void calc_compact_unitcell_vertices(int ecenter, const matrix box, rvec vert[])
{
rvec img[NTRICIMG], box_center;
int n, i, j, tmp[4], d;
const real oneFourth = 0.25;
calc_triclinic_images(box, img);
n = 0;
for (i = 2; i <= 5; i += 3)
{
tmp[0] = i-1;
if (i == 2)
{
tmp[1] = 8;
}
else
{
tmp[1] = 6;
}
tmp[2] = (i+1) % 6;
tmp[3] = tmp[1]+4;
for (j = 0; j < 4; j++)
{
for (d = 0; d < DIM; d++)
{
vert[n][d] = img[i][d]+img[tmp[j]][d]+img[tmp[(j+1)%4]][d];
}
n++;
}
}
for (i = 7; i <= 13; i += 6)
{
tmp[0] = (i-7)/2;
tmp[1] = tmp[0]+1;
if (i == 7)
{
tmp[2] = 8;
}
else
{
tmp[2] = 10;
}
tmp[3] = i-1;
for (j = 0; j < 4; j++)
{
for (d = 0; d < DIM; d++)
{
vert[n][d] = img[i][d]+img[tmp[j]][d]+img[tmp[(j+1)%4]][d];
}
n++;
}
}
for (i = 9; i <= 11; i += 2)
{
if (i == 9)
{
tmp[0] = 3;
}
else
{
tmp[0] = 0;
}
tmp[1] = tmp[0]+1;
if (i == 9)
{
tmp[2] = 6;
}
else
{
tmp[2] = 12;
}
tmp[3] = i-1;
for (j = 0; j < 4; j++)
{
for (d = 0; d < DIM; d++)
{
vert[n][d] = img[i][d]+img[tmp[j]][d]+img[tmp[(j+1)%4]][d];
}
n++;
}
}
calc_box_center(ecenter, box, box_center);
for (i = 0; i < NCUCVERT; i++)
{
for (d = 0; d < DIM; d++)
{
vert[i][d] = vert[i][d]*oneFourth+box_center[d];
}
}
}
int gmx_editconf(int argc, char *argv[])
{
static char *desc[] = {
"editconf converts generic structure format to [TT].gro[tt], [TT].g96[tt]",
"or [TT].pdb[tt].",
"[PAR]",
"The box can be modified with options [TT]-box[tt], [TT]-d[tt] and",
"[TT]-angles[tt]. Both [TT]-box[tt] and [TT]-d[tt]",
"will center the system in the box, unless [TT]-noc[tt] is used.",
"[PAR]",
"Option [TT]-bt[tt] determines the box type: [TT]triclinic[tt] is a",
"triclinic box, [TT]cubic[tt] is a rectangular box with all sides equal",
"[TT]dodecahedron[tt] represents a rhombic dodecahedron and "
"[TT]octahedron[tt] is a truncated octahedron.",
"The last two are special cases of a triclinic box.",
"The length of the three box vectors of the truncated octahedron is the",
"shortest distance between two opposite hexagons.",
"The volume of a dodecahedron is 0.71 and that of a truncated octahedron",
"is 0.77 of that of a cubic box with the same periodic image distance.",
"[PAR]",
"Option [TT]-box[tt] requires only",
"one value for a cubic box, dodecahedron and a truncated octahedron.",
"[PAR]",
"With [TT]-d[tt] and a [TT]triclinic[tt] box the size of the system in the x, y",
"and z directions is used. With [TT]-d[tt] and [TT]cubic[tt],",
"[TT]dodecahedron[tt] or [TT]octahedron[tt] boxes, the dimensions are set",
"to the diameter of the system (largest distance between atoms) plus twice",
"the specified distance.",
"[PAR]",
"Option [TT]-angles[tt] is only meaningful with option [TT]-box[tt] and",
"a triclinic box and can not be used with option [TT]-d[tt].",
"[PAR]",
"When [TT]-n[tt] or [TT]-ndef[tt] is set, a group",
"can be selected for calculating the size and the geometric center,",
"otherwise the whole system is used.",
"[PAR]",
"[TT]-rotate[tt] rotates the coordinates and velocities.",
"[PAR]",
"[TT]-princ[tt] aligns the principal axes of the system along the",
"coordinate axes, this may allow you to decrease the box volume,",
"but beware that molecules can rotate significantly in a nanosecond.",
"[PAR]",
"Scaling is applied before any of the other operations are",
"performed. Boxes and coordinates can be scaled to give a certain density (option",
"[TT]-density[tt]). Note that this may be inaccurate in case a gro",
"file is given as input. A special feature of the scaling option, when the",
"factor -1 is given in one dimension, one obtains a mirror image,",
"mirrored in one of the plains, when one uses -1 in three dimensions",
"a point-mirror image is obtained.[PAR]",
"Groups are selected after all operations have been applied.[PAR]",
"Periodicity can be removed in a crude manner.",
"It is important that the box sizes at the bottom of your input file",
"are correct when the periodicity is to be removed.",
"[PAR]",
"When writing [TT].pdb[tt] files, B-factors can be",
"added with the [TT]-bf[tt] option. B-factors are read",
"from a file with with following format: first line states number of",
"entries in the file, next lines state an index",
"followed by a B-factor. The B-factors will be attached per residue",
"unless an index is larger than the number of residues or unless the",
"[TT]-atom[tt] option is set. Obviously, any type of numeric data can",
"be added instead of B-factors. [TT]-legend[tt] will produce",
"a row of CA atoms with B-factors ranging from the minimum to the",
"maximum value found, effectively making a legend for viewing.",
"[PAR]",
"With the option -mead a special pdb (pqr) file for the MEAD electrostatics",
"program (Poisson-Boltzmann solver) can be made. A further prerequisite",
"is that the input file is a run input file.",
"The B-factor field is then filled with the Van der Waals radius",
"of the atoms while the occupancy field will hold the charge.",
"[PAR]",
"The option -grasp is similar, but it puts the charges in the B-factor",
"and the radius in the occupancy.",
"[PAR]",
"Finally with option [TT]-label[tt] editconf can add a chain identifier",
"to a pdb file, which can be useful for analysis with e.g. rasmol."
"[PAR]",
"To convert a truncated octrahedron file produced by a package which uses",
"a cubic box with the corners cut off (such as Gromos) use:[BR]",
"[TT]editconf -f <in> -rotate 0 45 35.264 -bt o -box <veclen> -o <out>[tt][BR]",
"where [TT]veclen[tt] is the size of the cubic box times sqrt(3)/2."
};
static char *bugs[] = {
"For complex molecules, the periodicity removal routine may break down, "
"in that case you can use trjconv"
};
static real dist=0.0,rbox=0.0,to_diam=0.0;
static bool bNDEF=FALSE,bRMPBC=FALSE,bCenter=FALSE,bReadVDW=FALSE;
static bool peratom=FALSE,bLegend=FALSE,bOrient=FALSE,bMead=FALSE,bGrasp=FALSE,bSig56=FALSE;
static rvec scale={1,1,1},newbox={0,0,0},newang={90,90,90};
static real rho=1000.0,rvdw=0.12;
static rvec center={0,0,0},translation={0,0,0},rotangles={0,0,0};
static char *btype[]={ NULL, "triclinic", "cubic", "dodecahedron", "octahedron", NULL },*label="A";
static rvec visbox={0,0,0};
t_pargs pa[] = {
{ "-ndef", FALSE, etBOOL, {&bNDEF},
"Choose output from default index groups" },
{ "-visbox", FALSE, etRVEC, {visbox},
"HIDDENVisualize a grid of boxes, -1 visualizes the 14 box images" },
{ "-bt", FALSE, etENUM, {btype},
"Box type for -box and -d" },
{ "-box", FALSE, etRVEC, {newbox}, "Box vector lengths (a,b,c)" },
{ "-angles", FALSE, etRVEC, {newang},
"Angles between the box vectors (bc,ac,ab)" },
{ "-d", FALSE, etREAL, {&dist},
"Distance between the solute and the box" },
{ "-c", FALSE, etBOOL, {&bCenter},
"Center molecule in box (implied by -box and -d)" },
{ "-center", FALSE, etRVEC, {center}, "Coordinates of geometrical center"},
{ "-translate", FALSE, etRVEC, {translation},
"Translation" },
{ "-rotate", FALSE, etRVEC, {rotangles},
"Rotation around the X, Y and Z axes in degrees" },
{ "-princ", FALSE, etBOOL, {&bOrient}, "Orient molecule(s) along their principal axes" },
{ "-scale", FALSE, etRVEC, {scale}, "Scaling factor" },
{ "-density",FALSE, etREAL, {&rho},
"Density (g/l) of the output box achieved by scaling" },
{ "-pbc", FALSE, etBOOL, {&bRMPBC},
"Remove the periodicity (make molecule whole again)" },
{ "-grasp", FALSE, etBOOL, {&bGrasp},
"Store the charge of the atom in the B-factor field and the radius of the atom in the occupancy field" },
{ "-rvdw", FALSE, etREAL, {&rvdw},
"Default Van der Waals radius (in nm) if one can not be found in the database or if no parameters are present in the topology file" },
{ "-sig56", FALSE, etREAL, {&bSig56},
"Use rmin/2 (minimum in the Van der Waals potential) rather than sigma/2 " },
{ "-vdwread",FALSE, etBOOL, {&bReadVDW},
"Read the Van der Waals radii from the file vdwradii.dat rather than computing the radii based on the force field" },
{ "-atom", FALSE, etBOOL, {&peratom}, "Force B-factor attachment per atom" },
{ "-legend", FALSE, etBOOL, {&bLegend}, "Make B-factor legend" },
{ "-label", FALSE, etSTR, {&label}, "Add chain label for all residues" }
};
#define NPA asize(pa)
FILE *out;
char *infile,*outfile,title[STRLEN];
int outftp,natom,i,j,n_bfac,itype,ntype;
double *bfac=NULL,c6,c12;
int *bfac_nr=NULL;
t_topology *top;
t_atoms atoms;
char *grpname,*sgrpname;
int isize,ssize,tsize;
atom_id *index,*sindex,*tindex;
rvec *x,*v,gc,min,max,size;
int ePBC;
matrix box;
bool bIndex,bSetSize,bSetAng,bCubic,bDist,bSetCenter;
bool bHaveV,bScale,bRho,bTranslate,bRotate,bCalcGeom,bCalcDiam;
real xs,ys,zs,xcent,ycent,zcent,diam=0,mass=0,d,vdw;
gmx_atomprop_t aps;
t_filenm fnm[] = {
{ efSTX, "-f", NULL, ffREAD },
{ efNDX, "-n", NULL, ffOPTRD },
{ efSTO, NULL, NULL, ffOPTWR },
{ efPQR, "-mead", "mead", ffOPTWR },
{ efDAT, "-bf", "bfact", ffOPTRD }
};
#define NFILE asize(fnm)
CopyRight(stderr,argv[0]);
parse_common_args(&argc,argv,PCA_CAN_VIEW,NFILE,fnm,NPA,pa,
asize(desc),desc,asize(bugs),bugs);
bIndex = opt2bSet("-n",NFILE,fnm) || bNDEF;
bMead = opt2bSet("-mead",NFILE,fnm);
bSetSize = opt2parg_bSet("-box" ,NPA,pa);
bSetAng = opt2parg_bSet("-angles" ,NPA,pa);
bSetCenter= opt2parg_bSet("-center" ,NPA,pa);
bDist = opt2parg_bSet("-d" ,NPA,pa);
/* Only automatically turn on centering without -noc */
if ((bDist || bSetSize || bSetCenter) && !opt2parg_bSet("-c",NPA,pa)) {
bCenter = TRUE;
}
bScale = opt2parg_bSet("-scale" ,NPA,pa);
bRho = opt2parg_bSet("-density",NPA,pa);
bTranslate= opt2parg_bSet("-translate",NPA,pa);
bRotate = opt2parg_bSet("-rotate",NPA,pa);
if (bScale && bRho)
fprintf(stderr,"WARNING: setting -density overrides -scale\n");
bScale = bScale || bRho;
bCalcGeom = bCenter || bRotate || bOrient || bScale;
bCalcDiam = btype[0][0]=='c' || btype[0][0]=='d' || btype[0][0]=='o';
infile = ftp2fn(efSTX,NFILE,fnm);
if (bMead)
outfile = ftp2fn(efPQR,NFILE,fnm);
else
outfile = ftp2fn(efSTO,NFILE,fnm);
outftp = fn2ftp(outfile);
aps = gmx_atomprop_init();
if (bMead && bGrasp) {
printf("Incompatible options -mead and -grasp. Turning off -grasp\n");
bGrasp = FALSE;
}
if (bGrasp && (outftp != efPDB))
gmx_fatal(FARGS,"Output file should be a .pdb file"
" when using the -grasp option\n");
if ((bMead || bGrasp) && !((fn2ftp(infile) == efTPR) ||
(fn2ftp(infile) == efTPA) ||
(fn2ftp(infile) == efTPB)))
gmx_fatal(FARGS,"Input file should be a .tp[abr] file"
" when using the -mead option\n");
get_stx_coordnum(infile,&natom);
init_t_atoms(&atoms,natom,TRUE);
snew(x,natom);
snew(v,natom);
read_stx_conf(infile,title,&atoms,x,v,&ePBC,box);
printf("Read %d atoms\n",atoms.nr);
if (ePBC != epbcNONE) {
real vol = det(box);
printf("Volume: %g nm^3, corresponds to roughly %d electrons\n",
vol,100*((int)(vol*4.5)));
}
if (bMead || bGrasp) {
top = read_top(infile,NULL);
if (atoms.nr != top->atoms.nr)
gmx_fatal(FARGS,"Atom numbers don't match (%d vs. %d)",
atoms.nr,top->atoms.nr);
snew(atoms.pdbinfo,top->atoms.nr);
ntype = top->idef.atnr;
for(i=0; (i<atoms.nr); i++) {
/* Determine the Van der Waals radius from the force field */
if (bReadVDW) {
if (!gmx_atomprop_query(aps,epropVDW,
*top->atoms.resname[top->atoms.atom[i].resnr],
*top->atoms.atomname[i],&vdw))
vdw = rvdw;
}
else {
itype = top->atoms.atom[i].type;
c12 = top->idef.iparams[itype*ntype+itype].lj.c12;
c6 = top->idef.iparams[itype*ntype+itype].lj.c6;
if ((c6 != 0) && (c12 != 0)) {
real sig6;
if (bSig56)
sig6 = 2*c12/c6;
else
sig6 = c12/c6;
vdw = 0.5*pow(sig6,1.0/6.0);
}
else
vdw = rvdw;
}
/* Factor of 10 for nm -> Angstroms */
vdw *= 10;
if (bMead) {
atoms.pdbinfo[i].occup = top->atoms.atom[i].q;
atoms.pdbinfo[i].bfac = vdw;
}
else {
atoms.pdbinfo[i].occup = vdw;
atoms.pdbinfo[i].bfac = top->atoms.atom[i].q;
}
}
}
bHaveV=FALSE;
for (i=0; (i<natom) && !bHaveV; i++)
for (j=0; (j<DIM) && !bHaveV; j++)
bHaveV=bHaveV || (v[i][j]!=0);
printf("%selocities found\n",bHaveV?"V":"No v");
if (visbox[0] > 0) {
if (bIndex)
gmx_fatal(FARGS,"Sorry, can not visualize box with index groups");
if (outftp != efPDB)
gmx_fatal(FARGS,"Sorry, can only visualize box with a pdb file");
} else if (visbox[0] == -1)
visualize_images("images.pdb",ePBC,box);
/* remove pbc */
if (bRMPBC)
rm_gropbc(&atoms,x,box);
if (bCalcGeom) {
if (bIndex) {
fprintf(stderr,"\nSelect a group for determining the system size:\n");
get_index(&atoms,ftp2fn_null(efNDX,NFILE,fnm),
1,&ssize,&sindex,&sgrpname);
} else {
ssize = atoms.nr;
sindex = NULL;
}
diam=calc_geom(ssize,sindex,x,gc,min,max,bCalcDiam);
rvec_sub(max, min, size);
printf(" system size :%7.3f%7.3f%7.3f (nm)\n",
size[XX], size[YY], size[ZZ]);
if (bCalcDiam)
printf(" diameter :%7.3f (nm)\n",diam);
printf(" center :%7.3f%7.3f%7.3f (nm)\n", gc[XX], gc[YY], gc[ZZ]);
printf(" box vectors :%7.3f%7.3f%7.3f (nm)\n",
norm(box[XX]), norm(box[YY]), norm(box[ZZ]));
printf(" box angles :%7.2f%7.2f%7.2f (degrees)\n",
norm2(box[ZZ])==0 ? 0 :
RAD2DEG*acos(cos_angle_no_table(box[YY],box[ZZ])),
norm2(box[ZZ])==0 ? 0 :
RAD2DEG*acos(cos_angle_no_table(box[XX],box[ZZ])),
norm2(box[YY])==0 ? 0 :
RAD2DEG*acos(cos_angle_no_table(box[XX],box[YY])));
printf(" box volume :%7.2f (nm^3)\n",det(box));
}
if (bRho || bOrient)
mass = calc_mass(&atoms,!fn2bTPX(infile),aps);
if (bOrient) {
atom_id *index;
char *grpnames;
/* Get a group for principal component analysis */
fprintf(stderr,"\nSelect group for the determining the orientation\n");
get_index(&atoms,ftp2fn_null(efNDX,NFILE,fnm),1,&isize,&index,&grpnames);
/* Orient the principal axes along the coordinate axes */
orient_princ(&atoms,isize,index,natom,x,bHaveV ? v : NULL, NULL);
sfree(index);
sfree(grpnames);
}
if ( bScale ) {
/* scale coordinates and box */
if (bRho) {
/* Compute scaling constant */
real vol,dens;
vol = det(box);
dens = (mass*AMU)/(vol*NANO*NANO*NANO);
fprintf(stderr,"Volume of input %g (nm^3)\n",vol);
fprintf(stderr,"Mass of input %g (a.m.u.)\n",mass);
fprintf(stderr,"Density of input %g (g/l)\n",dens);
if (vol==0 || mass==0)
gmx_fatal(FARGS,"Cannot scale density with "
"zero mass (%g) or volume (%g)\n",mass,vol);
scale[XX] = scale[YY] = scale[ZZ] = pow(dens/rho,1.0/3.0);
fprintf(stderr,"Scaling all box vectors by %g\n",scale[XX]);
}
scale_conf(atoms.nr,x,box,scale);
}
if (bTranslate) {
if (bIndex) {
fprintf(stderr,"\nSelect a group that you want to translate:\n");
get_index(&atoms,ftp2fn_null(efNDX,NFILE,fnm),
1,&ssize,&sindex,&sgrpname);
} else {
ssize = atoms.nr;
sindex = NULL;
}
printf("Translating %d atoms (out of %d) by %g %g %g nm\n",ssize,natom,
translation[XX],translation[YY],translation[ZZ]);
if (sindex) {
for(i=0; i<ssize; i++)
rvec_inc(x[sindex[i]],translation);
}
else {
for(i=0; i<natom; i++)
rvec_inc(x[i],translation);
}
}
if (bRotate) {
/* Rotate */
printf("Rotating %g, %g, %g degrees around the X, Y and Z axis respectively\n",rotangles[XX],rotangles[YY],rotangles[ZZ]);
for(i=0; i<DIM; i++)
rotangles[i] *= DEG2RAD;
rotate_conf(natom,x,v,rotangles[XX],rotangles[YY],rotangles[ZZ]);
}
if (bCalcGeom) {
/* recalc geometrical center and max and min coordinates and size */
calc_geom(ssize,sindex,x,gc,min,max,FALSE);
rvec_sub(max, min, size);
if (bScale || bOrient || bRotate)
printf("new system size : %6.3f %6.3f %6.3f\n",
size[XX],size[YY],size[ZZ]);
}
if (bSetSize || bDist || (btype[0][0]=='t' && bSetAng)) {
ePBC = epbcXYZ;
if (!(bSetSize || bDist))
for (i=0; i<DIM; i++)
newbox[i] = norm(box[i]);
clear_mat(box);
/* calculate new boxsize */
switch(btype[0][0]){
case 't':
if (bDist)
for(i=0; i<DIM; i++)
newbox[i] = size[i]+2*dist;
if (!bSetAng) {
box[XX][XX] = newbox[XX];
box[YY][YY] = newbox[YY];
box[ZZ][ZZ] = newbox[ZZ];
} else {
svmul(DEG2RAD,newang,newang);
box[XX][XX] = newbox[XX];
box[YY][XX] = newbox[YY]*cos(newang[ZZ]);
box[YY][YY] = newbox[YY]*sin(newang[ZZ]);
box[ZZ][XX] = newbox[ZZ]*cos(newang[YY]);
box[ZZ][YY] = newbox[ZZ]
*(cos(newang[XX])-cos(newang[YY])*cos(newang[ZZ]))/sin(newang[ZZ]);
box[ZZ][ZZ] = sqrt(sqr(newbox[ZZ])
-box[ZZ][XX]*box[ZZ][XX]-box[ZZ][YY]*box[ZZ][YY]);
}
break;
case 'c':
case 'd':
case 'o':
if (bSetSize)
d = newbox[0];
else
d = diam+2*dist;
if (btype[0][0] == 'c')
for(i=0; i<DIM; i++)
box[i][i] = d;
else if (btype[0][0] == 'd') {
box[XX][XX] = d;
box[YY][YY] = d;
box[ZZ][XX] = d/2;
box[ZZ][YY] = d/2;
box[ZZ][ZZ] = d*sqrt(2)/2;
} else {
box[XX][XX] = d;
box[YY][XX] = d/3;
box[YY][YY] = d*sqrt(2)*2/3;
box[ZZ][XX] = -d/3;
box[ZZ][YY] = d*sqrt(2)/3;
box[ZZ][ZZ] = d*sqrt(6)/3;
}
break;
}
}
/* calculate new coords for geometrical center */
if (!bSetCenter)
calc_box_center(ecenterDEF,box,center);
/* center molecule on 'center' */
if (bCenter)
center_conf(natom,x,center,gc);
/* print some */
if (bCalcGeom) {
calc_geom(ssize,sindex,x, gc, min, max, FALSE);
printf("new center :%7.3f%7.3f%7.3f (nm)\n",gc[XX],gc[YY],gc[ZZ]);
}
if (bOrient || bScale || bDist || bSetSize) {
printf("new box vectors :%7.3f%7.3f%7.3f (nm)\n",
norm(box[XX]), norm(box[YY]), norm(box[ZZ]));
printf("new box angles :%7.2f%7.2f%7.2f (degrees)\n",
norm2(box[ZZ])==0 ? 0 :
RAD2DEG*acos(cos_angle_no_table(box[YY],box[ZZ])),
norm2(box[ZZ])==0 ? 0 :
RAD2DEG*acos(cos_angle_no_table(box[XX],box[ZZ])),
norm2(box[YY])==0 ? 0 :
RAD2DEG*acos(cos_angle_no_table(box[XX],box[YY])));
printf("new box volume :%7.2f (nm^3)\n",det(box));
}
if (check_box(epbcXYZ,box))
printf("\nWARNING: %s\n",check_box(epbcXYZ,box));
if (bDist && btype[0][0]=='t')
{
if(TRICLINIC(box))
{
printf("\nWARNING: Your box is triclinic with non-orthogonal axes. In this case, the\n"
"distance from the solute to a box surface along the corresponding normal\n"
"vector might be somewhat smaller than your specified value %f.\n"
"You can check the actual value with g_mindist -pi\n",dist);
}
else
{
printf("\nWARNING: No boxtype specified - distance condition applied in each dimension.\n"
"If the molecule rotates the actual distance will be smaller. You might want\n"
"to use a cubic box instead, or why not try a dodecahedron today?\n");
}
}
if (bIndex) {
fprintf(stderr,"\nSelect a group for output:\n");
get_index(&atoms,opt2fn_null("-n",NFILE,fnm),
1,&isize,&index,&grpname);
if (opt2bSet("-bf",NFILE,fnm))
gmx_fatal(FARGS,"combination not implemented: -bf -n or -bf -ndef");
else
write_sto_conf_indexed(outfile,title,&atoms,x,bHaveV?v:NULL,ePBC,box,
isize,index);
}
else {
if ((outftp == efPDB) || (outftp == efPQR)) {
out=ffopen(outfile,"w");
if (bMead) {
set_pdb_wide_format(TRUE);
fprintf(out,"REMARK "
"The B-factors in this file hold atomic radii\n");
fprintf(out,"REMARK "
"The occupancy in this file hold atomic charges\n");
}
else if (bGrasp) {
fprintf(out,"GRASP PDB FILE\nFORMAT NUMBER=1\n");
fprintf(out,"REMARK "
"The B-factors in this file hold atomic charges\n");
fprintf(out,"REMARK "
"The occupancy in this file hold atomic radii\n");
}
else if (opt2bSet("-bf",NFILE,fnm)) {
read_bfac(opt2fn("-bf",NFILE,fnm),&n_bfac,&bfac,&bfac_nr);
set_pdb_conf_bfac(atoms.nr,atoms.nres,&atoms,
n_bfac,bfac,bfac_nr,peratom);
}
if (opt2parg_bSet("-label",NPA,pa)) {
for(i=0; (i<atoms.nr); i++)
atoms.atom[i].chain=label[0];
}
write_pdbfile(out,title,&atoms,x,ePBC,box,0,-1);
if (bLegend)
pdb_legend(out,atoms.nr,atoms.nres,&atoms,x);
if (visbox[0] > 0)
visualize_box(out,bLegend ? atoms.nr+12 : atoms.nr,
bLegend? atoms.nres=12 : atoms.nres,box,visbox);
fclose(out);
}
else
write_sto_conf(outfile,title,&atoms,x,bHaveV?v:NULL,ePBC,box);
}
gmx_atomprop_destroy(aps);
do_view(outfile,NULL);
thanx(stderr);
return 0;
}
