#include "gromacs/utility/futil.h"
#include "gromacs/utility/smalloc.h"
-int gmx_genrestr(int argc, char *argv[])
+int gmx_genrestr(int argc, char* argv[])
{
- const char *desc[] = {
+ const char* desc[] = {
"[THISMODULE] produces an #include file for a topology containing",
"a list of atom numbers and three force constants for the",
"[IT]x[it]-, [IT]y[it]-, and [IT]z[it]-direction based on",
"maintain the overall conformation of a protein without tieing it to",
"a specific position (as with position restraints)."
};
- static rvec fc = {1000.0, 1000.0, 1000.0};
- static real freeze_level = 0.0;
- static real disre_dist = 0.1;
- static real disre_frac = 0.0;
- static real disre_up2 = 1.0;
- static gmx_bool bDisre = FALSE;
- static gmx_bool bConstr = FALSE;
- static real cutoff = -1.0;
+ static rvec fc = { 1000.0, 1000.0, 1000.0 };
+ static real freeze_level = 0.0;
+ static real disre_dist = 0.1;
+ static real disre_frac = 0.0;
+ static real disre_up2 = 1.0;
+ static gmx_bool bDisre = FALSE;
+ static gmx_bool bConstr = FALSE;
+ static real cutoff = -1.0;
- t_pargs pa[] = {
- { "-fc", FALSE, etRVEC, {fc},
- "Force constants (kJ/mol nm^2)" },
- { "-freeze", FALSE, etREAL, {&freeze_level},
- "If the [TT]-of[tt] option or this one is given an index file will be written containing atom numbers of all atoms that have a B-factor less than the level given here" },
- { "-disre", FALSE, etBOOL, {&bDisre},
+ t_pargs pa[] = {
+ { "-fc", FALSE, etRVEC, { fc }, "Force constants (kJ/mol nm^2)" },
+ { "-freeze",
+ FALSE,
+ etREAL,
+ { &freeze_level },
+ "If the [TT]-of[tt] option or this one is given an index file will be written containing "
+ "atom numbers of all atoms that have a B-factor less than the level given here" },
+ { "-disre",
+ FALSE,
+ etBOOL,
+ { &bDisre },
"Generate a distance restraint matrix for all the atoms in index" },
- { "-disre_dist", FALSE, etREAL, {&disre_dist},
+ { "-disre_dist",
+ FALSE,
+ etREAL,
+ { &disre_dist },
"Distance range around the actual distance for generating distance restraints" },
- { "-disre_frac", FALSE, etREAL, {&disre_frac},
- "Fraction of distance to be used as interval rather than a fixed distance. If the fraction of the distance that you specify here is less than the distance given in the previous option, that one is used instead." },
- { "-disre_up2", FALSE, etREAL, {&disre_up2},
- "Distance between upper bound for distance restraints, and the distance at which the force becomes constant (see manual)" },
- { "-cutoff", FALSE, etREAL, {&cutoff},
+ { "-disre_frac",
+ FALSE,
+ etREAL,
+ { &disre_frac },
+ "Fraction of distance to be used as interval rather than a fixed distance. If the "
+ "fraction of the distance that you specify here is less than the distance given in the "
+ "previous option, that one is used instead." },
+ { "-disre_up2",
+ FALSE,
+ etREAL,
+ { &disre_up2 },
+ "Distance between upper bound for distance restraints, and the distance at which the "
+ "force becomes constant (see manual)" },
+ { "-cutoff",
+ FALSE,
+ etREAL,
+ { &cutoff },
"Only generate distance restraints for atoms pairs within cutoff (nm)" },
- { "-constr", FALSE, etBOOL, {&bConstr},
- "Generate a constraint matrix rather than distance restraints. Constraints of type 2 will be generated that do generate exclusions." }
+ { "-constr",
+ FALSE,
+ etBOOL,
+ { &bConstr },
+ "Generate a constraint matrix rather than distance restraints. Constraints of type 2 "
+ "will be generated that do generate exclusions." }
};
#define npargs asize(pa)
- gmx_output_env_t *oenv;
+ gmx_output_env_t* oenv;
t_atoms atoms;
int i, j, k;
- FILE *out;
+ FILE* out;
int igrp;
real d, dd, lo, hi;
- int *ind_grp;
- const char *xfn, *nfn;
- char *gn_grp;
+ int* ind_grp;
+ const char * xfn, *nfn;
+ char* gn_grp;
matrix box;
gmx_bool bFreeze;
rvec dx, *x = nullptr, *v = nullptr;
- t_filenm fnm[] = {
- { efSTX, "-f", nullptr, ffREAD },
- { efNDX, "-n", nullptr, ffOPTRD },
- { efITP, "-o", "posre", ffWRITE },
- { efNDX, "-of", "freeze", ffOPTWR }
- };
+ t_filenm fnm[] = { { efSTX, "-f", nullptr, ffREAD },
+ { efNDX, "-n", nullptr, ffOPTRD },
+ { efITP, "-o", "posre", ffWRITE },
+ { efNDX, "-of", "freeze", ffOPTWR } };
#define NFILE asize(fnm)
- if (!parse_common_args(&argc, argv, 0, NFILE, fnm, npargs, pa,
- asize(desc), desc, 0, nullptr, &oenv))
+ if (!parse_common_args(&argc, argv, 0, NFILE, fnm, npargs, pa, asize(desc), desc, 0, nullptr, &oenv))
{
return 0;
}
xfn = opt2fn_null("-f", NFILE, fnm);
nfn = opt2fn_null("-n", NFILE, fnm);
- if (( nfn == nullptr ) && ( xfn == nullptr))
+ if ((nfn == nullptr) && (xfn == nullptr))
{
gmx_fatal(FARGS, "no index file and no structure file supplied");
}
gmx_fatal(FARGS, "disre_dist should be >= 0");
}
- const char *title = "";
+ const char* title = "";
bool haveTopology = false;
if (xfn != nullptr)
{
{
if (!haveTopology || !atoms.pdbinfo)
{
- gmx_fatal(FARGS, "No B-factors in input file %s, use a pdb file next time.",
- xfn);
+ gmx_fatal(FARGS, "No B-factors in input file %s, use a pdb file next time.", xfn);
}
out = opt2FILE("-of", NFILE, fnm, "w");
{
if (atoms.pdbinfo[i].bfac <= freeze_level)
{
- fprintf(out, "%d\n", i+1);
+ fprintf(out, "%d\n", i + 1);
}
}
gmx_ffclose(out);
}
else if ((bDisre || bConstr) && x)
{
- printf("Select group to generate %s matrix from\n",
- bConstr ? "constraint" : "distance restraint");
+ printf("Select group to generate %s matrix from\n", bConstr ? "constraint" : "distance restraint");
get_index(&atoms, nfn, 1, &igrp, &ind_grp, &gn_grp);
out = ftp2FILE(efITP, NFILE, fnm, "w");
{
fprintf(out, "; distance restraints for %s of %s\n\n", gn_grp, title);
fprintf(out, "[ distance_restraints ]\n");
- fprintf(out, ";%4s %5s %1s %5s %10s %10s %10s %10s %10s\n", "i", "j", "?",
- "label", "funct", "lo", "up1", "up2", "weight");
+ fprintf(out, ";%4s %5s %1s %5s %10s %10s %10s %10s %10s\n", "i", "j", "?", "label",
+ "funct", "lo", "up1", "up2", "weight");
}
for (i = k = 0; i < igrp; i++)
{
- for (j = i+1; j < igrp; j++, k++)
+ for (j = i + 1; j < igrp; j++, k++)
{
rvec_sub(x[ind_grp[i]], x[ind_grp[j]], dx);
d = norm(dx);
if (bConstr)
{
- fprintf(out, "%5d %5d %1d %10g\n", ind_grp[i]+1, ind_grp[j]+1, 2, d);
+ fprintf(out, "%5d %5d %1d %10g\n", ind_grp[i] + 1, ind_grp[j] + 1, 2, d);
}
else
{
{
if (disre_frac > 0)
{
- dd = std::min(disre_dist, disre_frac*d);
+ dd = std::min(disre_dist, disre_frac * d);
}
else
{
dd = disre_dist;
}
- lo = std::max(0.0_real, d-dd);
- hi = d+dd;
- fprintf(out, "%5d %5d %1d %5d %10d %10g %10g %10g %10g\n",
- ind_grp[i]+1, ind_grp[j]+1, 1, k, 1,
- lo, hi, hi+disre_up2, 1.0);
+ lo = std::max(0.0_real, d - dd);
+ hi = d + dd;
+ fprintf(out, "%5d %5d %1d %5d %10d %10g %10g %10g %10g\n", ind_grp[i] + 1,
+ ind_grp[j] + 1, 1, k, 1, lo, hi, hi + disre_up2, 1.0);
}
}
}
fprintf(out, ";%3s %5s %9s %10s %10s\n", "i", "funct", "fcx", "fcy", "fcz");
for (i = 0; i < igrp; i++)
{
- fprintf(out, "%4d %4d %10g %10g %10g\n",
- ind_grp[i]+1, 1, fc[XX], fc[YY], fc[ZZ]);
+ fprintf(out, "%4d %4d %10g %10g %10g\n", ind_grp[i] + 1, 1, fc[XX], fc[YY], fc[ZZ]);
}
gmx_ffclose(out);
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff