*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017,2018,2019, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#define MAX_ENDS 3
-typedef struct {
+typedef struct
+{
int n;
int nend;
- rvec *end[MAX_ENDS];
- rvec *mid;
- rvec *dir;
- real *len;
+ rvec* end[MAX_ENDS];
+ rvec* mid;
+ rvec* dir;
+ real* len;
} t_bundle;
-static void rotate_ends(t_bundle *bun, rvec axis, int c0, int c1)
+static void rotate_ends(t_bundle* bun, rvec axis, int c0, int c1)
{
int end, i;
rvec ax, tmp;
for (i = 0; i < bun->n; i++)
{
copy_rvec(bun->end[end][i], tmp);
- bun->end[end][i][c0] = ax[c1]*tmp[c0] - ax[c0]*tmp[c1];
- bun->end[end][i][c1] = ax[c0]*tmp[c0] + ax[c1]*tmp[c1];
+ bun->end[end][i][c0] = ax[c1] * tmp[c0] - ax[c0] * tmp[c1];
+ bun->end[end][i][c1] = ax[c0] * tmp[c0] + ax[c1] * tmp[c1];
}
}
copy_rvec(axis, tmp);
- axis[c0] = ax[c1]*tmp[c0] - ax[c0]*tmp[c1];
- axis[c1] = ax[c0]*tmp[c0] + ax[c1]*tmp[c1];
+ axis[c0] = ax[c1] * tmp[c0] - ax[c0] * tmp[c1];
+ axis[c1] = ax[c0] * tmp[c0] + ax[c1] * tmp[c1];
}
-static void calc_axes(rvec x[], t_atom atom[], const int gnx[], int *index[],
- gmx_bool bRot, t_bundle *bun)
+static void calc_axes(rvec x[], t_atom atom[], const int gnx[], int* index[], gmx_bool bRot, t_bundle* bun)
{
int end, i, div, d;
real *mtot, m;
clear_rvec(bun->end[end][i]);
mtot[i] = 0;
}
- div = gnx[end]/bun->n;
+ div = gnx[end] / bun->n;
for (i = 0; i < gnx[end]; i++)
{
m = atom[index[end][i]].m;
for (d = 0; d < DIM; d++)
{
- bun->end[end][i/div][d] += m*x[index[end][i]][d];
+ bun->end[end][i / div][d] += m * x[index[end][i]][d];
}
- mtot[i/div] += m;
+ mtot[i / div] += m;
}
clear_rvec(axis[end]);
for (i = 0; i < bun->n; i++)
{
- svmul(1.0/mtot[i], bun->end[end][i], bun->end[end][i]);
+ svmul(1.0 / mtot[i], bun->end[end][i], bun->end[end][i]);
rvec_inc(axis[end], bun->end[end][i]);
}
- svmul(1.0/bun->n, axis[end], axis[end]);
+ svmul(1.0 / bun->n, axis[end], axis[end]);
}
sfree(mtot);
}
}
-static void dump_axes(t_trxstatus *status, t_trxframe *fr, t_atoms *outat,
- t_bundle *bun)
+static void dump_axes(t_trxstatus* status, t_trxframe* fr, t_atoms* outat, t_bundle* bun)
{
t_trxframe frout;
- static rvec *xout = nullptr;
+ static rvec* xout = nullptr;
int i;
GMX_ASSERT(outat->nr >= bun->n, "");
for (i = 0; i < bun->n; i++)
{
- copy_rvec(bun->end[0][i], xout[3*i]);
+ copy_rvec(bun->end[0][i], xout[3 * i]);
if (bun->nend >= 3)
{
- copy_rvec(bun->end[2][i], xout[3*i+1]);
+ copy_rvec(bun->end[2][i], xout[3 * i + 1]);
}
else
{
- copy_rvec(bun->mid[i], xout[3*i+1]);
+ copy_rvec(bun->mid[i], xout[3 * i + 1]);
}
- copy_rvec(bun->end[1][i], xout[3*i+2]);
+ copy_rvec(bun->end[1][i], xout[3 * i + 2]);
}
frout = *fr;
frout.bV = FALSE;
write_trxframe(status, &frout, nullptr);
}
-int gmx_bundle(int argc, char *argv[])
+int gmx_bundle(int argc, char* argv[])
{
- const char *desc[] = {
+ const char* desc[] = {
"[THISMODULE] analyzes bundles of axes. The axes can be for instance",
"helix axes. The program reads two index groups and divides both",
"of them in [TT]-na[tt] parts. The centers of mass of these parts",
"command line option [TT]-nmrpdb[tt], and type [TT]set axis true[tt] to",
"display the reference axis."
};
- static int n = 0;
- static gmx_bool bZ = FALSE;
- t_pargs pa[] = {
- { "-na", FALSE, etINT, {&n},
- "Number of axes" },
- { "-z", FALSE, etBOOL, {&bZ},
- "Use the [IT]z[it]-axis as reference instead of the average axis" }
- };
- FILE *flen, *fdist, *fz, *ftilt, *ftiltr, *ftiltl;
- FILE *fkink = nullptr, *fkinkr = nullptr, *fkinkl = nullptr;
- t_trxstatus *status;
- t_trxstatus *fpdb;
- t_topology top;
- int ePBC;
- rvec *xtop;
- matrix box;
- t_trxframe fr;
- t_atoms outatoms;
- real t, comp;
- char *grpname[MAX_ENDS];
+ static int n = 0;
+ static gmx_bool bZ = FALSE;
+ t_pargs pa[] = { { "-na", FALSE, etINT, { &n }, "Number of axes" },
+ { "-z",
+ FALSE,
+ etBOOL,
+ { &bZ },
+ "Use the [IT]z[it]-axis as reference instead of the average axis" } };
+ FILE * flen, *fdist, *fz, *ftilt, *ftiltr, *ftiltl;
+ FILE * fkink = nullptr, *fkinkr = nullptr, *fkinkl = nullptr;
+ t_trxstatus* status;
+ t_trxstatus* fpdb;
+ t_topology top;
+ int ePBC;
+ rvec* xtop;
+ matrix box;
+ t_trxframe fr;
+ t_atoms outatoms;
+ real t, comp;
+ char* grpname[MAX_ENDS];
/* FIXME: The constness should not be cast away */
- char *anm = const_cast<char*>("CA"), *rnm = const_cast<char*>("GLY");
+ char * anm = const_cast<char*>("CA"), *rnm = const_cast<char*>("GLY");
int i, gnx[MAX_ENDS];
- int *index[MAX_ENDS];
+ int* index[MAX_ENDS];
t_bundle bun;
gmx_bool bKink;
rvec va, vb, vc, vr, vl;
- gmx_output_env_t *oenv;
+ gmx_output_env_t* oenv;
gmx_rmpbc_t gpbc = nullptr;
#define NLEG asize(leg)
t_filenm fnm[] = {
- { efTRX, "-f", nullptr, ffREAD },
- { efTPS, nullptr, nullptr, ffREAD },
- { efNDX, nullptr, nullptr, ffOPTRD },
- { efXVG, "-ol", "bun_len", ffWRITE },
- { efXVG, "-od", "bun_dist", ffWRITE },
- { efXVG, "-oz", "bun_z", ffWRITE },
- { efXVG, "-ot", "bun_tilt", ffWRITE },
- { efXVG, "-otr", "bun_tiltr", ffWRITE },
- { efXVG, "-otl", "bun_tiltl", ffWRITE },
- { efXVG, "-ok", "bun_kink", ffOPTWR },
- { efXVG, "-okr", "bun_kinkr", ffOPTWR },
- { efXVG, "-okl", "bun_kinkl", ffOPTWR },
+ { efTRX, "-f", nullptr, ffREAD }, { efTPS, nullptr, nullptr, ffREAD },
+ { efNDX, nullptr, nullptr, ffOPTRD }, { efXVG, "-ol", "bun_len", ffWRITE },
+ { efXVG, "-od", "bun_dist", ffWRITE }, { efXVG, "-oz", "bun_z", ffWRITE },
+ { efXVG, "-ot", "bun_tilt", ffWRITE }, { efXVG, "-otr", "bun_tiltr", ffWRITE },
+ { efXVG, "-otl", "bun_tiltl", ffWRITE }, { efXVG, "-ok", "bun_kink", ffOPTWR },
+ { efXVG, "-okr", "bun_kinkr", ffOPTWR }, { efXVG, "-okl", "bun_kinkl", ffOPTWR },
{ efPDB, "-oa", "axes", ffOPTWR }
};
#define NFILE asize(fnm)
- if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_TIME_UNIT,
- NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, nullptr, &oenv))
+ if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_TIME_UNIT, NFILE, fnm, asize(pa), pa,
+ asize(desc), desc, 0, nullptr, &oenv))
{
return 0;
}
read_tps_conf(ftp2fn(efTPS, NFILE, fnm), &top, &ePBC, &xtop, nullptr, box, TRUE);
- bKink = opt2bSet("-ok", NFILE, fnm) || opt2bSet("-okr", NFILE, fnm)
- || opt2bSet("-okl", NFILE, fnm);
+ bKink = opt2bSet("-ok", NFILE, fnm) || opt2bSet("-okr", NFILE, fnm) || opt2bSet("-okl", NFILE, fnm);
if (bKink)
{
bun.nend = 3;
fprintf(stderr, "and a group of kink ");
}
fprintf(stderr, "atoms\n");
- get_index(&top.atoms, ftp2fn_null(efNDX, NFILE, fnm), bun.nend,
- gnx, index, grpname);
+ get_index(&top.atoms, ftp2fn_null(efNDX, NFILE, fnm), bun.nend, gnx, index, grpname);
if (n <= 0 || gnx[0] % n || gnx[1] % n || (bKink && gnx[2] % n))
{
- gmx_fatal(FARGS,
- "The size of one of your index groups is not a multiple of n");
+ gmx_fatal(FARGS, "The size of one of your index groups is not a multiple of n");
}
bun.n = n;
snew(bun.end[0], n);
snew(bun.dir, n);
snew(bun.len, n);
- flen = xvgropen(opt2fn("-ol", NFILE, fnm), "Axis lengths",
- output_env_get_xvgr_tlabel(oenv), "(nm)", oenv);
+ flen = xvgropen(opt2fn("-ol", NFILE, fnm), "Axis lengths", output_env_get_xvgr_tlabel(oenv),
+ "(nm)", oenv);
fdist = xvgropen(opt2fn("-od", NFILE, fnm), "Distance of axis centers",
- output_env_get_xvgr_tlabel(oenv), "(nm)", oenv);
+ output_env_get_xvgr_tlabel(oenv), "(nm)", oenv);
fz = xvgropen(opt2fn("-oz", NFILE, fnm), "Z-shift of axis centers",
- output_env_get_xvgr_tlabel(oenv), "(nm)", oenv);
- ftilt = xvgropen(opt2fn("-ot", NFILE, fnm), "Axis tilts",
- output_env_get_xvgr_tlabel(oenv), "(degrees)", oenv);
+ output_env_get_xvgr_tlabel(oenv), "(nm)", oenv);
+ ftilt = xvgropen(opt2fn("-ot", NFILE, fnm), "Axis tilts", output_env_get_xvgr_tlabel(oenv),
+ "(degrees)", oenv);
ftiltr = xvgropen(opt2fn("-otr", NFILE, fnm), "Radial axis tilts",
output_env_get_xvgr_tlabel(oenv), "(degrees)", oenv);
ftiltl = xvgropen(opt2fn("-otl", NFILE, fnm), "Lateral axis tilts",
if (bKink)
{
- fkink = xvgropen(opt2fn("-ok", NFILE, fnm), "Kink angles",
- output_env_get_xvgr_tlabel(oenv), "(degrees)", oenv);
+ fkink = xvgropen(opt2fn("-ok", NFILE, fnm), "Kink angles", output_env_get_xvgr_tlabel(oenv),
+ "(degrees)", oenv);
fkinkr = xvgropen(opt2fn("-okr", NFILE, fnm), "Radial kink angles",
output_env_get_xvgr_tlabel(oenv), "(degrees)", oenv);
if (output_env_get_print_xvgr_codes(oenv))
if (opt2bSet("-oa", NFILE, fnm))
{
- init_t_atoms(&outatoms, 3*n, FALSE);
- outatoms.nr = 3*n;
- for (i = 0; i < 3*n; i++)
+ init_t_atoms(&outatoms, 3 * n, FALSE);
+ outatoms.nr = 3 * n;
+ for (i = 0; i < 3 * n; i++)
{
- outatoms.atomname[i] = &anm;
- outatoms.atom[i].resind = i/3;
- outatoms.resinfo[i/3].name = &rnm;
- outatoms.resinfo[i/3].nr = i/3 + 1;
- outatoms.resinfo[i/3].ic = ' ';
+ outatoms.atomname[i] = &anm;
+ outatoms.atom[i].resind = i / 3;
+ outatoms.resinfo[i / 3].name = &rnm;
+ outatoms.resinfo[i / 3].nr = i / 3 + 1;
+ outatoms.resinfo[i / 3].ic = ' ';
}
fpdb = open_trx(opt2fn("-oa", NFILE, fnm), "w");
}
fprintf(flen, " %6g", bun.len[i]);
fprintf(fdist, " %6g", norm(bun.mid[i]));
fprintf(fz, " %6g", bun.mid[i][ZZ]);
- fprintf(ftilt, " %6g", RAD2DEG*acos(bun.dir[i][ZZ]));
- comp = bun.mid[i][XX]*bun.dir[i][XX]+bun.mid[i][YY]*bun.dir[i][YY];
- fprintf(ftiltr, " %6g", RAD2DEG*
- std::asin(comp/std::hypot(comp, bun.dir[i][ZZ])));
- comp = bun.mid[i][YY]*bun.dir[i][XX]-bun.mid[i][XX]*bun.dir[i][YY];
- fprintf(ftiltl, " %6g", RAD2DEG*
- std::asin(comp/std::hypot(comp, bun.dir[i][ZZ])));
+ fprintf(ftilt, " %6g", RAD2DEG * acos(bun.dir[i][ZZ]));
+ comp = bun.mid[i][XX] * bun.dir[i][XX] + bun.mid[i][YY] * bun.dir[i][YY];
+ fprintf(ftiltr, " %6g", RAD2DEG * std::asin(comp / std::hypot(comp, bun.dir[i][ZZ])));
+ comp = bun.mid[i][YY] * bun.dir[i][XX] - bun.mid[i][XX] * bun.dir[i][YY];
+ fprintf(ftiltl, " %6g", RAD2DEG * std::asin(comp / std::hypot(comp, bun.dir[i][ZZ])));
if (bKink)
{
rvec_sub(bun.end[0][i], bun.end[2][i], va);
rvec_sub(bun.end[2][i], bun.end[1][i], vb);
unitv(va, va);
unitv(vb, vb);
- fprintf(fkink, " %6g", RAD2DEG*acos(iprod(va, vb)));
+ fprintf(fkink, " %6g", RAD2DEG * acos(iprod(va, vb)));
cprod(va, vb, vc);
copy_rvec(bun.mid[i], vr);
vr[ZZ] = 0;
unitv(vr, vr);
- fprintf(fkinkr, " %6g", RAD2DEG*std::asin(iprod(vc, vr)));
+ fprintf(fkinkr, " %6g", RAD2DEG * std::asin(iprod(vc, vr)));
vl[XX] = vr[YY];
vl[YY] = -vr[XX];
vl[ZZ] = 0;
- fprintf(fkinkl, " %6g", RAD2DEG*std::asin(iprod(vc, vl)));
+ fprintf(fkinkl, " %6g", RAD2DEG * std::asin(iprod(vc, vl)));
}
}
fprintf(flen, "\n");
{
dump_axes(fpdb, &fr, &outatoms, &bun);
}
- }
- while (read_next_frame(oenv, status, &fr));
+ } while (read_next_frame(oenv, status, &fr));
gmx_rmpbc_done(gpbc);
close_trx(status);
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff