src/gromacs/gmxpreprocess/ter_db.cpp

   1 /*
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   3  *
   4  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
   5  * Copyright (c) 2001-2004, The GROMACS development team.
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   7  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
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  37 #include "gmxpre.h"
  38
  39 #include "ter_db.h"
  40
  41 #include <ctype.h>
  42 #include <string.h>
  43
  44 #include "gromacs/fileio/gmxfio.h"
  45 #include "gromacs/fileio/strdb.h"
  46 #include "gromacs/gmxpreprocess/fflibutil.h"
  47 #include "gromacs/gmxpreprocess/h_db.h"
  48 #include "gromacs/gmxpreprocess/notset.h"
  49 #include "gromacs/gmxpreprocess/resall.h"
  50 #include "gromacs/gmxpreprocess/toputil.h"
  51 #include "gromacs/legacyheaders/typedefs.h"
  52 #include "gromacs/utility/cstringutil.h"
  53 #include "gromacs/utility/fatalerror.h"
  54 #include "gromacs/utility/futil.h"
  55 #include "gromacs/utility/smalloc.h"
  56
  57 /* use bonded types definitions in hackblock.h */
  58 #define ekwRepl ebtsNR+1
  59 #define ekwAdd  ebtsNR+2
  60 #define ekwDel  ebtsNR+3
  61 #define ekwNR   3
  62 const char *kw_names[ekwNR] = {
  63     "replace", "add", "delete"
  64 };
  65
  66 int find_kw(char *keyw)
  67 {
  68     int i;
  69
  70     for (i = 0; i < ebtsNR; i++)
  71     {
  72         if (gmx_strcasecmp(btsNames[i], keyw) == 0)
  73         {
  74             return i;
  75         }
  76     }
  77     for (i = 0; i < ekwNR; i++)
  78     {
  79         if (gmx_strcasecmp(kw_names[i], keyw) == 0)
  80         {
  81             return ebtsNR + 1 + i;
  82         }
  83     }
  84
  85     return NOTSET;
  86 }
  87
  88 #define FATAL() gmx_fatal(FARGS, "Reading Termini Database: not enough items on line\n%s", line)
  89
  90 static void read_atom(char *line, gmx_bool bAdd,
  91                       char **nname, t_atom *a, gpp_atomtype_t atype, int *cgnr)
  92 {
  93     int    nr, i;
  94     char   buf[5][30];
  95     double m, q;
  96
  97     /* This code is messy, because of support for different formats:
  98      * for replace: [new name] <atom type> <m> <q> [cgnr (old format)]
  99      * for add:                <atom type> <m> <q> [cgnr]
 100      */
 101     nr = sscanf(line, "%s %s %s %s %s", buf[0], buf[1], buf[2], buf[3], buf[4]);
 102
 103     /* Here there an ambiguity due to the old replace format with cgnr,
 104      * which was read for years, but ignored in the rest of the code.
 105      * We have to assume that the atom type does not start with a digit
 106      * to make a line with 4 entries uniquely interpretable.
 107      */
 108     if (!bAdd && nr == 4 && isdigit(buf[1][0]))
 109     {
 110         nr = 3;
 111     }
 112
 113     if (nr < 3 || nr > 4)
 114     {
 115         gmx_fatal(FARGS, "Reading Termini Database: expected %d or %d items of atom data in stead of %d on line\n%s", 3, 4, nr, line);
 116     }
 117     i = 0;
 118     if (!bAdd)
 119     {
 120         if (nr == 4)
 121         {
 122             *nname = gmx_strdup(buf[i++]);
 123         }
 124         else
 125         {
 126             *nname = NULL;
 127         }
 128     }
 129     a->type = get_atomtype_type(buf[i++], atype);
 130     sscanf(buf[i++], "%lf", &m);
 131     a->m = m;
 132     sscanf(buf[i++], "%lf", &q);
 133     a->q = q;
 134     if (bAdd && nr == 4)
 135     {
 136         sscanf(buf[i++], "%d", cgnr);
 137     }
 138     else
 139     {
 140         *cgnr = NOTSET;
 141     }
 142 }
 143
 144 static void print_atom(FILE *out, t_atom *a, gpp_atomtype_t atype)
 145 {
 146     fprintf(out, "\t%s\t%g\t%g\n",
 147             get_atomtype_name(a->type, atype), a->m, a->q);
 148 }
 149
 150 static void print_ter_db(const char *ff, char C, int nb, t_hackblock tb[],
 151                          gpp_atomtype_t atype)
 152 {
 153     FILE *out;
 154     int   i, j, k, bt, nrepl, nadd, ndel;
 155     char  buf[STRLEN];
 156
 157     sprintf(buf, "%s-%c.tdb", ff, C);
 158     out = gmx_fio_fopen(buf, "w");
 159
 160     for (i = 0; (i < nb); i++)
 161     {
 162         fprintf(out, "[ %s ]\n", tb[i].name);
 163
 164         /* first count: */
 165         nrepl = 0;
 166         nadd  = 0;
 167         ndel  = 0;
 168         for (j = 0; j < tb[i].nhack; j++)
 169         {
 170             if (tb[i].hack[j].oname != NULL && tb[i].hack[j].nname != NULL)
 171             {
 172                 nrepl++;
 173             }
 174             else if (tb[i].hack[j].oname == NULL && tb[i].hack[j].nname != NULL)
 175             {
 176                 nadd++;
 177             }
 178             else if (tb[i].hack[j].oname != NULL && tb[i].hack[j].nname == NULL)
 179             {
 180                 ndel++;
 181             }
 182             else if (tb[i].hack[j].oname == NULL && tb[i].hack[j].nname == NULL)
 183             {
 184                 gmx_fatal(FARGS, "invalid hack (%s) in termini database", tb[i].name);
 185             }
 186         }
 187         if (nrepl)
 188         {
 189             fprintf(out, "[ %s ]\n", kw_names[ekwRepl-ebtsNR-1]);
 190             for (j = 0; j < tb[i].nhack; j++)
 191             {
 192                 if (tb[i].hack[j].oname != NULL && tb[i].hack[j].nname != NULL)
 193                 {
 194                     fprintf(out, "%s\t", tb[i].hack[j].oname);
 195                     print_atom(out, tb[i].hack[j].atom, atype);
 196                 }
 197             }
 198         }
 199         if (nadd)
 200         {
 201             fprintf(out, "[ %s ]\n", kw_names[ekwAdd-ebtsNR-1]);
 202             for (j = 0; j < tb[i].nhack; j++)
 203             {
 204                 if (tb[i].hack[j].oname == NULL && tb[i].hack[j].nname != NULL)
 205                 {
 206                     print_ab(out, &(tb[i].hack[j]), tb[i].hack[j].nname);
 207                     print_atom(out, tb[i].hack[j].atom, atype);
 208                 }
 209             }
 210         }
 211         if (ndel)
 212         {
 213             fprintf(out, "[ %s ]\n", kw_names[ekwDel-ebtsNR-1]);
 214             for (j = 0; j < tb[i].nhack; j++)
 215             {
 216                 if (tb[i].hack[j].oname != NULL && tb[i].hack[j].nname == NULL)
 217                 {
 218                     fprintf(out, "%s\n", tb[i].hack[j].oname);
 219                 }
 220             }
 221         }
 222         for (bt = 0; bt < ebtsNR; bt++)
 223         {
 224             if (tb[i].rb[bt].nb)
 225             {
 226                 fprintf(out, "[ %s ]\n", btsNames[bt]);
 227                 for (j = 0; j < tb[i].rb[bt].nb; j++)
 228                 {
 229                     for (k = 0; k < btsNiatoms[bt]; k++)
 230                     {
 231                         fprintf(out, "%s%s", k ? "\t" : "", tb[i].rb[bt].b[j].a[k]);
 232                     }
 233                     if (tb[i].rb[bt].b[j].s)
 234                     {
 235                         fprintf(out, "\t%s", tb[i].rb[bt].b[j].s);
 236                     }
 237                     fprintf(out, "\n");
 238                 }
 239             }
 240         }
 241         fprintf(out, "\n");
 242     }
 243     gmx_fio_fclose(out);
 244 }
 245
 246 static void read_ter_db_file(char *fn,
 247                              int *ntbptr, t_hackblock **tbptr,
 248                              gpp_atomtype_t atype)
 249 {
 250     char         filebase[STRLEN], *ptr;
 251     FILE        *in;
 252     char         header[STRLEN], buf[STRLEN], line[STRLEN];
 253     t_hackblock *tb;
 254     int          i, j, n, ni, kwnr, nb, maxnb, nh;
 255
 256     fflib_filename_base(fn, filebase, STRLEN);
 257     /* Remove the C/N termini extension */
 258     ptr = strrchr(filebase, '.');
 259     if (ptr != NULL)
 260     {
 261         ptr[0] = '\0';
 262     }
 263
 264     in = fflib_open(fn);
 265     if (debug)
 266     {
 267         fprintf(debug, "Opened %s\n", fn);
 268     }
 269
 270     tb    = *tbptr;
 271     nb    = *ntbptr - 1;
 272     maxnb = 0;
 273     kwnr  = NOTSET;
 274     get_a_line(in, line, STRLEN);
 275     while (!feof(in))
 276     {
 277         if (get_header(line, header))
 278         {
 279             /* this is a new block, or a new keyword */
 280             kwnr = find_kw(header);
 281
 282             if (kwnr == NOTSET)
 283             {
 284                 nb++;
 285                 /* here starts a new block */
 286                 if (nb >= maxnb)
 287                 {
 288                     maxnb = nb + 100;
 289                     srenew(tb, maxnb);
 290                 }
 291                 clear_t_hackblock(&tb[nb]);
 292                 tb[nb].name     = gmx_strdup(header);
 293                 tb[nb].filebase = gmx_strdup(filebase);
 294             }
 295         }
 296         else
 297         {
 298             if (nb < 0)
 299             {
 300                 gmx_fatal(FARGS, "reading termini database: "
 301                           "directive expected before line:\n%s\n"
 302                           "This might be a file in an old format.", line);
 303             }
 304             /* this is not a header, so it must be data */
 305             if (kwnr >= ebtsNR)
 306             {
 307                 /* this is a hack: add/rename/delete atoms */
 308                 /* make space for hacks */
 309                 if (tb[nb].nhack >= tb[nb].maxhack)
 310                 {
 311                     tb[nb].maxhack += 10;
 312                     srenew(tb[nb].hack, tb[nb].maxhack);
 313                 }
 314                 nh = tb[nb].nhack;
 315                 clear_t_hack(&(tb[nb].hack[nh]));
 316                 for (i = 0; i < 4; i++)
 317                 {
 318                     tb[nb].hack[nh].a[i] = NULL;
 319                 }
 320                 tb[nb].nhack++;
 321
 322                 /* get data */
 323                 n = 0;
 324                 if (kwnr == ekwRepl || kwnr == ekwDel)
 325                 {
 326                     if (sscanf(line, "%s%n", buf, &n) != 1)
 327                     {
 328                         gmx_fatal(FARGS, "Reading Termini Database '%s': "
 329                                   "expected atom name on line\n%s", fn, line);
 330                     }
 331                     tb[nb].hack[nh].oname = gmx_strdup(buf);
 332                     /* we only replace or delete one atom at a time */
 333                     tb[nb].hack[nh].nr = 1;
 334                 }
 335                 else if (kwnr == ekwAdd)
 336                 {
 337                     read_ab(line, fn, &(tb[nb].hack[nh]));
 338                     get_a_line(in, line, STRLEN);
 339                 }
 340                 else
 341                 {
 342                     gmx_fatal(FARGS, "unimplemented keyword number %d (%s:%d)",
 343                               kwnr, __FILE__, __LINE__);
 344                 }
 345                 if (kwnr == ekwRepl || kwnr == ekwAdd)
 346                 {
 347                     snew(tb[nb].hack[nh].atom, 1);
 348                     read_atom(line+n, kwnr == ekwAdd,
 349                               &tb[nb].hack[nh].nname, tb[nb].hack[nh].atom, atype,
 350                               &tb[nb].hack[nh].cgnr);
 351                     if (tb[nb].hack[nh].nname == NULL)
 352                     {
 353                         if (tb[nb].hack[nh].oname != NULL)
 354                         {
 355                             tb[nb].hack[nh].nname = gmx_strdup(tb[nb].hack[nh].oname);
 356                         }
 357                         else
 358                         {
 359                             gmx_fatal(FARGS, "Reading Termini Database '%s': don't know which name the new atom should have on line\n%s", fn, line);
 360                         }
 361                     }
 362                 }
 363             }
 364             else if (kwnr >= 0 && kwnr < ebtsNR)
 365             {
 366                 /* this is bonded data: bonds, angles, dihedrals or impropers */
 367                 srenew(tb[nb].rb[kwnr].b, tb[nb].rb[kwnr].nb+1);
 368                 n = 0;
 369                 for (j = 0; j < btsNiatoms[kwnr]; j++)
 370                 {
 371                     if (sscanf(line+n, "%s%n", buf, &ni) == 1)
 372                     {
 373                         tb[nb].rb[kwnr].b[tb[nb].rb[kwnr].nb].a[j] = gmx_strdup(buf);
 374                     }
 375                     else
 376                     {
 377                         gmx_fatal(FARGS, "Reading Termini Database '%s': expected %d atom names (found %d) on line\n%s", fn, btsNiatoms[kwnr], j-1, line);
 378                     }
 379                     n += ni;
 380                 }
 381                 for (; j < MAXATOMLIST; j++)
 382                 {
 383                     tb[nb].rb[kwnr].b[tb[nb].rb[kwnr].nb].a[j] = NULL;
 384                 }
 385                 strcpy(buf, "");
 386                 sscanf(line+n, "%s", buf);
 387                 tb[nb].rb[kwnr].b[tb[nb].rb[kwnr].nb].s = gmx_strdup(buf);
 388                 tb[nb].rb[kwnr].nb++;
 389             }
 390             else
 391             {
 392                 gmx_fatal(FARGS, "Reading Termini Database: Expecting a header at line\n"
 393                           "%s", line);
 394             }
 395         }
 396         get_a_line(in, line, STRLEN);
 397     }
 398     nb++;
 399     srenew(tb, nb);
 400
 401     gmx_ffclose(in);
 402
 403     *ntbptr = nb;
 404     *tbptr  = tb;
 405 }
 406
 407 int read_ter_db(const char *ffdir, char ter,
 408                 t_hackblock **tbptr, gpp_atomtype_t atype)
 409 {
 410     char   ext[STRLEN];
 411     int    ntdbf, f;
 412     char **tdbf;
 413     int    ntb;
 414
 415     sprintf(ext, ".%c.tdb", ter);
 416
 417     /* Search for termini database files.
 418      * Do not generate an error when none are found.
 419      */
 420     ntdbf  = fflib_search_file_end(ffdir, ext, FALSE, &tdbf);
 421     ntb    = 0;
 422     *tbptr = NULL;
 423     for (f = 0; f < ntdbf; f++)
 424     {
 425         read_ter_db_file(tdbf[f], &ntb, tbptr, atype);
 426         sfree(tdbf[f]);
 427     }
 428     sfree(tdbf);
 429
 430     if (debug)
 431     {
 432         print_ter_db("new", ter, ntb, *tbptr, atype);
 433     }
 434
 435     return ntb;
 436 }
 437
 438 t_hackblock **filter_ter(int nrtp, t_restp rtp[],
 439                          int nb, t_hackblock tb[],
 440                          const char *resname,
 441                          const char *rtpname,
 442                          int *nret)
 443 {
 444     // TODO Four years later, no force fields have ever used this, so decide status of this feature
 445     /* Since some force fields (e.g. OPLS) needs different
 446      * atomtypes for different residues there could be a lot
 447      * of entries in the databases for specific residues
 448      * (e.g. GLY-NH3+, SER-NH3+, ALA-NH3+).
 449      *
 450      * To reduce the database size, we assume that a terminus specifier liker
 451      *
 452      * [ GLY|SER|ALA-NH3+ ]
 453      *
 454      * would cover all of the three residue types above.
 455      * Wildcards (*,?) are not OK. Don't worry about e.g. GLU vs. GLUH since
 456      * pdb2gmx only uses the first 3 letters when calling this routine.
 457      *
 458      * To automate this, this routines scans a list of termini
 459      * for the residue name "resname" and returns an allocated list of
 460      * pointers to the termini that could be applied to the
 461      * residue in question. The variable pointed to by nret will
 462      * contain the number of valid pointers in the list.
 463      * Remember to free the list when you are done with it...
 464      */
 465
 466     t_restp     *   restp;
 467     int             i, j, n, none_idx;
 468     gmx_bool        found;
 469     char           *rtpname_match, *s;
 470     t_hackblock   **list;
 471
 472     rtpname_match = search_rtp(rtpname, nrtp, rtp);
 473     restp         = get_restp(rtpname_match, nrtp, rtp);
 474
 475     n    = 0;
 476     list = NULL;
 477
 478     for (i = 0; i < nb; i++)
 479     {
 480         s     = tb[i].name;
 481         found = FALSE;
 482         do
 483         {
 484             /* The residue name should appear in a tdb file with the same base name
 485              * as the file containing the rtp entry.
 486              * This makes termini selection for different molecule types
 487              * much cleaner.
 488              */
 489             if (gmx_strcasecmp(restp->filebase, tb[i].filebase) == 0 &&
 490                 gmx_strncasecmp(resname, s, 3) == 0)
 491             {
 492                 found = TRUE;
 493                 srenew(list, n+1);
 494                 list[n] = &(tb[i]);
 495                 n++;
 496             }
 497             else
 498             {
 499                 /* advance to next |-separated field */
 500                 s = strchr(s, '|');
 501                 if (s != NULL)
 502                 {
 503                     s++;
 504                 }
 505             }
 506         }
 507         while (!found && s != NULL);
 508     }
 509
 510     /* All residue-specific termini have been added. We might have to fall
 511      * back on generic termini, which are characterized by not having
 512      * '-' in the name prior to the last position (which indicates charge).
 513      * The [ None ] alternative is special since we don't want that
 514      * to be the default, so we put it last in the list we return.
 515      */
 516     none_idx = -1;
 517     for (i = 0; i < nb; i++)
 518     {
 519         s = tb[i].name;
 520         /* The residue name should appear in a tdb file with the same base name
 521          * as the file containing the rtp entry.
 522          * This makes termini selection for different molecule types
 523          * much cleaner.
 524          */
 525         if (gmx_strcasecmp(restp->filebase, tb[i].filebase) == 0)
 526         {
 527             if (!gmx_strcasecmp("None", s))
 528             {
 529                 none_idx = i;
 530             }
 531             else
 532             {
 533                 /* Time to see if there's a generic terminus that matches.
 534                    Is there a hyphen? */
 535                 char *c = strchr(s, '-');
 536
 537                 /* A conjunction hyphen normally indicates a residue-specific
 538                    terminus, which is named like "GLY-COOH". A generic terminus
 539                    won't have a hyphen. */
 540                 bool bFoundAnyHyphen = (c != NULL);
 541                 /* '-' as the last character indicates charge, so if that's
 542                    the only one found e.g. "COO-", then it was not a conjunction
 543                    hyphen, so this is a generic terminus */
 544                 bool bOnlyFoundChargeHyphen = (bFoundAnyHyphen &&
 545                                                *(c+1) == '\0');
 546                 /* Thus, "GLY-COO-" is not recognized as a generic terminus. */
 547                 bool bFoundGenericTerminus = !bFoundAnyHyphen || bOnlyFoundChargeHyphen;
 548                 if (bFoundGenericTerminus)
 549                 {
 550                     /* Check that we haven't already added a residue-specific version
 551                      * of this terminus.
 552                      */
 553                     for (j = 0; j < n && strstr((*list[j]).name, s) == NULL; j++)
 554                     {
 555                         ;
 556                     }
 557                     if (j == n)
 558                     {
 559                         srenew(list, n+1);
 560                         list[n] = &(tb[i]);
 561                         n++;
 562                     }
 563                 }
 564             }
 565         }
 566     }
 567     if (none_idx >= 0)
 568     {
 569         srenew(list, n+1);
 570         list[n] = &(tb[none_idx]);
 571         n++;
 572     }
 573
 574     *nret = n;
 575     return list;
 576 }
 577
 578
 579 t_hackblock *choose_ter(int nb, t_hackblock **tb, const char *title)
 580 {
 581     int i, sel, ret;
 582
 583     printf("%s\n", title);
 584     for (i = 0; (i < nb); i++)
 585     {
 586         bool bIsZwitterion = (0 == gmx_wcmatch("*ZWITTERION*", (*tb[i]).name));
 587         printf("%2d: %s%s\n", i, (*tb[i]).name,
 588                bIsZwitterion ? " (only use with zwitterions containing exactly one residue)" : "");
 589     }
 590     do
 591     {
 592         ret = fscanf(stdin, "%d", &sel);
 593     }
 594     while ((ret != 1) || (sel < 0) || (sel >= nb));
 595
 596     return tb[sel];
 597 }