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.
44 #include "gromacs/commandline/pargs.h"
45 #include "gromacs/utility/smalloc.h"
47 #include "gromacs/fileio/confio.h"
48 #include "gromacs/utility/futil.h"
50 #include "gromacs/math/vec.h"
51 #include "gromacs/topology/index.h"
52 #include "gromacs/utility/cstringutil.h"
53 #include "gromacs/utility/fatalerror.h"
56 int gmx_genpr(int argc, char *argv[])
58 const char *desc[] = {
59 "[THISMODULE] produces an #include file for a topology containing",
60 "a list of atom numbers and three force constants for the",
61 "[IT]x[it]-, [IT]y[it]-, and [IT]z[it]-direction based on",
62 "the contents of the [TT]-f[tt] file. A single isotropic force constant may",
63 "be given on the command line instead of three components.[PAR]",
64 "WARNING: Position restraints are interactions within molecules, therefore",
65 "they must be included within the correct [TT][ moleculetype ][tt]",
66 "block in the topology. The atom indices within the",
67 "[TT][ position_restraints ][tt] block must be within the range of the",
68 "atom indices for that molecule type. Since the atom numbers in every",
69 "moleculetype in the topology start at 1 and the numbers in the input file",
70 "for [THISMODULE] number consecutively from 1, [THISMODULE] will only",
71 "produce a useful file for the first molecule. You may wish to",
72 "edit the resulting index file to remove the lines for later atoms,",
73 "or construct a suitable index group to provide",
74 "as input to [THISMODULE].[PAR]",
75 "The [TT]-of[tt] option produces an index file that can be used for",
76 "freezing atoms. In this case, the input file must be a [TT].pdb[tt] file.[PAR]",
77 "With the [TT]-disre[tt] option, half a matrix of distance restraints",
78 "is generated instead of position restraints. With this matrix, that",
79 "one typically would apply to C[GRK]alpha[grk] atoms in a protein, one can",
80 "maintain the overall conformation of a protein without tieing it to",
81 "a specific position (as with position restraints)."
83 static rvec fc = {1000.0, 1000.0, 1000.0};
84 static real freeze_level = 0.0;
85 static real disre_dist = 0.1;
86 static real disre_frac = 0.0;
87 static real disre_up2 = 1.0;
88 static gmx_bool bDisre = FALSE;
89 static gmx_bool bConstr = FALSE;
90 static real cutoff = -1.0;
93 { "-fc", FALSE, etRVEC, {fc},
94 "Force constants (kJ/mol nm^2)" },
95 { "-freeze", FALSE, etREAL, {&freeze_level},
96 "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" },
97 { "-disre", FALSE, etBOOL, {&bDisre},
98 "Generate a distance restraint matrix for all the atoms in index" },
99 { "-disre_dist", FALSE, etREAL, {&disre_dist},
100 "Distance range around the actual distance for generating distance restraints" },
101 { "-disre_frac", FALSE, etREAL, {&disre_frac},
102 "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." },
103 { "-disre_up2", FALSE, etREAL, {&disre_up2},
104 "Distance between upper bound for distance restraints, and the distance at which the force becomes constant (see manual)" },
105 { "-cutoff", FALSE, etREAL, {&cutoff},
106 "Only generate distance restraints for atoms pairs within cutoff (nm)" },
107 { "-constr", FALSE, etBOOL, {&bConstr},
108 "Generate a constraint matrix rather than distance restraints. Constraints of type 2 will be generated that do generate exclusions." }
110 #define npargs asize(pa)
113 t_atoms *atoms = NULL;
119 const char *xfn, *nfn;
124 rvec dx, *x = NULL, *v = NULL;
127 { efSTX, "-f", NULL, ffREAD },
128 { efNDX, "-n", NULL, ffOPTRD },
129 { efITP, "-o", "posre", ffWRITE },
130 { efNDX, "-of", "freeze", ffOPTWR }
132 #define NFILE asize(fnm)
134 if (!parse_common_args(&argc, argv, 0, NFILE, fnm, npargs, pa,
135 asize(desc), desc, 0, NULL, &oenv))
140 bFreeze = opt2bSet("-of", NFILE, fnm) || opt2parg_bSet("-freeze", asize(pa), pa);
141 bDisre = bDisre || opt2parg_bSet("-disre_dist", npargs, pa);
142 xfn = opt2fn_null("-f", NFILE, fnm);
143 nfn = opt2fn_null("-n", NFILE, fnm);
145 if (( nfn == NULL ) && ( xfn == NULL))
147 gmx_fatal(FARGS, "no index file and no structure file supplied");
150 if ((disre_frac < 0) || (disre_frac >= 1))
152 gmx_fatal(FARGS, "disre_frac should be between 0 and 1");
156 gmx_fatal(FARGS, "disre_dist should be >= 0");
162 get_stx_coordnum(xfn, &(atoms->nr));
163 init_t_atoms(atoms, atoms->nr, TRUE);
166 fprintf(stderr, "\nReading structure file\n");
167 read_stx_conf(xfn, title, atoms, x, v, NULL, box);
172 if (!atoms || !atoms->pdbinfo)
174 gmx_fatal(FARGS, "No B-factors in input file %s, use a pdb file next time.",
178 out = opt2FILE("-of", NFILE, fnm, "w");
179 fprintf(out, "[ freeze ]\n");
180 for (i = 0; (i < atoms->nr); i++)
182 if (atoms->pdbinfo[i].bfac <= freeze_level)
184 fprintf(out, "%d\n", i+1);
189 else if ((bDisre || bConstr) && x)
191 printf("Select group to generate %s matrix from\n",
192 bConstr ? "constraint" : "distance restraint");
193 get_index(atoms, nfn, 1, &igrp, &ind_grp, &gn_grp);
195 out = ftp2FILE(efITP, NFILE, fnm, "w");
198 fprintf(out, "; constraints for %s of %s\n\n", gn_grp, title);
199 fprintf(out, "[ constraints ]\n");
200 fprintf(out, ";%4s %5s %1s %10s\n", "i", "j", "tp", "dist");
204 fprintf(out, "; distance restraints for %s of %s\n\n", gn_grp, title);
205 fprintf(out, "[ distance_restraints ]\n");
206 fprintf(out, ";%4s %5s %1s %5s %10s %10s %10s %10s %10s\n", "i", "j", "?",
207 "label", "funct", "lo", "up1", "up2", "weight");
209 for (i = k = 0; i < igrp; i++)
211 for (j = i+1; j < igrp; j++, k++)
213 rvec_sub(x[ind_grp[i]], x[ind_grp[j]], dx);
217 fprintf(out, "%5d %5d %1d %10g\n", ind_grp[i]+1, ind_grp[j]+1, 2, d);
221 if (cutoff < 0 || d < cutoff)
225 dd = min(disre_dist, disre_frac*d);
233 fprintf(out, "%5d %5d %1d %5d %10d %10g %10g %10g %10g\n",
234 ind_grp[i]+1, ind_grp[j]+1, 1, k, 1,
235 lo, hi, hi+disre_up2, 1.0);
244 printf("Select group to position restrain\n");
245 get_index(atoms, nfn, 1, &igrp, &ind_grp, &gn_grp);
247 out = ftp2FILE(efITP, NFILE, fnm, "w");
248 fprintf(out, "; position restraints for %s of %s\n\n", gn_grp, title);
249 fprintf(out, "[ position_restraints ]\n");
250 fprintf(out, ";%3s %5s %9s %10s %10s\n", "i", "funct", "fcx", "fcy", "fcz");
251 for (i = 0; i < igrp; i++)
253 fprintf(out, "%4d %4d %10g %10g %10g\n",
254 ind_grp[i]+1, 1, fc[XX], fc[YY], fc[ZZ]);