2 * This file is part of the GROMACS molecular simulation package.
4 * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
5 * Copyright (c) 2001-2004, The GROMACS development team.
6 * Copyright (c) 2013,2014, by the GROMACS development team, led by
7 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
8 * and including many others, as listed in the AUTHORS file in the
9 * top-level source directory and at http://www.gromacs.org.
11 * GROMACS is free software; you can redistribute it and/or
12 * modify it under the terms of the GNU Lesser General Public License
13 * as published by the Free Software Foundation; either version 2.1
14 * of the License, or (at your option) any later version.
16 * GROMACS is distributed in the hope that it will be useful,
17 * but WITHOUT ANY WARRANTY; without even the implied warranty of
18 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
19 * Lesser General Public License for more details.
21 * You should have received a copy of the GNU Lesser General Public
22 * License along with GROMACS; if not, see
23 * http://www.gnu.org/licenses, or write to the Free Software Foundation,
24 * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
26 * If you want to redistribute modifications to GROMACS, please
27 * consider that scientific software is very special. Version
28 * control is crucial - bugs must be traceable. We will be happy to
29 * consider code for inclusion in the official distribution, but
30 * derived work must not be called official GROMACS. Details are found
31 * in the README & COPYING files - if they are missing, get the
32 * official version at http://www.gromacs.org.
34 * To help us fund GROMACS development, we humbly ask that you cite
35 * the research papers on the package. Check out http://www.gromacs.org.
42 #include "gromacs/commandline/pargs.h"
43 #include "gromacs/utility/smalloc.h"
45 #include "gromacs/fileio/confio.h"
46 #include "gromacs/utility/futil.h"
48 #include "gromacs/math/vec.h"
49 #include "gromacs/topology/index.h"
50 #include "gromacs/utility/cstringutil.h"
51 #include "gromacs/utility/fatalerror.h"
54 int gmx_genpr(int argc, char *argv[])
56 const char *desc[] = {
57 "[THISMODULE] produces an #include file for a topology containing",
58 "a list of atom numbers and three force constants for the",
59 "[IT]x[it]-, [IT]y[it]-, and [IT]z[it]-direction based on",
60 "the contents of the [TT]-f[tt] file. A single isotropic force constant may",
61 "be given on the command line instead of three components.[PAR]",
62 "WARNING: Position restraints are interactions within molecules, therefore",
63 "they must be included within the correct [TT][ moleculetype ][tt]",
64 "block in the topology. The atom indices within the",
65 "[TT][ position_restraints ][tt] block must be within the range of the",
66 "atom indices for that molecule type. Since the atom numbers in every",
67 "moleculetype in the topology start at 1 and the numbers in the input file",
68 "for [THISMODULE] number consecutively from 1, [THISMODULE] will only",
69 "produce a useful file for the first molecule. You may wish to",
70 "edit the resulting index file to remove the lines for later atoms,",
71 "or construct a suitable index group to provide",
72 "as input to [THISMODULE].[PAR]",
73 "The [TT]-of[tt] option produces an index file that can be used for",
74 "freezing atoms. In this case, the input file must be a [TT].pdb[tt] file.[PAR]",
75 "With the [TT]-disre[tt] option, half a matrix of distance restraints",
76 "is generated instead of position restraints. With this matrix, that",
77 "one typically would apply to C[GRK]alpha[grk] atoms in a protein, one can",
78 "maintain the overall conformation of a protein without tieing it to",
79 "a specific position (as with position restraints)."
81 static rvec fc = {1000.0, 1000.0, 1000.0};
82 static real freeze_level = 0.0;
83 static real disre_dist = 0.1;
84 static real disre_frac = 0.0;
85 static real disre_up2 = 1.0;
86 static gmx_bool bDisre = FALSE;
87 static gmx_bool bConstr = FALSE;
88 static real cutoff = -1.0;
91 { "-fc", FALSE, etRVEC, {fc},
92 "Force constants (kJ/mol nm^2)" },
93 { "-freeze", FALSE, etREAL, {&freeze_level},
94 "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" },
95 { "-disre", FALSE, etBOOL, {&bDisre},
96 "Generate a distance restraint matrix for all the atoms in index" },
97 { "-disre_dist", FALSE, etREAL, {&disre_dist},
98 "Distance range around the actual distance for generating distance restraints" },
99 { "-disre_frac", FALSE, etREAL, {&disre_frac},
100 "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." },
101 { "-disre_up2", FALSE, etREAL, {&disre_up2},
102 "Distance between upper bound for distance restraints, and the distance at which the force becomes constant (see manual)" },
103 { "-cutoff", FALSE, etREAL, {&cutoff},
104 "Only generate distance restraints for atoms pairs within cutoff (nm)" },
105 { "-constr", FALSE, etBOOL, {&bConstr},
106 "Generate a constraint matrix rather than distance restraints. Constraints of type 2 will be generated that do generate exclusions." }
108 #define npargs asize(pa)
111 t_atoms *atoms = NULL;
117 const char *xfn, *nfn;
122 rvec dx, *x = NULL, *v = NULL;
125 { efSTX, "-f", NULL, ffREAD },
126 { efNDX, "-n", NULL, ffOPTRD },
127 { efITP, "-o", "posre", ffWRITE },
128 { efNDX, "-of", "freeze", ffOPTWR }
130 #define NFILE asize(fnm)
132 if (!parse_common_args(&argc, argv, 0, NFILE, fnm, npargs, pa,
133 asize(desc), desc, 0, NULL, &oenv))
138 bFreeze = opt2bSet("-of", NFILE, fnm) || opt2parg_bSet("-freeze", asize(pa), pa);
139 bDisre = bDisre || opt2parg_bSet("-disre_dist", npargs, pa);
140 xfn = opt2fn_null("-f", NFILE, fnm);
141 nfn = opt2fn_null("-n", NFILE, fnm);
143 if (( nfn == NULL ) && ( xfn == NULL))
145 gmx_fatal(FARGS, "no index file and no structure file supplied");
148 if ((disre_frac < 0) || (disre_frac >= 1))
150 gmx_fatal(FARGS, "disre_frac should be between 0 and 1");
154 gmx_fatal(FARGS, "disre_dist should be >= 0");
160 get_stx_coordnum(xfn, &(atoms->nr));
161 init_t_atoms(atoms, atoms->nr, TRUE);
164 fprintf(stderr, "\nReading structure file\n");
165 read_stx_conf(xfn, title, atoms, x, v, NULL, box);
170 if (!atoms || !atoms->pdbinfo)
172 gmx_fatal(FARGS, "No B-factors in input file %s, use a pdb file next time.",
176 out = opt2FILE("-of", NFILE, fnm, "w");
177 fprintf(out, "[ freeze ]\n");
178 for (i = 0; (i < atoms->nr); i++)
180 if (atoms->pdbinfo[i].bfac <= freeze_level)
182 fprintf(out, "%d\n", i+1);
187 else if ((bDisre || bConstr) && x)
189 printf("Select group to generate %s matrix from\n",
190 bConstr ? "constraint" : "distance restraint");
191 get_index(atoms, nfn, 1, &igrp, &ind_grp, &gn_grp);
193 out = ftp2FILE(efITP, NFILE, fnm, "w");
196 fprintf(out, "; constraints for %s of %s\n\n", gn_grp, title);
197 fprintf(out, "[ constraints ]\n");
198 fprintf(out, ";%4s %5s %1s %10s\n", "i", "j", "tp", "dist");
202 fprintf(out, "; distance restraints for %s of %s\n\n", gn_grp, title);
203 fprintf(out, "[ distance_restraints ]\n");
204 fprintf(out, ";%4s %5s %1s %5s %10s %10s %10s %10s %10s\n", "i", "j", "?",
205 "label", "funct", "lo", "up1", "up2", "weight");
207 for (i = k = 0; i < igrp; i++)
209 for (j = i+1; j < igrp; j++, k++)
211 rvec_sub(x[ind_grp[i]], x[ind_grp[j]], dx);
215 fprintf(out, "%5d %5d %1d %10g\n", ind_grp[i]+1, ind_grp[j]+1, 2, d);
219 if (cutoff < 0 || d < cutoff)
223 dd = min(disre_dist, disre_frac*d);
231 fprintf(out, "%5d %5d %1d %5d %10d %10g %10g %10g %10g\n",
232 ind_grp[i]+1, ind_grp[j]+1, 1, k, 1,
233 lo, hi, hi+disre_up2, 1.0);
242 printf("Select group to position restrain\n");
243 get_index(atoms, nfn, 1, &igrp, &ind_grp, &gn_grp);
245 out = ftp2FILE(efITP, NFILE, fnm, "w");
246 fprintf(out, "; position restraints for %s of %s\n\n", gn_grp, title);
247 fprintf(out, "[ position_restraints ]\n");
248 fprintf(out, ";%3s %5s %9s %10s %10s\n", "i", "funct", "fcx", "fcy", "fcz");
249 for (i = 0; i < igrp; i++)
251 fprintf(out, "%4d %4d %10g %10g %10g\n",
252 ind_grp[i]+1, 1, fc[XX], fc[YY], fc[ZZ]);