static void write_constr_pdb(const char *fn, const char *title,
gmx_mtop_t *mtop,
int start, int homenr, t_commrec *cr,
rvec x[], matrix box)
{
char fname[STRLEN], format[STRLEN];
FILE *out;
int dd_ac0 = 0, dd_ac1 = 0, i, ii, resnr;
gmx_domdec_t *dd;
char *anm, *resnm;
dd = NULL;
if (DOMAINDECOMP(cr))
{
dd = cr->dd;
dd_get_constraint_range(dd, &dd_ac0, &dd_ac1);
start = 0;
homenr = dd_ac1;
}
if (PAR(cr))
{
sprintf(fname, "%s_n%d.pdb", fn, cr->sim_nodeid);
}
else
{
sprintf(fname, "%s.pdb", fn);
}
sprintf(format, "%s\n", get_pdbformat());
out = gmx_fio_fopen(fname, "w");
fprintf(out, "TITLE %s\n", title);
gmx_write_pdb_box(out, -1, box);
for (i = start; i < start+homenr; i++)
{
if (dd != NULL)
{
if (i >= dd->nat_home && i < dd_ac0)
{
continue;
}
ii = dd->gatindex[i];
}
else
{
ii = i;
}
gmx_mtop_atominfo_global(mtop, ii, &anm, &resnr, &resnm);
fprintf(out, format, "ATOM", (ii+1)%100000,
anm, resnm, ' ', resnr%10000, ' ',
10*x[i][XX], 10*x[i][YY], 10*x[i][ZZ]);
}
fprintf(out, "TER\n");
gmx_fio_fclose(out);
}
void dump_as_pdb(char *pdb,t_ana_struct *anal)
{
FILE *kp;
int i,j;
real t;
kp = ffopen(pdb,"w");
for(i=0; (i<anal->nstruct); i++) {
t = 1000*anal->t[i];
fprintf(kp,"MODEL %d time %g fs\n",i+1,t);
for(j=0; (j<anal->nparticle); j++) {
fprintf(kp,get_pdbformat(),"ATOM",i+1,(j < anal->nion[i]) ? "O" : "N",
"PLS",' ',1,
anal->x[i][j][XX]/100,
anal->x[i][j][YY]/100,
anal->x[i][j][ZZ]/100);
fprintf(kp,"\n");
}
fprintf(kp,"ENDMDL\n");
}
ffclose(kp);
}
static void project(const char *trajfile,t_topology *top,int ePBC,matrix topbox,
const char *projfile,const char *twodplotfile,
const char *threedplotfile, const char *filterfile,int skip,
const char *extremefile,gmx_bool bExtrAll,real extreme,
int nextr, t_atoms *atoms,int natoms,atom_id *index,
gmx_bool bFit,rvec *xref,int nfit,atom_id *ifit,real *w_rls,
real *sqrtm,rvec *xav,
int *eignr,rvec **eigvec,
int noutvec,int *outvec, gmx_bool bSplit,
const output_env_t oenv)
{
FILE *xvgrout=NULL;
int nat,i,j,d,v,vec,nfr,nframes=0,snew_size,frame;
t_trxstatus *out=NULL;
t_trxstatus *status;
int noutvec_extr,imin,imax;
real *pmin,*pmax;
atom_id *all_at;
matrix box;
rvec *xread,*x;
real t,inp,**inprod=NULL,min=0,max=0;
char str[STRLEN],str2[STRLEN],**ylabel,*c;
real fact;
gmx_rmpbc_t gpbc=NULL;
snew(x,natoms);
if (bExtrAll)
noutvec_extr=noutvec;
else
noutvec_extr=1;
if (trajfile) {
snew(inprod,noutvec+1);
if (filterfile) {
fprintf(stderr,"Writing a filtered trajectory to %s using eigenvectors\n",
filterfile);
for(i=0; i<noutvec; i++)
fprintf(stderr,"%d ",outvec[i]+1);
fprintf(stderr,"\n");
out=open_trx(filterfile,"w");
}
snew_size=0;
nfr=0;
nframes=0;
nat=read_first_x(oenv,&status,trajfile,&t,&xread,box);
if (nat>atoms->nr)
gmx_fatal(FARGS,"the number of atoms in your trajectory (%d) is larger than the number of atoms in your structure file (%d)",nat,atoms->nr);
snew(all_at,nat);
if (top)
gpbc = gmx_rmpbc_init(&top->idef,ePBC,nat,box);
for(i=0; i<nat; i++)
all_at[i]=i;
do {
if (nfr % skip == 0) {
if (top)
gmx_rmpbc(gpbc,nat,box,xread);
if (nframes>=snew_size) {
snew_size+=100;
for(i=0; i<noutvec+1; i++)
srenew(inprod[i],snew_size);
}
inprod[noutvec][nframes]=t;
/* calculate x: a fitted struture of the selected atoms */
if (bFit) {
reset_x(nfit,ifit,nat,NULL,xread,w_rls);
do_fit(nat,w_rls,xref,xread);
}
for (i=0; i<natoms; i++)
copy_rvec(xread[index[i]],x[i]);
for(v=0; v<noutvec; v++) {
vec=outvec[v];
/* calculate (mass-weighted) projection */
inp=0;
for (i=0; i<natoms; i++) {
inp+=(eigvec[vec][i][0]*(x[i][0]-xav[i][0])+
eigvec[vec][i][1]*(x[i][1]-xav[i][1])+
eigvec[vec][i][2]*(x[i][2]-xav[i][2]))*sqrtm[i];
}
inprod[v][nframes]=inp;
}
if (filterfile) {
for(i=0; i<natoms; i++)
for(d=0; d<DIM; d++) {
/* misuse xread for output */
xread[index[i]][d] = xav[i][d];
for(v=0; v<noutvec; v++)
xread[index[i]][d] +=
inprod[v][nframes]*eigvec[outvec[v]][i][d]/sqrtm[i];
}
write_trx(out,natoms,index,atoms,0,t,box,xread,NULL,NULL);
}
nframes++;
}
nfr++;
} while (read_next_x(oenv,status,&t,nat,xread,box));
close_trx(status);
sfree(x);
if (filterfile)
close_trx(out);
}
else
snew(xread,atoms->nr);
if (top)
gmx_rmpbc_done(gpbc);
if (projfile) {
snew(ylabel,noutvec);
for(v=0; v<noutvec; v++) {
sprintf(str,"vec %d",eignr[outvec[v]]+1);
ylabel[v]=strdup(str);
}
sprintf(str,"projection on eigenvectors (%s)",proj_unit);
write_xvgr_graphs(projfile, noutvec, 1, str, NULL, output_env_get_xvgr_tlabel(oenv),
(const char **)ylabel,
nframes, inprod[noutvec], inprod, NULL,
output_env_get_time_factor(oenv), FALSE, bSplit,oenv);
}
if (twodplotfile) {
sprintf(str,"projection on eigenvector %d (%s)",
eignr[outvec[0]]+1,proj_unit);
sprintf(str2,"projection on eigenvector %d (%s)",
eignr[outvec[noutvec-1]]+1,proj_unit);
xvgrout=xvgropen(twodplotfile,"2D projection of trajectory",str,str2,
oenv);
for(i=0; i<nframes; i++) {
if ( bSplit && i>0 && abs(inprod[noutvec][i])<1e-5 )
fprintf(xvgrout,"&\n");
fprintf(xvgrout,"%10.5f %10.5f\n",inprod[0][i],inprod[noutvec-1][i]);
}
ffclose(xvgrout);
}
if (threedplotfile) {
t_atoms atoms;
rvec *x;
real *b=NULL;
matrix box;
char *resnm,*atnm, pdbform[STRLEN];
gmx_bool bPDB, b4D;
FILE *out;
if (noutvec < 3)
gmx_fatal(FARGS,"You have selected less than 3 eigenvectors");
/* initialize */
bPDB = fn2ftp(threedplotfile)==efPDB;
clear_mat(box);
box[XX][XX] = box[YY][YY] = box[ZZ][ZZ] = 1;
b4D = bPDB && (noutvec >= 4);
if (b4D) {
fprintf(stderr, "You have selected four or more eigenvectors:\n"
"fourth eigenvector will be plotted "
"in bfactor field of pdb file\n");
sprintf(str,"4D proj. of traj. on eigenv. %d, %d, %d and %d",
eignr[outvec[0]]+1,eignr[outvec[1]]+1,
eignr[outvec[2]]+1,eignr[outvec[3]]+1);
} else {
sprintf(str,"3D proj. of traj. on eigenv. %d, %d and %d",
eignr[outvec[0]]+1,eignr[outvec[1]]+1,eignr[outvec[2]]+1);
}
init_t_atoms(&atoms,nframes,FALSE);
snew(x,nframes);
snew(b,nframes);
atnm=strdup("C");
resnm=strdup("PRJ");
if(nframes>10000)
fact=10000.0/nframes;
else
fact=1.0;
for(i=0; i<nframes; i++) {
atoms.atomname[i] = &atnm;
atoms.atom[i].resind = i;
atoms.resinfo[i].name = &resnm;
atoms.resinfo[i].nr = ceil(i*fact);
atoms.resinfo[i].ic = ' ';
x[i][XX]=inprod[0][i];
x[i][YY]=inprod[1][i];
x[i][ZZ]=inprod[2][i];
if (b4D)
b[i] =inprod[3][i];
}
if ( ( b4D || bSplit ) && bPDB ) {
strcpy(pdbform,get_pdbformat());
strcat(pdbform,"%8.4f%8.4f\n");
out=ffopen(threedplotfile,"w");
fprintf(out,"HEADER %s\n",str);
if ( b4D )
fprintf(out,"REMARK %s\n","fourth dimension plotted as B-factor");
j=0;
for(i=0; i<atoms.nr; i++) {
if ( j>0 && bSplit && abs(inprod[noutvec][i])<1e-5 ) {
fprintf(out,"TER\n");
j=0;
}
fprintf(out,pdbform,"ATOM",i+1,"C","PRJ",' ',j+1,
PR_VEC(10*x[i]), 1.0, 10*b[i]);
if (j>0)
fprintf(out,"CONECT%5d%5d\n", i, i+1);
j++;
}
fprintf(out,"TER\n");
ffclose(out);
} else
write_sto_conf(threedplotfile,str,&atoms,x,NULL,ePBC,box);
free_t_atoms(&atoms,FALSE);
}
if (extremefile) {
snew(pmin,noutvec_extr);
snew(pmax,noutvec_extr);
if (extreme==0) {
fprintf(stderr,"%11s %17s %17s\n","eigenvector","Minimum","Maximum");
fprintf(stderr,
"%11s %10s %10s %10s %10s\n","","value","frame","value","frame");
imin = 0;
imax = 0;
for(v=0; v<noutvec_extr; v++) {
for(i=0; i<nframes; i++) {
if (inprod[v][i]<inprod[v][imin])
imin = i;
if (inprod[v][i]>inprod[v][imax])
imax = i;
}
pmin[v] = inprod[v][imin];
pmax[v] = inprod[v][imax];
fprintf(stderr,"%7d %10.6f %10d %10.6f %10d\n",
eignr[outvec[v]]+1,
pmin[v],imin,pmax[v],imax);
}
}
else {
pmin[0] = -extreme;
pmax[0] = extreme;
}
/* build format string for filename: */
strcpy(str,extremefile);/* copy filename */
c=strrchr(str,'.'); /* find where extention begins */
strcpy(str2,c); /* get extention */
sprintf(c,"%%d%s",str2); /* append '%s' and extention to filename */
for(v=0; v<noutvec_extr; v++) {
/* make filename using format string */
if (noutvec_extr==1)
strcpy(str2,extremefile);
else
sprintf(str2,str,eignr[outvec[v]]+1);
fprintf(stderr,"Writing %d frames along eigenvector %d to %s\n",
nextr,outvec[v]+1,str2);
out=open_trx(str2,"w");
for(frame=0; frame<nextr; frame++) {
if ((extreme==0) && (nextr<=3))
for(i=0; i<natoms; i++) {
atoms->resinfo[atoms->atom[index[i]].resind].chainid = 'A' + frame;
}
for(i=0; i<natoms; i++)
for(d=0; d<DIM; d++)
xread[index[i]][d] =
(xav[i][d] + (pmin[v]*(nextr-frame-1)+pmax[v]*frame)/(nextr-1)
*eigvec[outvec[v]][i][d]/sqrtm[i]);
write_trx(out,natoms,index,atoms,0,frame,topbox,xread,NULL,NULL);
}
close_trx(out);
}
sfree(pmin);
sfree(pmax);
}
fprintf(stderr,"\n");
}
