int write_trxframe(t_trxstatus *status,t_trxframe *fr,gmx_conect gc)
{
char title[STRLEN];
real prec;
if (fr->bPrec)
prec = fr->prec;
else
prec = 1000.0;
switch (gmx_fio_getftp(status->fio)) {
case efTRJ:
case efTRR:
break;
default:
if (!fr->bX)
gmx_fatal(FARGS,"Need coordinates to write a %s trajectory",
ftp2ext(gmx_fio_getftp(status->fio)));
break;
}
switch (gmx_fio_getftp(status->fio)) {
case efXTC:
write_xtc(status->fio,fr->natoms,fr->step,fr->time,fr->box,fr->x,prec);
break;
case efTRJ:
case efTRR:
fwrite_trn(status->fio,fr->step,fr->time,fr->lambda,fr->box,fr->natoms,
fr->bX ? fr->x:NULL,fr->bV ? fr->v:NULL ,fr->bF ? fr->f:NULL);
break;
case efGRO:
case efPDB:
case efBRK:
case efENT:
if (!fr->bAtoms)
gmx_fatal(FARGS,"Can not write a %s file without atom names",
ftp2ext(gmx_fio_getftp(status->fio)));
sprintf(title,"frame t= %.3f",fr->time);
if (gmx_fio_getftp(status->fio) == efGRO)
write_hconf_p(gmx_fio_getfp(status->fio),title,fr->atoms,
prec2ndec(prec),fr->x,fr->bV ? fr->v : NULL,fr->box);
else
write_pdbfile(gmx_fio_getfp(status->fio),title,
fr->atoms,fr->x,fr->bPBC ? fr->ePBC : -1,fr->box,
' ',fr->step,gc,TRUE);
break;
case efG87:
write_gms(gmx_fio_getfp(status->fio),fr->natoms,fr->x,fr->box);
break;
case efG96:
write_g96_conf(gmx_fio_getfp(status->fio),fr,-1,NULL);
break;
default:
gmx_fatal(FARGS,"Sorry, write_trxframe can not write %s",
ftp2ext(gmx_fio_getftp(status->fio)));
break;
}
return 0;
}
int main(int argc,char *argv[])
{
const char *desc[] = {
"[TT]do_multiprot[tt] ",
"reads a trajectory file and aligns it to a reference structure ",
"each time frame",
"calling the multiprot program. This allows you to use a reference",
"structure whose sequence is different than that of the protein in the ",
"trajectory, since the alignment is based on the geometry, not sequence.",
"The output of [TT]do_multiprot[tt] includes the rmsd and the number of residues",
"on which it was calculated.",
"[PAR]",
"An aligned trajectory file is generated with the [TT]-ox[tt] option.[PAR]",
"With the [TT]-cr[tt] option, the number of hits in the alignment is given",
"per residue. This number can be between 0 and the number of frames, and",
"indicates the structural conservation of this residue.[PAR]",
"If you do not have the [TT]multiprot[tt] program, get it. [TT]do_multiprot[tt] assumes",
"that the [TT]multiprot[tt] executable is [TT]/usr/local/bin/multiprot[tt]. If this is ",
"not the case, then you should set an environment variable [BB]MULTIPROT[bb]",
"pointing to the [TT]multiprot[tt] executable, e.g.: [PAR]",
"[TT]setenv MULTIPROT /usr/MultiProtInstall/multiprot.Linux[tt][PAR]",
"Note that at the current implementation only binary alignment (your",
"molecule to a reference) is supported. In addition, note that the ",
"by default [TT]multiprot[tt] aligns the two proteins on their C-alpha carbons.",
"and that this depends on the [TT]multiprot[tt] parameters which are not dealt ",
"with here. Thus, the C-alpha carbons is expected to give the same "
"results as choosing the whole protein and will be slightly faster.[PAR]",
"For information about [TT]multiprot[tt], see:",
"http://bioinfo3d.cs.tau.ac.il/MultiProt/.[PAR]"
};
static bool bVerbose;
t_pargs pa[] = {
{ "-v", FALSE, etBOOL, {&bVerbose},
"HIDDENGenerate miles of useless information" }
};
const char *bugs[] = {
"The program is very slow, since multiprot is run externally"
};
t_trxstatus *status;
t_trxstatus *trxout=NULL;
FILE *tapein,*fo,*frc,*tmpf,*out=NULL,*fres=NULL;
const char *fnRef;
const char *fn="2_sol.res";
t_topology top;
int ePBC;
t_atoms *atoms,ratoms,useatoms;
t_trxframe fr;
t_pdbinfo p;
int nres,nres2,nr0;
real t;
int i,j,natoms,nratoms,nframe=0,model_nr=-1;
int cur_res,prev_res;
int nout;
t_countres *countres=NULL;
matrix box,rbox;
int gnx;
char *grpnm,*ss_str;
atom_id *index;
rvec *xp,*x,*xr;
char pdbfile[32],refpdb[256],title[256],rtitle[256],filemode[5];
char out_title[256];
char multiprot[256],*mptr;
int ftp;
int outftp=-1;
real rmsd;
bool bTrjout,bCountres;
const char *TrjoutFile=NULL;
output_env_t oenv;
static rvec translation={0,0,0},rotangles={0,0,0};
gmx_rmpbc_t gpbc=NULL;
t_filenm fnm[] = {
{ efTRX, "-f", NULL, ffREAD },
{ efTPS, NULL, NULL, ffREAD },
{ efNDX, NULL, NULL, ffOPTRD },
{ efSTX, "-r", NULL , ffREAD },
{ efXVG, "-o", "rmss", ffWRITE },
{ efXVG, "-rc", "rescount", ffWRITE},
{ efXVG, "-cr", "countres", ffOPTWR},
{ efTRX, "-ox", "aligned", ffOPTWR }
};
#define NFILE asize(fnm)
CopyRight(stderr,argv[0]);
parse_common_args(&argc,argv,PCA_CAN_TIME | PCA_CAN_VIEW | PCA_TIME_UNIT,
NFILE,fnm, asize(pa),pa, asize(desc),desc,
asize(bugs),bugs,&oenv
);
fnRef=opt2fn("-r",NFILE,fnm);
bTrjout = opt2bSet("-ox",NFILE,fnm);
bCountres= opt2bSet("-cr",NFILE,fnm);
if (bTrjout) {
TrjoutFile = opt2fn_null("-ox",NFILE,fnm);
}
read_tps_conf(ftp2fn(efTPS,NFILE,fnm),title,&top,&ePBC,&xp,NULL,box,FALSE);
gpbc = gmx_rmpbc_init(&top.idef,ePBC,top.atoms.nr,box);
atoms=&(top.atoms);
ftp=fn2ftp(fnRef);
get_stx_coordnum(fnRef,&nratoms);
init_t_atoms(&ratoms,nratoms,TRUE);
snew(xr,nratoms);
read_stx_conf(fnRef,rtitle,&ratoms,xr,NULL,&ePBC,rbox);
if (bVerbose) {
fprintf(stderr,"Read %d atoms\n",atoms->nr);
fprintf(stderr,"Read %d reference atoms\n",ratoms.nr);
}
if (bCountres) {
snew(countres,ratoms.nres);
j=0;
cur_res=0;
for (i=0;i<ratoms.nr;i++) {
prev_res=cur_res;
cur_res=ratoms.atom[i].resind;
if (cur_res != prev_res) {
countres[j].resnr=cur_res;
countres[j].count=0;
j++;
}
}
}
get_index(atoms,ftp2fn_null(efNDX,NFILE,fnm),1,&gnx,&index,&grpnm);
nres=0;
nr0=-1;
for(i=0; (i<gnx); i++) {
if (atoms->atom[index[i]].resind != nr0) {
nr0=atoms->atom[index[i]].resind;
nres++;
}
}
fprintf(stderr,"There are %d residues in your selected group\n",nres);
strcpy(pdbfile,"ddXXXXXX");
gmx_tmpnam(pdbfile);
if ((tmpf = fopen(pdbfile,"w")) == NULL) {
sprintf(pdbfile,"%ctmp%cfilterXXXXXX",DIR_SEPARATOR,DIR_SEPARATOR);
gmx_tmpnam(pdbfile);
if ((tmpf = fopen(pdbfile,"w")) == NULL) {
gmx_fatal(FARGS,"Can not open tmp file %s",pdbfile);
}
}
else {
gmx_ffclose(tmpf);
}
if (ftp != efPDB) {
strcpy(refpdb,"ddXXXXXX");
gmx_tmpnam(refpdb);
strcat(refpdb,".pdb");
write_sto_conf(refpdb,rtitle,&ratoms,xr,NULL,ePBC,rbox);
}
else {
strcpy(refpdb,fnRef);
}
if ((mptr=getenv("MULTIPROT")) == NULL) {
mptr="/usr/local/bin/multiprot";
}
if (!gmx_fexist(mptr)) {
gmx_fatal(FARGS,"MULTIPROT executable (%s) does not exist (use setenv MULTIPROT)",
mptr);
}
sprintf (multiprot,"%s %s %s > /dev/null %s",
mptr, refpdb, pdbfile, "2> /dev/null");
if (bVerbose)
fprintf(stderr,"multiprot cmd='%s'\n",multiprot);
if (!read_first_frame(oenv,&status,ftp2fn(efTRX,NFILE,fnm),&fr,TRX_READ_X))
gmx_fatal(FARGS,"Could not read a frame from %s",ftp2fn(efTRX,NFILE,fnm));
natoms = fr.natoms;
if (bTrjout) {
nout=natoms;
/* open file now */
outftp=fn2ftp(TrjoutFile);
if (bVerbose)
fprintf(stderr,"Will write %s: %s\n",ftp2ext(ftp),ftp2desc(outftp));
strcpy(filemode,"w");
switch (outftp) {
case efXTC:
case efG87:
case efTRR:
case efTRJ:
out=NULL;
trxout = open_trx(TrjoutFile,filemode);
break;
case efGRO:
case efG96:
case efPDB:
/* Make atoms struct for output in GRO or PDB files */
/* get memory for stuff to go in pdb file */
init_t_atoms(&useatoms,nout,FALSE);
sfree(useatoms.resinfo);
useatoms.resinfo=atoms->resinfo;
for(i=0;(i<nout);i++) {
useatoms.atomname[i]=atoms->atomname[i];
useatoms.atom[i]=atoms->atom[i];
useatoms.nres=max(useatoms.nres,useatoms.atom[i].resind+1);
}
useatoms.nr=nout;
out=gmx_ffopen(TrjoutFile,filemode);
break;
}
}
if (natoms > atoms->nr) {
gmx_fatal(FARGS,"\nTrajectory does not match topology!");
}
if (gnx > natoms) {
gmx_fatal(FARGS,"\nTrajectory does not match selected group!");
}
fo = xvgropen(opt2fn("-o",NFILE,fnm),"RMSD","Time (ps)","RMSD (nm)",oenv);
frc = xvgropen(opt2fn("-rc",NFILE,fnm),"Number of Residues in the alignment","Time (ps)","Residues",oenv);
do {
t = output_env_conv_time(oenv,fr.time);
gmx_rmpbc(gpbc,natoms,fr.box,fr.x);
tapein=gmx_ffopen(pdbfile,"w");
write_pdbfile_indexed(tapein,NULL,atoms,fr.x,ePBC,fr.box,' ',-1,gnx,index,NULL,TRUE);
gmx_ffclose(tapein);
system(multiprot);
remove(pdbfile);
process_multiprot_output(fn, &rmsd, &nres2,rotangles,translation,bCountres,countres);
fprintf(fo,"%12.7f",t);
fprintf(fo," %12.7f\n",rmsd);
fprintf(frc,"%12.7f",t);
fprintf(frc,"%12d\n",nres2);
if (bTrjout) {
rotate_conf(natoms,fr.x,NULL,rotangles[XX],rotangles[YY],rotangles[ZZ]);
for(i=0; i<natoms; i++) {
rvec_inc(fr.x[i],translation);
}
switch(outftp) {
case efTRJ:
case efTRR:
case efG87:
case efXTC:
write_trxframe(trxout,&fr,NULL);
break;
case efGRO:
case efG96:
case efPDB:
sprintf(out_title,"Generated by do_multiprot : %s t= %g %s",
title,output_env_conv_time(oenv,fr.time),output_env_get_time_unit(oenv));
switch(outftp) {
case efGRO:
write_hconf_p(out,out_title,&useatoms,prec2ndec(fr.prec),
fr.x,NULL,fr.box);
break;
case efPDB:
fprintf(out,"REMARK GENERATED BY DO_MULTIPROT\n");
sprintf(out_title,"%s t= %g %s",title,output_env_conv_time(oenv,fr.time),output_env_get_time_unit(oenv));
/* if reading from pdb, we want to keep the original
model numbering else we write the output frame
number plus one, because model 0 is not allowed in pdb */
if (ftp==efPDB && fr.step > model_nr) {
model_nr = fr.step;
}
else {
model_nr++;
}
write_pdbfile(out,out_title,&useatoms,fr.x,ePBC,fr.box,' ',model_nr,NULL,TRUE);
break;
case efG96:
fr.title = out_title;
fr.bTitle = (nframe == 0);
fr.bAtoms = FALSE;
fr.bStep = TRUE;
fr.bTime = TRUE;
write_g96_conf(out,&fr,-1,NULL);
}
break;
}
}
nframe++;
} while(read_next_frame(oenv,status,&fr));
if (bCountres) {
fres= xvgropen(opt2fn("-cr",NFILE,fnm),"Number of frames in which the residues are aligned to","Residue","Number",oenv);
for (i=0;i<ratoms.nres;i++) {
fprintf(fres,"%10d %12d\n",countres[i].resnr,countres[i].count);
}
gmx_ffclose(fres);
}
gmx_ffclose(fo);
gmx_ffclose(frc);
fprintf(stderr,"\n");
close_trj(status);
if (trxout != NULL) {
close_trx(trxout);
}
else if (out != NULL) {
gmx_ffclose(out);
}
view_all(oenv,NFILE, fnm);
sfree(xr);
if (bCountres) {
sfree(countres);
}
free_t_atoms(&ratoms,TRUE);
if (bTrjout) {
if (outftp==efPDB || outftp==efGRO || outftp==efG96) {
free_t_atoms(&useatoms,TRUE);
}
}
gmx_thanx(stderr);
return 0;
}
int write_trxframe_indexed(t_trxstatus *status, t_trxframe *fr, int nind,
const atom_id *ind, gmx_conect gc)
{
char title[STRLEN];
rvec *xout = NULL, *vout = NULL, *fout = NULL;
int i, ftp = -1;
real prec;
if (fr->bPrec)
{
prec = fr->prec;
}
else
{
prec = 1000.0;
}
if (status->tng)
{
ftp = efTNG;
}
else if (status->fio)
{
ftp = gmx_fio_getftp(status->fio);
}
else
{
gmx_incons("No input file available");
}
switch (ftp)
{
case efTRR:
case efTNG:
break;
default:
if (!fr->bX)
{
gmx_fatal(FARGS, "Need coordinates to write a %s trajectory",
ftp2ext(ftp));
}
break;
}
switch (ftp)
{
case efTRR:
case efTNG:
if (fr->bV)
{
snew(vout, nind);
for (i = 0; i < nind; i++)
{
copy_rvec(fr->v[ind[i]], vout[i]);
}
}
if (fr->bF)
{
snew(fout, nind);
for (i = 0; i < nind; i++)
{
copy_rvec(fr->f[ind[i]], fout[i]);
}
}
/* no break */
case efXTC:
if (fr->bX)
{
snew(xout, nind);
for (i = 0; i < nind; i++)
{
copy_rvec(fr->x[ind[i]], xout[i]);
}
}
break;
default:
break;
}
switch (ftp)
{
case efTNG:
gmx_write_tng_from_trxframe(status->tng, fr, nind);
break;
case efXTC:
write_xtc(status->fio, nind, fr->step, fr->time, fr->box, xout, prec);
break;
case efTRR:
fwrite_trn(status->fio, nframes_read(status),
fr->time, fr->step, fr->box, nind, xout, vout, fout);
break;
case efGRO:
case efPDB:
case efBRK:
case efENT:
if (!fr->bAtoms)
{
gmx_fatal(FARGS, "Can not write a %s file without atom names",
ftp2ext(ftp));
}
sprintf(title, "frame t= %.3f", fr->time);
if (ftp == efGRO)
{
write_hconf_indexed_p(gmx_fio_getfp(status->fio), title, fr->atoms, nind, ind,
prec2ndec(prec),
fr->x, fr->bV ? fr->v : NULL, fr->box);
}
else
{
write_pdbfile_indexed(gmx_fio_getfp(status->fio), title, fr->atoms,
fr->x, -1, fr->box, ' ', fr->step, nind, ind, gc, TRUE);
}
break;
case efG96:
write_g96_conf(gmx_fio_getfp(status->fio), fr, nind, ind);
break;
default:
gmx_fatal(FARGS, "Sorry, write_trxframe_indexed can not write %s",
ftp2ext(ftp));
break;
}
switch (ftp)
{
case efTRR:
case efTNG:
if (vout)
{
sfree(vout);
}
if (fout)
{
sfree(fout);
}
/* no break */
case efXTC:
sfree(xout);
break;
default:
break;
}
return 0;
}
int write_trxframe_indexed(t_trxstatus *status,t_trxframe *fr,int nind,
atom_id *ind, gmx_conect gc)
{
char title[STRLEN];
rvec *xout=NULL,*vout=NULL,*fout=NULL;
int i;
real prec;
if (fr->bPrec)
prec = fr->prec;
else
prec = 1000.0;
switch (gmx_fio_getftp(status->fio)) {
case efTRJ:
case efTRR:
break;
default:
if (!fr->bX)
gmx_fatal(FARGS,"Need coordinates to write a %s trajectory",
ftp2ext(gmx_fio_getftp(status->fio)));
break;
}
switch (gmx_fio_getftp(status->fio)) {
case efTRJ:
case efTRR:
if (fr->bV) {
snew(vout,nind);
for(i=0; i<nind; i++)
copy_rvec(fr->v[ind[i]],vout[i]);
}
if (fr->bF) {
snew(fout,nind);
for(i=0; i<nind; i++)
copy_rvec(fr->f[ind[i]],fout[i]);
}
case efXTC:
case efG87:
if (fr->bX) {
snew(xout,nind);
for(i=0; i<nind; i++)
copy_rvec(fr->x[ind[i]],xout[i]);
}
break;
default:
break;
}
switch (gmx_fio_getftp(status->fio)) {
case efXTC:
write_xtc(status->fio,nind,fr->step,fr->time,fr->box,xout,prec);
break;
case efTRJ:
case efTRR:
fwrite_trn(status->fio,nframes_read(status),
fr->time,fr->step,fr->box,nind,xout,vout,fout);
break;
case efGRO:
case efPDB:
case efBRK:
case efENT:
if (!fr->bAtoms)
gmx_fatal(FARGS,"Can not write a %s file without atom names",
ftp2ext(gmx_fio_getftp(status->fio)));
sprintf(title,"frame t= %.3f",fr->time);
if (gmx_fio_getftp(status->fio) == efGRO)
write_hconf_indexed_p(gmx_fio_getfp(status->fio),title,fr->atoms,nind,ind,
prec2ndec(prec),
fr->x,fr->bV ? fr->v : NULL,fr->box);
else
write_pdbfile_indexed(gmx_fio_getfp(status->fio),title,fr->atoms,
fr->x,-1,fr->box,' ',fr->step,nind,ind,gc,TRUE);
break;
case efG87:
write_gms(gmx_fio_getfp(status->fio),nind,xout,fr->box);
break;
case efG96:
write_g96_conf(gmx_fio_getfp(status->fio),fr,nind,ind);
break;
default:
gmx_fatal(FARGS,"Sorry, write_trxframe_indexed can not write %s",
ftp2ext(gmx_fio_getftp(status->fio)));
break;
}
switch (gmx_fio_getftp(status->fio)) {
case efTRN:
case efTRJ:
case efTRR:
if (vout) sfree(vout);
if (fout) sfree(fout);
case efXTC:
case efG87:
sfree(xout);
break;
default:
break;
}
return 0;
}
