#include "initial_distribution.h"
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#include "io.h"
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ts_vesicle *parseDump(char *dumpfname) {
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xmlDocPtr doc;
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xmlNodePtr cur, cur1,cur2;
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ts_vesicle *vesicle=NULL;
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doc = xmlParseFile(dumpfname);
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if (doc == NULL ) {
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fatal("Dump file could not be found or parsed. It is correct file?",1);
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}
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cur = xmlDocGetRootElement(doc);
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if (cur == NULL) {
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fatal("Dump file is empty.",1);
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}
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if (xmlStrcmp(cur->name, (const xmlChar *) "VTKFile")) {
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fatal("document of the wrong type, root node != story",1);
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}
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cur = cur->xmlChildrenNode;
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while (cur != NULL) {
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if ((!xmlStrcmp(cur->name, (const xmlChar *)"tape"))){
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setGlobalTapeTXTfromTapeTag(doc, cur);
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}
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if ((!xmlStrcmp(cur->name, (const xmlChar *)"trisurf"))){
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vesicle=parseTrisurfTag(doc, cur);
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}
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// START Point Position data & Bonds
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if ((!xmlStrcmp(cur->name, (const xmlChar *)"UnstructuredGrid"))){
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cur1 = cur->xmlChildrenNode;
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while(cur1!=NULL){
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if ((!xmlStrcmp(cur1->name, (const xmlChar *)"Piece"))){
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cur2=cur1->xmlChildrenNode;
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while(cur2!=NULL){
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if ((!xmlStrcmp(cur2->name, (const xmlChar *)"PointData"))){
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if(vesicle!=NULL)
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parseXMLPointData(vesicle,doc,cur2);
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}
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if ((!xmlStrcmp(cur2->name, (const xmlChar *)"Points"))){
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//fprintf(stderr,"Found point data\n");
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if(vesicle!=NULL)
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//fprintf(stderr,"Fils: %ld, Nfono: %ld\n", vesicle->tape->nfil, vesicle->tape->nfono);
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parseXMLVertexPosition(vesicle, doc, cur2);
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}
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if ((!xmlStrcmp(cur2->name, (const xmlChar *)"Cells"))){
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//fprintf(stderr,"Found cell(Bonds) data\n");
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if(vesicle!=NULL)
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parseXMLBonds(vesicle, doc, cur2);
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}
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cur2=cur2->next;
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}
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}
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cur1 = cur1->next;
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}
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}
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// END Point Position data & Bonds
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cur = cur->next;
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}
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xmlFreeDoc(doc);
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// vesicle->poly_list=init_poly_list(0, 0, vesicle->vlist, vesicle);
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init_normal_vectors(vesicle->tlist);
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mean_curvature_and_energy(vesicle);
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sweep_attraction_bond_energy(vesicle);
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/* TODO: filaments */
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// ts_fprintf(stdout,"Restoration completed\n");
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// write_vertex_xml_file(vesicle,999);
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// vesicle_free(vesicle);
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// exit(0);
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return vesicle;
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}
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ts_bool setGlobalTapeTXTfromTapeTag(xmlDocPtr doc, xmlNodePtr cur){
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xmlChar *tape = xmlNodeListGetString(doc, cur->xmlChildrenNode, 1);
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strcpy(tapetxt,(char *)tape);
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xmlFree(tape);
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return TS_SUCCESS;
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}
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/* this is a parser of additional data in xml */
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ts_vesicle *parseTrisurfTag(xmlDocPtr doc, xmlNodePtr cur){
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//fprintf(stderr,"Parsing trisurf tag\n");
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xmlNodePtr child;
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#ifdef COMPRESS
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/* base64decode */
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size_t cLen;
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/*size_t tLen;
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const unsigned char test[]="Test";
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char *cTest=base64_encode(test, 4,&tLen);
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unsigned char *cuTest=base64_decode((char *)cTest,tLen,&tLen);
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cuTest[tLen]=0;
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fprintf(stderr,"%s\n",cuTest);
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*/
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xmlChar *b64=xmlNodeListGetString(doc, cur->xmlChildrenNode, 1);
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unsigned char *compressed=base64_decode((char *)b64,strlen((char *)b64)-1,&cLen);
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/* uncompress */
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unsigned char *subtree=(unsigned char *)malloc(512000*sizeof(unsigned char)); /* TODO: again, the uncompressed string must not exceed this */
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z_stream infstream;
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infstream.zalloc = Z_NULL;
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infstream.zfree = Z_NULL;
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infstream.opaque = Z_NULL;
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infstream.avail_in = (ts_uint)cLen; // size of input
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infstream.next_in = compressed; // input char array
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infstream.avail_out = (ts_uint)512000; // size of output
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infstream.next_out = subtree; // output char array
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// the actual DE-compression work.
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inflateInit(&infstream);
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inflate(&infstream, Z_NO_FLUSH);
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inflateEnd(&infstream);
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//fprintf(stderr,"%lu\n",cLen);
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subtree[infstream.total_out]='\0'; //zero terminate string
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//fprintf(stderr,"%s\n",subtree);
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free(subtree);
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#endif
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/*parse xml subtree */
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xmlChar *nvtx, *npoly, *nmono;
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nvtx = xmlGetProp(cur, (xmlChar *)"nvtx");
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npoly=xmlGetProp(cur, (xmlChar *)"npoly");
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nmono=xmlGetProp(cur, (xmlChar *)"nmono");
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ts_tape *tape=parsetapebuffer(tapetxt);
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//fprintf(stderr,"nvtx=%u\n",atoi((char *)nvtx));
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//TODO: check if nvtx is in agreement with nshell from tape
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ts_vesicle *vesicle=init_vesicle(atoi((char *)nvtx),tape->ncxmax,tape->ncymax,tape->nczmax,tape->stepsize);
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//vesicle->poly_list=init_poly_list(atoi((char *)npoly),atoi((char *)nmono), vesicle->vlist, vesicle);
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xmlFree(nvtx);
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xmlFree(npoly);
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xmlFree(nmono);
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child = cur->xmlChildrenNode;
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while (child != NULL) {
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if ((!xmlStrcmp(child->name, (const xmlChar *)"vtxn"))){
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parseTrisurfVtxn(vesicle->vlist, doc, child);
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}
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if ((!xmlStrcmp(child->name, (const xmlChar *)"tria"))){
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parseTrisurfTria(vesicle, doc, child);
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}
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if ((!xmlStrcmp(child->name, (const xmlChar *)"trianeigh"))){
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parseTrisurfTriaNeigh(vesicle, doc, child);
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}
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if ((!xmlStrcmp(child->name, (const xmlChar *)"tristar"))){
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parseTrisurfTristar(vesicle, doc, child);
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}
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if ((!xmlStrcmp(child->name, (const xmlChar *)"nucleus"))){
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parseTrisurfNucleus(vesicle, doc, child);
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}
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if ((!xmlStrcmp(child->name, (const xmlChar *)"constant_volume"))){
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parseTrisurfConstantVolume(doc, child);
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}
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if ((!xmlStrcmp(child->name, (const xmlChar *)"constant_area"))){
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parseTrisurfConstantArea(doc, child);
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}
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child = child->next;
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}
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vesicle->tape=tape;
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set_vesicle_values_from_tape(vesicle);
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return vesicle;
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}
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/* Low level tags parsers */
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ts_bool parseTrisurfConstantVolume(xmlDocPtr doc, xmlNodePtr cur){
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xmlChar *cvol = xmlNodeListGetString(doc, cur->xmlChildrenNode, 1);
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char *n=(char *)cvol;
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V0=atof(n);
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xmlFree(cvol);
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return TS_SUCCESS;
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}
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ts_bool parseTrisurfConstantArea(xmlDocPtr doc, xmlNodePtr cur){
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xmlChar *carea = xmlNodeListGetString(doc, cur->xmlChildrenNode, 1);
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char *n=(char *)carea;
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A0=atof(n);
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xmlFree(carea);
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return TS_SUCCESS;
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}
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ts_bool parseTrisurfNucleus(ts_vesicle *vesicle, xmlDocPtr doc, xmlNodePtr cur){
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xmlChar *coords = xmlNodeListGetString(doc, cur->xmlChildrenNode, 1);
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char *n=(char *)coords;
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char *token=strtok(n," ");
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ts_uint i;
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for(i=0;i<3;i++){
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vesicle->nucleus_center[i]=atof(token);
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token=strtok(NULL," ");
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}
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xmlFree(coords);
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return TS_SUCCESS;
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}
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ts_bool parseTrisurfVtxn(ts_vertex_list *vlist, xmlDocPtr doc, xmlNodePtr cur){
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xmlChar *chari;
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xmlChar *neighs;
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char *n;
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char *token;
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ts_uint neighi;
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ts_uint i;
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chari = xmlGetProp(cur, (xmlChar *)"idx");
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i=atoi((char *)chari);
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xmlFree(chari);
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ts_vertex *vtx=vlist->vtx[i];
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neighs = xmlNodeListGetString(doc, cur->xmlChildrenNode, 1);
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//fprintf(stderr,"Found neigh for vtx %u that seems to have index %u with neighs=%s\n",i,vtx->idx,neighs);
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n=(char *)neighs;
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token=strtok(n," ");
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while(token!=NULL){
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neighi=atoi(token);
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//fprintf(stderr,"%u", neighi);
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vtx_add_neighbour(vtx,vlist->vtx[neighi]);
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token=strtok(NULL," ");
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}
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xmlFree(neighs);
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return TS_SUCCESS;
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}
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ts_bool parseTrisurfTria(ts_vesicle *vesicle, xmlDocPtr doc, xmlNodePtr cur){
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xmlChar *triangles;
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char *tria;
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char *vtx[3];
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ts_uint i,j;
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triangles = xmlNodeListGetString(doc, cur->xmlChildrenNode, 1);
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tria=(char *)triangles;
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vtx[0]=strtok(tria," ");
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for(i=1;i<3;i++) vtx[i]=strtok(NULL," ");
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j=0;
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while(vtx[2]!=NULL){
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triangle_add(vesicle->tlist, vesicle->vlist->vtx[atoi(vtx[0])],vesicle->vlist->vtx[atoi(vtx[1])],vesicle->vlist->vtx[atoi(vtx[2])]);
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for(i=0;i<3;i++) vtx[i]=strtok(NULL," ");
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j++;
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}
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//fprintf(stderr,"Parsing triangles %s j=%d\n",triangles,j);
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xmlFree(triangles);
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return TS_SUCCESS;
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}
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ts_bool parseTrisurfTriaNeigh(ts_vesicle *vesicle, xmlDocPtr doc, xmlNodePtr cur){
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xmlChar *triangles;
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char *tria;
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char *ntria[3];
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ts_uint i,j;
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triangles = xmlNodeListGetString(doc, cur->xmlChildrenNode, 1);
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tria=(char *)triangles;
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ntria[0]=strtok(tria," ");
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for(i=1;i<3;i++) ntria[i]=strtok(NULL," ");
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j=0;
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while(ntria[2]!=NULL){
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triangle_add_neighbour(vesicle->tlist->tria[j],vesicle->tlist->tria[atoi(ntria[0])]);
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triangle_add_neighbour(vesicle->tlist->tria[j],vesicle->tlist->tria[atoi(ntria[1])]);
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triangle_add_neighbour(vesicle->tlist->tria[j],vesicle->tlist->tria[atoi(ntria[2])]);
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j++;
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for(i=0;i<3;i++) ntria[i]=strtok(NULL," ");
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}
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//fprintf(stderr,"Parsing triangle neighbors j=%d\n",j);
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xmlFree(triangles);
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return TS_SUCCESS;
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}
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ts_bool parseTrisurfTristar(ts_vesicle *vesicle, xmlDocPtr doc, xmlNodePtr cur){
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xmlChar *chari;
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xmlChar *tristar;
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char *t;
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char *token;
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ts_uint neighi;
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ts_uint i;
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chari = xmlGetProp(cur, (xmlChar *)"idx");
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i=atoi((char *)chari);
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xmlFree(chari);
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ts_vertex *vtx=vesicle->vlist->vtx[i];
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tristar = xmlNodeListGetString(doc, cur->xmlChildrenNode, 1);
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// fprintf(stderr,"Found tristar for vtx %u that seems to have index %u with tristar=%s\n",i,vtx->idx,tristar);
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t=(char *)tristar;
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token=strtok(t," ");
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while(token!=NULL){
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neighi=atoi(token);
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//fprintf(stderr,"%u", neighi);
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vertex_add_tristar(vtx,vesicle->tlist->tria[neighi]);
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token=strtok(NULL," ");
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}
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xmlFree(tristar);
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return TS_SUCCESS;
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}
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/* this parses the data for vertices (like spontaneous curvature, etc.) */
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ts_bool parseXMLPointData(ts_vesicle *vesicle,xmlDocPtr doc, xmlNodePtr cur){
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xmlNodePtr child = cur->xmlChildrenNode;
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xmlChar *property_name;
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xmlChar *values;
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char *vals;
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char *token;
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int idx, polyidx, monoidx, filidx, fonoidx;
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while (child != NULL) {
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if ((!xmlStrcmp(child->name, (const xmlChar *)"DataArray"))){
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property_name=xmlGetProp(child, (xmlChar *)"Name");
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// fprintf(stderr,"Name: %s\n", property_name);
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if(!xmlStrcmp(property_name,(const xmlChar *)"spontaneous_curvature")){
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values=xmlNodeListGetString(doc,child->xmlChildrenNode,1);
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vals=(char *)values;
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token=strtok(vals," ");
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idx=0;
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while(token!=NULL){
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if(idx<vesicle->vlist->n){
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vesicle->vlist->vtx[idx]->c=atof(token);
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} else if(vesicle->tape->nmono && vesicle->tape->npoly && idx<vesicle->vlist->n+vesicle->tape->nmono*vesicle->tape->npoly) {
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polyidx=(idx-vesicle->vlist->n)/vesicle->tape->nmono;
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monoidx=(idx-vesicle->vlist->n)%vesicle->tape->nmono;
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vesicle->poly_list->poly[polyidx]->vlist->vtx[monoidx]->c=atof(token);
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} else {
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filidx=(idx-vesicle->vlist->n-vesicle->tape->nmono*vesicle->tape->npoly)/vesicle->tape->nfono;
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fonoidx=(idx-vesicle->vlist->n-vesicle->tape->nmono*vesicle->tape->npoly)%vesicle->tape->nfono;
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//fprintf(stderr,"filidx=%d, fonoidx=%d, coord=%s,%s,%s\n",filidx,fonoidx,token[0],token[1],token[2]);
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vesicle->filament_list->poly[filidx]->vlist->vtx[fonoidx]->c=atof(token);
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}
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idx++;
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token=strtok(NULL," ");
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}
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xmlFree(values);
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}
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xmlFree(property_name);
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}
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child=child->next;
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}
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return TS_SUCCESS;
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}
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/* this is a parser of vertex positions and bonds from main xml data */
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ts_bool parseXMLVertexPosition(ts_vesicle *vesicle,xmlDocPtr doc, xmlNodePtr cur){
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xmlNodePtr child = cur->xmlChildrenNode;
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xmlChar *points;
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char *pts;
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int i, idx, polyidx, monoidx, filidx, fonoidx;
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char *token[3];
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while (child != NULL) {
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if ((!xmlStrcmp(child->name, (const xmlChar *)"DataArray"))){
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points = xmlNodeListGetString(doc, child->xmlChildrenNode, 1);
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pts=(char *)points;
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token[0]=strtok(pts," ");
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token[1]=strtok(NULL," ");
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token[2]=strtok(NULL,"\n");
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idx=0;
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while(token[0]!=NULL){
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if(idx<vesicle->vlist->n){
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vesicle->vlist->vtx[idx]->x=atof(token[0]);
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vesicle->vlist->vtx[idx]->y=atof(token[1]);
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vesicle->vlist->vtx[idx]->z=atof(token[2]);
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} else if(vesicle->tape->nmono && vesicle->tape->npoly && idx<vesicle->vlist->n+vesicle->tape->nmono*vesicle->tape->npoly) {
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polyidx=(idx-vesicle->vlist->n)/vesicle->tape->nmono;
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monoidx=(idx-vesicle->vlist->n)%vesicle->tape->nmono;
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vesicle->poly_list->poly[polyidx]->vlist->vtx[monoidx]->x=atof(token[0]);
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vesicle->poly_list->poly[polyidx]->vlist->vtx[monoidx]->y=atof(token[1]);
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vesicle->poly_list->poly[polyidx]->vlist->vtx[monoidx]->z=atof(token[2]);
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} else {
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filidx=(idx-vesicle->vlist->n-vesicle->tape->nmono*vesicle->tape->npoly)/vesicle->tape->nfono;
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fonoidx=(idx-vesicle->vlist->n-vesicle->tape->nmono*vesicle->tape->npoly)%vesicle->tape->nfono;
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//fprintf(stderr,"filidx=%d, fonoidx=%d, coord=%s,%s,%s\n",filidx,fonoidx,token[0],token[1],token[2]);
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vesicle->filament_list->poly[filidx]->vlist->vtx[fonoidx]->x=atof(token[0]);
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vesicle->filament_list->poly[filidx]->vlist->vtx[fonoidx]->y=atof(token[1]);
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vesicle->filament_list->poly[filidx]->vlist->vtx[fonoidx]->z=atof(token[2]);
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}
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for(i=0;i<2;i++) token[i]=strtok(NULL," ");
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token[2]=strtok(NULL,"\n");
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idx++;
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}
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xmlFree(points);
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}
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child=child->next;
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}
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//fprintf(stderr,"Came here\n");
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//fprintf(stderr,"Vertices position j=%d\n",idx);
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return TS_SUCCESS;
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}
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ts_bool parseXMLBonds(ts_vesicle *vesicle,xmlDocPtr doc, xmlNodePtr cur){
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xmlNodePtr child = cur->xmlChildrenNode;
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xmlChar *bonds, *conname;
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char *b;
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int idx, polyidx;
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char *token[2];
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while (child != NULL) {
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conname=xmlGetProp(child, (xmlChar *)"Name");
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if ((!xmlStrcmp(child->name, (const xmlChar *)"DataArray")) && !xmlStrcmp(conname, (const xmlChar *)"connectivity") ){
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bonds = xmlNodeListGetString(doc, child->xmlChildrenNode, 1);
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b=(char *)bonds;
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token[0]=strtok(b," ");
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token[1]=strtok(NULL,"\n");
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idx=0;
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while(token[0]!=NULL){
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if(idx<3*(vesicle->vlist->n-2)){
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bond_add(vesicle->blist, vesicle->vlist->vtx[atoi(token[0])], vesicle->vlist->vtx[atoi(token[1])]);
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}
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else {
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//find grafted vtx
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if(vesicle->tape->npoly && vesicle->tape->nmono && (vesicle->tape->nmono-1)==(idx-3*(vesicle->vlist->n-2))%(vesicle->tape->nmono)
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&& idx<(3*vesicle->vlist->n-2+vesicle->tape->nmono*vesicle->tape->npoly+vesicle->tape->npoly)){
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polyidx=(idx-3*(vesicle->vlist->n-2))/(vesicle->tape->nmono);
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//fprintf(stderr,"poly=%d, vertex=%d\n",polyidx,atoi(token[0]));
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vesicle->poly_list->poly[polyidx]->grafted_vtx=vesicle->vlist->vtx[atoi(token[0])];
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vesicle->vlist->vtx[atoi(token[0])]->grafted_poly=vesicle->poly_list->poly[polyidx];
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}
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}
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token[0]=strtok(NULL," ");
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token[1]=strtok(NULL,"\n");
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idx++;
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}
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xmlFree(bonds);
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}
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xmlFree(conname);
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child=child->next;
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}
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//fprintf(stderr,"Bond data j=%d\n",idx);
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return TS_SUCCESS;
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}
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