src/gromacs/gmxpreprocess/add_par.cpp

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
   5  * Copyright (c) 2001-2004, The GROMACS development team.
   6  * Copyright (c) 2011,2014,2015,2017, 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.
  10  *
  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.
  15  *
  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.
  20  *
  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.
  25  *
  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.
  33  *
  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.
  36  */
  37 /* This file is completely threadsafe - keep it that way! */
  38 #include "gmxpre.h"
  39
  40 #include "add_par.h"
  41
  42 #include <string.h>
  43
  44 #include <algorithm>
  45
  46 #include "gromacs/gmxpreprocess/grompp-impl.h"
  47 #include "gromacs/gmxpreprocess/hackblock.h"
  48 #include "gromacs/gmxpreprocess/notset.h"
  49 #include "gromacs/gmxpreprocess/toputil.h"
  50 #include "gromacs/utility/cstringutil.h"
  51 #include "gromacs/utility/fatalerror.h"
  52 #include "gromacs/utility/smalloc.h"
  53
  54 static void clear_atom_list(int i0, int a[])
  55 {
  56     int i;
  57
  58     for (i = i0; i < MAXATOMLIST; i++)
  59     {
  60         a[i] = -1;
  61     }
  62 }
  63
  64 static void clear_force_param(int i0, real c[])
  65 {
  66     int i;
  67
  68     for (i = i0; i < MAXFORCEPARAM; i++)
  69     {
  70         c[i] = NOTSET;
  71     }
  72 }
  73
  74 void add_param(t_params *ps, int ai, int aj, real *c, char *s)
  75 {
  76     int i;
  77
  78     if ((ai < 0) || (aj < 0))
  79     {
  80         gmx_fatal(FARGS, "Trying to add impossible atoms: ai=%d, aj=%d", ai, aj);
  81     }
  82     pr_alloc(1, ps);
  83     ps->param[ps->nr].ai() = ai;
  84     ps->param[ps->nr].aj() = aj;
  85     clear_atom_list(2, ps->param[ps->nr].a);
  86     if (c == nullptr)
  87     {
  88         clear_force_param(0, ps->param[ps->nr].c);
  89     }
  90     else
  91     {
  92         for (i = 0; (i < MAXFORCEPARAM); i++)
  93         {
  94             ps->param[ps->nr].c[i] = c[i];
  95         }
  96     }
  97     set_p_string(&(ps->param[ps->nr]), s);
  98     ps->nr++;
  99 }
 100
 101 void add_imp_param(t_params *ps, int ai, int aj, int ak, int al, real c0, real c1,
 102                    char *s)
 103 {
 104     pr_alloc(1, ps);
 105     ps->param[ps->nr].ai() = ai;
 106     ps->param[ps->nr].aj() = aj;
 107     ps->param[ps->nr].ak() = ak;
 108     ps->param[ps->nr].al() = al;
 109     clear_atom_list  (4, ps->param[ps->nr].a);
 110     ps->param[ps->nr].c0() = c0;
 111     ps->param[ps->nr].c1() = c1;
 112     clear_force_param(2, ps->param[ps->nr].c);
 113     set_p_string(&(ps->param[ps->nr]), s);
 114     ps->nr++;
 115 }
 116
 117 void add_dih_param(t_params *ps, int ai, int aj, int ak, int al, real c0, real c1,
 118                    real c2, char *s)
 119 {
 120     pr_alloc(1, ps);
 121     ps->param[ps->nr].ai() = ai;
 122     ps->param[ps->nr].aj() = aj;
 123     ps->param[ps->nr].ak() = ak;
 124     ps->param[ps->nr].al() = al;
 125     clear_atom_list  (4, ps->param[ps->nr].a);
 126     ps->param[ps->nr].c0() = c0;
 127     ps->param[ps->nr].c1() = c1;
 128     ps->param[ps->nr].c2() = c2;
 129     clear_force_param(3, ps->param[ps->nr].c);
 130     set_p_string(&(ps->param[ps->nr]), s);
 131     ps->nr++;
 132 }
 133
 134 void add_cmap_param(t_params *ps, int ai, int aj, int ak, int al, int am, char *s)
 135 {
 136     pr_alloc(1, ps);
 137     ps->param[ps->nr].ai() = ai;
 138     ps->param[ps->nr].aj() = aj;
 139     ps->param[ps->nr].ak() = ak;
 140     ps->param[ps->nr].al() = al;
 141     ps->param[ps->nr].am() = am;
 142     clear_atom_list(5, ps->param[ps->nr].a);
 143     clear_force_param(0, ps->param[ps->nr].c);
 144     set_p_string(&(ps->param[ps->nr]), s);
 145     ps->nr++;
 146 }
 147
 148 void add_vsite2_atoms(t_params *ps, int ai, int aj, int ak)
 149 {
 150     pr_alloc(1, ps);
 151     ps->param[ps->nr].ai() = ai;
 152     ps->param[ps->nr].aj() = aj;
 153     ps->param[ps->nr].ak() = ak;
 154     clear_atom_list  (3, ps->param[ps->nr].a);
 155     clear_force_param(0, ps->param[ps->nr].c);
 156     set_p_string(&(ps->param[ps->nr]), "");
 157     ps->nr++;
 158 }
 159
 160 void add_vsite2_param(t_params *ps, int ai, int aj, int ak, real c0)
 161 {
 162     pr_alloc(1, ps);
 163     ps->param[ps->nr].ai() = ai;
 164     ps->param[ps->nr].aj() = aj;
 165     ps->param[ps->nr].ak() = ak;
 166     clear_atom_list  (3, ps->param[ps->nr].a);
 167     ps->param[ps->nr].c0() = c0;
 168     clear_force_param(1, ps->param[ps->nr].c);
 169     set_p_string(&(ps->param[ps->nr]), "");
 170     ps->nr++;
 171 }
 172
 173 void add_vsite3_param(t_params *ps, int ai, int aj, int ak, int al,
 174                       real c0, real c1)
 175 {
 176     pr_alloc(1, ps);
 177     ps->param[ps->nr].ai() = ai;
 178     ps->param[ps->nr].aj() = aj;
 179     ps->param[ps->nr].ak() = ak;
 180     ps->param[ps->nr].al() = al;
 181     clear_atom_list  (4, ps->param[ps->nr].a);
 182     ps->param[ps->nr].c0() = c0;
 183     ps->param[ps->nr].c1() = c1;
 184     clear_force_param(2, ps->param[ps->nr].c);
 185     set_p_string(&(ps->param[ps->nr]), "");
 186     ps->nr++;
 187 }
 188
 189 void add_vsite3_atoms(t_params *ps, int ai, int aj, int ak, int al, gmx_bool bSwapParity)
 190 {
 191     pr_alloc(1, ps);
 192     ps->param[ps->nr].ai() = ai;
 193     ps->param[ps->nr].aj() = aj;
 194     ps->param[ps->nr].ak() = ak;
 195     ps->param[ps->nr].al() = al;
 196     clear_atom_list  (4, ps->param[ps->nr].a);
 197     clear_force_param(0, ps->param[ps->nr].c);
 198     if (bSwapParity)
 199     {
 200         ps->param[ps->nr].c1() = -1;
 201     }
 202     set_p_string(&(ps->param[ps->nr]), "");
 203     ps->nr++;
 204 }
 205
 206 void add_vsite4_atoms(t_params *ps, int ai, int aj, int ak, int al, int am)
 207 {
 208     pr_alloc(1, ps);
 209     ps->param[ps->nr].ai() = ai;
 210     ps->param[ps->nr].aj() = aj;
 211     ps->param[ps->nr].ak() = ak;
 212     ps->param[ps->nr].al() = al;
 213     ps->param[ps->nr].am() = am;
 214     clear_atom_list  (5, ps->param[ps->nr].a);
 215     clear_force_param(0, ps->param[ps->nr].c);
 216     set_p_string(&(ps->param[ps->nr]), "");
 217     ps->nr++;
 218 }
 219
 220 int search_jtype(t_restp *rtp, char *name, gmx_bool bNterm)
 221 {
 222     int    niter, iter, j, jmax;
 223     size_t k, kmax, minstrlen;
 224     char  *rtpname, searchname[12];
 225
 226     strcpy(searchname, name);
 227
 228     /* Do a best match comparison */
 229     /* for protein N-terminus, allow renaming of H1, H2 and H3 to H */
 230     if (bNterm && (strlen(searchname) == 2) && (searchname[0] == 'H') &&
 231         ( (searchname[1] == '1') || (searchname[1] == '2') ||
 232           (searchname[1] == '3') ) )
 233     {
 234         niter = 2;
 235     }
 236     else
 237     {
 238         niter = 1;
 239     }
 240     kmax = 0;
 241     jmax = -1;
 242     for (iter = 0; (iter < niter && jmax == -1); iter++)
 243     {
 244         if (iter == 1)
 245         {
 246             /* Try without the hydrogen number in the N-terminus */
 247             searchname[1] = '\0';
 248         }
 249         for (j = 0; (j < rtp->natom); j++)
 250         {
 251             rtpname = *(rtp->atomname[j]);
 252             if (gmx_strcasecmp(searchname, rtpname) == 0)
 253             {
 254                 jmax = j;
 255                 kmax = strlen(searchname);
 256                 break;
 257             }
 258             if (iter == niter - 1)
 259             {
 260                 minstrlen = std::min(strlen(searchname), strlen(rtpname));
 261                 for (k = 0; k < minstrlen; k++)
 262                 {
 263                     if (searchname[k] != rtpname[k])
 264                     {
 265                         break;
 266                     }
 267                 }
 268                 if (k > kmax)
 269                 {
 270                     kmax = k;
 271                     jmax = j;
 272                 }
 273             }
 274         }
 275     }
 276     if (jmax == -1)
 277     {
 278         gmx_fatal(FARGS, "Atom %s not found in rtp database in residue %s",
 279                   searchname, rtp->resname);
 280     }
 281     if (kmax != strlen(searchname))
 282     {
 283         gmx_fatal(FARGS, "Atom %s not found in rtp database in residue %s, "
 284                   "it looks a bit like %s",
 285                   searchname, rtp->resname, *(rtp->atomname[jmax]));
 286     }
 287     return jmax;
 288 }