*
* 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 FARAWAY 10000
-static int *res_ndx(t_atoms *atoms)
+static int* res_ndx(t_atoms* atoms)
{
- int *rndx;
+ int* rndx;
int i, r0;
if (atoms->nr <= 0)
r0 = atoms->atom[0].resind;
for (i = 0; (i < atoms->nr); i++)
{
- rndx[i] = atoms->atom[i].resind-r0;
+ rndx[i] = atoms->atom[i].resind - r0;
}
return rndx;
}
-static int *res_natm(t_atoms *atoms)
+static int* res_natm(t_atoms* atoms)
{
- int *natm;
+ int* natm;
int i, j, r0;
if (atoms->nr <= 0)
j = 0;
for (i = 0; (i < atoms->nres); i++)
{
- while ((atoms->atom[j].resind)-r0 == i)
+ while ((atoms->atom[j].resind) - r0 == i)
{
natm[i]++;
j++;
return natm;
}
-static void calc_mat(int nres, int natoms, const int rndx[],
- rvec x[], const int *index,
- real trunc, real **mdmat, int **nmat, int ePBC, matrix box)
+static void calc_mat(int nres,
+ int natoms,
+ const int rndx[],
+ rvec x[],
+ const int* index,
+ real trunc,
+ real** mdmat,
+ int** nmat,
+ int ePBC,
+ matrix box)
{
int i, j, resi, resj;
real trunc2, r, r2;
for (i = 0; (i < natoms); i++)
{
resi = rndx[i];
- for (j = i+1; (j < natoms); j++)
+ for (j = i + 1; (j < natoms); j++)
{
resj = rndx[j];
pbc_dx(&pbc, x[index[i]], x[index[j]], ddx);
for (resi = 0; (resi < nres); resi++)
{
mdmat[resi][resi] = 0;
- for (resj = resi+1; (resj < nres); resj++)
+ for (resj = resi + 1; (resj < nres); resj++)
{
r = std::sqrt(mdmat[resi][resj]);
mdmat[resi][resj] = r;
}
}
-static void tot_nmat(int nres, int natoms, int nframes, int **nmat,
- int *tot_n, real *mean_n)
+static void tot_nmat(int nres, int natoms, int nframes, int** nmat, int* tot_n, real* mean_n)
{
int i, j;
}
}
-int gmx_mdmat(int argc, char *argv[])
+int gmx_mdmat(int argc, char* argv[])
{
- const char *desc[] = {
+ const char* desc[] = {
"[THISMODULE] makes distance matrices consisting of the smallest distance",
"between residue pairs. With [TT]-frames[tt], these distance matrices can be",
"stored in order to see differences in tertiary structure as a",
"residues over the whole trajectory can be made.",
"The output can be processed with [gmx-xpm2ps] to make a PostScript (tm) plot."
};
- static real truncate = 1.5;
- static int nlevels = 40;
- t_pargs pa[] = {
- { "-t", FALSE, etREAL, {&truncate},
- "trunc distance" },
- { "-nlevels", FALSE, etINT, {&nlevels},
- "Discretize distance in this number of levels" }
+ static real truncate = 1.5;
+ static int nlevels = 40;
+ t_pargs pa[] = {
+ { "-t", FALSE, etREAL, { &truncate }, "trunc distance" },
+ { "-nlevels", FALSE, etINT, { &nlevels }, "Discretize distance in this number of levels" }
};
- t_filenm fnm[] = {
- { efTRX, "-f", nullptr, ffREAD },
- { efTPS, nullptr, nullptr, ffREAD },
- { efNDX, nullptr, nullptr, ffOPTRD },
- { efXPM, "-mean", "dm", ffWRITE },
- { efXPM, "-frames", "dmf", ffOPTWR },
- { efXVG, "-no", "num", ffOPTWR },
+ t_filenm fnm[] = {
+ { efTRX, "-f", nullptr, ffREAD }, { efTPS, nullptr, nullptr, ffREAD },
+ { efNDX, nullptr, nullptr, ffOPTRD }, { efXPM, "-mean", "dm", ffWRITE },
+ { efXPM, "-frames", "dmf", ffOPTWR }, { efXVG, "-no", "num", ffOPTWR },
};
#define NFILE asize(fnm)
- FILE *out = nullptr, *fp;
- t_topology top;
- int ePBC;
- t_atoms useatoms;
- int isize;
- int *index;
- char *grpname;
- int *rndx, *natm, prevres, newres;
+ FILE * out = nullptr, *fp;
+ t_topology top;
+ int ePBC;
+ t_atoms useatoms;
+ int isize;
+ int* index;
+ char* grpname;
+ int * rndx, *natm, prevres, newres;
int i, j, nres, natoms, nframes, trxnat;
- t_trxstatus *status;
+ t_trxstatus* status;
gmx_bool bCalcN, bFrames;
real t, ratio;
char label[234];
t_rgb rlo, rhi;
- rvec *x;
- real **mdmat, *resnr, **totmdmat;
- int **nmat, **totnmat;
- real *mean_n;
- int *tot_n;
- matrix box = {{0}};
- gmx_output_env_t *oenv;
+ rvec* x;
+ real ** mdmat, *resnr, **totmdmat;
+ int ** nmat, **totnmat;
+ real* mean_n;
+ int* tot_n;
+ matrix box = { { 0 } };
+ gmx_output_env_t* oenv;
gmx_rmpbc_t gpbc = nullptr;
- if (!parse_common_args(&argc, argv, PCA_CAN_TIME, NFILE, fnm,
- asize(pa), pa, asize(desc), desc, 0, nullptr, &oenv))
+ if (!parse_common_args(&argc, argv, PCA_CAN_TIME, NFILE, fnm, asize(pa), pa, asize(desc), desc,
+ 0, nullptr, &oenv))
{
return 0;
}
newres = 0;
for (i = 0; (i < isize); i++)
{
- int ii = index[i];
+ int ii = index[i];
useatoms.atomname[i] = top.atoms.atomname[ii];
if (top.atoms.atom[ii].resind != prevres)
{
{
fprintf(debug, "New residue: atom %5s %5s %6d, index entry %5d, newres %5d\n",
*(top.atoms.resinfo[top.atoms.atom[ii].resind].name),
- *(top.atoms.atomname[ii]),
- ii, i, newres);
+ *(top.atoms.atomname[ii]), ii, i, newres);
}
}
useatoms.atom[i].resind = newres;
}
- useatoms.nres = newres+1;
+ useatoms.nres = newres + 1;
useatoms.nr = isize;
rndx = res_ndx(&(useatoms));
snew(mdmat[i], nres);
snew(nmat[i], natoms);
snew(totnmat[i], natoms);
- resnr[i] = i+1;
+ resnr[i] = i + 1;
}
snew(totmdmat, nres);
for (i = 0; (i < nres); i++)
nframes = 0;
- rlo.r = 1.0; rlo.g = 1.0; rlo.b = 1.0;
- rhi.r = 0.0; rhi.g = 0.0; rhi.b = 0.0;
+ rlo.r = 1.0;
+ rlo.g = 1.0;
+ rlo.b = 1.0;
+ rhi.r = 0.0;
+ rhi.g = 0.0;
+ rhi.b = 0.0;
gpbc = gmx_rmpbc_init(&top.idef, ePBC, trxnat);
if (bFrames)
{
sprintf(label, "t=%.0f ps", t);
- write_xpm(out, 0, label, "Distance (nm)", "Residue Index", "Residue Index",
- nres, nres, resnr, resnr, mdmat, 0, truncate, rlo, rhi, &nlevels);
+ write_xpm(out, 0, label, "Distance (nm)", "Residue Index", "Residue Index", nres, nres,
+ resnr, resnr, mdmat, 0, truncate, rlo, rhi, &nlevels);
}
- }
- while (read_next_x(oenv, status, &t, x, box));
+ } while (read_next_x(oenv, status, &t, x, box));
fprintf(stderr, "\n");
close_trx(status);
gmx_rmpbc_done(gpbc);
totmdmat[i][j] /= nframes;
}
}
- write_xpm(opt2FILE("-mean", NFILE, fnm, "w"), 0, "Mean smallest distance",
- "Distance (nm)", "Residue Index", "Residue Index",
- nres, nres, resnr, resnr, totmdmat, 0, truncate, rlo, rhi, &nlevels);
+ write_xpm(opt2FILE("-mean", NFILE, fnm, "w"), 0, "Mean smallest distance", "Distance (nm)",
+ "Residue Index", "Residue Index", nres, nres, resnr, resnr, totmdmat, 0, truncate,
+ rlo, rhi, &nlevels);
if (bCalcN)
{
- char **legend;
+ char** legend;
snew(legend, 5);
for (i = 0; i < 5; i++)
snew(legend[i], STRLEN);
}
tot_nmat(nres, natoms, nframes, totnmat, tot_n, mean_n);
- fp = xvgropen(ftp2fn(efXVG, NFILE, fnm),
- "Increase in number of contacts", "Residue", "Ratio", oenv);
+ fp = xvgropen(ftp2fn(efXVG, NFILE, fnm), "Increase in number of contacts", "Residue",
+ "Ratio", oenv);
sprintf(legend[0], "Total/mean");
sprintf(legend[1], "Total");
sprintf(legend[2], "Mean");
}
else
{
- ratio = tot_n[i]/mean_n[i];
+ ratio = tot_n[i] / mean_n[i];
}
- fprintf(fp, "%3d %8.3f %3d %8.3f %3d %8.3f\n",
- i+1, ratio, tot_n[i], mean_n[i], natm[i], mean_n[i]/natm[i]);
+ fprintf(fp, "%3d %8.3f %3d %8.3f %3d %8.3f\n", i + 1, ratio, tot_n[i], mean_n[i],
+ natm[i], mean_n[i] / natm[i]);
}
xvgrclose(fp);
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff