src/gromacs/gmxpreprocess/add_par.c

   1 /*
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  37 /* This file is completely threadsafe - keep it that way! */
  38 #include "config.h"
  39
  40 #include <string.h>
  41 #include "typedefs.h"
  42 #include "gromacs/utility/smalloc.h"
  43 #include "grompp-impl.h"
  44 #include "macros.h"
  45 #include "toputil.h"
  46 #include "hackblock.h"
  47 #include "gromacs/utility/cstringutil.h"
  48 #include "gromacs/utility/fatalerror.h"
  49
  50 static void clear_atom_list(int i0, atom_id a[])
  51 {
  52     int i;
  53
  54     for (i = i0; i < MAXATOMLIST; i++)
  55     {
  56         a[i] = -1;
  57     }
  58 }
  59
  60 static void clear_force_param(int i0, real c[])
  61 {
  62     int i;
  63
  64     for (i = i0; i < MAXFORCEPARAM; i++)
  65     {
  66         c[i] = NOTSET;
  67     }
  68 }
  69
  70 void add_param(t_params *ps, int ai, int aj, real *c, char *s)
  71 {
  72     int i;
  73
  74     if ((ai < 0) || (aj < 0))
  75     {
  76         gmx_fatal(FARGS, "Trying to add impossible atoms: ai=%d, aj=%d", ai, aj);
  77     }
  78     pr_alloc(1, ps);
  79     ps->param[ps->nr].AI = ai;
  80     ps->param[ps->nr].AJ = aj;
  81     clear_atom_list(2, ps->param[ps->nr].a);
  82     if (c == NULL)
  83     {
  84         clear_force_param(0, ps->param[ps->nr].c);
  85     }
  86     else
  87     {
  88         for (i = 0; (i < MAXFORCEPARAM); i++)
  89         {
  90             ps->param[ps->nr].c[i] = c[i];
  91         }
  92     }
  93     set_p_string(&(ps->param[ps->nr]), s);
  94     ps->nr++;
  95 }
  96
  97 void add_imp_param(t_params *ps, int ai, int aj, int ak, int al, real c0, real c1,
  98                    char *s)
  99 {
 100     pr_alloc(1, ps);
 101     ps->param[ps->nr].AI = ai;
 102     ps->param[ps->nr].AJ = aj;
 103     ps->param[ps->nr].AK = ak;
 104     ps->param[ps->nr].AL = al;
 105     clear_atom_list  (4, ps->param[ps->nr].a);
 106     ps->param[ps->nr].C0 = c0;
 107     ps->param[ps->nr].C1 = c1;
 108     clear_force_param(2, ps->param[ps->nr].c);
 109     set_p_string(&(ps->param[ps->nr]), s);
 110     ps->nr++;
 111 }
 112
 113 void add_dih_param(t_params *ps, int ai, int aj, int ak, int al, real c0, real c1,
 114                    real c2, char *s)
 115 {
 116     pr_alloc(1, ps);
 117     ps->param[ps->nr].AI = ai;
 118     ps->param[ps->nr].AJ = aj;
 119     ps->param[ps->nr].AK = ak;
 120     ps->param[ps->nr].AL = al;
 121     clear_atom_list  (4, ps->param[ps->nr].a);
 122     ps->param[ps->nr].C0 = c0;
 123     ps->param[ps->nr].C1 = c1;
 124     ps->param[ps->nr].C2 = c2;
 125     clear_force_param(3, ps->param[ps->nr].c);
 126     set_p_string(&(ps->param[ps->nr]), s);
 127     ps->nr++;
 128 }
 129
 130 void add_cmap_param(t_params *ps, int ai, int aj, int ak, int al, int am, char *s)
 131 {
 132     pr_alloc(1, ps);
 133     ps->param[ps->nr].AI = ai;
 134     ps->param[ps->nr].AJ = aj;
 135     ps->param[ps->nr].AK = ak;
 136     ps->param[ps->nr].AL = al;
 137     ps->param[ps->nr].AM = am;
 138     clear_atom_list(5, ps->param[ps->nr].a);
 139     clear_force_param(0, ps->param[ps->nr].c);
 140     set_p_string(&(ps->param[ps->nr]), s);
 141     ps->nr++;
 142 }
 143
 144 void add_vsite2_atoms(t_params *ps, int ai, int aj, int ak)
 145 {
 146     pr_alloc(1, ps);
 147     ps->param[ps->nr].AI = ai;
 148     ps->param[ps->nr].AJ = aj;
 149     ps->param[ps->nr].AK = ak;
 150     clear_atom_list  (3, ps->param[ps->nr].a);
 151     clear_force_param(0, ps->param[ps->nr].c);
 152     set_p_string(&(ps->param[ps->nr]), "");
 153     ps->nr++;
 154 }
 155
 156 void add_vsite2_param(t_params *ps, int ai, int aj, int ak, real c0)
 157 {
 158     pr_alloc(1, ps);
 159     ps->param[ps->nr].AI = ai;
 160     ps->param[ps->nr].AJ = aj;
 161     ps->param[ps->nr].AK = ak;
 162     clear_atom_list  (3, ps->param[ps->nr].a);
 163     ps->param[ps->nr].C0 = c0;
 164     clear_force_param(1, ps->param[ps->nr].c);
 165     set_p_string(&(ps->param[ps->nr]), "");
 166     ps->nr++;
 167 }
 168
 169 void add_vsite3_param(t_params *ps, int ai, int aj, int ak, int al,
 170                       real c0, real c1)
 171 {
 172     pr_alloc(1, ps);
 173     ps->param[ps->nr].AI = ai;
 174     ps->param[ps->nr].AJ = aj;
 175     ps->param[ps->nr].AK = ak;
 176     ps->param[ps->nr].AL = al;
 177     clear_atom_list  (4, ps->param[ps->nr].a);
 178     ps->param[ps->nr].C0 = c0;
 179     ps->param[ps->nr].C1 = c1;
 180     clear_force_param(2, ps->param[ps->nr].c);
 181     set_p_string(&(ps->param[ps->nr]), "");
 182     ps->nr++;
 183 }
 184
 185 void add_vsite3_atoms(t_params *ps, int ai, int aj, int ak, int al, gmx_bool bSwapParity)
 186 {
 187     pr_alloc(1, ps);
 188     ps->param[ps->nr].AI = ai;
 189     ps->param[ps->nr].AJ = aj;
 190     ps->param[ps->nr].AK = ak;
 191     ps->param[ps->nr].AL = al;
 192     clear_atom_list  (4, ps->param[ps->nr].a);
 193     clear_force_param(0, ps->param[ps->nr].c);
 194     if (bSwapParity)
 195     {
 196         ps->param[ps->nr].C1 = -1;
 197     }
 198     set_p_string(&(ps->param[ps->nr]), "");
 199     ps->nr++;
 200 }
 201
 202 void add_vsite4_atoms(t_params *ps, int ai, int aj, int ak, int al, int am)
 203 {
 204     pr_alloc(1, ps);
 205     ps->param[ps->nr].AI = ai;
 206     ps->param[ps->nr].AJ = aj;
 207     ps->param[ps->nr].AK = ak;
 208     ps->param[ps->nr].AL = al;
 209     ps->param[ps->nr].AM = am;
 210     clear_atom_list  (5, ps->param[ps->nr].a);
 211     clear_force_param(0, ps->param[ps->nr].c);
 212     set_p_string(&(ps->param[ps->nr]), "");
 213     ps->nr++;
 214 }
 215
 216 int search_jtype(t_restp *rtp, char *name, gmx_bool bNterm)
 217 {
 218     int   niter, iter, j, k, kmax, jmax, minstrlen;
 219     char *rtpname, searchname[12];
 220
 221     strcpy(searchname, name);
 222
 223     /* Do a best match comparison */
 224     /* for protein N-terminus, allow renaming of H1, H2 and H3 to H */
 225     if (bNterm && (strlen(searchname) == 2) && (searchname[0] == 'H') &&
 226         ( (searchname[1] == '1') || (searchname[1] == '2') ||
 227           (searchname[1] == '3') ) )
 228     {
 229         niter = 2;
 230     }
 231     else
 232     {
 233         niter = 1;
 234     }
 235     kmax = 0;
 236     jmax = -1;
 237     for (iter = 0; (iter < niter && jmax == -1); iter++)
 238     {
 239         if (iter == 1)
 240         {
 241             /* Try without the hydrogen number in the N-terminus */
 242             searchname[1] = '\0';
 243         }
 244         for (j = 0; (j < rtp->natom); j++)
 245         {
 246             rtpname = *(rtp->atomname[j]);
 247             if (gmx_strcasecmp(searchname, rtpname) == 0)
 248             {
 249                 jmax = j;
 250                 kmax = strlen(searchname);
 251                 break;
 252             }
 253             if (iter == niter - 1)
 254             {
 255                 minstrlen = min(strlen(searchname), strlen(rtpname));
 256                 for (k = 0; k < minstrlen; k++)
 257                 {
 258                     if (searchname[k] != rtpname[k])
 259                     {
 260                         break;
 261                     }
 262                 }
 263                 if (k > kmax)
 264                 {
 265                     kmax = k;
 266                     jmax = j;
 267                 }
 268             }
 269         }
 270     }
 271     if (jmax == -1)
 272     {
 273         gmx_fatal(FARGS, "Atom %s not found in rtp database in residue %s",
 274                   searchname, rtp->resname);
 275     }
 276     if (kmax != strlen(searchname))
 277     {
 278         gmx_fatal(FARGS, "Atom %s not found in rtp database in residue %s, "
 279                   "it looks a bit like %s",
 280                   searchname, rtp->resname, *(rtp->atomname[jmax]));
 281     }
 282     return jmax;
 283 }