static gmx_bool pdb_next_x(t_trxstatus *status, FILE *fp, t_trxframe *fr)
{
t_atoms atoms;
t_symtab *symtab;
matrix boxpdb;
// Initiate model_nr to -1 rather than NOTSET.
// It is not worthwhile introducing extra variables in the
// read_pdbfile call to verify that a model_nr was read.
int ePBC, model_nr = -1, na;
char title[STRLEN], *time, *step;
double dbl;
atoms.nr = fr->natoms;
atoms.atom = nullptr;
atoms.pdbinfo = nullptr;
/* the other pointers in atoms should not be accessed if these are NULL */
snew(symtab, 1);
open_symtab(symtab);
na = read_pdbfile(fp, title, &model_nr, &atoms, symtab, fr->x, &ePBC, boxpdb, TRUE, nullptr);
free_symtab(symtab);
sfree(symtab);
set_trxframe_ePBC(fr, ePBC);
if (nframes_read(status) == 0)
{
fprintf(stderr, " '%s', %d atoms\n", title, fr->natoms);
}
fr->bPrec = TRUE;
fr->prec = 10000;
fr->bX = TRUE;
fr->bBox = (boxpdb[XX][XX] != 0.0);
if (fr->bBox)
{
copy_mat(boxpdb, fr->box);
}
fr->step = 0;
step = std::strstr(title, " step= ");
fr->bStep = ((step != nullptr) && sscanf(step+7, "%" SCNd64, &fr->step) == 1);
dbl = 0.0;
time = std::strstr(title, " t= ");
fr->bTime = ((time != nullptr) && sscanf(time+4, "%lf", &dbl) == 1);
fr->time = dbl;
if (na == 0)
{
return FALSE;
}
else
{
if (na != fr->natoms)
{
gmx_fatal(FARGS, "Number of atoms in pdb frame %d is %d instead of %d",
nframes_read(status), na, fr->natoms);
}
return TRUE;
}
}
static gmx_bool pdb_next_x(t_trxstatus *status, FILE *fp,t_trxframe *fr)
{
t_atoms atoms;
matrix boxpdb;
int ePBC,model_nr,na;
char title[STRLEN],*time;
double dbl;
atoms.nr = fr->natoms;
atoms.atom=NULL;
atoms.pdbinfo=NULL;
/* the other pointers in atoms should not be accessed if these are NULL */
model_nr=NOTSET;
na=read_pdbfile(fp,title,&model_nr,&atoms,fr->x,&ePBC,boxpdb,TRUE,NULL);
set_trxframe_ePBC(fr,ePBC);
if (nframes_read(status)==0)
fprintf(stderr," '%s', %d atoms\n",title, fr->natoms);
fr->bPrec = TRUE;
fr->prec = 10000;
fr->bX = TRUE;
fr->bBox = (boxpdb[XX][XX] != 0.0);
if (fr->bBox) {
copy_mat(boxpdb,fr->box);
}
if (model_nr!=NOTSET) {
fr->bStep = TRUE;
fr->step = model_nr;
}
time=strstr(title," t= ");
if (time) {
fr->bTime = TRUE;
sscanf(time+4,"%lf",&dbl);
fr->time=(real)dbl;
} else {
fr->bTime = FALSE;
/* this is a bit dirty, but it will work: if no time is read from
comment line in pdb file, set time to current frame number */
if (fr->bStep)
fr->time=(real)fr->step;
else
fr->time=(real)nframes_read(status);
}
if (na == 0) {
return FALSE;
} else {
if (na != fr->natoms)
gmx_fatal(FARGS,"Number of atoms in pdb frame %d is %d instead of %d",
nframes_read(status),na,fr->natoms);
return TRUE;
}
}
int write_trxframe_indexed(t_trxstatus *status, const t_trxframe *fr, int nind,
const int *ind, gmx_conect gc)
{
char title[STRLEN];
rvec *xout = nullptr, *vout = nullptr, *fout = nullptr;
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]);
}
}
// fallthrough
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:
gmx_trr_write_frame(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,
fr->x, fr->bV ? fr->v : nullptr, 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:
sprintf(title, "frame t= %.3f", fr->time);
write_g96_conf(gmx_fio_getfp(status->fio), title, 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);
}
// fallthrough
case efXTC:
sfree(xout);
break;
default:
break;
}
return 0;
}
static gmx_bool pdb_next_x(t_trxstatus *status, FILE *fp, t_trxframe *fr)
{
t_atoms atoms;
t_symtab *symtab;
matrix boxpdb;
// Initiate model_nr to -1 rather than NOTSET.
// It is not worthwhile introducing extra variables in the
// read_pdbfile call to verify that a model_nr was read.
int ePBC, model_nr = -1, na;
char title[STRLEN], *time;
double dbl;
atoms.nr = fr->natoms;
atoms.atom = NULL;
atoms.pdbinfo = NULL;
/* the other pointers in atoms should not be accessed if these are NULL */
snew(symtab, 1);
open_symtab(symtab);
na = read_pdbfile(fp, title, &model_nr, &atoms, symtab, fr->x, &ePBC, boxpdb, TRUE, NULL);
free_symtab(symtab);
sfree(symtab);
set_trxframe_ePBC(fr, ePBC);
if (nframes_read(status) == 0)
{
fprintf(stderr, " '%s', %d atoms\n", title, fr->natoms);
}
fr->bPrec = TRUE;
fr->prec = 10000;
fr->bX = TRUE;
fr->bBox = (boxpdb[XX][XX] != 0.0);
if (fr->bBox)
{
copy_mat(boxpdb, fr->box);
}
if (model_nr != -1)
{
fr->bStep = TRUE;
fr->step = model_nr;
}
time = std::strstr(title, " t= ");
if (time)
{
fr->bTime = TRUE;
sscanf(time+4, "%lf", &dbl);
fr->time = (real)dbl;
}
else
{
fr->bTime = FALSE;
/* this is a bit dirty, but it will work: if no time is read from
comment line in pdb file, set time to current frame number */
if (fr->bStep)
{
fr->time = (real)fr->step;
}
else
{
fr->time = (real)nframes_read(status);
}
}
if (na == 0)
{
return FALSE;
}
else
{
if (na != fr->natoms)
{
gmx_fatal(FARGS, "Number of atoms in pdb frame %d is %d instead of %d",
nframes_read(status), na, fr->natoms);
}
return TRUE;
}
}
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;
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]);
}
}
/* no break */
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);
}
/* no break */
case efXTC:
case efG87:
sfree(xout);
break;
default:
break;
}
return 0;
}
int gmx_rmsdist(int argc, char *argv[])
{
const char *desc[] = {
"[THISMODULE] computes the root mean square deviation of atom distances,",
"which has the advantage that no fit is needed like in standard RMS",
"deviation as computed by [gmx-rms].",
"The reference structure is taken from the structure file.",
"The RMSD at time t is calculated as the RMS",
"of the differences in distance between atom-pairs in the reference",
"structure and the structure at time t.[PAR]",
"[THISMODULE] can also produce matrices of the rms distances, rms distances",
"scaled with the mean distance and the mean distances and matrices with",
"NMR averaged distances (1/r^3 and 1/r^6 averaging). Finally, lists",
"of atom pairs with 1/r^3 and 1/r^6 averaged distance below the",
"maximum distance ([TT]-max[tt], which will default to 0.6 in this case)",
"can be generated, by default averaging over equivalent hydrogens",
"(all triplets of hydrogens named *[123]). Additionally a list of",
"equivalent atoms can be supplied ([TT]-equiv[tt]), each line containing",
"a set of equivalent atoms specified as residue number and name and",
"atom name; e.g.:[PAR]",
"[TT]3 SER HB1 3 SER HB2[tt][PAR]",
"Residue and atom names must exactly match those in the structure",
"file, including case. Specifying non-sequential atoms is undefined."
};
int natom, i, j, teller, gi, gj;
real t;
t_topology top;
int ePBC;
t_atoms *atoms;
matrix box;
rvec *x;
FILE *fp;
t_trxstatus *status;
int isize, gnr = 0;
atom_id *index, *noe_index;
char *grpname;
real **d_r, **d, **dtot, **dtot2, **mean, **rms, **rmsc, *resnr;
real **dtot1_3 = NULL, **dtot1_6 = NULL;
real rmsnow, meanmax, rmsmax, rmscmax;
real max1_3, max1_6;
t_noe_gr *noe_gr = NULL;
t_noe **noe = NULL;
t_rgb rlo, rhi;
char buf[255];
gmx_bool bRMS, bScale, bMean, bNOE, bNMR3, bNMR6, bNMR;
static int nlevels = 40;
static real scalemax = -1.0;
static gmx_bool bSumH = TRUE;
static gmx_bool bPBC = TRUE;
output_env_t oenv;
t_pargs pa[] = {
{ "-nlevels", FALSE, etINT, {&nlevels},
"Discretize RMS in this number of levels" },
{ "-max", FALSE, etREAL, {&scalemax},
"Maximum level in matrices" },
{ "-sumh", FALSE, etBOOL, {&bSumH},
"Average distance over equivalent hydrogens" },
{ "-pbc", FALSE, etBOOL, {&bPBC},
"Use periodic boundary conditions when computing distances" }
};
t_filenm fnm[] = {
{ efTRX, "-f", NULL, ffREAD },
{ efTPS, NULL, NULL, ffREAD },
{ efNDX, NULL, NULL, ffOPTRD },
{ efDAT, "-equiv", "equiv", ffOPTRD },
{ efXVG, NULL, "distrmsd", ffWRITE },
{ efXPM, "-rms", "rmsdist", ffOPTWR },
{ efXPM, "-scl", "rmsscale", ffOPTWR },
{ efXPM, "-mean", "rmsmean", ffOPTWR },
{ efXPM, "-nmr3", "nmr3", ffOPTWR },
{ efXPM, "-nmr6", "nmr6", ffOPTWR },
{ efDAT, "-noe", "noe", ffOPTWR },
};
#define NFILE asize(fnm)
if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
{
return 0;
}
bRMS = opt2bSet("-rms", NFILE, fnm);
bScale = opt2bSet("-scl", NFILE, fnm);
bMean = opt2bSet("-mean", NFILE, fnm);
bNOE = opt2bSet("-noe", NFILE, fnm);
bNMR3 = opt2bSet("-nmr3", NFILE, fnm);
bNMR6 = opt2bSet("-nmr6", NFILE, fnm);
bNMR = bNMR3 || bNMR6 || bNOE;
max1_3 = 0;
max1_6 = 0;
/* check input */
if (bNOE && scalemax < 0)
{
scalemax = 0.6;
fprintf(stderr, "WARNING: using -noe without -max "
"makes no sense, setting -max to %g\n\n", scalemax);
}
/* get topology and index */
read_tps_conf(ftp2fn(efTPS, NFILE, fnm), buf, &top, &ePBC, &x, NULL, box, FALSE);
if (!bPBC)
{
ePBC = epbcNONE;
}
atoms = &(top.atoms);
get_index(atoms, ftp2fn_null(efNDX, NFILE, fnm), 1, &isize, &index, &grpname);
/* initialize arrays */
snew(d, isize);
snew(dtot, isize);
snew(dtot2, isize);
if (bNMR)
{
snew(dtot1_3, isize);
snew(dtot1_6, isize);
}
snew(mean, isize);
snew(rms, isize);
snew(rmsc, isize);
snew(d_r, isize);
snew(resnr, isize);
for (i = 0; (i < isize); i++)
{
snew(d[i], isize);
snew(dtot[i], isize);
snew(dtot2[i], isize);
if (bNMR)
{
snew(dtot1_3[i], isize);
snew(dtot1_6[i], isize);
}
snew(mean[i], isize);
snew(rms[i], isize);
snew(rmsc[i], isize);
snew(d_r[i], isize);
resnr[i] = i+1;
}
/*set box type*/
calc_dist(isize, index, x, ePBC, box, d_r);
sfree(x);
/*open output files*/
fp = xvgropen(ftp2fn(efXVG, NFILE, fnm), "RMS Deviation", "Time (ps)", "RMSD (nm)",
oenv);
if (output_env_get_print_xvgr_codes(oenv))
{
fprintf(fp, "@ subtitle \"of distances between %s atoms\"\n", grpname);
}
/*do a first step*/
natom = read_first_x(oenv, &status, ftp2fn(efTRX, NFILE, fnm), &t, &x, box);
do
{
calc_dist_tot(isize, index, x, ePBC, box, d, dtot, dtot2, bNMR, dtot1_3, dtot1_6);
rmsnow = rms_diff(isize, d, d_r);
fprintf(fp, "%g %g\n", t, rmsnow);
}
while (read_next_x(oenv, status, &t, x, box));
fprintf(stderr, "\n");
gmx_ffclose(fp);
teller = nframes_read(status);
close_trj(status);
calc_rms(isize, teller, dtot, dtot2, mean, &meanmax, rms, &rmsmax, rmsc, &rmscmax);
fprintf(stderr, "rmsmax = %g, rmscmax = %g\n", rmsmax, rmscmax);
if (bNMR)
{
calc_nmr(isize, teller, dtot1_3, dtot1_6, &max1_3, &max1_6);
}
if (scalemax > -1.0)
{
rmsmax = scalemax;
rmscmax = scalemax;
meanmax = scalemax;
max1_3 = scalemax;
max1_6 = scalemax;
}
if (bNOE)
{
/* make list of noe atom groups */
snew(noe_index, isize+1);
snew(noe_gr, isize);
gnr = analyze_noe_equivalent(opt2fn_null("-equiv", NFILE, fnm),
atoms, isize, index, bSumH, noe_index, noe_gr);
fprintf(stdout, "Found %d non-equivalent atom-groups in %d atoms\n",
gnr, isize);
/* make half matrix of of noe-group distances from atom distances */
snew(noe, gnr);
for (i = 0; i < gnr; i++)
{
snew(noe[i], gnr);
}
calc_noe(isize, noe_index, dtot1_3, dtot1_6, gnr, noe);
}
rlo.r = 1.0, rlo.g = 1.0, rlo.b = 1.0;
rhi.r = 0.0, rhi.g = 0.0, rhi.b = 0.0;
if (bRMS)
{
write_xpm(opt2FILE("-rms", NFILE, fnm, "w"), 0,
"RMS of distance", "RMS (nm)", "Atom Index", "Atom Index",
isize, isize, resnr, resnr, rms, 0.0, rmsmax, rlo, rhi, &nlevels);
}
if (bScale)
{
write_xpm(opt2FILE("-scl", NFILE, fnm, "w"), 0,
"Relative RMS", "RMS", "Atom Index", "Atom Index",
isize, isize, resnr, resnr, rmsc, 0.0, rmscmax, rlo, rhi, &nlevels);
}
if (bMean)
{
write_xpm(opt2FILE("-mean", NFILE, fnm, "w"), 0,
"Mean Distance", "Distance (nm)", "Atom Index", "Atom Index",
isize, isize, resnr, resnr, mean, 0.0, meanmax, rlo, rhi, &nlevels);
}
if (bNMR3)
{
write_xpm(opt2FILE("-nmr3", NFILE, fnm, "w"), 0, "1/r^3 averaged distances",
"Distance (nm)", "Atom Index", "Atom Index",
isize, isize, resnr, resnr, dtot1_3, 0.0, max1_3, rlo, rhi, &nlevels);
}
if (bNMR6)
{
write_xpm(opt2FILE("-nmr6", NFILE, fnm, "w"), 0, "1/r^6 averaged distances",
"Distance (nm)", "Atom Index", "Atom Index",
isize, isize, resnr, resnr, dtot1_6, 0.0, max1_6, rlo, rhi, &nlevels);
}
if (bNOE)
{
write_noe(opt2FILE("-noe", NFILE, fnm, "w"), gnr, noe, noe_gr, scalemax);
}
do_view(oenv, ftp2fn(efXVG, NFILE, fnm), NULL);
return 0;
}
