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43 #include "gromacs/commandline/pargs.h"
45 #include "gromacs/utility/smalloc.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 based on",
61 "the contents of the [TT]-f[tt] file. A single isotropic force constant may",
62 "be given on the command line instead of three components.[PAR]",
63 "WARNING: Position restraints are interactions within molecules, therefore",
64 "they must be included within the correct [TT][ moleculetype ][tt]",
65 "block in the topology. The atom indices within the",
66 "[TT][ position_restraints ][tt] block must be within the range of the",
67 "atom indices for that molecule type. Since the atom numbers in every",
68 "moleculetype in the topology start at 1 and the numbers in the input file",
69 "for [THISMODULE] number consecutively from 1, [THISMODULE] will only",
70 "produce a useful file for the first molecule. You may wish to",
71 "edit the resulting index file to remove the lines for later atoms,",
72 "or construct a suitable index group to provide",
73 "as input to [THISMODULE].[PAR]",
74 "The [TT]-of[tt] option produces an index file that can be used for",
75 "freezing atoms. In this case, the input file must be a [TT].pdb[tt] file.[PAR]",
76 "With the [TT]-disre[tt] option, half a matrix of distance restraints",
77 "is generated instead of position restraints. With this matrix, that",
78 "one typically would apply to C[GRK]alpha[grk] atoms in a protein, one can",
79 "maintain the overall conformation of a protein without tieing it to",
80 "a specific position (as with position restraints)."
82 static rvec fc = {1000.0, 1000.0, 1000.0};
83 static real freeze_level = 0.0;
84 static real disre_dist = 0.1;
85 static real disre_frac = 0.0;
86 static real disre_up2 = 1.0;
87 static gmx_bool bDisre = FALSE;
88 static gmx_bool bConstr = FALSE;
89 static real cutoff = -1.0;
92 { "-fc", FALSE, etRVEC, {fc},
93 "Force constants (kJ/mol nm^2)" },
94 { "-freeze", FALSE, etREAL, {&freeze_level},
95 "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" },
96 { "-disre", FALSE, etBOOL, {&bDisre},
97 "Generate a distance restraint matrix for all the atoms in index" },
98 { "-disre_dist", FALSE, etREAL, {&disre_dist},
99 "Distance range around the actual distance for generating distance restraints" },
100 { "-disre_frac", FALSE, etREAL, {&disre_frac},
101 "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." },
102 { "-disre_up2", FALSE, etREAL, {&disre_up2},
103 "Distance between upper bound for distance restraints, and the distance at which the force becomes constant (see manual)" },
104 { "-cutoff", FALSE, etREAL, {&cutoff},
105 "Only generate distance restraints for atoms pairs within cutoff (nm)" },
106 { "-constr", FALSE, etBOOL, {&bConstr},
107 "Generate a constraint matrix rather than distance restraints. Constraints of type 2 will be generated that do generate exclusions." }
109 #define npargs asize(pa)
112 t_atoms *atoms = NULL;
118 const char *xfn, *nfn;
123 rvec dx, *x = NULL, *v = NULL;
126 { efSTX, "-f", NULL, ffREAD },
127 { efNDX, "-n", NULL, ffOPTRD },
128 { efITP, "-o", "posre", ffWRITE },
129 { efNDX, "-of", "freeze", ffOPTWR }
131 #define NFILE asize(fnm)
133 if (!parse_common_args(&argc, argv, 0, NFILE, fnm, npargs, pa,
134 asize(desc), desc, 0, NULL, &oenv))
139 bFreeze = opt2bSet("-of", NFILE, fnm) || opt2parg_bSet("-freeze", asize(pa), pa);
140 bDisre = bDisre || opt2parg_bSet("-disre_dist", npargs, pa);
141 xfn = opt2fn_null("-f", NFILE, fnm);
142 nfn = opt2fn_null("-n", NFILE, fnm);
144 if (( nfn == NULL ) && ( xfn == NULL))
146 gmx_fatal(FARGS, "no index file and no structure file supplied");
149 if ((disre_frac < 0) || (disre_frac >= 1))
151 gmx_fatal(FARGS, "disre_frac should be between 0 and 1");
155 gmx_fatal(FARGS, "disre_dist should be >= 0");
161 get_stx_coordnum(xfn, &(atoms->nr));
162 init_t_atoms(atoms, atoms->nr, TRUE);
165 fprintf(stderr, "\nReading structure file\n");
166 read_stx_conf(xfn, title, atoms, x, v, NULL, box);
171 if (!atoms || !atoms->pdbinfo)
173 gmx_fatal(FARGS, "No B-factors in input file %s, use a pdb file next time.",
177 out = opt2FILE("-of", NFILE, fnm, "w");
178 fprintf(out, "[ freeze ]\n");
179 for (i = 0; (i < atoms->nr); i++)
181 if (atoms->pdbinfo[i].bfac <= freeze_level)
183 fprintf(out, "%d\n", i+1);
188 else if ((bDisre || bConstr) && x)
190 printf("Select group to generate %s matrix from\n",
191 bConstr ? "constraint" : "distance restraint");
192 get_index(atoms, nfn, 1, &igrp, &ind_grp, &gn_grp);
194 out = ftp2FILE(efITP, NFILE, fnm, "w");
197 fprintf(out, "; constraints for %s of %s\n\n", gn_grp, title);
198 fprintf(out, "[ constraints ]\n");
199 fprintf(out, ";%4s %5s %1s %10s\n", "i", "j", "tp", "dist");
203 fprintf(out, "; distance restraints for %s of %s\n\n", gn_grp, title);
204 fprintf(out, "[ distance_restraints ]\n");
205 fprintf(out, ";%4s %5s %1s %5s %10s %10s %10s %10s %10s\n", "i", "j", "?",
206 "label", "funct", "lo", "up1", "up2", "weight");
208 for (i = k = 0; i < igrp; i++)
210 for (j = i+1; j < igrp; j++, k++)
212 rvec_sub(x[ind_grp[i]], x[ind_grp[j]], dx);
216 fprintf(out, "%5d %5d %1d %10g\n", ind_grp[i]+1, ind_grp[j]+1, 2, d);
220 if (cutoff < 0 || d < cutoff)
224 dd = min(disre_dist, disre_frac*d);
232 fprintf(out, "%5d %5d %1d %5d %10d %10g %10g %10g %10g\n",
233 ind_grp[i]+1, ind_grp[j]+1, 1, k, 1,
243 printf("Select group to position restrain\n");
244 get_index(atoms, nfn, 1, &igrp, &ind_grp, &gn_grp);
246 out = ftp2FILE(efITP, NFILE, fnm, "w");
247 fprintf(out, "; position restraints for %s of %s\n\n", gn_grp, title);
248 fprintf(out, "[ position_restraints ]\n");
249 fprintf(out, ";%3s %5s %9s %10s %10s\n", "i", "funct", "fcx", "fcy", "fcz");
250 for (i = 0; i < igrp; i++)
252 fprintf(out, "%4d %4d %10g %10g %10g\n",
253 ind_grp[i]+1, 1, fc[XX], fc[YY], fc[ZZ]);