void do_fit(int natoms,real *w_rls,rvec *xp,rvec *x)
{
do_fit_ndim(3,natoms,w_rls,xp,x);
}
int gmx_rotmat(int argc, char *argv[])
{
const char *desc[] = {
"[THISMODULE] plots the rotation matrix required for least squares fitting",
"a conformation onto the reference conformation provided with",
"[TT]-s[tt]. Translation is removed before fitting.",
"The output are the three vectors that give the new directions",
"of the x, y and z directions of the reference conformation,",
"for example: (zx,zy,zz) is the orientation of the reference",
"z-axis in the trajectory frame.",
"[PAR]",
"This tool is useful for, for instance,",
"determining the orientation of a molecule",
"at an interface, possibly on a trajectory produced with",
"[TT]gmx trjconv -fit rotxy+transxy[tt] to remove the rotation",
"in the [IT]x-y[it] plane.",
"[PAR]",
"Option [TT]-ref[tt] determines a reference structure for fitting,",
"instead of using the structure from [TT]-s[tt]. The structure with",
"the lowest sum of RMSD's to all other structures is used.",
"Since the computational cost of this procedure grows with",
"the square of the number of frames, the [TT]-skip[tt] option",
"can be useful. A full fit or only a fit in the [IT]x-y[it] plane can",
"be performed.",
"[PAR]",
"Option [TT]-fitxy[tt] fits in the [IT]x-y[it] plane before determining",
"the rotation matrix."
};
const char *reffit[] =
{ NULL, "none", "xyz", "xy", NULL };
static int skip = 1;
static gmx_bool bFitXY = FALSE, bMW = TRUE;
t_pargs pa[] = {
{ "-ref", FALSE, etENUM, {reffit},
"Determine the optimal reference structure" },
{ "-skip", FALSE, etINT, {&skip},
"Use every nr-th frame for [TT]-ref[tt]" },
{ "-fitxy", FALSE, etBOOL, {&bFitXY},
"Fit the x/y rotation before determining the rotation" },
{ "-mw", FALSE, etBOOL, {&bMW},
"Use mass weighted fitting" }
};
FILE *out;
t_trxstatus *status;
t_topology top;
int ePBC;
rvec *x_ref, *x;
matrix box, R;
real t;
int natoms, i;
char *grpname, title[256];
int gnx;
gmx_rmpbc_t gpbc = NULL;
atom_id *index;
output_env_t oenv;
real *w_rls;
const char *leg[] = { "xx", "xy", "xz", "yx", "yy", "yz", "zx", "zy", "zz" };
#define NLEG asize(leg)
t_filenm fnm[] = {
{ efTRX, "-f", NULL, ffREAD },
{ efTPS, NULL, NULL, ffREAD },
{ efNDX, NULL, NULL, ffOPTRD },
{ efXVG, NULL, "rotmat", ffWRITE }
};
#define NFILE asize(fnm)
if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW | PCA_BE_NICE,
NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
{
return 0;
}
read_tps_conf(ftp2fn(efTPS, NFILE, fnm), title, &top, &ePBC, &x_ref, NULL, box, bMW);
gpbc = gmx_rmpbc_init(&top.idef, ePBC, top.atoms.nr);
gmx_rmpbc(gpbc, top.atoms.nr, box, x_ref);
get_index(&top.atoms, ftp2fn_null(efNDX, NFILE, fnm), 1, &gnx, &index, &grpname);
if (reffit[0][0] != 'n')
{
get_refx(oenv, ftp2fn(efTRX, NFILE, fnm), reffit[0][2] == 'z' ? 3 : 2, skip,
gnx, index, bMW, &top, ePBC, x_ref);
}
natoms = read_first_x(oenv, &status, ftp2fn(efTRX, NFILE, fnm), &t, &x, box);
snew(w_rls, natoms);
for (i = 0; i < gnx; i++)
{
if (index[i] >= natoms)
{
gmx_fatal(FARGS, "Atom index (%d) is larger than the number of atoms in the trajecory (%d)", index[i]+1, natoms);
}
w_rls[index[i]] = (bMW ? top.atoms.atom[index[i]].m : 1.0);
}
if (reffit[0][0] == 'n')
{
reset_x(gnx, index, natoms, NULL, x_ref, w_rls);
}
out = xvgropen(ftp2fn(efXVG, NFILE, fnm),
"Fit matrix", "Time (ps)", "", oenv);
xvgr_legend(out, NLEG, leg, oenv);
do
{
gmx_rmpbc(gpbc, natoms, box, x);
reset_x(gnx, index, natoms, NULL, x, w_rls);
if (bFitXY)
{
do_fit_ndim(2, natoms, w_rls, x_ref, x);
}
calc_fit_R(DIM, natoms, w_rls, x_ref, x, R);
fprintf(out,
"%7g %7.4f %7.4f %7.4f %7.4f %7.4f %7.4f %7.4f %7.4f %7.4f\n",
t,
R[XX][XX], R[XX][YY], R[XX][ZZ],
R[YY][XX], R[YY][YY], R[YY][ZZ],
R[ZZ][XX], R[ZZ][YY], R[ZZ][ZZ]);
}
while (read_next_x(oenv, status, &t, x, box));
gmx_rmpbc_done(gpbc);
close_trj(status);
gmx_ffclose(out);
do_view(oenv, ftp2fn(efXVG, NFILE, fnm), "-nxy");
return 0;
}
