trisurf-ng.git - Gitblit

Fixed most problems, some still persists.

Samo Penic

2019-10-19 201659654a328f84c229d16fe85d8709a4183957

commit \| author \| age
7f6076	1	/* vim: set ts=4 sts=4 sw=4 noet : */
8c1bb1	2	#include <stdio.h>
SP	3	#include <string.h>
	4	#include <stdlib.h>
	5	#include <libxml/xmlmemory.h>
	6	#include <libxml/parser.h>
	7	#include <general.h>
	8	#include <restore.h>
	9	#include <snapshot.h>
1eb75b	10	#include <b64zlib_compression.h>
8c1bb1	11	#include "vesicle.h"
487968	12	#include "vertex.h"
a011d2	13	#include "triangle.h"
a3dbf0	14	#include "bond.h"
SP	15	#include "energy.h"
bb4033	16	#include "poly.h"
a3dbf0	17	#include "initial_distribution.h"
698ae1	18	#include "io.h"
002513	19	#include <math.h>
a011d2	20
ab798b	21	ts_vesicle parseDump(char dumpfname) {
8c1bb1	22	xmlDocPtr doc;
8fa1c0	23	xmlNodePtr cur, cur1,cur2;
SP	24	ts_vesicle *vesicle=NULL;
8c1bb1	25	doc = xmlParseFile(dumpfname);
002513	26	int i;
8c1bb1	27	if (doc == NULL ) {
SP	28	fatal("Dump file could not be found or parsed. It is correct file?",1);
	29	}
	30
	31	cur = xmlDocGetRootElement(doc);
	32
	33	if (cur == NULL) {
	34	fatal("Dump file is empty.",1);
	35	}
	36
	37	if (xmlStrcmp(cur->name, (const xmlChar *) "VTKFile")) {
	38	fatal("document of the wrong type, root node != story",1);
	39	}
	40
	41	cur = cur->xmlChildrenNode;
	42	while (cur != NULL) {
698ae1	43
SP	44	if ((!xmlStrcmp(cur->name, (const xmlChar *)"tape"))){
	45	setGlobalTapeTXTfromTapeTag(doc, cur);
	46	}
	47
8c1bb1	48	if ((!xmlStrcmp(cur->name, (const xmlChar *)"trisurf"))){
3c772b	49	vesicle=parseTrisurfTag(doc, cur);
8c1bb1	50	}
8fa1c0	51	// START Point Position data & Bonds
SP	52	if ((!xmlStrcmp(cur->name, (const xmlChar *)"UnstructuredGrid"))){
	53	cur1 = cur->xmlChildrenNode;
	54	while(cur1!=NULL){
	55	if ((!xmlStrcmp(cur1->name, (const xmlChar *)"Piece"))){
	56	cur2=cur1->xmlChildrenNode;
	57	while(cur2!=NULL){
def8b5	58	if ((!xmlStrcmp(cur2->name, (const xmlChar *)"PointData"))){
SP	59	if(vesicle!=NULL)
	60	parseXMLPointData(vesicle,doc,cur2);
	61	}
8fa1c0	62	if ((!xmlStrcmp(cur2->name, (const xmlChar *)"Points"))){
720bd4	63	//fprintf(stderr,"Found point data\n");
8fa1c0	64	if(vesicle!=NULL)
f62178	65	//fprintf(stderr,"Fils: %ld, Nfono: %ld\n", vesicle->tape->nfil, vesicle->tape->nfono);
28efdb	66	parseXMLVertexPosition(vesicle, doc, cur2);
8fa1c0	67	}
SP	68	if ((!xmlStrcmp(cur2->name, (const xmlChar *)"Cells"))){
720bd4	69	//fprintf(stderr,"Found cell(Bonds) data\n");
a3dbf0	70	if(vesicle!=NULL)
28efdb	71	parseXMLBonds(vesicle, doc, cur2);
8fa1c0	72	}
SP	73	cur2=cur2->next;
	74	}
	75	}
	76	cur1 = cur1->next;
	77	}
	78	}
	79	// END Point Position data & Bonds
8c1bb1	80	cur = cur->next;
SP	81	}
	82	xmlFreeDoc(doc);
bb4033	83
86b69b	84	// vesicle->poly_list=init_poly_list(0, 0, vesicle->vlist, vesicle);
d43116	85	set_vesicle_values_from_tape(vesicle);
a3dbf0	86	init_normal_vectors(vesicle->tlist);
SP	87	mean_curvature_and_energy(vesicle);
89434d	88	sweep_attraction_bond_energy(vesicle);
002513	89	if(vesicle->tape->stretchswitch==1){
699ac4	90	vesicle->tlist->a0=sqrt(3)/4.0*pow((vesicle->tape->dmax+1.0)/2.0,2);
002513	91	for(i=0;i<vesicle->tlist->n;i++){
SP	92	stretchenergy(vesicle, vesicle->tlist->tria[i]);
	93	}
	94	}
ab798b	95	/* TODO: filaments */
a3dbf0	96
f4d6ca	97	// ts_fprintf(stdout,"Restoration completed\n");
ab798b	98	// write_vertex_xml_file(vesicle,999);
SP	99	// vesicle_free(vesicle);
	100	// exit(0);
	101	return vesicle;
8c1bb1	102	}
SP	103
698ae1	104	ts_bool setGlobalTapeTXTfromTapeTag(xmlDocPtr doc, xmlNodePtr cur){
SP	105	xmlChar *tape = xmlNodeListGetString(doc, cur->xmlChildrenNode, 1);
	106	strcpy(tapetxt,(char *)tape);
	107	xmlFree(tape);
	108	return TS_SUCCESS;
	109	}
8fa1c0	110
SP	111
	112	/* this is a parser of additional data in xml */
8c1bb1	113	ts_vesicle *parseTrisurfTag(xmlDocPtr doc, xmlNodePtr cur){
720bd4	114	//fprintf(stderr,"Parsing trisurf tag\n");
487968	115	xmlNodePtr child;
SP	116
	117	#ifdef COMPRESS
8c1bb1	118	/* base64decode */
SP	119	size_t cLen;
	120	/*size_t tLen;
	121	const unsigned char test[]="Test";
	122	char *cTest=base64_encode(test, 4,&tLen);
	123	unsigned char cuTest=base64_decode((char )cTest,tLen,&tLen);
	124	cuTest[tLen]=0;
	125	fprintf(stderr,"%s\n",cuTest);
	126	*/
	127	xmlChar *b64=xmlNodeListGetString(doc, cur->xmlChildrenNode, 1);
	128	unsigned char compressed=base64_decode((char )b64,strlen((char *)b64)-1,&cLen);
	129	/* uncompress */
	130	unsigned char subtree=(unsigned char )malloc(512000sizeof(unsigned char)); / TODO: again, the uncompressed string must not exceed this */
	131	z_stream infstream;
	132	infstream.zalloc = Z_NULL;
	133	infstream.zfree = Z_NULL;
	134	infstream.opaque = Z_NULL;
	135	infstream.avail_in = (ts_uint)cLen; // size of input
	136	infstream.next_in = compressed; // input char array
	137	infstream.avail_out = (ts_uint)512000; // size of output
	138	infstream.next_out = subtree; // output char array
	139
	140	// the actual DE-compression work.
	141	inflateInit(&infstream);
	142	inflate(&infstream, Z_NO_FLUSH);
	143	inflateEnd(&infstream);
720bd4	144	//fprintf(stderr,"%lu\n",cLen);
8c1bb1	145	subtree[infstream.total_out]='\0'; //zero terminate string
720bd4	146	//fprintf(stderr,"%s\n",subtree);
8c1bb1	147
SP	148	free(subtree);
487968	149	#endif
8c1bb1	150	/parse xml subtree /
86b69b	151	xmlChar nvtx, npoly, *nmono;
8c1bb1	152	nvtx = xmlGetProp(cur, (xmlChar *)"nvtx");
SP	153	npoly=xmlGetProp(cur, (xmlChar *)"npoly");
86b69b	154	nmono=xmlGetProp(cur, (xmlChar *)"nmono");
698ae1	155	ts_tape *tape=parsetapebuffer(tapetxt);
SP	156	//fprintf(stderr,"nvtx=%u\n",atoi((char *)nvtx));
	157	//TODO: check if nvtx is in agreement with nshell from tape
	158	ts_vesicle vesicle=init_vesicle(atoi((char )nvtx),tape->ncxmax,tape->ncymax,tape->nczmax,tape->stepsize);
d43116	159	// vesicle->poly_list=init_poly_list(atoi((char )npoly),atoi((char )nmono), vesicle->vlist, vesicle);
SP	160	vesicle->poly_list=init_empty_poly_list(atoi((char )npoly),atoi((char )nmono));
8c1bb1	161	xmlFree(nvtx);
SP	162	xmlFree(npoly);
86b69b	163	xmlFree(nmono);
487968	164
SP	165	child = cur->xmlChildrenNode;
	166	while (child != NULL) {
	167	if ((!xmlStrcmp(child->name, (const xmlChar *)"vtxn"))){
	168	parseTrisurfVtxn(vesicle->vlist, doc, child);
	169	}
a011d2	170	if ((!xmlStrcmp(child->name, (const xmlChar *)"tria"))){
SP	171	parseTrisurfTria(vesicle, doc, child);
	172	}
e9ac7b	173	if ((!xmlStrcmp(child->name, (const xmlChar *)"trianeigh"))){
SP	174	parseTrisurfTriaNeigh(vesicle, doc, child);
	175	}
a011d2	176	if ((!xmlStrcmp(child->name, (const xmlChar *)"tristar"))){
SP	177	parseTrisurfTristar(vesicle, doc, child);
	178	}
4891eb	179	if ((!xmlStrcmp(child->name, (const xmlChar *)"nucleus"))){
SP	180	parseTrisurfNucleus(vesicle, doc, child);
	181	}
49981c	182	if ((!xmlStrcmp(child->name, (const xmlChar *)"constant_volume"))){
SP	183	parseTrisurfConstantVolume(doc, child);
	184	}
	185	if ((!xmlStrcmp(child->name, (const xmlChar *)"constant_area"))){
	186	parseTrisurfConstantArea(doc, child);
	187	}
	188
a011d2	189
487968	190	child = child->next;
SP	191	}
	192
698ae1	193	vesicle->tape=tape;
d43116	194	// set_vesicle_values_from_tape(vesicle);
8c1bb1	195	return vesicle;
SP	196	}
487968	197
a011d2	198
SP	199
	200	/* Low level tags parsers */
49981c	201	ts_bool parseTrisurfConstantVolume(xmlDocPtr doc, xmlNodePtr cur){
SP	202	xmlChar *cvol = xmlNodeListGetString(doc, cur->xmlChildrenNode, 1);
	203	char n=(char )cvol;
	204	V0=atof(n);
	205	xmlFree(cvol);
	206	return TS_SUCCESS;
	207	}
	208	ts_bool parseTrisurfConstantArea(xmlDocPtr doc, xmlNodePtr cur){
	209	xmlChar *carea = xmlNodeListGetString(doc, cur->xmlChildrenNode, 1);
	210	char n=(char )carea;
	211	A0=atof(n);
	212	xmlFree(carea);
	213	return TS_SUCCESS;
	214	}
	215
4891eb	216	ts_bool parseTrisurfNucleus(ts_vesicle *vesicle, xmlDocPtr doc, xmlNodePtr cur){
SP	217	xmlChar *coords = xmlNodeListGetString(doc, cur->xmlChildrenNode, 1);
	218	char n=(char )coords;
	219	char *token=strtok(n," ");
	220	ts_uint i;
	221	for(i=0;i<3;i++){
	222	vesicle->nucleus_center[i]=atof(token);
	223	token=strtok(NULL," ");
	224	}
	225	xmlFree(coords);
	226	return TS_SUCCESS;
	227	}
a011d2	228
SP	229	ts_bool parseTrisurfVtxn(ts_vertex_list *vlist, xmlDocPtr doc, xmlNodePtr cur){
487968	230
SP	231	xmlChar *chari;
	232	xmlChar *neighs;
	233	char *n;
	234	char *token;
	235	ts_uint neighi;
	236	ts_uint i;
	237	chari = xmlGetProp(cur, (xmlChar *)"idx");
	238	i=atoi((char *)chari);
	239	xmlFree(chari);
	240	ts_vertex *vtx=vlist->vtx[i];
	241	neighs = xmlNodeListGetString(doc, cur->xmlChildrenNode, 1);
	242	//fprintf(stderr,"Found neigh for vtx %u that seems to have index %u with neighs=%s\n",i,vtx->idx,neighs);
	243
	244	n=(char *)neighs;
	245	token=strtok(n," ");
	246	while(token!=NULL){
	247	neighi=atoi(token);
	248	//fprintf(stderr,"%u", neighi);
	249	vtx_add_neighbour(vtx,vlist->vtx[neighi]);
	250	token=strtok(NULL," ");
	251	}
	252	xmlFree(neighs);
	253	return TS_SUCCESS;
	254	}
	255
a011d2	256	ts_bool parseTrisurfTria(ts_vesicle *vesicle, xmlDocPtr doc, xmlNodePtr cur){
SP	257	xmlChar *triangles;
	258	char *tria;
	259	char *vtx[3];
	260
e87e4e	261	ts_uint i,j;
a011d2	262	triangles = xmlNodeListGetString(doc, cur->xmlChildrenNode, 1);
SP	263	tria=(char *)triangles;
e87e4e	264	vtx[0]=strtok(tria," ");
SP	265	for(i=1;i<3;i++) vtx[i]=strtok(NULL," ");
	266	j=0;
a011d2	267	while(vtx[2]!=NULL){
SP	268	triangle_add(vesicle->tlist, vesicle->vlist->vtx[atoi(vtx[0])],vesicle->vlist->vtx[atoi(vtx[1])],vesicle->vlist->vtx[atoi(vtx[2])]);
	269	for(i=0;i<3;i++) vtx[i]=strtok(NULL," ");
e87e4e	270	j++;
a011d2	271	}
720bd4	272	//fprintf(stderr,"Parsing triangles %s j=%d\n",triangles,j);
a011d2	273
SP	274	xmlFree(triangles);
	275	return TS_SUCCESS;
	276	}
	277
	278
e9ac7b	279	ts_bool parseTrisurfTriaNeigh(ts_vesicle *vesicle, xmlDocPtr doc, xmlNodePtr cur){
SP	280	xmlChar *triangles;
	281	char *tria;
	282	char *ntria[3];
	283	ts_uint i,j;
	284	triangles = xmlNodeListGetString(doc, cur->xmlChildrenNode, 1);
	285	tria=(char *)triangles;
e87e4e	286	ntria[0]=strtok(tria," ");
SP	287	for(i=1;i<3;i++) ntria[i]=strtok(NULL," ");
e9ac7b	288	j=0;
SP	289	while(ntria[2]!=NULL){
	290	triangle_add_neighbour(vesicle->tlist->tria[j],vesicle->tlist->tria[atoi(ntria[0])]);
	291	triangle_add_neighbour(vesicle->tlist->tria[j],vesicle->tlist->tria[atoi(ntria[1])]);
	292	triangle_add_neighbour(vesicle->tlist->tria[j],vesicle->tlist->tria[atoi(ntria[2])]);
	293	j++;
	294	for(i=0;i<3;i++) ntria[i]=strtok(NULL," ");
	295	}
720bd4	296	//fprintf(stderr,"Parsing triangle neighbors j=%d\n",j);
e9ac7b	297
SP	298	xmlFree(triangles);
	299	return TS_SUCCESS;
	300	}
	301
	302
a011d2	303	ts_bool parseTrisurfTristar(ts_vesicle *vesicle, xmlDocPtr doc, xmlNodePtr cur){
SP	304
	305	xmlChar *chari;
	306	xmlChar *tristar;
	307	char *t;
	308	char *token;
	309	ts_uint neighi;
	310	ts_uint i;
	311	chari = xmlGetProp(cur, (xmlChar *)"idx");
	312	i=atoi((char *)chari);
	313	xmlFree(chari);
	314	ts_vertex *vtx=vesicle->vlist->vtx[i];
	315	tristar = xmlNodeListGetString(doc, cur->xmlChildrenNode, 1);
	316	// fprintf(stderr,"Found tristar for vtx %u that seems to have index %u with tristar=%s\n",i,vtx->idx,tristar);
	317
	318	t=(char *)tristar;
	319	token=strtok(t," ");
	320	while(token!=NULL){
	321	neighi=atoi(token);
	322	//fprintf(stderr,"%u", neighi);
	323	vertex_add_tristar(vtx,vesicle->tlist->tria[neighi]);
	324	token=strtok(NULL," ");
	325	}
	326	xmlFree(tristar);
	327	return TS_SUCCESS;
	328	}
	329
def8b5	330	/* this parses the data for vertices (like spontaneous curvature, etc.) */
SP	331	ts_bool parseXMLPointData(ts_vesicle *vesicle,xmlDocPtr doc, xmlNodePtr cur){
	332	xmlNodePtr child = cur->xmlChildrenNode;
	333	xmlChar *property_name;
	334	xmlChar *values;
1eb75b	335	// char *vals;
SP	336	// char *token;
def8b5	337	int idx, polyidx, monoidx, filidx, fonoidx;
SP	338	while (child != NULL) {
	339	if ((!xmlStrcmp(child->name, (const xmlChar *)"DataArray"))){
	340	property_name=xmlGetProp(child, (xmlChar *)"Name");
	341	// fprintf(stderr,"Name: %s\n", property_name);
	342	if(!xmlStrcmp(property_name,(const xmlChar *)"spontaneous_curvature")){
	343	values=xmlNodeListGetString(doc,child->xmlChildrenNode,1);
1eb75b	344	// vals=(char *)values;
SP	345	unsigned long data_len=0;
	346	ts_double curv_values=(double )ts_decompress((unsigned char )values,strlen((char )values), &data_len);
201659	347	data_len=data_len/sizeof(ts_double);
1eb75b	348	// token=strtok(vals," ");
SP	349	for(idx=0;idx<data_len;idx++){
	350	// while(token!=NULL){
def8b5	351	if(idx<vesicle->vlist->n){
1eb75b	352	vesicle->vlist->vtx[idx]->c=curv_values[idx]; //atof(token);
def8b5	353	} else if(vesicle->tape->nmono && vesicle->tape->npoly && idx<vesicle->vlist->n+vesicle->tape->nmono*vesicle->tape->npoly) {
SP	354	polyidx=(idx-vesicle->vlist->n)/vesicle->tape->nmono;
	355	monoidx=(idx-vesicle->vlist->n)%vesicle->tape->nmono;
1eb75b	356	vesicle->poly_list->poly[polyidx]->vlist->vtx[monoidx]->c=curv_values[idx];//atof(token);
def8b5	357	} else {
SP	358	filidx=(idx-vesicle->vlist->n-vesicle->tape->nmono*vesicle->tape->npoly)/vesicle->tape->nfono;
	359	fonoidx=(idx-vesicle->vlist->n-vesicle->tape->nmono*vesicle->tape->npoly)%vesicle->tape->nfono;
	360	//fprintf(stderr,"filidx=%d, fonoidx=%d, coord=%s,%s,%s\n",filidx,fonoidx,token[0],token[1],token[2]);
1eb75b	361	vesicle->filament_list->poly[filidx]->vlist->vtx[fonoidx]->c=curv_values[idx];//atof(token);
def8b5	362	}
1eb75b	363	//idx++;
SP	364	//token=strtok(NULL," ");
def8b5	365	}
201659	366
def8b5	367	xmlFree(values);
201659	368	free(curv_values);
def8b5	369	}
SP	370	xmlFree(property_name);
	371	}
	372
	373	child=child->next;
	374	}
	375	return TS_SUCCESS;
	376	}
8fa1c0	377	/* this is a parser of vertex positions and bonds from main xml data */
SP	378	ts_bool parseXMLVertexPosition(ts_vesicle *vesicle,xmlDocPtr doc, xmlNodePtr cur){
	379	xmlNodePtr child = cur->xmlChildrenNode;
	380	xmlChar *points;
1eb75b	381	// char *pts;
201659	382	int i,idx, polyidx, monoidx, filidx, fonoidx;
1eb75b	383	// char *token[3];
8fa1c0	384	while (child != NULL) {
SP	385	if ((!xmlStrcmp(child->name, (const xmlChar *)"DataArray"))){
	386	points = xmlNodeListGetString(doc, child->xmlChildrenNode, 1);
1eb75b	387	unsigned long data_len=0;
SP	388	ts_double coords=(double )ts_decompress((unsigned char )points,strlen((char )points), &data_len);
201659	389	data_len=data_len/sizeof(ts_double);
1eb75b	390	//pts=(char *)points;
SP	391	//token[0]=strtok(pts," ");
	392	//token[1]=strtok(NULL," ");
	393	//token[2]=strtok(NULL,"\n");
201659	394	for(i=0,idx=0;i<data_len;i+=3,idx++){
1eb75b	395	// while(token[0]!=NULL){
86b69b	396	if(idx<vesicle->vlist->n){
1eb75b	397	vesicle->vlist->vtx[idx]->x=coords[idx];//atof(token[0]);
SP	398	vesicle->vlist->vtx[idx]->y=coords[idx+1];//atof(token[1]);
	399	vesicle->vlist->vtx[idx]->z=coords[idx+2];//atof(token[2]);
301c87	400	} else if(vesicle->tape->nmono && vesicle->tape->npoly && idx<vesicle->vlist->n+vesicle->tape->nmono*vesicle->tape->npoly) {
86b69b	401	polyidx=(idx-vesicle->vlist->n)/vesicle->tape->nmono;
SP	402	monoidx=(idx-vesicle->vlist->n)%vesicle->tape->nmono;
1eb75b	403	vesicle->poly_list->poly[polyidx]->vlist->vtx[monoidx]->x=coords[idx];//atof(token[0]);
SP	404	vesicle->poly_list->poly[polyidx]->vlist->vtx[monoidx]->y=coords[idx+1];//atof(token[1]);
	405	vesicle->poly_list->poly[polyidx]->vlist->vtx[monoidx]->z=coords[idx+2];//atof(token[2]);
301c87	406	} else {
SP	407	filidx=(idx-vesicle->vlist->n-vesicle->tape->nmono*vesicle->tape->npoly)/vesicle->tape->nfono;
	408	fonoidx=(idx-vesicle->vlist->n-vesicle->tape->nmono*vesicle->tape->npoly)%vesicle->tape->nfono;
f62178	409	//fprintf(stderr,"filidx=%d, fonoidx=%d, coord=%s,%s,%s\n",filidx,fonoidx,token[0],token[1],token[2]);
1eb75b	410	vesicle->filament_list->poly[filidx]->vlist->vtx[fonoidx]->x=coords[idx];//atof(token[0]);
SP	411	vesicle->filament_list->poly[filidx]->vlist->vtx[fonoidx]->y=coords[idx+1];//atof(token[1]);
	412	vesicle->filament_list->poly[filidx]->vlist->vtx[fonoidx]->z=coords[idx+2];//atof(token[2]);
86b69b	413	}
1eb75b	414	//for(i=0;i<2;i++) token[i]=strtok(NULL," ");
SP	415	//token[2]=strtok(NULL,"\n");
	416	//idx++;
8fa1c0	417	}
SP	418	xmlFree(points);
	419	}
	420	child=child->next;
	421	}
f62178	422	//fprintf(stderr,"Came here\n");
720bd4	423	//fprintf(stderr,"Vertices position j=%d\n",idx);
28efdb	424
8fa1c0	425	return TS_SUCCESS;
SP	426	}
a3dbf0	427	ts_bool parseXMLBonds(ts_vesicle *vesicle,xmlDocPtr doc, xmlNodePtr cur){
SP	428	xmlNodePtr child = cur->xmlChildrenNode;
bb4033	429	xmlChar bonds, conname;
1eb75b	430	// char *b;
201659	431	int i,idx, polyidx;
1eb75b	432	// char *token[2];
SP	433	// int temp_cnt=0;
a3dbf0	434	while (child != NULL) {
bb4033	435	conname=xmlGetProp(child, (xmlChar *)"Name");
SP	436	if ((!xmlStrcmp(child->name, (const xmlChar )"DataArray")) && !xmlStrcmp(conname, (const xmlChar )"connectivity") ){
a3dbf0	437	bonds = xmlNodeListGetString(doc, child->xmlChildrenNode, 1);
1eb75b	438	unsigned long data_len=0;
SP	439	unsigned long conn=(unsigned long )ts_decompress((unsigned char )bonds,strlen((char )bonds), &data_len);
201659	440	data_len=data_len/sizeof(unsigned long);
1eb75b	441	//token[0]=strtok(b," ");
SP	442	//token[1]=strtok(NULL,"\n");
201659	443	for(i=0,idx=0;i<data_len;i+=2,idx++){
1eb75b	444	// while(token[0]!=NULL){
86b69b	445	if(idx<3*(vesicle->vlist->n-2)){
1eb75b	446	bond_add(vesicle->blist, vesicle->vlist->vtx[conn[idx]], vesicle->vlist->vtx[conn[idx+1]]);
3cd5f4	447	//fprintf(stderr,"Bonds in vesicle count idx=%d\n",idx);
86b69b	448	}
SP	449	else {
	450	//find grafted vtx
301c87	451	if(vesicle->tape->npoly && vesicle->tape->nmono && (vesicle->tape->nmono-1)==(idx-3*(vesicle->vlist->n-2))%(vesicle->tape->nmono)
3cd5f4	452	&& idx<(3vesicle->vlist->n-2+vesicle->tape->nmonovesicle->tape->npoly)){
1eb75b	453	// temp_cnt++;
3cd5f4	454	//fprintf(stderr,"%d: Bonds in poly count idx=%d, t1=%s t2=%s\n",temp_cnt,idx, token[0], token[1]);
SP	455
86b69b	456	polyidx=(idx-3*(vesicle->vlist->n-2))/(vesicle->tape->nmono);
720bd4	457	//fprintf(stderr,"poly=%d, vertex=%d\n",polyidx,atoi(token[0]));
1eb75b	458	vesicle->poly_list->poly[polyidx]->grafted_vtx=vesicle->vlist->vtx[conn[idx]];
SP	459	vesicle->vlist->vtx[conn[idx]]->grafted_poly=vesicle->poly_list->poly[polyidx];
86b69b	460	}
SP	461	}
a3dbf0	462	}
SP	463	xmlFree(bonds);
	464	}
bb4033	465	xmlFree(conname);
a3dbf0	466	child=child->next;
SP	467	}
720bd4	468	//fprintf(stderr,"Bond data j=%d\n",idx);
a3dbf0	469	return TS_SUCCESS;
SP	470	}
	471
8fa1c0	472
SP	473