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45 #include "gromacs/utility/smalloc.h"
48 #include "gromacs/fileio/futil.h"
51 #include "gromacs/utility/cstringutil.h"
52 #include "gmx_fatal.h"
55 #include "gromacs/fileio/gmxfio.h"
56 #include "fflibutil.h"
58 #include "gromacs/fileio/strdb.h"
60 /* use bonded types definitions in hackblock.h */
61 #define ekwRepl ebtsNR+1
62 #define ekwAdd ebtsNR+2
63 #define ekwDel ebtsNR+3
65 const char *kw_names[ekwNR] = {
66 "replace", "add", "delete"
69 int find_kw(char *keyw)
73 for (i = 0; i < ebtsNR; i++)
75 if (gmx_strcasecmp(btsNames[i], keyw) == 0)
80 for (i = 0; i < ekwNR; i++)
82 if (gmx_strcasecmp(kw_names[i], keyw) == 0)
84 return ebtsNR + 1 + i;
91 #define FATAL() gmx_fatal(FARGS, "Reading Termini Database: not enough items on line\n%s", line)
93 static void read_atom(char *line, gmx_bool bAdd,
94 char **nname, t_atom *a, gpp_atomtype_t atype, int *cgnr)
97 char buf[5][30], type[12];
100 /* This code is messy, because of support for different formats:
101 * for replace: [new name] <atom type> <m> <q> [cgnr (old format)]
102 * for add: <atom type> <m> <q> [cgnr]
104 nr = sscanf(line, "%s %s %s %s %s", buf[0], buf[1], buf[2], buf[3], buf[4]);
106 /* Here there an ambiguity due to the old replace format with cgnr,
107 * which was read for years, but ignored in the rest of the code.
108 * We have to assume that the atom type does not start with a digit
109 * to make a line with 4 entries uniquely interpretable.
111 if (!bAdd && nr == 4 && isdigit(buf[1][0]))
116 if (nr < 3 || nr > 4)
118 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);
125 *nname = strdup(buf[i++]);
132 a->type = get_atomtype_type(buf[i++], atype);
133 sscanf(buf[i++], "%lf", &m);
135 sscanf(buf[i++], "%lf", &q);
139 sscanf(buf[i++], "%d", cgnr);
147 static void print_atom(FILE *out, t_atom *a, gpp_atomtype_t atype)
149 fprintf(out, "\t%s\t%g\t%g\n",
150 get_atomtype_name(a->type, atype), a->m, a->q);
153 static void print_ter_db(const char *ff, char C, int nb, t_hackblock tb[],
154 gpp_atomtype_t atype)
157 int i, j, k, bt, nrepl, nadd, ndel;
158 char buf[STRLEN], nname[STRLEN];
160 sprintf(buf, "%s-%c.tdb", ff, C);
161 out = gmx_fio_fopen(buf, "w");
163 for (i = 0; (i < nb); i++)
165 fprintf(out, "[ %s ]\n", tb[i].name);
171 for (j = 0; j < tb[i].nhack; j++)
173 if (tb[i].hack[j].oname != NULL && tb[i].hack[j].nname != NULL)
177 else if (tb[i].hack[j].oname == NULL && tb[i].hack[j].nname != NULL)
181 else if (tb[i].hack[j].oname != NULL && tb[i].hack[j].nname == NULL)
185 else if (tb[i].hack[j].oname == NULL && tb[i].hack[j].nname == NULL)
187 gmx_fatal(FARGS, "invalid hack (%s) in termini database", tb[i].name);
192 fprintf(out, "[ %s ]\n", kw_names[ekwRepl-ebtsNR-1]);
193 for (j = 0; j < tb[i].nhack; j++)
195 if (tb[i].hack[j].oname != NULL && tb[i].hack[j].nname != NULL)
197 fprintf(out, "%s\t", tb[i].hack[j].oname);
198 print_atom(out, tb[i].hack[j].atom, atype);
204 fprintf(out, "[ %s ]\n", kw_names[ekwAdd-ebtsNR-1]);
205 for (j = 0; j < tb[i].nhack; j++)
207 if (tb[i].hack[j].oname == NULL && tb[i].hack[j].nname != NULL)
209 print_ab(out, &(tb[i].hack[j]), tb[i].hack[j].nname);
210 print_atom(out, tb[i].hack[j].atom, atype);
216 fprintf(out, "[ %s ]\n", kw_names[ekwDel-ebtsNR-1]);
217 for (j = 0; j < tb[i].nhack; j++)
219 if (tb[i].hack[j].oname != NULL && tb[i].hack[j].nname == NULL)
221 fprintf(out, "%s\n", tb[i].hack[j].oname);
225 for (bt = 0; bt < ebtsNR; bt++)
229 fprintf(out, "[ %s ]\n", btsNames[bt]);
230 for (j = 0; j < tb[i].rb[bt].nb; j++)
232 for (k = 0; k < btsNiatoms[bt]; k++)
234 fprintf(out, "%s%s", k ? "\t" : "", tb[i].rb[bt].b[j].a[k]);
236 if (tb[i].rb[bt].b[j].s)
238 fprintf(out, "\t%s", tb[i].rb[bt].b[j].s);
249 static void read_ter_db_file(char *fn,
250 int *ntbptr, t_hackblock **tbptr,
251 gpp_atomtype_t atype)
253 char filebase[STRLEN], *ptr;
255 char header[STRLEN], buf[STRLEN], line[STRLEN];
257 int i, j, n, ni, kwnr, nb, maxnb, nh;
259 fflib_filename_base(fn, filebase, STRLEN);
260 /* Remove the C/N termini extension */
261 ptr = strrchr(filebase, '.');
270 fprintf(debug, "Opened %s\n", fn);
277 get_a_line(in, line, STRLEN);
280 if (get_header(line, header))
282 /* this is a new block, or a new keyword */
283 kwnr = find_kw(header);
288 /* here starts a new block */
294 clear_t_hackblock(&tb[nb]);
295 tb[nb].name = strdup(header);
296 tb[nb].filebase = strdup(filebase);
303 gmx_fatal(FARGS, "reading termini database: "
304 "directive expected before line:\n%s\n"
305 "This might be a file in an old format.", line);
307 /* this is not a header, so it must be data */
310 /* this is a hack: add/rename/delete atoms */
311 /* make space for hacks */
312 if (tb[nb].nhack >= tb[nb].maxhack)
314 tb[nb].maxhack += 10;
315 srenew(tb[nb].hack, tb[nb].maxhack);
318 clear_t_hack(&(tb[nb].hack[nh]));
319 for (i = 0; i < 4; i++)
321 tb[nb].hack[nh].a[i] = NULL;
327 if (kwnr == ekwRepl || kwnr == ekwDel)
329 if (sscanf(line, "%s%n", buf, &n) != 1)
331 gmx_fatal(FARGS, "Reading Termini Database '%s': "
332 "expected atom name on line\n%s", fn, line);
334 tb[nb].hack[nh].oname = strdup(buf);
335 /* we only replace or delete one atom at a time */
336 tb[nb].hack[nh].nr = 1;
338 else if (kwnr == ekwAdd)
340 read_ab(line, fn, &(tb[nb].hack[nh]));
341 get_a_line(in, line, STRLEN);
345 gmx_fatal(FARGS, "unimplemented keyword number %d (%s:%d)",
346 kwnr, __FILE__, __LINE__);
348 if (kwnr == ekwRepl || kwnr == ekwAdd)
350 snew(tb[nb].hack[nh].atom, 1);
351 read_atom(line+n, kwnr == ekwAdd,
352 &tb[nb].hack[nh].nname, tb[nb].hack[nh].atom, atype,
353 &tb[nb].hack[nh].cgnr);
354 if (tb[nb].hack[nh].nname == NULL)
356 if (tb[nb].hack[nh].oname != NULL)
358 tb[nb].hack[nh].nname = strdup(tb[nb].hack[nh].oname);
362 gmx_fatal(FARGS, "Reading Termini Database '%s': don't know which name the new atom should have on line\n%s", fn, line);
367 else if (kwnr >= 0 && kwnr < ebtsNR)
369 /* this is bonded data: bonds, angles, dihedrals or impropers */
370 srenew(tb[nb].rb[kwnr].b, tb[nb].rb[kwnr].nb+1);
372 for (j = 0; j < btsNiatoms[kwnr]; j++)
374 if (sscanf(line+n, "%s%n", buf, &ni) == 1)
376 tb[nb].rb[kwnr].b[tb[nb].rb[kwnr].nb].a[j] = strdup(buf);
380 gmx_fatal(FARGS, "Reading Termini Database '%s': expected %d atom names (found %d) on line\n%s", fn, btsNiatoms[kwnr], j-1, line);
384 for (; j < MAXATOMLIST; j++)
386 tb[nb].rb[kwnr].b[tb[nb].rb[kwnr].nb].a[j] = NULL;
389 sscanf(line+n, "%s", buf);
390 tb[nb].rb[kwnr].b[tb[nb].rb[kwnr].nb].s = strdup(buf);
391 tb[nb].rb[kwnr].nb++;
395 gmx_fatal(FARGS, "Reading Termini Database: Expecting a header at line\n"
399 get_a_line(in, line, STRLEN);
410 int read_ter_db(const char *ffdir, char ter,
411 t_hackblock **tbptr, gpp_atomtype_t atype)
418 sprintf(ext, ".%c.tdb", ter);
420 /* Search for termini database files.
421 * Do not generate an error when none are found.
423 ntdbf = fflib_search_file_end(ffdir, ext, FALSE, &tdbf);
426 for (f = 0; f < ntdbf; f++)
428 read_ter_db_file(tdbf[f], &ntb, tbptr, atype);
435 print_ter_db("new", ter, ntb, *tbptr, atype);
441 t_hackblock **filter_ter(int nrtp, t_restp rtp[],
442 int nb, t_hackblock tb[],
447 /* Since some force fields (e.g. OPLS) needs different
448 * atomtypes for different residues there could be a lot
449 * of entries in the databases for specific residues
450 * (e.g. GLY-NH3+, SER-NH3+, ALA-NH3+).
452 * To reduce the database size, we assume that a terminus specifier liker
454 * [ GLY|SER|ALA-NH3+ ]
456 * would cover all of the three residue types above.
457 * Wildcards (*,?) are not OK. Don't worry about e.g. GLU vs. GLUH since
458 * pdb2gmx only uses the first 3 letters when calling this routine.
460 * To automate this, this routines scans a list of termini
461 * for the residue name "resname" and returns an allocated list of
462 * pointers to the termini that could be applied to the
463 * residue in question. The variable pointed to by nret will
464 * contain the number of valid pointers in the list.
465 * Remember to free the list when you are done with it...
469 int i, j, n, len, none_idx;
471 char *rtpname_match, *s, *s2, *c;
474 rtpname_match = search_rtp(rtpname, nrtp, rtp);
475 restp = get_restp(rtpname_match, nrtp, rtp);
480 for (i = 0; i < nb; i++)
486 /* The residue name should appear in a tdb file with the same base name
487 * as the file containing the rtp entry.
488 * This makes termini selection for different molecule types
491 if (gmx_strcasecmp(restp->filebase, tb[i].filebase) == 0 &&
492 gmx_strncasecmp(resname, s, 3) == 0)
501 /* advance to next |-separated field */
509 while (!found && s != NULL);
512 /* All residue-specific termini have been added. See if there
513 * are some generic ones by searching for the occurence of
514 * '-' in the name prior to the last position (which indicates charge).
515 * The [ None ] alternative is special since we don't want that
516 * to be the default, so we put it last in the list we return.
519 for (i = 0; i < nb; i++)
522 /* The residue name should appear in a tdb file with the same base name
523 * as the file containing the rtp entry.
524 * This makes termini selection for different molecule types
527 if (gmx_strcasecmp(restp->filebase, tb[i].filebase) == 0)
529 if (!gmx_strcasecmp("None", s))
536 if (c == NULL || ((c-s+1) == strlen(s)))
538 /* Check that we haven't already added a residue-specific version
541 for (j = 0; j < n && strstr((*list[j]).name, s) == NULL; j++)
558 list[n] = &(tb[none_idx]);
567 t_hackblock *choose_ter(int nb, t_hackblock **tb, const char *title)
571 printf("%s\n", title);
572 for (i = 0; (i < nb); i++)
574 char *advice_string = "";
575 if (0 == gmx_wcmatch("*ZWITTERION*", (*tb[i]).name))
577 advice_string = " (only use with zwitterions containing exactly one residue)";
579 printf("%2d: %s%s\n", i, (*tb[i]).name, advice_string);
583 ret = fscanf(stdin, "%d", &sel);
585 while ((ret != 1) || (sel < 0) || (sel >= nb));