static void dump_axes(t_trxstatus *status,t_trxframe *fr,t_atoms *outat,
t_bundle *bun)
{
t_trxframe frout;
static rvec *xout=NULL;
int i,end;
if (xout==NULL)
snew(xout,outat->nr);
for(i=0; i<bun->n; i++) {
copy_rvec(bun->end[0][i],xout[3*i]);
if (bun->nend >= 3)
copy_rvec(bun->end[2][i],xout[3*i+1]);
else
copy_rvec(bun->mid[i],xout[3*i+1]);
copy_rvec(bun->end[1][i],xout[3*i+2]);
}
frout = *fr;
frout.bV = FALSE;
frout.bF = FALSE;
frout.bBox = FALSE;
frout.bAtoms = TRUE;
frout.natoms = outat->nr;
frout.atoms = outat;
frout.x = xout;
write_trxframe(status,&frout,NULL);
}
static void write_trx_x(int status,t_trxframe *fr,real *mass,bool bCom,
int ngrps,int isize[],atom_id **index)
{
static rvec *xav=NULL;
static t_atoms *atoms=NULL;
t_trxframe fr_av;
int i;
fr->bV = FALSE;
fr->bF = FALSE;
if (bCom) {
if (xav==NULL) {
snew(xav,ngrps);
snew(atoms,1);
*atoms = *fr->atoms;
snew(atoms->atom,ngrps);
atoms->nr = ngrps;
/* Note that atom and residue names will be the ones of the first atom
* in each group.
*/
for(i=0; i<ngrps; i++) {
atoms->atom[i] = fr->atoms->atom[index[i][0]];
atoms->atomname[i] = fr->atoms->atomname[index[i][0]];
}
}
average_data(fr->x,xav,mass,ngrps,isize,index);
fr_av = *fr;
fr_av.natoms = ngrps;
fr_av.atoms = atoms;
fr_av.x = xav;
write_trxframe(status,&fr_av);
} else {
write_trxframe_indexed(status,fr,isize[0],index[0]);
}
}
int gmx_trjcat(int argc,char *argv[])
{
static char *desc[] = {
"trjcat concatenates several input trajectory files in sorted order. ",
"In case of double time frames the one in the later file is used. ",
"By specifying [TT]-settime[tt] you will be asked for the start time ",
"of each file. The input files are taken from the command line, ",
"such that a command like [TT]trjcat -o fixed.trr *.trr[tt] should do ",
"the trick. Using [TT]-cat[tt] you can simply paste several files ",
"together without removal of frames with identical time stamps.[PAR]",
"One important option is inferred when the output file is amongst the",
"input files. In that case that particular file will be appended to",
"which implies you do not need to store double the amount of data.",
"Obviously the file to append to has to be the one with lowest starting",
"time since one can only append at the end of a file.[PAR]",
"If the [TT]-demux[tt] option is given, the N trajectories that are",
"read, are written in another order as specified in the xvg file."
"The xvg file should contain something like:[PAR]",
"0 0 1 2 3 4 5[BR]",
"2 1 0 2 3 5 4[BR]",
"Where the first number is the time, and subsequent numbers point to",
"trajectory indices.",
"The frames corresponding to the numbers present at the first line",
"are collected into the output trajectory. If the number of frames in",
"the trajectory does not match that in the xvg file then the program",
"tries to be smart. Beware."
};
static bool bVels=TRUE;
static int prec=3;
static bool bCat=FALSE;
static bool bSort=TRUE;
static bool bKeepLast=FALSE;
static bool bSetTime=FALSE;
static bool bDeMux;
static real begin=-1;
static real end=-1;
static real dt=0;
t_pargs pa[] = {
{ "-b", FALSE, etTIME, {&begin},
"First time to use (%t)"},
{ "-e", FALSE, etTIME, {&end},
"Last time to use (%t)"},
{ "-dt", FALSE, etTIME, {&dt},
"Only write frame when t MOD dt = first time (%t)" },
{ "-prec", FALSE, etINT, {&prec},
"Precision for .xtc and .gro writing in number of decimal places" },
{ "-vel", FALSE, etBOOL, {&bVels},
"Read and write velocities if possible" },
{ "-settime", FALSE, etBOOL, {&bSetTime},
"Change starting time interactively" },
{ "-sort", FALSE, etBOOL, {&bSort},
"Sort trajectory files (not frames)" },
{ "-keeplast",FALSE, etBOOL, {&bKeepLast},
"keep overlapping frames at end of trajectory" },
{ "-cat", FALSE, etBOOL, {&bCat},
"do not discard double time frames" }
};
#define npargs asize(pa)
int status,ftpin,i,frame,frame_out,step=0,trjout=0;
rvec *x,*v;
real xtcpr,t_corr;
t_trxframe fr,frout;
char **fnms,**fnms_out,*in_file,*out_file;
int n_append;
int trxout=-1;
bool bNewFile,bIndex,bWrite;
int earliersteps,nfile_in,nfile_out,*cont_type,last_ok_step;
real *readtime,*timest,*settime;
real first_time=0,lasttime=NOTSET,last_ok_t=-1,timestep;
int isize,j;
atom_id *index=NULL,imax;
char *grpname;
real **val=NULL,*t=NULL,dt_remd;
int n,nset;
t_filenm fnm[] = {
{ efTRX, "-f", NULL, ffRDMULT },
{ efTRO, "-o", NULL, ffWRMULT },
{ efNDX, "-n", "index", ffOPTRD },
{ efXVG, "-demux", "remd", ffOPTRD }
};
#define NFILE asize(fnm)
CopyRight(stderr,argv[0]);
parse_common_args(&argc,argv,PCA_BE_NICE|PCA_TIME_UNIT,
NFILE,fnm,asize(pa),pa,asize(desc),desc,
0,NULL);
bIndex = ftp2bSet(efNDX,NFILE,fnm);
bDeMux = ftp2bSet(efXVG,NFILE,fnm);
bSort = bSort && !bDeMux;
imax=NO_ATID;
if (bIndex) {
printf("Select group for output\n");
rd_index(ftp2fn(efNDX,NFILE,fnm),1,&isize,&index,&grpname);
/* scan index */
imax=index[0];
for(i=1; i<isize; i++)
imax = max(imax, index[i]);
}
if (bDeMux) {
nset = 0;
dt_remd = 0;
val=read_xvg_time(opt2fn("-demux",NFILE,fnm),TRUE,
opt2parg_bSet("-b",npargs,pa),begin,
opt2parg_bSet("-e",npargs,pa),end,
1,&nset,&n,&dt_remd,&t);
printf("Read %d sets of %d points, dt = %g\n\n",nset,n,dt_remd);
if (debug) {
fprintf(debug,"Dump of replica_index.xvg\n");
for(i=0; (i<n); i++) {
fprintf(debug,"%10g",t[i]);
for(j=0; (j<nset); j++) {
fprintf(debug," %3d",gmx_nint(val[j][i]));
}
fprintf(debug,"\n");
}
}
}
/* prec is in nr of decimal places, xtcprec is a multiplication factor: */
xtcpr=1;
for (i=0; i<prec; i++)
xtcpr*=10;
nfile_in = opt2fns(&fnms,"-f",NFILE,fnm);
if (!nfile_in)
gmx_fatal(FARGS,"No input files!");
if (bDeMux && (nfile_in != nset))
gmx_fatal(FARGS,"You have specified %d files and %d entries in the demux table",nfile_in,nset);
nfile_out = opt2fns(&fnms_out,"-o",NFILE,fnm);
if (!nfile_out)
gmx_fatal(FARGS,"No output files!");
if ((nfile_out > 1) && !bDeMux)
gmx_fatal(FARGS,"Don't know what to do with more than 1 output file if not demultiplexing");
else if (bDeMux && (nfile_out != nset) && (nfile_out != 1))
gmx_fatal(FARGS,"Number of output files should be 1 or %d (#input files), not %d",nset,nfile_out);
if (bDeMux) {
if (nfile_out != nset) {
char *buf = strdup(fnms_out[0]);
snew(fnms_out,nset);
for(i=0; (i<nset); i++) {
snew(fnms_out[i],strlen(buf)+32);
sprintf(fnms_out[i],"%d_%s",i,buf);
}
}
do_demux(nfile_in,fnms,fnms_out,n,val,t,dt_remd,isize,index,dt);
}
else {
snew(readtime,nfile_in+1);
snew(timest,nfile_in+1);
scan_trj_files(fnms,nfile_in,readtime,timest,imax);
snew(settime,nfile_in+1);
snew(cont_type,nfile_in+1);
edit_files(fnms,nfile_in,readtime,timest,settime,cont_type,bSetTime,bSort);
/* Check whether the output file is amongst the input files
* This has to be done after sorting etc.
*/
out_file = fnms_out[0];
n_append = -1;
for(i=0; ((i<nfile_in) && (n_append==-1)); i++) {
if (strcmp(fnms[i],out_file) == 0) {
n_append = i;
}
}
if (n_append == 0)
fprintf(stderr,"Will append to %s rather than creating a new file\n",
out_file);
else if (n_append != -1)
gmx_fatal(FARGS,"Can only append to the first file which is %s (not %s)",
fnms[0],out_file);
earliersteps=0;
/* Not checking input format, could be dangerous :-) */
/* Not checking output format, equally dangerous :-) */
frame=-1;
frame_out=-1;
/* the default is not to change the time at all,
* but this is overridden by the edit_files routine
*/
t_corr=0;
if (n_append == -1) {
trxout = open_trx(out_file,"w");
memset(&frout,0,sizeof(frout));
}
else {
/* Read file to find what is the last frame in it */
if (!read_first_frame(&status,out_file,&fr,FLAGS))
gmx_fatal(FARGS,"Reading first frame from %s",out_file);
while (read_next_frame(status,&fr))
;
close_trj(status);
lasttime = fr.time;
bKeepLast = TRUE;
trxout = open_trx(out_file,"a");
frout = fr;
}
/* Lets stitch up some files */
timestep = timest[0];
for(i=n_append+1; (i<nfile_in); i++) {
/* Open next file */
/* set the next time from the last frame in previous file */
if (i > 0) {
if (frame_out >= 0) {
if(cont_type[i]==TIME_CONTINUE) {
begin =frout.time;
begin += 0.5*timestep;
settime[i]=frout.time;
cont_type[i]=TIME_EXPLICIT;
}
else if(cont_type[i]==TIME_LAST) {
begin=frout.time;
begin += 0.5*timestep;
}
/* Or, if the time in the next part should be changed by the
* same amount, start at half a timestep from the last time
* so we dont repeat frames.
*/
/* I don't understand the comment above, but for all the cases
* I tried the code seems to work properly. B. Hess 2008-4-2.
*/
}
/* Or, if time is set explicitly, we check for overlap/gap */
if(cont_type[i]==TIME_EXPLICIT)
if( ( i < nfile_in ) &&
( frout.time < settime[i]-1.5*timestep ) )
fprintf(stderr, "WARNING: Frames around t=%f %s have a different "
"spacing than the rest,\n"
"might be a gap or overlap that couldn't be corrected "
"automatically.\n",convert_time(frout.time),time_unit());
}
/* if we don't have a timestep in the current file, use the old one */
if ( timest[i] != 0 )
timestep = timest[i];
read_first_frame(&status,fnms[i],&fr,FLAGS);
if(!fr.bTime) {
fr.time=0;
fprintf(stderr,"\nWARNING: Couldn't find a time in the frame.\n");
}
if(cont_type[i]==TIME_EXPLICIT)
t_corr=settime[i]-fr.time;
/* t_corr is the amount we want to change the time.
* If the user has chosen not to change the time for
* this part of the trajectory t_corr remains at
* the value it had in the last part, changing this
* by the same amount.
* If no value was given for the first trajectory part
* we let the time start at zero, see the edit_files routine.
*/
bNewFile=TRUE;
printf("\n");
if (lasttime != NOTSET)
printf("lasttime %g\n", lasttime);
do {
/* copy the input frame to the output frame */
frout=fr;
/* set the new time by adding the correct calculated above */
frout.time += t_corr;
/* quit if we have reached the end of what should be written */
if((end > 0) && (frout.time > end+GMX_REAL_EPS)) {
i=nfile_in;
break;
}
/* determine if we should write this frame (dt is handled elsewhere) */
if (bCat) /* write all frames of all files */
bWrite = TRUE;
else if ( bKeepLast ) /* write till last frame of this traj
and skip first frame(s) of next traj */
bWrite = ( frout.time > lasttime+0.5*timestep );
else /* write till first frame of next traj */
bWrite = ( frout.time < settime[i+1]-0.5*timestep );
if( bWrite && (frout.time >= begin) ) {
frame++;
if (frame_out == -1)
first_time = frout.time;
lasttime = frout.time;
if (dt==0 || bRmod(frout.time,first_time,dt)) {
frame_out++;
last_ok_t=frout.time;
if(bNewFile) {
fprintf(stderr,"\nContinue writing frames from %s t=%g %s, "
"frame=%d \n",
fnms[i],convert_time(frout.time),time_unit(),frame);
bNewFile=FALSE;
}
if (bIndex)
write_trxframe_indexed(trxout,&frout,isize,index);
else
write_trxframe(trxout,&frout);
if ( ((frame % 10) == 0) || (frame < 10) )
fprintf(stderr," -> frame %6d time %8.3f %s \r",
frame_out,convert_time(frout.time),time_unit());
}
}
} while( read_next_frame(status,&fr));
close_trj(status);
earliersteps+=step;
}
if (trxout >= 0)
close_trx(trxout);
fprintf(stderr,"\nLast frame written was %d, time %f %s\n",
frame,convert_time(last_ok_t),time_unit());
}
thanx(stderr);
return 0;
}
static void do_demux(int nset,char *fnms[],char *fnms_out[],
int nval,real **value,real *time,real dt_remd,
int isize,atom_id index[],real dt)
{
int i,j,k,natoms,nnn;
int *fp_in,*fp_out;
bool bCont,*bSet;
real t,first_time=0;
t_trxframe *trx;
snew(fp_in,nset);
snew(trx,nset);
snew(bSet,nset);
natoms = -1;
t = -1;
for(i=0; (i<nset); i++) {
nnn = read_first_frame(&(fp_in[i]),fnms[i],&(trx[i]),TRX_NEED_X);
if (natoms == -1) {
natoms = nnn;
first_time = trx[i].time;
}
else if (natoms != nnn)
gmx_fatal(FARGS,"Trajectory file %s has %d atoms while previous trajs had %d atoms",fnms[i],nnn,natoms);
if (t == -1)
t = trx[i].time;
else if (t != trx[i].time)
gmx_fatal(FARGS,"Trajectory file %s has time %f while previous trajs had time %f",fnms[i],trx[i].time,t);
}
snew(fp_out,nset);
for(i=0; (i<nset); i++)
fp_out[i] = open_trx(fnms_out[i],"w");
k = 0;
if (gmx_nint(time[k] - t) != 0)
gmx_fatal(FARGS,"First time in demuxing table does not match trajectories");
do {
while ((k+1 < nval) && ((trx[0].time - time[k+1]) > dt_remd*0.1))
k++;
if (debug)
fprintf(debug,"trx[0].time = %g, time[k] = %g\n",trx[0].time,time[k]);
for(i=0; (i<nset); i++)
bSet[i] = FALSE;
for(i=0; (i<nset); i++) {
j = gmx_nint(value[i][k]);
range_check(j,0,nset);
if (bSet[j])
gmx_fatal(FARGS,"Demuxing the same replica %d twice at time %f",
j,trx[0].time);
bSet[j] = TRUE;
if (dt==0 || bRmod(trx[i].time,first_time,dt)) {
if (index)
write_trxframe_indexed(fp_out[j],&trx[i],isize,index);
else
write_trxframe(fp_out[j],&trx[i]);
}
}
bCont = (k < nval);
for(i=0; (i<nset); i++)
bCont = bCont && read_next_frame(fp_in[i],&trx[i]);
} while (bCont);
for(i=0; (i<nset); i++) {
close_trx(fp_in[i]);
close_trx(fp_out[i]);
}
}
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 main (int argc,char *argv[])
{
const char *desc[] = {
"[TT]g_protonate[tt] reads (a) conformation(s) and adds all missing",
"hydrogens as defined in [TT]gmx2.ff/aminoacids.hdb[tt]. If only [TT]-s[tt] is",
"specified, this conformation will be protonated, if also [TT]-f[tt]",
"is specified, the conformation(s) will be read from this file, ",
"which can be either a single conformation or a trajectory.",
"[PAR]",
"If a [TT].pdb[tt] file is supplied, residue names might not correspond to",
"to the GROMACS naming conventions, in which case these residues will",
"probably not be properly protonated.",
"[PAR]",
"If an index file is specified, please note that the atom numbers",
"should correspond to the [BB]protonated[bb] state."
};
char title[STRLEN+1];
const char *infile;
char *grpnm;
t_topology top;
int ePBC;
t_atoms *atoms,*iatoms;
t_protonate protdata;
atom_id *index;
t_trxstatus *status;
t_trxstatus *out;
t_trxframe fr,frout;
rvec *x,*ix;
int nidx,natoms,natoms_out;
matrix box;
int i,frame,resind;
gmx_bool bReadMultiple;
output_env_t oenv;
const char *bugs[] = {
"For the moment, only .pdb files are accepted to the -s flag"
};
t_filenm fnm[] = {
{ efTPS, NULL, NULL, ffREAD },
{ efTRX, "-f", NULL, ffOPTRD },
{ efNDX, NULL, NULL, ffOPTRD },
{ efTRO, "-o", "protonated", ffWRITE }
};
#define NFILE asize(fnm)
CopyRight(stderr,argv[0]);
parse_common_args(&argc,argv,PCA_CAN_TIME,
NFILE,fnm,0,NULL,asize(desc),desc,asize(bugs),bugs,&oenv);
infile=opt2fn("-s",NFILE,fnm);
read_tps_conf(infile,title,&top,&ePBC,&x,NULL,box,FALSE);
atoms=&(top.atoms);
printf("Select group to process:\n");
get_index(atoms,ftp2fn_null(efNDX,NFILE,fnm),1,&nidx,&index,&grpnm);
bReadMultiple = opt2bSet("-f",NFILE,fnm);
if (bReadMultiple) {
infile = opt2fn("-f",NFILE,fnm);
if ( !read_first_frame(oenv,&status, infile, &fr, TRX_NEED_X ) ) {
gmx_fatal(FARGS,"cannot read coordinate file %s",infile);
}
natoms = fr.natoms;
} else {
clear_trxframe(&fr,TRUE);
fr.natoms = atoms->nr;
fr.bTitle = TRUE;
fr.title = title;
fr.bX = TRUE;
fr.x = x;
fr.bBox = TRUE;
copy_mat(box, fr.box);
natoms = fr.natoms;
}
/* check input */
if ( natoms == 0 ) {
gmx_fatal(FARGS,"no atoms in coordinate file %s",infile);
}
if ( natoms > atoms->nr ) {
gmx_fatal(FARGS,"topology with %d atoms does not match "
"coordinates with %d atoms",atoms->nr,natoms);
}
for(i=0; i<nidx; i++) {
if (index[i] > natoms) {
gmx_fatal(FARGS,"An atom number in group %s is larger than the number of "
"atoms (%d) in the coordinate file %s",grpnm,natoms,infile);
}
}
/* get indexed copy of atoms */
snew(iatoms,1);
init_t_atoms(iatoms,nidx,FALSE);
snew(iatoms->atom, iatoms->nr);
resind = 0;
for(i=0; i<nidx; i++) {
iatoms->atom[i] = atoms->atom[index[i]];
iatoms->atomname[i] = atoms->atomname[index[i]];
if ( i>0 && (atoms->atom[index[i]].resind!=atoms->atom[index[i-1]].resind) ) {
resind++;
}
iatoms->atom[i].resind = resind;
iatoms->resinfo[resind] = atoms->resinfo[atoms->atom[index[i]].resind];
/* allocate some space for the rtp name and copy from name */
snew(iatoms->resinfo[resind].rtp,1);
*iatoms->resinfo[resind].rtp = gmx_strdup(*atoms->resinfo[resind].name);
iatoms->nres = max(iatoms->nres, iatoms->atom[i].resind+1);
}
init_t_protonate(&protdata);
out = open_trx(opt2fn("-o",NFILE,fnm),"w");
snew(ix, nidx);
frame=0;
do {
if (debug) {
fprintf(debug,"FRAME %d (%d %g)\n",frame,fr.step,fr.time);
}
/* get indexed copy of x */
for(i=0; i<nidx; i++) {
copy_rvec(fr.x[index[i]], ix[i]);
}
/* protonate */
natoms_out = protonate(&iatoms, &ix, &protdata);
/* setup output frame */
frout = fr;
frout.natoms = natoms_out;
frout.bAtoms = TRUE;
frout.atoms = iatoms;
frout.bV = FALSE;
frout.bF = FALSE;
frout.x = ix;
/* write output */
write_trxframe(out,&frout,NULL);
frame++;
} while ( bReadMultiple && read_next_frame(oenv,status, &fr) );
sfree(ix);
sfree(iatoms);
thanx(stderr);
return 0;
}
int gmx_trjcat(int argc, char *argv[])
{
const char *desc[] =
{
"[THISMODULE] concatenates several input trajectory files in sorted order. ",
"In case of double time frames the one in the later file is used. ",
"By specifying [TT]-settime[tt] you will be asked for the start time ",
"of each file. The input files are taken from the command line, ",
"such that a command like [TT]gmx trjcat -f *.trr -o fixed.trr[tt] should do ",
"the trick. Using [TT]-cat[tt], you can simply paste several files ",
"together without removal of frames with identical time stamps.[PAR]",
"One important option is inferred when the output file is amongst the",
"input files. In that case that particular file will be appended to",
"which implies you do not need to store double the amount of data.",
"Obviously the file to append to has to be the one with lowest starting",
"time since one can only append at the end of a file.[PAR]",
"If the [TT]-demux[tt] option is given, the N trajectories that are",
"read, are written in another order as specified in the [REF].xvg[ref] file.",
"The [REF].xvg[ref] file should contain something like::",
"",
" 0 0 1 2 3 4 5",
" 2 1 0 2 3 5 4",
"",
"The first number is the time, and subsequent numbers point to",
"trajectory indices.",
"The frames corresponding to the numbers present at the first line",
"are collected into the output trajectory. If the number of frames in",
"the trajectory does not match that in the [REF].xvg[ref] file then the program",
"tries to be smart. Beware."
};
static gmx_bool bCat = FALSE;
static gmx_bool bSort = TRUE;
static gmx_bool bKeepLast = FALSE;
static gmx_bool bKeepLastAppend = FALSE;
static gmx_bool bOverwrite = FALSE;
static gmx_bool bSetTime = FALSE;
static gmx_bool bDeMux;
static real begin = -1;
static real end = -1;
static real dt = 0;
t_pargs
pa[] =
{
{ "-b", FALSE, etTIME,
{ &begin }, "First time to use (%t)" },
{ "-e", FALSE, etTIME,
{ &end }, "Last time to use (%t)" },
{ "-dt", FALSE, etTIME,
{ &dt }, "Only write frame when t MOD dt = first time (%t)" },
{ "-settime", FALSE, etBOOL,
{ &bSetTime }, "Change starting time interactively" },
{ "-sort", FALSE, etBOOL,
{ &bSort }, "Sort trajectory files (not frames)" },
{ "-keeplast", FALSE, etBOOL,
{ &bKeepLast }, "Keep overlapping frames at end of trajectory" },
{ "-overwrite", FALSE, etBOOL,
{ &bOverwrite }, "Overwrite overlapping frames during appending" },
{ "-cat", FALSE, etBOOL,
{ &bCat }, "Do not discard double time frames" }
};
#define npargs asize(pa)
int ftpin, i, frame, frame_out;
t_trxstatus *status, *trxout = NULL;
real t_corr;
t_trxframe fr, frout;
char **fnms, **fnms_out, *out_file;
int n_append;
gmx_bool bNewFile, bIndex, bWrite;
int nfile_in, nfile_out, *cont_type;
real *readtime, *timest, *settime;
real first_time = 0, lasttime, last_ok_t = -1, timestep;
gmx_bool lastTimeSet = FALSE;
real last_frame_time, searchtime;
int isize = 0, j;
int *index = NULL, imax;
char *grpname;
real **val = NULL, *t = NULL, dt_remd;
int n, nset, ftpout = -1, prevEndStep = 0, filetype;
gmx_off_t fpos;
gmx_output_env_t *oenv;
t_filenm fnm[] =
{
{ efTRX, "-f", NULL, ffRDMULT },
{ efTRO, "-o", NULL, ffWRMULT },
{ efNDX, "-n", "index", ffOPTRD },
{ efXVG, "-demux", "remd", ffOPTRD }
};
#define NFILE asize(fnm)
if (!parse_common_args(&argc, argv, PCA_TIME_UNIT, NFILE, fnm,
asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
{
return 0;
}
bIndex = ftp2bSet(efNDX, NFILE, fnm);
bDeMux = ftp2bSet(efXVG, NFILE, fnm);
bSort = bSort && !bDeMux;
imax = -1;
if (bIndex)
{
printf("Select group for output\n");
rd_index(ftp2fn(efNDX, NFILE, fnm), 1, &isize, &index, &grpname);
/* scan index */
imax = index[0];
for (i = 1; i < isize; i++)
{
imax = std::max(imax, index[i]);
}
}
if (bDeMux)
{
nset = 0;
dt_remd = 0;
val = read_xvg_time(opt2fn("-demux", NFILE, fnm), TRUE,
opt2parg_bSet("-b", npargs, pa), begin,
opt2parg_bSet("-e", npargs, pa), end, 1, &nset, &n,
&dt_remd, &t);
printf("Read %d sets of %d points, dt = %g\n\n", nset, n, dt_remd);
if (debug)
{
fprintf(debug, "Dump of replica_index.xvg\n");
for (i = 0; (i < n); i++)
{
fprintf(debug, "%10g", t[i]);
for (j = 0; (j < nset); j++)
{
fprintf(debug, " %3d", static_cast<int>(std::round(val[j][i])));
}
fprintf(debug, "\n");
}
}
}
nfile_in = opt2fns(&fnms, "-f", NFILE, fnm);
if (!nfile_in)
{
gmx_fatal(FARGS, "No input files!" );
}
if (bDeMux && (nfile_in != nset))
{
gmx_fatal(FARGS, "You have specified %d files and %d entries in the demux table", nfile_in, nset);
}
ftpin = fn2ftp(fnms[0]);
for (i = 1; i < nfile_in; i++)
{
if (ftpin != fn2ftp(fnms[i]))
{
gmx_fatal(FARGS, "All input files must be of the same format");
}
}
nfile_out = opt2fns(&fnms_out, "-o", NFILE, fnm);
if (!nfile_out)
{
gmx_fatal(FARGS, "No output files!");
}
if ((nfile_out > 1) && !bDeMux)
{
gmx_fatal(FARGS, "Don't know what to do with more than 1 output file if not demultiplexing");
}
else if (bDeMux && (nfile_out != nset) && (nfile_out != 1))
{
gmx_fatal(FARGS, "Number of output files should be 1 or %d (#input files), not %d", nset, nfile_out);
}
if (bDeMux)
{
if (nfile_out != nset)
{
char *buf = gmx_strdup(fnms_out[0]);
snew(fnms_out, nset);
for (i = 0; (i < nset); i++)
{
snew(fnms_out[i], std::strlen(buf)+32);
sprintf(fnms_out[i], "%d_%s", i, buf);
}
sfree(buf);
}
do_demux(nfile_in, fnms, fnms_out, n, val, t, dt_remd, isize, index, dt, oenv);
}
else
{
snew(readtime, nfile_in+1);
snew(timest, nfile_in+1);
scan_trj_files(fnms, nfile_in, readtime, timest, imax, oenv);
snew(settime, nfile_in+1);
snew(cont_type, nfile_in+1);
edit_files(fnms, nfile_in, readtime, timest, settime, cont_type, bSetTime, bSort,
oenv);
/* Check whether the output file is amongst the input files
* This has to be done after sorting etc.
*/
out_file = fnms_out[0];
ftpout = fn2ftp(out_file);
n_append = -1;
for (i = 0; ((i < nfile_in) && (n_append == -1)); i++)
{
if (std::strcmp(fnms[i], out_file) == 0)
{
n_append = i;
}
}
if (n_append == 0)
{
fprintf(stderr, "Will append to %s rather than creating a new file\n",
out_file);
}
else if (n_append != -1)
{
gmx_fatal(FARGS, "Can only append to the first file which is %s (not %s)",
fnms[0], out_file);
}
/* Not checking input format, could be dangerous :-) */
/* Not checking output format, equally dangerous :-) */
frame = -1;
frame_out = -1;
/* the default is not to change the time at all,
* but this is overridden by the edit_files routine
*/
t_corr = 0;
if (n_append == -1)
{
if (ftpout == efTNG)
{
if (ftpout != ftpin)
{
gmx_fatal(FARGS, "When writing TNG the input file format must also be TNG");
}
if (bIndex)
{
trjtools_gmx_prepare_tng_writing(out_file, 'w', NULL, &trxout,
fnms[0], isize, NULL, index, grpname);
}
else
{
trjtools_gmx_prepare_tng_writing(out_file, 'w', NULL, &trxout,
fnms[0], -1, NULL, NULL, NULL);
}
}
else
{
trxout = open_trx(out_file, "w");
}
std::memset(&frout, 0, sizeof(frout));
}
else
{
t_fileio *stfio;
if (!read_first_frame(oenv, &status, out_file, &fr, FLAGS))
{
gmx_fatal(FARGS, "Reading first frame from %s", out_file);
}
stfio = trx_get_fileio(status);
if (!bKeepLast && !bOverwrite)
{
fprintf(stderr, "\n\nWARNING: Appending without -overwrite implies -keeplast "
"between the first two files. \n"
"If the trajectories have an overlap and have not been written binary \n"
"reproducible this will produce an incorrect trajectory!\n\n");
filetype = gmx_fio_getftp(stfio);
/* Fails if last frame is incomplete
* We can't do anything about it without overwriting
* */
if (filetype == efXTC || filetype == efTNG)
{
lasttime = trx_get_time_of_final_frame(status);
fr.time = lasttime;
}
else
{
while (read_next_frame(oenv, status, &fr))
{
;
}
lasttime = fr.time;
}
lastTimeSet = TRUE;
bKeepLastAppend = TRUE;
close_trj(status);
trxout = open_trx(out_file, "a");
}
else if (bOverwrite)
{
if (gmx_fio_getftp(stfio) != efXTC)
{
gmx_fatal(FARGS, "Overwrite only supported for XTC." );
}
last_frame_time = trx_get_time_of_final_frame(status);
/* xtc_seek_time broken for trajectories containing only 1 or 2 frames
* or when seek time = 0 */
if (nfile_in > 1 && settime[1] < last_frame_time+timest[0]*0.5)
{
/* Jump to one time-frame before the start of next
* trajectory file */
searchtime = settime[1]-timest[0]*1.25;
}
else
{
searchtime = last_frame_time;
}
if (xtc_seek_time(stfio, searchtime, fr.natoms, TRUE))
{
gmx_fatal(FARGS, "Error seeking to append position.");
}
read_next_frame(oenv, status, &fr);
if (std::abs(searchtime - fr.time) > timest[0]*0.5)
{
gmx_fatal(FARGS, "Error seeking: attempted to seek to %f but got %f.",
searchtime, fr.time);
}
lasttime = fr.time;
lastTimeSet = TRUE;
fpos = gmx_fio_ftell(stfio);
close_trj(status);
trxout = open_trx(out_file, "r+");
if (gmx_fio_seek(trx_get_fileio(trxout), fpos))
{
gmx_fatal(FARGS, "Error seeking to append position.");
}
}
if (lastTimeSet)
{
printf("\n Will append after %f \n", lasttime);
}
frout = fr;
}
/* Lets stitch up some files */
timestep = timest[0];
for (i = n_append+1; (i < nfile_in); i++)
{
/* Open next file */
/* set the next time from the last frame in previous file */
if (i > 0)
{
/* When writing TNG the step determine which frame to write. Use an
* offset to be able to increase steps properly when changing files. */
if (ftpout == efTNG)
{
prevEndStep = frout.step;
}
if (frame_out >= 0)
{
if (cont_type[i] == TIME_CONTINUE)
{
begin = frout.time;
begin += 0.5*timestep;
settime[i] = frout.time;
cont_type[i] = TIME_EXPLICIT;
}
else if (cont_type[i] == TIME_LAST)
{
begin = frout.time;
begin += 0.5*timestep;
}
/* Or, if the time in the next part should be changed by the
* same amount, start at half a timestep from the last time
* so we dont repeat frames.
*/
/* I don't understand the comment above, but for all the cases
* I tried the code seems to work properly. B. Hess 2008-4-2.
*/
}
/* Or, if time is set explicitly, we check for overlap/gap */
if (cont_type[i] == TIME_EXPLICIT)
{
if ( ( i < nfile_in ) &&
( frout.time < settime[i]-1.5*timestep ) )
{
fprintf(stderr, "WARNING: Frames around t=%f %s have a different "
"spacing than the rest,\n"
"might be a gap or overlap that couldn't be corrected "
"automatically.\n", output_env_conv_time(oenv, frout.time),
output_env_get_time_unit(oenv));
}
}
}
/* if we don't have a timestep in the current file, use the old one */
if (timest[i] != 0)
{
timestep = timest[i];
}
read_first_frame(oenv, &status, fnms[i], &fr, FLAGS);
if (!fr.bTime)
{
fr.time = 0;
fprintf(stderr, "\nWARNING: Couldn't find a time in the frame.\n");
}
if (cont_type[i] == TIME_EXPLICIT)
{
t_corr = settime[i]-fr.time;
}
/* t_corr is the amount we want to change the time.
* If the user has chosen not to change the time for
* this part of the trajectory t_corr remains at
* the value it had in the last part, changing this
* by the same amount.
* If no value was given for the first trajectory part
* we let the time start at zero, see the edit_files routine.
*/
bNewFile = TRUE;
if (!lastTimeSet)
{
lasttime = 0;
lastTimeSet = true;
}
printf("\n");
printf("lasttime %g\n", lasttime);
do
{
/* copy the input frame to the output frame */
frout = fr;
/* set the new time by adding the correct calculated above */
frout.time += t_corr;
if (ftpout == efTNG)
{
frout.step += prevEndStep;
}
/* quit if we have reached the end of what should be written */
if ((end > 0) && (frout.time > end+GMX_REAL_EPS))
{
i = nfile_in;
break;
}
/* determine if we should write this frame (dt is handled elsewhere) */
if (bCat) /* write all frames of all files */
{
bWrite = TRUE;
}
else if (bKeepLast || (bKeepLastAppend && i == 1))
/* write till last frame of this traj
and skip first frame(s) of next traj */
{
bWrite = ( frout.time > lasttime+0.5*timestep );
}
else /* write till first frame of next traj */
{
bWrite = ( frout.time < settime[i+1]-0.5*timestep );
}
if (bWrite && (frout.time >= begin) )
{
frame++;
if (frame_out == -1)
{
first_time = frout.time;
}
lasttime = frout.time;
lastTimeSet = TRUE;
if (dt == 0 || bRmod(frout.time, first_time, dt))
{
frame_out++;
last_ok_t = frout.time;
if (bNewFile)
{
fprintf(stderr, "\nContinue writing frames from %s t=%g %s, "
"frame=%d \n",
fnms[i], output_env_conv_time(oenv, frout.time), output_env_get_time_unit(oenv),
frame);
bNewFile = FALSE;
}
if (bIndex)
{
write_trxframe_indexed(trxout, &frout, isize, index,
NULL);
}
else
{
write_trxframe(trxout, &frout, NULL);
}
if ( ((frame % 10) == 0) || (frame < 10) )
{
fprintf(stderr, " -> frame %6d time %8.3f %s \r",
frame_out, output_env_conv_time(oenv, frout.time), output_env_get_time_unit(oenv));
fflush(stderr);
}
}
}
}
while (read_next_frame(oenv, status, &fr));
close_trj(status);
}
if (trxout)
{
close_trx(trxout);
}
fprintf(stderr, "\nLast frame written was %d, time %f %s\n",
frame, output_env_conv_time(oenv, last_ok_t), output_env_get_time_unit(oenv));
}
return 0;
}
static void do_demux(int nset, char *fnms[], char *fnms_out[], int nval,
real **value, real *time, real dt_remd, int isize,
int index[], real dt, const gmx_output_env_t *oenv)
{
int i, j, k, natoms, nnn;
t_trxstatus **fp_in, **fp_out;
gmx_bool bCont, *bSet;
real t, first_time = 0;
t_trxframe *trx;
snew(fp_in, nset);
snew(trx, nset);
snew(bSet, nset);
natoms = -1;
t = -1;
for (i = 0; (i < nset); i++)
{
nnn = read_first_frame(oenv, &(fp_in[i]), fnms[i], &(trx[i]),
TRX_NEED_X);
if (natoms == -1)
{
natoms = nnn;
first_time = trx[i].time;
}
else if (natoms != nnn)
{
gmx_fatal(FARGS, "Trajectory file %s has %d atoms while previous trajs had %d atoms", fnms[i], nnn, natoms);
}
if (t == -1)
{
t = trx[i].time;
}
else if (t != trx[i].time)
{
gmx_fatal(FARGS, "Trajectory file %s has time %f while previous trajs had time %f", fnms[i], trx[i].time, t);
}
}
snew(fp_out, nset);
for (i = 0; (i < nset); i++)
{
fp_out[i] = open_trx(fnms_out[i], "w");
}
k = 0;
if (std::round(time[k] - t) != 0)
{
gmx_fatal(FARGS, "First time in demuxing table does not match trajectories");
}
do
{
while ((k+1 < nval) && ((trx[0].time - time[k+1]) > dt_remd*0.1))
{
k++;
}
if (debug)
{
fprintf(debug, "trx[0].time = %g, time[k] = %g\n", trx[0].time, time[k]);
}
for (i = 0; (i < nset); i++)
{
bSet[i] = FALSE;
}
for (i = 0; (i < nset); i++)
{
j = std::round(value[i][k]);
range_check(j, 0, nset);
if (bSet[j])
{
gmx_fatal(FARGS, "Demuxing the same replica %d twice at time %f",
j, trx[0].time);
}
bSet[j] = TRUE;
if (dt == 0 || bRmod(trx[i].time, first_time, dt))
{
if (index)
{
write_trxframe_indexed(fp_out[j], &trx[i], isize, index, NULL);
}
else
{
write_trxframe(fp_out[j], &trx[i], NULL);
}
}
}
bCont = (k < nval);
for (i = 0; (i < nset); i++)
{
bCont = bCont && read_next_frame(oenv, fp_in[i], &trx[i]);
}
}
while (bCont);
for (i = 0; (i < nset); i++)
{
close_trx(fp_in[i]);
close_trx(fp_out[i]);
}
}
int gmx_insert_dummy_atom(int argc, char *argv[])
{
const char *desc[] = {
"\tAdd a dummy atom between atoms -a1 and -a2",
};
gmx_bool bVerbose = FALSE;
int a1=-1,a2=-1;
int insert_at=-1;
const char *tpr_file, *traj_file, *out_file;
t_pargs pa[] = {
{ "-a1", TRUE, etINT,
{&a1}, "Starting atom for bond vector--ie: CD in CNC"},
{ "-a2", TRUE, etINT,
{&a2}, "Ending atom for bond vector--ie: NE in CNC"},
{ "-insert_at", TRUE, etINT,
{&insert_at}, "Desired index for dummy atom. Default = 0"},
{ "-v", FALSE, etBOOL,
{&bVerbose}, "Be slightly more verbose"}
};
t_filenm fnm[] = {
{efTPS, NULL, NULL, ffREAD},
{efTRX, NULL, NULL, ffREAD},
{efTRO, "-o","tilt",ffWRITE},
};
#define NFILE asize(fnm)
#define NPA asize(pa)
output_env_t oenv;
int ngrps, nrefgrps;
t_topology top;
t_atoms *atoms=NULL;
t_trxframe fr,frout;
t_trxstatus *status;
rvec *xtop;
matrix box;
int ePBC;
int flags=TRX_READ_X;
char buffer[1024];
int ftp;
FILE *out_gro = NULL;
t_trxstatus *trxout = NULL;
CopyRight(stderr,argv[0]);
parse_common_args(&argc, argv,
PCA_CAN_BEGIN | PCA_CAN_END | PCA_CAN_VIEW |
PCA_TIME_UNIT | PCA_BE_NICE | PCA_CAN_TIME,
NFILE, fnm, NPA, pa, asize(desc), desc,
0, NULL, &oenv);
/* Get inputs */
tpr_file = ftp2fn(efTPS, NFILE, fnm);
traj_file = opt2fn( "-f", NFILE, fnm);
out_file = opt2fn("-o", NFILE, fnm);
ftp = fn2ftp(out_file);
std::cout << "\n\n" << out_file << " " << ftp << std::endl;
/* Open inputs */
read_tps_conf(tpr_file, buffer, &top, &ePBC,
&xtop, NULL, box, TRUE);
sfree(xtop);
atoms = &top.atoms;
gmx_conect gc = NULL;
gc = gmx_conect_generate(&top);
/* Make sure -a1 and -a2 are included and increment by -1 to match internal numbering */
if ( a1<1 || a2<1 || a1==a2 || a1>top.atoms.nr || a2>top.atoms.nr ) {
gmx_fatal(FARGS, "\nAtom numbers -a1 and -a2 defining the bond vector must be specified and different\n");
}
a1--; a2--;
/* Read first frame */
gmx_bool bHaveFirstFrame = read_first_frame(oenv, &status, traj_file, &fr, flags);
if (bHaveFirstFrame) {
set_trxframe_ePBC(&fr,ePBC);
}
if (ftp == efGRO) {
out_gro = ffopen(out_file,"w");
}
else if (ftp == efXTC) {
trxout = open_trx(out_file,"w");
}
/* read file and loop through frames */
int frameN = 0;
do {
if (ftp == efGRO) {
fprintf(out_gro,"Dummy atom inserted into %s, FRAME %i\n",traj_file,frameN);
fprintf(out_gro,"%i\n",top.atoms.nr+1);
float CD[3] = { fr.x[a1][0], fr.x[a1][1], fr.x[a1][2] };
float NE[3] = { fr.x[a2][0], fr.x[a2][1], fr.x[a2][2] };
float MP[3] ;
for (int i=0;i<3;i++) {
MP[i] = (CD[i]+NE[i])*0.5;
}
// GRO format:
// RESID, RESNAME, ATOM, INDEX, X, Y, Z, vX, vY, vZ
//"%5d%-5s%5s%5d%8.3f%8.3f%8.3f%8.4f%8.4f%8.4f"
int index = 1;
if (insert_at <= 0) {
fprintf(out_gro,"%5d%-5s%5s%5d%8.4f%8.4f%8.4f%8.4f%8.4f%8.4f\n",
0,"TCHG","TCHG",0,MP[0],MP[1],MP[2],0.0f,0.0f,0.0f);
index++;
}
/* Loop over atoms */
int i;
int resid_offset = 0;
for (i=0;i<top.atoms.nr;i++){
if (insert_at == index) {
fprintf(out_gro,"%5d%-5s%5s%5d%8.4f%8.4f%8.4f%8.4f%8.4f%8.4f\n",
top.atoms.atom[i-1].resind+2,"TCHG","TCHG",index,MP[0],MP[1],MP[2],0.0f,0.0f,0.0f);
index++;
resid_offset++;
}
// Ignoring velocities since I'm using this with mdrun -rerun for
// force calculations only, which don't care about velocities
fprintf(out_gro,"%5d%-5s%5s%5d%8.4f%8.4f%8.4f%8.4f%8.4f%8.4f\n",
top.atoms.atom[i].resind+1 + resid_offset,
*top.atoms.resinfo[top.atoms.atom[i].resind].name,
*top.atoms.atomname[i],
index,
fr.x[i][0], fr.x[i][1], fr.x[i][2],
0.0f,0.0f,0.0f);
index++;
if (index > 99999) {
index = 0;
}
}
/* Get box information */
write_hconf_box(out_gro,1,box);
}
else if (ftp == efXTC) {
float CD[3] = { fr.x[a1][0], fr.x[a1][1], fr.x[a1][2] };
float NE[3] = { fr.x[a2][0], fr.x[a2][1], fr.x[a2][2] };
rvec MP ;
for (int i=0;i<3;i++) {
MP[i] = (CD[i]+NE[i])*0.5;
}
rvec * newX = new rvec [top.atoms.nr+1];
int i = 0;
int offset = 0;
if (insert_at <= 0) {
for (int j=0;j<3;j++) {
newX[i][j] = MP[j];
}
offset++;
}
for (i=0; i<top.atoms.nr; i++) {
if (insert_at == i) {
for (int j=0;j<3;j++) {
newX[i][j] = MP[j];
}
offset++;
}
for (int j=0;j<3;j++) {
newX[i+offset][j] = fr.x[i][j];
}
}
frout = fr;
frout.x = newX;
frout.natoms++;
write_trxframe(trxout,&frout,gc);
delete[] newX;
}
frameN++;
} while(read_next_frame(oenv, status, &fr));
if (trxout) {
close_trx(trxout);
}
if (out_gro) {
ffclose(out_gro);
}
return 0;
}
static void do_demux(gmx::ArrayRef<const std::string> inFiles,
gmx::ArrayRef<const std::string> outFiles, int nval,
real **value, real *time, real dt_remd, int isize,
int index[], real dt, const gmx_output_env_t *oenv)
{
int k, natoms;
t_trxstatus **fp_in, **fp_out;
gmx_bool bCont, *bSet;
real t, first_time = 0;
t_trxframe *trx;
snew(fp_in, inFiles.size());
snew(trx, inFiles.size());
snew(bSet, inFiles.size());
natoms = -1;
t = -1;
for (gmx::index i = 0; i < inFiles.ssize(); i++)
{
read_first_frame(oenv, &(fp_in[i]), inFiles[i].c_str(), &(trx[i]),
TRX_NEED_X);
if (natoms == -1)
{
natoms = trx[i].natoms;
first_time = trx[i].time;
}
else if (natoms != trx[i].natoms)
{
gmx_fatal(FARGS, "Trajectory file %s has %d atoms while previous trajs had %d atoms", inFiles[i].c_str(), trx[i].natoms, natoms);
}
if (t == -1)
{
t = trx[i].time;
}
else if (t != trx[i].time)
{
gmx_fatal(FARGS, "Trajectory file %s has time %f while previous trajs had time %f", inFiles[i].c_str(), trx[i].time, t);
}
}
snew(fp_out, inFiles.size());
for (gmx::index i = 0; i < inFiles.ssize(); i++)
{
fp_out[i] = open_trx(outFiles[i].c_str(), "w");
}
k = 0;
if (std::round(time[k] - t) != 0)
{
gmx_fatal(FARGS, "First time in demuxing table does not match trajectories");
}
do
{
while ((k+1 < nval) && ((trx[0].time - time[k+1]) > dt_remd*0.1))
{
k++;
}
if (debug)
{
fprintf(debug, "trx[0].time = %g, time[k] = %g\n", trx[0].time, time[k]);
}
for (gmx::index i = 0; i < inFiles.ssize(); i++)
{
bSet[i] = FALSE;
}
for (gmx::index i = 0; i < inFiles.ssize(); i++)
{
int j = gmx::roundToInt(value[i][k]);
range_check(j, 0, inFiles.size());
if (bSet[j])
{
gmx_fatal(FARGS, "Demuxing the same replica %d twice at time %f",
j, trx[0].time);
}
bSet[j] = TRUE;
if (dt == 0 || bRmod(trx[i].time, first_time, dt))
{
if (index)
{
write_trxframe_indexed(fp_out[j], &trx[i], isize, index, nullptr);
}
else
{
write_trxframe(fp_out[j], &trx[i], nullptr);
}
}
}
bCont = (k < nval);
for (gmx::index i = 0; i < inFiles.ssize(); i++)
{
bCont = bCont && read_next_frame(oenv, fp_in[i], &trx[i]);
}
}
while (bCont);
for (gmx::index i = 0; i < inFiles.ssize(); i++)
{
close_trx(fp_in[i]);
close_trx(fp_out[i]);
}
}
