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43 #include "gromacs/commandline/pargs.h"
47 #include "gromacs/fileio/confio.h"
48 #include "gromacs/fileio/futil.h"
52 #include "gmx_fatal.h"
55 int gmx_genpr(int argc, char *argv[])
57 const char *desc[] = {
58 "[THISMODULE] produces an include file for a topology containing",
59 "a list of atom numbers and three force constants for the",
60 "[IT]x[it]-, [IT]y[it]-, and [IT]z[it]-direction. A single isotropic force constant may",
61 "be given on the command line instead of three components.[PAR]",
62 "WARNING: position restraints only work for the one molecule at a time.",
63 "Position restraints are interactions within molecules, therefore",
64 "they should be included within the correct [TT][ moleculetype ][tt]",
65 "block in the topology. Since the atom numbers in every moleculetype",
66 "in the topology start at 1 and the numbers in the input file for",
67 "[THISMODULE] number consecutively from 1, [THISMODULE] will only",
68 "produce a useful file for the first molecule.[PAR]",
69 "The [TT]-of[tt] option produces an index file that can be used for",
70 "freezing atoms. In this case, the input file must be a [TT].pdb[tt] file.[PAR]",
71 "With the [TT]-disre[tt] option, half a matrix of distance restraints",
72 "is generated instead of position restraints. With this matrix, that",
73 "one typically would apply to C[GRK]alpha[grk] atoms in a protein, one can",
74 "maintain the overall conformation of a protein without tieing it to",
75 "a specific position (as with position restraints)."
77 static rvec fc = {1000.0, 1000.0, 1000.0};
78 static real freeze_level = 0.0;
79 static real disre_dist = 0.1;
80 static real disre_frac = 0.0;
81 static real disre_up2 = 1.0;
82 static gmx_bool bDisre = FALSE;
83 static gmx_bool bConstr = FALSE;
84 static real cutoff = -1.0;
87 { "-fc", FALSE, etRVEC, {fc},
88 "Force constants (kJ/mol nm^2)" },
89 { "-freeze", FALSE, etREAL, {&freeze_level},
90 "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" },
91 { "-disre", FALSE, etBOOL, {&bDisre},
92 "Generate a distance restraint matrix for all the atoms in index" },
93 { "-disre_dist", FALSE, etREAL, {&disre_dist},
94 "Distance range around the actual distance for generating distance restraints" },
95 { "-disre_frac", FALSE, etREAL, {&disre_frac},
96 "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." },
97 { "-disre_up2", FALSE, etREAL, {&disre_up2},
98 "Distance between upper bound for distance restraints, and the distance at which the force becomes constant (see manual)" },
99 { "-cutoff", FALSE, etREAL, {&cutoff},
100 "Only generate distance restraints for atoms pairs within cutoff (nm)" },
101 { "-constr", FALSE, etBOOL, {&bConstr},
102 "Generate a constraint matrix rather than distance restraints. Constraints of type 2 will be generated that do generate exclusions." }
104 #define npargs asize(pa)
107 t_atoms *atoms = NULL;
113 const char *xfn, *nfn;
118 rvec dx, *x = NULL, *v = NULL;
121 { efSTX, "-f", NULL, ffREAD },
122 { efNDX, "-n", NULL, ffOPTRD },
123 { efITP, "-o", "posre", ffWRITE },
124 { efNDX, "-of", "freeze", ffOPTWR }
126 #define NFILE asize(fnm)
128 if (!parse_common_args(&argc, argv, 0, NFILE, fnm, npargs, pa,
129 asize(desc), desc, 0, NULL, &oenv))
134 bFreeze = opt2bSet("-of", NFILE, fnm) || opt2parg_bSet("-freeze", asize(pa), pa);
135 bDisre = bDisre || opt2parg_bSet("-disre_dist", npargs, pa);
136 xfn = opt2fn_null("-f", NFILE, fnm);
137 nfn = opt2fn_null("-n", NFILE, fnm);
139 if (( nfn == NULL ) && ( xfn == NULL))
141 gmx_fatal(FARGS, "no index file and no structure file supplied");
144 if ((disre_frac < 0) || (disre_frac >= 1))
146 gmx_fatal(FARGS, "disre_frac should be between 0 and 1");
150 gmx_fatal(FARGS, "disre_dist should be >= 0");
156 get_stx_coordnum(xfn, &(atoms->nr));
157 init_t_atoms(atoms, atoms->nr, TRUE);
160 fprintf(stderr, "\nReading structure file\n");
161 read_stx_conf(xfn, title, atoms, x, v, NULL, box);
166 if (!atoms || !atoms->pdbinfo)
168 gmx_fatal(FARGS, "No B-factors in input file %s, use a pdb file next time.",
172 out = opt2FILE("-of", NFILE, fnm, "w");
173 fprintf(out, "[ freeze ]\n");
174 for (i = 0; (i < atoms->nr); i++)
176 if (atoms->pdbinfo[i].bfac <= freeze_level)
178 fprintf(out, "%d\n", i+1);
183 else if ((bDisre || bConstr) && x)
185 printf("Select group to generate %s matrix from\n",
186 bConstr ? "constraint" : "distance restraint");
187 get_index(atoms, nfn, 1, &igrp, &ind_grp, &gn_grp);
189 out = ftp2FILE(efITP, NFILE, fnm, "w");
192 fprintf(out, "; constraints for %s of %s\n\n", gn_grp, title);
193 fprintf(out, "[ constraints ]\n");
194 fprintf(out, ";%4s %5s %1s %10s\n", "i", "j", "tp", "dist");
198 fprintf(out, "; distance restraints for %s of %s\n\n", gn_grp, title);
199 fprintf(out, "[ distance_restraints ]\n");
200 fprintf(out, ";%4s %5s %1s %5s %10s %10s %10s %10s %10s\n", "i", "j", "?",
201 "label", "funct", "lo", "up1", "up2", "weight");
203 for (i = k = 0; i < igrp; i++)
205 for (j = i+1; j < igrp; j++, k++)
207 rvec_sub(x[ind_grp[i]], x[ind_grp[j]], dx);
211 fprintf(out, "%5d %5d %1d %10g\n", ind_grp[i]+1, ind_grp[j]+1, 2, d);
215 if (cutoff < 0 || d < cutoff)
219 dd = min(disre_dist, disre_frac*d);
227 fprintf(out, "%5d %5d %1d %5d %10d %10g %10g %10g %10g\n",
228 ind_grp[i]+1, ind_grp[j]+1, 1, k, 1,
238 printf("Select group to position restrain\n");
239 get_index(atoms, nfn, 1, &igrp, &ind_grp, &gn_grp);
241 out = ftp2FILE(efITP, NFILE, fnm, "w");
242 fprintf(out, "; position restraints for %s of %s\n\n", gn_grp, title);
243 fprintf(out, "[ position_restraints ]\n");
244 fprintf(out, ";%3s %5s %9s %10s %10s\n", "i", "funct", "fcx", "fcy", "fcz");
245 for (i = 0; i < igrp; i++)
247 fprintf(out, "%4d %4d %10g %10g %10g\n",
248 ind_grp[i]+1, 1, fc[XX], fc[YY], fc[ZZ]);