src/gromacs/gmxpreprocess/nm2type.c

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  37 /* This file is completely threadsafe - keep it that way! */
  38 #ifdef HAVE_CONFIG_H
  39 #include <config.h>
  40 #endif
  41
  42 #include <string.h>
  43
  44 #include "gromacs/math/utilities.h"
  45 #include "macros.h"
  46 #include "bondf.h"
  47 #include "gromacs/utility/cstringutil.h"
  48 #include "gromacs/utility/smalloc.h"
  49 #include "gromacs/fileio/confio.h"
  50 #include "gromacs/math/vec.h"
  51 #include "gromacs/math/3dview.h"
  52 #include "txtdump.h"
  53 #include "readinp.h"
  54 #include "names.h"
  55 #include "toppush.h"
  56 #include "pdb2top.h"
  57 #include "gpp_nextnb.h"
  58 #include "gpp_atomtype.h"
  59 #include "fflibutil.h"
  60
  61 #include "nm2type.h"
  62
  63 #include "gromacs/utility/fatalerror.h"
  64
  65 static void rd_nm2type_file(const char *fn, int *nnm, t_nm2type **nmp)
  66 {
  67     FILE         *fp;
  68     gmx_bool      bCont;
  69     char          libfilename[128];
  70     char          format[128], f1[128];
  71     char          buf[1024], elem[16], type[16], nbbuf[16], **newbuf;
  72     int           i, nb, nnnm, line = 1;
  73     double        qq, mm, *blen;
  74     t_nm2type    *nm2t = NULL;
  75
  76     fp = fflib_open(fn);
  77     if (NULL == fp)
  78     {
  79         gmx_fatal(FARGS, "Can not find %s in library directory", fn);
  80     }
  81
  82     nnnm = *nnm;
  83     nm2t = *nmp;
  84     do
  85     {
  86         /* Read a line from the file */
  87         bCont = (fgets2(buf, 1023, fp) != NULL);
  88
  89         if (bCont)
  90         {
  91             /* Remove comment */
  92             strip_comment(buf);
  93             if (sscanf(buf, "%s%s%lf%lf%d", elem, type, &qq, &mm, &nb) == 5)
  94             {
  95                 /* If we can read the first four, there probably is more */
  96                 srenew(nm2t, nnnm+1);
  97                 snew(nm2t[nnnm].blen, nb);
  98                 if (nb > 0)
  99                 {
 100                     snew(newbuf, nb);
 101                     strcpy(format, "%*s%*s%*s%*s%*s");
 102                     for (i = 0; (i < nb); i++)
 103                     {
 104                         /* Complicated format statement */
 105                         strcpy(f1, format);
 106                         strcat(f1, "%s%lf");
 107                         if (sscanf(buf, f1, nbbuf, &(nm2t[nnnm].blen[i])) != 2)
 108                         {
 109                             gmx_fatal(FARGS, "Error on line %d of %s", line, libfilename);
 110                         }
 111                         newbuf[i] = strdup(nbbuf);
 112                         strcat(format, "%*s%*s");
 113                     }
 114                 }
 115                 else
 116                 {
 117                     newbuf = NULL;
 118                 }
 119                 nm2t[nnnm].elem   = strdup(elem);
 120                 nm2t[nnnm].type   = strdup(type);
 121                 nm2t[nnnm].q      = qq;
 122                 nm2t[nnnm].m      = mm;
 123                 nm2t[nnnm].nbonds = nb;
 124                 nm2t[nnnm].bond   = newbuf;
 125                 nnnm++;
 126             }
 127             line++;
 128         }
 129     }
 130     while (bCont);
 131     gmx_ffclose(fp);
 132
 133     *nnm = nnnm;
 134     *nmp = nm2t;
 135 }
 136
 137 t_nm2type *rd_nm2type(const char *ffdir, int *nnm)
 138 {
 139     int        nff, f;
 140     char     **ff;
 141     t_nm2type *nm;
 142
 143     nff  = fflib_search_file_end(ffdir, ".n2t", FALSE, &ff);
 144     *nnm = 0;
 145     nm   = NULL;
 146     for (f = 0; f < nff; f++)
 147     {
 148         rd_nm2type_file(ff[f], nnm, &nm);
 149         sfree(ff[f]);
 150     }
 151     sfree(ff);
 152
 153     return nm;
 154 }
 155
 156 void dump_nm2type(FILE *fp, int nnm, t_nm2type nm2t[])
 157 {
 158     int i, j;
 159
 160     fprintf(fp, "; nm2type database\n");
 161     for (i = 0; (i < nnm); i++)
 162     {
 163         fprintf(fp, "%-8s %-8s %8.4f %8.4f %-4d",
 164                 nm2t[i].elem, nm2t[i].type,
 165                 nm2t[i].q, nm2t[i].m, nm2t[i].nbonds);
 166         for (j = 0; (j < nm2t[i].nbonds); j++)
 167         {
 168             fprintf(fp, " %-5s %6.4f", nm2t[i].bond[j], nm2t[i].blen[j]);
 169         }
 170         fprintf(fp, "\n");
 171     }
 172 }
 173
 174 enum {
 175     ematchNone, ematchWild, ematchElem, ematchExact, ematchNR
 176 };
 177
 178 static int match_str(const char *atom, const char *template_string)
 179 {
 180     if (!atom || !template_string)
 181     {
 182         return ematchNone;
 183     }
 184     else if (gmx_strcasecmp(atom, template_string) == 0)
 185     {
 186         return ematchExact;
 187     }
 188     else if (atom[0] == template_string[0])
 189     {
 190         return ematchElem;
 191     }
 192     else if (strcmp(template_string, "*") == 0)
 193     {
 194         return ematchWild;
 195     }
 196     else
 197     {
 198         return ematchNone;
 199     }
 200 }
 201
 202 int nm2type(int nnm, t_nm2type nm2t[], t_symtab *tab, t_atoms *atoms,
 203             gpp_atomtype_t atype, int *nbonds, t_params *bonds)
 204 {
 205     int      cur = 0;
 206 #define prev (1-cur)
 207     int      i, j, k, m, n, nresolved, nb, maxbond, ai, aj, best, im, nqual[2][ematchNR];
 208     int     *bbb, *n_mask, *m_mask, **match, **quality;
 209     char    *aname_i, *aname_m, *aname_n, *type;
 210     double   qq, mm;
 211     t_param *param;
 212
 213     snew(param, 1);
 214     maxbond = 0;
 215     for (i = 0; (i < atoms->nr); i++)
 216     {
 217         maxbond = max(maxbond, nbonds[i]);
 218     }
 219     if (debug)
 220     {
 221         fprintf(debug, "Max number of bonds per atom is %d\n", maxbond);
 222     }
 223     snew(bbb, maxbond);
 224     snew(n_mask, maxbond);
 225     snew(m_mask, maxbond);
 226     snew(match, maxbond);
 227     for (i = 0; (i < maxbond); i++)
 228     {
 229         snew(match[i], maxbond);
 230     }
 231
 232     nresolved = 0;
 233     for (i = 0; (i < atoms->nr); i++)
 234     {
 235         aname_i = *atoms->atomname[i];
 236         nb      = 0;
 237         for (j = 0; (j < bonds->nr); j++)
 238         {
 239             ai = bonds->param[j].AI;
 240             aj = bonds->param[j].AJ;
 241             if (ai == i)
 242             {
 243                 bbb[nb++] = aj;
 244             }
 245             else if (aj == i)
 246             {
 247                 bbb[nb++] = ai;
 248             }
 249         }
 250         if (nb != nbonds[i])
 251         {
 252             gmx_fatal(FARGS, "Counting number of bonds nb = %d, nbonds[%d] = %d",
 253                       nb, i, nbonds[i]);
 254         }
 255         if (debug)
 256         {
 257             fprintf(debug, "%4s has bonds to", aname_i);
 258             for (j = 0; (j < nb); j++)
 259             {
 260                 fprintf(debug, " %4s", *atoms->atomname[bbb[j]]);
 261             }
 262             fprintf(debug, "\n");
 263         }
 264         best = -1;
 265         for (k = 0; (k < ematchNR); k++)
 266         {
 267             nqual[prev][k] = 0;
 268         }
 269
 270         /* First check for names */
 271         for (k = 0; (k < nnm); k++)
 272         {
 273             if (nm2t[k].nbonds == nb)
 274             {
 275                 im = match_str(*atoms->atomname[i], nm2t[k].elem);
 276                 if (im > ematchWild)
 277                 {
 278                     for (j = 0; (j < ematchNR); j++)
 279                     {
 280                         nqual[cur][j] = 0;
 281                     }
 282
 283                     /* Fill a matrix with matching quality */
 284                     for (m = 0; (m < nb); m++)
 285                     {
 286                         aname_m = *atoms->atomname[bbb[m]];
 287                         for (n = 0; (n < nb); n++)
 288                         {
 289                             aname_n     = nm2t[k].bond[n];
 290                             match[m][n] = match_str(aname_m, aname_n);
 291                         }
 292                     }
 293                     /* Now pick the best matches */
 294                     for (m = 0; (m < nb); m++)
 295                     {
 296                         n_mask[m] = 0;
 297                         m_mask[m] = 0;
 298                     }
 299                     for (j = ematchNR-1; (j > 0); j--)
 300                     {
 301                         for (m = 0; (m < nb); m++)
 302                         {
 303                             for (n = 0; (n < nb); n++)
 304                             {
 305                                 if ((n_mask[n] == 0) &&
 306                                     (m_mask[m] == 0) &&
 307                                     (match[m][n] == j))
 308                                 {
 309                                     n_mask[n] = 1;
 310                                     m_mask[m] = 1;
 311                                     nqual[cur][j]++;
 312                                 }
 313                             }
 314                         }
 315                     }
 316                     if ((nqual[cur][ematchExact]+
 317                          nqual[cur][ematchElem]+
 318                          nqual[cur][ematchWild]) == nb)
 319                     {
 320                         if ((nqual[cur][ematchExact] > nqual[prev][ematchExact]) ||
 321
 322                             ((nqual[cur][ematchExact] == nqual[prev][ematchExact]) &&
 323                              (nqual[cur][ematchElem] > nqual[prev][ematchElem])) ||
 324
 325                             ((nqual[cur][ematchExact] == nqual[prev][ematchExact]) &&
 326                              (nqual[cur][ematchElem] == nqual[prev][ematchElem]) &&
 327                              (nqual[cur][ematchWild] > nqual[prev][ematchWild])))
 328                         {
 329                             best = k;
 330                             cur  = prev;
 331                         }
 332                     }
 333                 }
 334             }
 335         }
 336         if (best != -1)
 337         {
 338             int  atomnr = 0;
 339             real alpha  = 0;
 340
 341             qq   = nm2t[best].q;
 342             mm   = nm2t[best].m;
 343             type = nm2t[best].type;
 344
 345             if ((k = get_atomtype_type(type, atype)) == NOTSET)
 346             {
 347                 atoms->atom[i].qB = alpha;
 348                 atoms->atom[i].m  = atoms->atom[i].mB = mm;
 349                 k                 = add_atomtype(atype, tab, &(atoms->atom[i]), type, param,
 350                                                  atoms->atom[i].type, 0, 0, 0, atomnr, 0, 0);
 351             }
 352             atoms->atom[i].type  = k;
 353             atoms->atom[i].typeB = k;
 354             atoms->atom[i].q     = qq;
 355             atoms->atom[i].qB    = qq;
 356             atoms->atom[i].m     = mm;
 357             atoms->atom[i].mB    = mm;
 358             nresolved++;
 359         }
 360         else
 361         {
 362             fprintf(stderr, "Can not find forcefield for atom %s-%d with %d bonds\n",
 363                     *atoms->atomname[i], i+1, nb);
 364         }
 365     }
 366     sfree(bbb);
 367     sfree(n_mask);
 368     sfree(m_mask);
 369     sfree(param);
 370
 371     return nresolved;
 372 }