/*!
* \param[in,out] d Trajectory analysis data structure.
* \returns 0 on success, a non-zero error code on error.
*/
static int
init_first_frame(gmx_ana_traj_t *d)
{
int i;
/* Return if we have already initialized the trajectory */
if (d->fr)
{
return 0;
}
d->frflags |= TRX_NEED_X;
snew(d->fr, 1);
if (!read_first_frame(&d->status, d->trjfile, d->fr, d->frflags))
{
gmx_input("could not read coordinates from trajectory");
return EIO;
}
if (d->top && d->fr->natoms > d->top->atoms.nr)
{
gmx_fatal(FARGS, "Trajectory (%d atoms) does not match topology (%d atoms)",
d->fr->natoms, d->top->atoms.nr);
return -1;
}
/* check index groups */
for (i = 0; i < d->ngrps; ++i)
{
gmx_ana_index_check(d->sel[i]->g, d->fr->natoms);
}
set_trxframe_ePBC(d->fr, d->ePBC);
return 0;
}
void init_membed(FILE *fplog, gmx_membed_t *membed, int nfile, const t_filenm fnm[], gmx_mtop_t *mtop, t_inputrec *inputrec, t_state *state, t_commrec *cr,real *cpt)
{
char *ins;
int i,rm_bonded_at,fr_id,fr_i=0,tmp_id,warn=0;
int ng,j,max_lip_rm,ins_grp_id,ins_nat,mem_nat,ntype,lip_rm,tpr_version;
real prot_area;
rvec *r_ins=NULL;
t_block *ins_at,*rest_at;
pos_ins_t *pos_ins;
mem_t *mem_p;
rm_t *rm_p;
gmx_groups_t *groups;
gmx_bool bExcl=FALSE;
t_atoms atoms;
t_pbc *pbc;
char **piecename=NULL;
/* input variables */
const char *membed_input;
real xy_fac = 0.5;
real xy_max = 1.0;
real z_fac = 1.0;
real z_max = 1.0;
int it_xy = 1000;
int it_z = 0;
real probe_rad = 0.22;
int low_up_rm = 0;
int maxwarn=0;
int pieces=1;
gmx_bool bALLOW_ASYMMETRY=FALSE;
snew(ins_at,1);
snew(pos_ins,1);
if(MASTER(cr))
{
/* get input data out membed file */
membed_input = opt2fn("-membed",nfile,fnm);
get_input(membed_input,&xy_fac,&xy_max,&z_fac,&z_max,&it_xy,&it_z,&probe_rad,&low_up_rm,&maxwarn,&pieces,&bALLOW_ASYMMETRY);
tpr_version = get_tpr_version(ftp2fn(efTPX,nfile,fnm));
if (tpr_version<58)
gmx_fatal(FARGS,"Version of *.tpr file to old (%d). Rerun grompp with gromacs VERSION 4.0.3 or newer.\n",tpr_version);
if( !EI_DYNAMICS(inputrec->eI) )
gmx_input("Change integrator to a dynamics integrator in mdp file (e.g. md or sd).");
if(PAR(cr))
gmx_input("Sorry, parallel g_membed is not yet fully functional.");
#ifdef GMX_OPENMM
gmx_input("Sorry, g_membed does not work with openmm.");
#endif
if(*cpt>=0)
{
fprintf(stderr,"\nSetting -cpt to -1, because embedding cannot be restarted from cpt-files.\n");
*cpt=-1;
}
groups=&(mtop->groups);
atoms=gmx_mtop_global_atoms(mtop);
snew(mem_p,1);
fprintf(stderr,"\nSelect a group to embed in the membrane:\n");
get_index(&atoms,opt2fn_null("-mn",nfile,fnm),1,&(ins_at->nr),&(ins_at->index),&ins);
ins_grp_id = search_string(ins,groups->ngrpname,(groups->grpname));
fprintf(stderr,"\nSelect a group to embed %s into (e.g. the membrane):\n",ins);
get_index(&atoms,opt2fn_null("-mn",nfile,fnm),1,&(mem_p->mem_at.nr),&(mem_p->mem_at.index),&(mem_p->name));
pos_ins->pieces=pieces;
snew(pos_ins->nidx,pieces);
snew(pos_ins->subindex,pieces);
snew(piecename,pieces);
if (pieces>1)
{
fprintf(stderr,"\nSelect pieces to embed:\n");
get_index(&atoms,opt2fn_null("-mn",nfile,fnm),pieces,pos_ins->nidx,pos_ins->subindex,piecename);
}
else
{
/*use whole embedded group*/
snew(pos_ins->nidx,1);
snew(pos_ins->subindex,1);
pos_ins->nidx[0]=ins_at->nr;
pos_ins->subindex[0]=ins_at->index;
}
if(probe_rad<0.2199999)
{
warn++;
fprintf(stderr,"\nWarning %d:\nA probe radius (-rad) smaller than 0.2 can result in overlap between waters "
"and the group to embed, which will result in Lincs errors etc.\nIf you are sure, you can increase maxwarn.\n\n",warn);
}
if(xy_fac<0.09999999)
{
warn++;
fprintf(stderr,"\nWarning %d:\nThe initial size of %s is probably too smal.\n"
"If you are sure, you can increase maxwarn.\n\n",warn,ins);
}
if(it_xy<1000)
{
warn++;
fprintf(stderr,"\nWarning %d;\nThe number of steps used to grow the xy-coordinates of %s (%d) is probably too small.\n"
"Increase -nxy or, if you are sure, you can increase maxwarn.\n\n",warn,ins,it_xy);
}
if( (it_z<100) && ( z_fac<0.99999999 || z_fac>1.0000001) )
{
warn++;
fprintf(stderr,"\nWarning %d;\nThe number of steps used to grow the z-coordinate of %s (%d) is probably too small.\n"
"Increase -nz or, if you are sure, you can increase maxwarn.\n\n",warn,ins,it_z);
}
if(it_xy+it_z>inputrec->nsteps)
{
warn++;
fprintf(stderr,"\nWarning %d:\nThe number of growth steps (-nxy + -nz) is larger than the number of steps in the tpr.\n"
"If you are sure, you can increase maxwarn.\n\n",warn);
}
fr_id=-1;
if( inputrec->opts.ngfrz==1)
gmx_fatal(FARGS,"You did not specify \"%s\" as a freezegroup.",ins);
for(i=0;i<inputrec->opts.ngfrz;i++)
{
tmp_id = mtop->groups.grps[egcFREEZE].nm_ind[i];
if(ins_grp_id==tmp_id)
{
fr_id=tmp_id;
fr_i=i;
}
}
if (fr_id == -1 )
gmx_fatal(FARGS,"\"%s\" not as freezegroup defined in the mdp-file.",ins);
for(i=0;i<DIM;i++)
if( inputrec->opts.nFreeze[fr_i][i] != 1)
gmx_fatal(FARGS,"freeze dimensions for %s are not Y Y Y\n",ins);
ng = groups->grps[egcENER].nr;
if (ng == 1)
gmx_input("No energy groups defined. This is necessary for energy exclusion in the freeze group");
for(i=0;i<ng;i++)
{
for(j=0;j<ng;j++)
{
if (inputrec->opts.egp_flags[ng*i+j] == EGP_EXCL)
{
bExcl = TRUE;
if ( (groups->grps[egcENER].nm_ind[i] != ins_grp_id) || (groups->grps[egcENER].nm_ind[j] != ins_grp_id) )
gmx_fatal(FARGS,"Energy exclusions \"%s\" and \"%s\" do not match the group to embed \"%s\"",
*groups->grpname[groups->grps[egcENER].nm_ind[i]],
*groups->grpname[groups->grps[egcENER].nm_ind[j]],ins);
}
}
}
if (!bExcl)
gmx_input("No energy exclusion groups defined. This is necessary for energy exclusion in the freeze group");
/* Guess the area the protein will occupy in the membrane plane Calculate area per lipid*/
snew(rest_at,1);
ins_nat = init_ins_at(ins_at,rest_at,state,pos_ins,groups,ins_grp_id,xy_max);
/* Check moleculetypes in insertion group */
check_types(ins_at,rest_at,mtop);
mem_nat = init_mem_at(mem_p,mtop,state->x,state->box,pos_ins);
prot_area = est_prot_area(pos_ins,state->x,ins_at,mem_p);
if ( (prot_area>7.5) && ( (state->box[XX][XX]*state->box[YY][YY]-state->box[XX][YY]*state->box[YY][XX])<50) )
{
warn++;
fprintf(stderr,"\nWarning %d:\nThe xy-area is very small compared to the area of the protein.\n"
"This might cause pressure problems during the growth phase. Just try with\n"
"current setup (-maxwarn + 1), but if pressure problems occur, lower the\n"
"compressibility in the mdp-file or use no pressure coupling at all.\n\n",warn);
}
if(warn>maxwarn)
gmx_fatal(FARGS,"Too many warnings.\n");
printf("The estimated area of the protein in the membrane is %.3f nm^2\n",prot_area);
printf("\nThere are %d lipids in the membrane part that overlaps the protein.\nThe area per lipid is %.4f nm^2.\n",mem_p->nmol,mem_p->lip_area);
/* Maximum number of lipids to be removed*/
max_lip_rm=(int)(2*prot_area/mem_p->lip_area);
printf("Maximum number of lipids that will be removed is %d.\n",max_lip_rm);
printf("\nWill resize the protein by a factor of %.3f in the xy plane and %.3f in the z direction.\n"
"This resizing will be done with respect to the geometrical center of all protein atoms\n"
"that span the membrane region, i.e. z between %.3f and %.3f\n\n",xy_fac,z_fac,mem_p->zmin,mem_p->zmax);
/* resize the protein by xy and by z if necessary*/
snew(r_ins,ins_at->nr);
init_resize(ins_at,r_ins,pos_ins,mem_p,state->x,bALLOW_ASYMMETRY);
membed->fac[0]=membed->fac[1]=xy_fac;
membed->fac[2]=z_fac;
membed->xy_step =(xy_max-xy_fac)/(double)(it_xy);
membed->z_step =(z_max-z_fac)/(double)(it_z-1);
resize(r_ins,state->x,pos_ins,membed->fac);
/* remove overlapping lipids and water from the membrane box*/
/*mark molecules to be removed*/
snew(pbc,1);
set_pbc(pbc,inputrec->ePBC,state->box);
snew(rm_p,1);
lip_rm = gen_rm_list(rm_p,ins_at,rest_at,pbc,mtop,state->x, r_ins, mem_p,pos_ins,probe_rad,low_up_rm,bALLOW_ASYMMETRY);
lip_rm -= low_up_rm;
if(fplog)
for(i=0;i<rm_p->nr;i++)
fprintf(fplog,"rm mol %d\n",rm_p->mol[i]);
for(i=0;i<mtop->nmolblock;i++)
{
ntype=0;
for(j=0;j<rm_p->nr;j++)
if(rm_p->block[j]==i)
ntype++;
printf("Will remove %d %s molecules\n",ntype,*(mtop->moltype[mtop->molblock[i].type].name));
}
if(lip_rm>max_lip_rm)
{
warn++;
fprintf(stderr,"\nWarning %d:\nTrying to remove a larger lipid area than the estimated protein area\n"
"Try making the -xyinit resize factor smaller.\n\n",warn);
}
/*remove all lipids and waters overlapping and update all important structures*/
rm_group(inputrec,groups,mtop,rm_p,state,ins_at,pos_ins);
rm_bonded_at = rm_bonded(ins_at,mtop);
if (rm_bonded_at != ins_at->nr)
{
fprintf(stderr,"Warning: The number of atoms for which the bonded interactions are removed is %d, "
"while %d atoms are embedded. Make sure that the atoms to be embedded are not in the same"
"molecule type as atoms that are not to be embedded.\n",rm_bonded_at,ins_at->nr);
}
if(warn>maxwarn)
gmx_fatal(FARGS,"Too many warnings.\nIf you are sure these warnings are harmless, you can increase -maxwarn");
if (ftp2bSet(efTOP,nfile,fnm))
top_update(opt2fn("-mp",nfile,fnm),ins,rm_p,mtop);
sfree(pbc);
sfree(rest_at);
if (pieces>1) { sfree(piecename); }
membed->it_xy=it_xy;
membed->it_z=it_z;
membed->pos_ins=pos_ins;
membed->r_ins=r_ins;
}
}
void read_xpm_entry(FILE *in,t_matrix *mm)
{
t_mapping *map;
char *line=NULL,*str,buf[256];
int i,m,col_len,nch,n_axis_x,n_axis_y,llmax;
unsigned int r,g,b;
double u;
bool bGetOnWithIt;
t_xpmelmt c;
mm->flags=0;
mm->title[0]=0;
mm->legend[0]=0;
mm->label_x[0]=0;
mm->label_y[0]=0;
mm->matrix=NULL;
mm->axis_x=NULL;
mm->axis_y=NULL;
mm->bDiscrete=FALSE;
llmax = STRLEN;
while (fgetline(&line,llmax,in) && (strncmp(line,"static",6) != 0)) {
parsestring(line,"title",(mm->title));
parsestring(line,"legend",(mm->legend));
parsestring(line,"x-label",(mm->label_x));
parsestring(line,"y-label",(mm->label_y));
parsestring(line,"type",buf);
}
if (buf[0] && (strcasecmp(buf,"Discrete")==0))
mm->bDiscrete=TRUE;
if (debug)
fprintf(debug,"%s %s %s %s\n",
mm->title,mm->legend,mm->label_x,mm->label_y);
if (strncmp(line,"static",6) != 0)
gmx_input("Invalid XPixMap");
/* Read sizes */
bGetOnWithIt=FALSE;
while (!bGetOnWithIt && fgetline(&line,llmax,in)) {
while (( line[0] != '\"' ) && ( line[0] != '\0' ))
line++;
if ( line[0] == '\"' ) {
line2string(&line);
sscanf(line,"%d %d %d %d",&(mm->nx),&(mm->ny),&(mm->nmap),&nch);
if (nch > 2)
gmx_fatal(FARGS,"Sorry can only read xpm's with at most 2 caracters per pixel\n");
llmax = max(STRLEN,mm->nx+10);
bGetOnWithIt=TRUE;
}
}
if (debug)
fprintf(debug,"mm->nx %d mm->ny %d mm->nmap %d nch %d\n",
mm->nx,mm->ny,mm->nmap,nch);
/* Read color map */
snew(map,mm->nmap);
m=0;
while ((m < mm->nmap) && fgetline(&line,llmax,in)) {
line=strchr(line,'\"');
if (line) {
line++;
/* Read xpm color map entry */
map[m].code.c1 = line[0];
if (nch==1)
map[m].code.c2 = 0;
else
map[m].code.c2 = line[1];
line += nch;
str = strchr(line,'#');
if (str) {
str++;
col_len = 0;
while (isxdigit(str[col_len]))
col_len++;
if (col_len==6) {
sscanf(line,"%*s #%2x%2x%2x",&r,&g,&b);
map[m].rgb.r=r/255.0;
map[m].rgb.g=g/255.0;
map[m].rgb.b=b/255.0;
} else if (col_len==12) {
sscanf(line,"%*s #%4x%4x%4x",&r,&g,&b);
map[m].rgb.r=r/65535.0;
map[m].rgb.g=g/65535.0;
map[m].rgb.b=b/65535.0;
} else
gmx_file("Unsupported or invalid colormap in X PixMap");
} else {
str = strchr(line,'c');
if (str)
str += 2;
else
gmx_file("Unsupported or invalid colormap in X PixMap");
fprintf(stderr,"Using white for color \"%s",str);
map[m].rgb.r = 1;
map[m].rgb.g = 1;
map[m].rgb.b = 1;
}
line=strchr(line,'\"');
line++;
line2string(&line);
map[m].desc = strdup(line);
m++;
}
}
if ( m != mm->nmap )
gmx_fatal(FARGS,"Number of read colors map entries (%d) does not match the number in the header (%d)",m,mm->nmap);
mm->map = map;
/* Read axes, if there are any */
n_axis_x=0;
n_axis_y=0;
bGetOnWithIt=FALSE;
do {
if (strstr(line,"x-axis")) {
line=strstr(line,"x-axis");
skipstr(&line);
if (mm->axis_x==NULL)
snew(mm->axis_x,mm->nx + 1);
while (sscanf(line,"%lf",&u)==1) {
if (n_axis_x > mm->nx) {
gmx_fatal(FARGS,"Too many x-axis labels in xpm (max %d)",mm->nx);
} else if (n_axis_x == mm->nx) {
mm->flags |= MAT_SPATIAL_X;
}
mm->axis_x[n_axis_x] = u;
n_axis_x++;
skipstr(&line);
}
}
else if (strstr(line,"y-axis")) {
line=strstr(line,"y-axis");
skipstr(&line);
if (mm->axis_y==NULL)
snew(mm->axis_y,mm->ny + 1);
while (sscanf(line,"%lf",&u)==1) {
if (n_axis_y > mm->ny) {
gmx_file("Too many y-axis labels in xpm");
} else if (n_axis_y == mm->ny) {
mm->flags |= MAT_SPATIAL_Y;
}
mm->axis_y[n_axis_y] = u;
n_axis_y++;
skipstr(&line);
}
}
} while ((line[0] != '\"') && fgetline(&line,llmax,in));
/* Read matrix */
snew(mm->matrix,mm->nx);
for(i=0; i<mm->nx; i++)
snew(mm->matrix[i],mm->ny);
m=mm->ny-1;
do {
if(m%(1+mm->ny/100)==0)
fprintf(stderr,"%3d%%\b\b\b\b",(100*(mm->ny-m))/mm->ny);
while ((line[0] != '\"') && (line[0] != '\0'))
line++;
if (line[0] != '\"')
gmx_fatal(FARGS,"Not enough caracters in row %d of the matrix\n",m+1);
else {
line++;
for(i=0; i<mm->nx; i++) {
c.c1=line[nch*i];
if (nch==1)
c.c2=0;
else
c.c2=line[nch*i+1];
mm->matrix[i][m]=searchcmap(mm->nmap,mm->map,c);
}
m--;
}
} while ((m>=0) && fgetline(&line,llmax,in));
if (m>=0)
gmx_incons("Not enough rows in the matrix");
}
/*!
* \param[in,out] d Trajectory analysis data structure.
* \returns 0 on success, a non-zero error code on error.
*
* Initializes the selection data in \c gmx_ana_traj_t based on
* the selection options and/or index files provided on the command line.
*
* This function is called automatically by parse_trjana_args() and should
* not be called directly unless \ref ANA_USER_SELINIT is specified.
*
* \see ANA_USER_SELINIT
*/
int
gmx_ana_init_selections(gmx_ana_traj_t *d)
{
int rc;
int i;
int nr;
gmx_ana_indexgrps_t *grps;
int natoms;
bool bStdIn;
bool bInteractive;
bool bOk;
if (d->sel)
{
gmx_call("init_selections called more than once\n"
"perhaps you forgot ANA_USER_SELINIT");
return -1;
}
/* Check if we need some information from the topology */
if (gmx_ana_selcollection_requires_top(d->sc))
{
rc = load_topology(d, TRUE);
if (rc != 0)
{
return rc;
}
}
/* Load the topology and init the index groups */
gmx_ana_indexgrps_init(&grps, d->top, d->ndxfile);
/* Parse the selection */
rc = gmx_ana_selmethod_register_defaults(d->sc);
if (rc != 0)
{
gmx_fatal(FARGS, "default selection method registration failed");
return rc;
}
bStdIn = (d->selfile && d->selfile[0] == '-' && d->selfile[1] == 0)
|| (d->selection && d->selection[0] == 0)
|| (!d->selfile && !d->selection);
bInteractive = bStdIn && isatty(fileno(stdin));
if (bStdIn && bInteractive)
{
/* Parse from stdin */
/* First we parse the reference groups if there are any */
if (d->nrefgrps > 0)
{
fprintf(stderr, "\nSpecify ");
if (d->nrefgrps == 1)
{
fprintf(stderr, "a reference selection");
}
else
{
fprintf(stderr, "%d reference selections", d->nrefgrps);
}
fprintf(stderr, ":\n");
fprintf(stderr, "(one selection per line, use \\ for line continuation)\n");
rc = gmx_ana_selcollection_parse_stdin(d->sc, d->nrefgrps, grps, TRUE);
nr = gmx_ana_selcollection_get_count(d->sc);
if (rc != 0 || nr != d->nrefgrps)
{
gmx_ana_traj_free(d);
gmx_input("unrecoverable error in selection parsing");
return rc;
}
}
/* Then, we parse the analysis groups */
fprintf(stderr, "\nSpecify ");
if (d->nanagrps == 1)
{
fprintf(stderr, "a selection");
}
else if (d->nanagrps == -1)
{
fprintf(stderr, "any number of selections");
}
else
{
fprintf(stderr, "%d selections", d->nanagrps);
}
fprintf(stderr, " for analysis:\n");
fprintf(stderr, "(one selection per line, use \\ for line continuation%s)\n",
d->nanagrps == -1 ? ", Ctrl-D to end" : "");
rc = gmx_ana_selcollection_parse_stdin(d->sc, d->nanagrps, grps, TRUE);
fprintf(stderr, "\n");
}
else if (bStdIn)
{
rc = gmx_ana_selcollection_parse_stdin(d->sc, -1, grps, FALSE);
}
else if (d->selection)
{
rc = gmx_ana_selcollection_parse_str(d->sc, d->selection, grps);
}
else
{
rc = gmx_ana_selcollection_parse_file(d->sc, d->selfile, grps);
}
gmx_ana_indexgrps_free(grps);
if (rc != 0)
{
/* Free memory for memory leak checking */
gmx_ana_traj_free(d);
gmx_input("selection(s) could not be parsed");
return rc;
}
/* Check the number of groups */
nr = gmx_ana_selcollection_get_count(d->sc);
if (nr <= d->nrefgrps)
{
gmx_input("selection does not specify enough index groups");
return -1;
}
if (d->nanagrps <= 0)
{
d->nanagrps = nr - d->nrefgrps;
}
else if (nr != d->nrefgrps + d->nanagrps)
{
gmx_input("selection does not specify the correct number of index groups");
return -1;
}
if (d->flags & ANA_DEBUG_SELECTION)
{
gmx_ana_selcollection_print_tree(stderr, d->sc, FALSE);
}
if (gmx_ana_selcollection_requires_top(d->sc))
{
rc = load_topology(d, TRUE);
if (rc != 0)
{
return rc;
}
}
if (d->top)
{
natoms = -1;
}
else
{
rc = init_first_frame(d);
if (rc != 0)
{
return rc;
}
natoms = d->fr->natoms;
}
gmx_ana_selcollection_set_topology(d->sc, d->top, natoms);
rc = gmx_ana_selcollection_compile(d->sc);
if (rc != 0)
{
/* Free memory for memory leak checking */
gmx_ana_traj_free(d);
gmx_input("selection could not be compiled");
return rc;
}
/* Create the selection array */
d->ngrps = gmx_ana_selcollection_get_count(d->sc);
if (!(d->flags & ANA_USE_FULLGRPS))
{
d->ngrps -= d->nrefgrps;
}
snew(d->sel, d->ngrps);
for (i = 0; i < d->ngrps; ++i)
{
if (d->flags & ANA_USE_FULLGRPS)
{
d->sel[i] = gmx_ana_selcollection_get_selection(d->sc, i);
}
else
{
d->sel[i] = gmx_ana_selcollection_get_selection(d->sc, i + d->nrefgrps);
}
}
if (d->flags & ANA_DEBUG_SELECTION)
{
fprintf(stderr, "\n");
gmx_ana_selcollection_print_tree(stderr, d->sc, FALSE);
fprintf(stderr, "\n");
gmx_ana_poscalc_coll_print_tree(stderr, d->pcc);
fprintf(stderr, "\n");
}
/* Initialize the position evaluation */
gmx_ana_poscalc_init_eval(d->pcc);
if (d->flags & ANA_DEBUG_SELECTION)
{
gmx_ana_poscalc_coll_print_tree(stderr, d->pcc);
fprintf(stderr, "\n");
}
/* Check that dynamic selections are not provided if not allowed */
if (d->flags & ANA_NO_DYNSEL)
{
for (i = 0; i < d->nrefgrps + d->nanagrps; ++i)
{
gmx_ana_selection_t *sel;
sel = gmx_ana_selcollection_get_selection(d->sc, i);
if (sel->bDynamic)
{
gmx_fatal(FARGS, "%s does not support dynamic selections",
ShortProgram());
return -1;
}
}
}
/* Check that non-atom positions are not provided if not allowed.
* TODO: It would be better to have these checks in the parser. */
if (d->flags & ANA_ONLY_ATOMPOS)
{
for (i = 0; i < d->nanagrps; ++i)
{
gmx_ana_selection_t *sel;
sel = gmx_ana_selcollection_get_selection(d->sc, i + d->nrefgrps);
if (sel->p.m.type != INDEX_ATOM)
{
gmx_fatal(FARGS, "%s does not support non-atom positions",
ShortProgram());
return -1;
}
}
}
/* Create the names array */
snew(d->grpnames, d->ngrps);
for (i = 0; i < d->ngrps; ++i)
{
d->grpnames[i] = gmx_ana_selection_name(d->sel[i]);
}
return 0;
}
