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46 #include "gromacs/utility/smalloc.h"
47 #include "gromacs/fileio/confio.h"
50 #include "gromacs/fileio/futil.h"
51 #include "gmx_fatal.h"
62 static void copy_atom(t_atoms *atoms1, int a1, t_atoms *atoms2, int a2)
64 atoms2->atom[a2] = atoms1->atom[a1];
65 snew(atoms2->atomname[a2], 1);
66 *atoms2->atomname[a2] = strdup(*atoms1->atomname[a1]);
69 static atom_id pdbasearch_atom(const char *name, int resind, t_atoms *pdba,
70 const char *searchtype, gmx_bool bAllowMissing)
74 for (i = 0; (i < pdba->nr) && (pdba->atom[i].resind != resind); i++)
79 return search_atom(name, i, pdba,
80 searchtype, bAllowMissing);
83 static void hacksearch_atom(int *ii, int *jj, char *name,
84 int nab[], t_hack *ab[],
85 int resind, t_atoms *pdba)
95 for (i = 0; (i < pdba->nr) && (pdba->atom[i].resind != resind); i++)
99 for (; (i < pdba->nr) && (pdba->atom[i].resind == resind) && (*ii < 0); i++)
101 for (j = 0; (j < nab[i]) && (*ii < 0); j++)
103 if (ab[i][j].nname && strcmp(name, ab[i][j].nname) == 0)
114 void dump_ab(FILE *out, int natom, int nab[], t_hack *ab[], gmx_bool bHeader)
118 #define SS(s) (s) ? (s) : "-"
122 fprintf(out, "ADDBLOCK (t_hack) natom=%d\n"
123 "%4s %2s %-4s %-4s %2s %-4s %-4s %-4s %-4s %1s %s\n",
124 natom, "atom", "nr", "old", "new", "tp", "ai", "aj", "ak", "al", "a", "x");
126 for (i = 0; i < natom; i++)
128 for (j = 0; j < nab[i]; j++)
130 fprintf(out, "%4d %2d %-4s %-4s %2d %-4s %-4s %-4s %-4s %s %g %g %g\n",
131 i+1, ab[i][j].nr, SS(ab[i][j].oname), SS(ab[i][j].nname),
133 SS(ab[i][j].AI), SS(ab[i][j].AJ),
134 SS(ab[i][j].AK), SS(ab[i][j].AL),
135 ab[i][j].atom ? "+" : "",
136 ab[i][j].newx[XX], ab[i][j].newx[YY], ab[i][j].newx[ZZ]);
142 static t_hackblock *get_hackblocks(t_atoms *pdba, int nah, t_hackblock ah[],
144 t_hackblock **ntdb, t_hackblock **ctdb,
148 t_hackblock *hb, *ahptr;
151 snew(hb, pdba->nres);
152 /* first the termini */
153 for (i = 0; i < nterpairs; i++)
157 copy_t_hackblock(ntdb[i], &hb[rN[i]]);
161 merge_t_hackblock(ctdb[i], &hb[rC[i]]);
164 /* then the whole hdb */
165 for (rnr = 0; rnr < pdba->nres; rnr++)
167 ahptr = search_h_db(nah, ah, *pdba->resinfo[rnr].rtp);
170 if (hb[rnr].name == NULL)
172 hb[rnr].name = strdup(ahptr->name);
174 merge_hacks(ahptr, &hb[rnr]);
180 static void expand_hackblocks_one(t_hackblock *hbr, char *atomname,
181 int *nabi, t_hack **abi, gmx_bool bN, gmx_bool bC)
186 /* we'll recursively add atoms to atoms */
187 for (j = 0; j < hbr->nhack; j++)
189 /* first check if we're in the N- or C-terminus, then we should ignore
190 all hacks involving atoms from resp. previous or next residue
191 (i.e. which name begins with '-' (N) or '+' (C) */
193 if (bN) /* N-terminus: ignore '-' */
195 for (k = 0; k < 4 && hbr->hack[j].a[k] && !bIgnore; k++)
197 bIgnore = hbr->hack[j].a[k][0] == '-';
200 if (bC) /* C-terminus: ignore '+' */
202 for (k = 0; k < 4 && hbr->hack[j].a[k] && !bIgnore; k++)
204 bIgnore = hbr->hack[j].a[k][0] == '+';
207 /* must be either hdb entry (tp>0) or add from tdb (oname==NULL)
208 and first control aton (AI) matches this atom or
209 delete/replace from tdb (oname!=NULL) and oname matches this atom */
212 fprintf(debug, " %s", hbr->hack[j].oname ? hbr->hack[j].oname : hbr->hack[j].AI);
216 ( ( ( hbr->hack[j].tp > 0 || hbr->hack[j].oname == NULL ) &&
217 strcmp(atomname, hbr->hack[j].AI) == 0 ) ||
218 ( hbr->hack[j].oname != NULL &&
219 strcmp(atomname, hbr->hack[j].oname) == 0) ) )
221 /* now expand all hacks for this atom */
224 fprintf(debug, " +%dh", hbr->hack[j].nr);
226 srenew(*abi, *nabi + hbr->hack[j].nr);
227 for (k = 0; k < hbr->hack[j].nr; k++)
229 copy_t_hack(&hbr->hack[j], &(*abi)[*nabi + k]);
230 (*abi)[*nabi + k].bXSet = FALSE;
231 /* if we're adding (oname==NULL) and don't have a new name (nname)
232 yet, build it from atomname */
233 if ( (*abi)[*nabi + k].nname == NULL)
235 if ( (*abi)[*nabi + k].oname == NULL)
237 (*abi)[*nabi + k].nname = strdup(atomname);
238 (*abi)[*nabi + k].nname[0] = 'H';
245 fprintf(debug, "Hack '%s' %d, replacing nname '%s' with '%s' (old name '%s')\n",
247 (*abi)[*nabi + k].nname, hbr->hack[j].nname,
248 (*abi)[*nabi + k].oname ? (*abi)[*nabi + k].oname : "");
250 sfree((*abi)[*nabi + k].nname);
251 (*abi)[*nabi + k].nname = strdup(hbr->hack[j].nname);
254 if (hbr->hack[j].tp == 10 && k == 2)
256 /* This is a water virtual site, not a hydrogen */
257 /* Ugly hardcoded name hack */
258 (*abi)[*nabi + k].nname[0] = 'M';
260 else if (hbr->hack[j].tp == 11 && k >= 2)
262 /* This is a water lone pair, not a hydrogen */
263 /* Ugly hardcoded name hack */
264 srenew((*abi)[*nabi + k].nname, 4);
265 (*abi)[*nabi + k].nname[0] = 'L';
266 (*abi)[*nabi + k].nname[1] = 'P';
267 (*abi)[*nabi + k].nname[2] = '1' + k - 2;
268 (*abi)[*nabi + k].nname[3] = '\0';
270 else if (hbr->hack[j].nr > 1)
272 /* adding more than one atom, number them */
273 l = strlen((*abi)[*nabi + k].nname);
274 srenew((*abi)[*nabi + k].nname, l+2);
275 (*abi)[*nabi + k].nname[l] = '1' + k;
276 (*abi)[*nabi + k].nname[l+1] = '\0';
279 (*nabi) += hbr->hack[j].nr;
281 /* add hacks to atoms we've just added */
282 if (hbr->hack[j].tp > 0 || hbr->hack[j].oname == NULL)
284 for (k = 0; k < hbr->hack[j].nr; k++)
286 expand_hackblocks_one(hbr, (*abi)[*nabi-hbr->hack[j].nr+k].nname,
294 static void expand_hackblocks(t_atoms *pdba, t_hackblock hb[],
295 int nab[], t_hack *ab[],
296 int nterpairs, int *rN, int *rC)
301 for (i = 0; i < pdba->nr; i++)
304 for (j = 0; j < nterpairs && !bN; j++)
306 bN = pdba->atom[i].resind == rN[j];
309 for (j = 0; j < nterpairs && !bC; j++)
311 bC = pdba->atom[i].resind == rC[j];
314 /* add hacks to this atom */
315 expand_hackblocks_one(&hb[pdba->atom[i].resind], *pdba->atomname[i],
316 &nab[i], &ab[i], bN, bC);
320 fprintf(debug, "\n");
324 static int check_atoms_present(t_atoms *pdba, int nab[], t_hack *ab[])
326 int i, j, k, d, rnr, nadd;
329 for (i = 0; i < pdba->nr; i++)
331 rnr = pdba->atom[i].resind;
332 for (j = 0; j < nab[i]; j++)
334 if (ab[i][j].oname == NULL)
337 if (ab[i][j].nname == NULL)
339 gmx_incons("ab[i][j].nname not allocated");
341 /* check if the atom is already present */
342 k = pdbasearch_atom(ab[i][j].nname, rnr, pdba, "check", TRUE);
345 /* We found the added atom. */
346 ab[i][j].bAlreadyPresent = TRUE;
349 fprintf(debug, "Atom '%s' in residue '%s' %d is already present\n",
351 *pdba->resinfo[rnr].name, pdba->resinfo[rnr].nr);
356 ab[i][j].bAlreadyPresent = FALSE;
357 /* count how many atoms we'll add */
361 else if (ab[i][j].nname == NULL)
372 static void calc_all_pos(t_atoms *pdba, rvec x[], int nab[], t_hack *ab[],
373 gmx_bool bCheckMissing)
375 int i, j, ii, jj, m, ia, d, rnr, l = 0;
377 rvec xa[4]; /* control atoms for calc_h_pos */
378 rvec xh[MAXH]; /* hydrogen positions from calc_h_pos */
383 for (i = 0; i < pdba->nr; i++)
385 rnr = pdba->atom[i].resind;
386 for (j = 0; j < nab[i]; j += ab[i][j].nr)
388 /* check if we're adding: */
389 if (ab[i][j].oname == NULL && ab[i][j].tp > 0)
392 for (m = 0; (m < ab[i][j].nctl && bFoundAll); m++)
394 ia = pdbasearch_atom(ab[i][j].a[m], rnr, pdba,
395 bCheckMissing ? "atom" : "check",
399 /* not found in original atoms, might still be in t_hack (ab) */
400 hacksearch_atom(&ii, &jj, ab[i][j].a[m], nab, ab, rnr, pdba);
403 copy_rvec(ab[ii][jj].newx, xa[m]);
410 gmx_fatal(FARGS, "Atom %s not found in residue %s %d"
412 " while adding hydrogens",
414 *pdba->resinfo[rnr].name,
415 pdba->resinfo[rnr].nr,
416 *pdba->resinfo[rnr].rtp);
422 copy_rvec(x[ia], xa[m]);
427 for (m = 0; (m < MAXH); m++)
429 for (d = 0; d < DIM; d++)
441 calc_h_pos(ab[i][j].tp, xa, xh, &l);
442 for (m = 0; m < ab[i][j].nr; m++)
444 copy_rvec(xh[m], ab[i][j+m].newx);
445 ab[i][j+m].bXSet = TRUE;
453 static void free_ab(int natoms, int *nab, t_hack **ab)
457 for (i = 0; i < natoms; i++)
459 free_t_hack(nab[i], &ab[i]);
465 static int add_h_low(t_atoms **pdbaptr, rvec *xptr[],
466 int nah, t_hackblock ah[],
467 int nterpairs, t_hackblock **ntdb, t_hackblock **ctdb,
468 int *rN, int *rC, gmx_bool bCheckMissing,
469 int **nabptr, t_hack ***abptr,
470 gmx_bool bUpdate_pdba, gmx_bool bKeep_old_pdba)
472 t_atoms *newpdba = NULL, *pdba = NULL;
474 int i, newi, j, d, natoms, nalreadypresent;
481 /* set flags for adding hydrogens (according to hdb) */
487 /* the first time these will be pointers to NULL, but we will
488 return in them the completed arrays, which we will get back
495 fprintf(debug, "pointer to ab found\n");
505 /* WOW, everything was already figured out */
506 bUpdate_pdba = FALSE;
509 fprintf(debug, "pointer to non-null ab found\n");
514 /* We'll have to do all the hard work */
516 /* first get all the hackblocks for each residue: */
517 hb = get_hackblocks(pdba, nah, ah, nterpairs, ntdb, ctdb, rN, rC);
520 dump_hb(debug, pdba->nres, hb);
523 /* expand the hackblocks to atom level */
526 expand_hackblocks(pdba, hb, nab, ab, nterpairs, rN, rC);
527 free_t_hackblock(pdba->nres, &hb);
532 fprintf(debug, "before calc_all_pos\n");
533 dump_ab(debug, natoms, nab, ab, TRUE);
536 /* Now calc the positions */
537 calc_all_pos(pdba, *xptr, nab, ab, bCheckMissing);
541 fprintf(debug, "after calc_all_pos\n");
542 dump_ab(debug, natoms, nab, ab, TRUE);
547 /* we don't have to add atoms that are already present in pdba,
548 so we will remove them from the ab (t_hack) */
549 nadd = check_atoms_present(pdba, nab, ab);
552 fprintf(debug, "removed add hacks that were already in pdba:\n");
553 dump_ab(debug, natoms, nab, ab, TRUE);
554 fprintf(debug, "will be adding %d atoms\n", nadd);
557 /* Copy old atoms, making space for new ones */
559 init_t_atoms(newpdba, natoms+nadd, FALSE);
560 newpdba->nres = pdba->nres;
561 sfree(newpdba->resinfo);
562 newpdba->resinfo = pdba->resinfo;
570 fprintf(debug, "snew xn for %d old + %d new atoms %d total)\n",
571 natoms, nadd, natoms+nadd);
576 /* There is nothing to do: return now */
579 free_ab(natoms, nab, ab);
585 snew(xn, natoms+nadd);
587 for (i = 0; (i < natoms); i++)
589 /* check if this atom wasn't scheduled for deletion */
590 if (nab[i] == 0 || (ab[i][0].nname != NULL) )
592 if (newi >= natoms+nadd)
594 /*gmx_fatal(FARGS,"Not enough space for adding atoms");*/
596 srenew(xn, natoms+nadd);
599 srenew(newpdba->atom, natoms+nadd);
600 srenew(newpdba->atomname, natoms+nadd);
606 fprintf(debug, "(%3d) %3d %4s %4s%3d %3d",
607 i+1, newi+1, *pdba->atomname[i],
608 *pdba->resinfo[pdba->atom[i].resind].name,
609 pdba->resinfo[pdba->atom[i].resind].nr, nab[i]);
613 copy_atom(pdba, i, newpdba, newi);
615 copy_rvec((*xptr)[i], xn[newi]);
616 /* process the hacks for this atom */
618 for (j = 0; j < nab[i]; j++)
620 if (ab[i][j].oname == NULL) /* add */
623 if (newi >= natoms+nadd)
625 /* gmx_fatal(FARGS,"Not enough space for adding atoms");*/
627 srenew(xn, natoms+nadd);
630 srenew(newpdba->atom, natoms+nadd);
631 srenew(newpdba->atomname, natoms+nadd);
637 newpdba->atom[newi].resind = pdba->atom[i].resind;
641 fprintf(debug, " + %d", newi+1);
644 if (ab[i][j].nname != NULL &&
645 (ab[i][j].oname == NULL ||
646 strcmp(ab[i][j].oname, *newpdba->atomname[newi]) == 0))
649 if (ab[i][j].oname == NULL && ab[i][j].bAlreadyPresent)
651 /* This atom is already present, copy it from the input. */
655 copy_atom(pdba, i+nalreadypresent, newpdba, newi);
657 copy_rvec((*xptr)[i+nalreadypresent], xn[newi]);
665 fprintf(debug, "Replacing %d '%s' with (old name '%s') %s\n",
667 (newpdba->atomname[newi] && *newpdba->atomname[newi]) ? *newpdba->atomname[newi] : "",
668 ab[i][j].oname ? ab[i][j].oname : "",
671 snew(newpdba->atomname[newi], 1);
672 *newpdba->atomname[newi] = strdup(ab[i][j].nname);
673 if (ab[i][j].oname != NULL && ab[i][j].atom) /* replace */
674 { /* newpdba->atom[newi].m = ab[i][j].atom->m; */
675 /* newpdba->atom[newi].q = ab[i][j].atom->q; */
676 /* newpdba->atom[newi].type = ab[i][j].atom->type; */
681 copy_rvec(ab[i][j].newx, xn[newi]);
684 if (bUpdate_pdba && debug)
686 fprintf(debug, " %s %g %g", *newpdba->atomname[newi],
687 newpdba->atom[newi].m, newpdba->atom[newi].q);
692 i += nalreadypresent;
695 fprintf(debug, "\n");
712 free_ab(natoms, nab, ab);
719 for (i = 0; i < natoms; i++)
721 /* Do not free the atomname string itself, it might be in symtab */
722 /* sfree(*(pdba->atomname[i])); */
723 /* sfree(pdba->atomname[i]); */
725 sfree(pdba->atomname);
727 sfree(pdba->pdbinfo);
743 void deprotonate(t_atoms *atoms, rvec *x)
748 for (i = 0; i < atoms->nr; i++)
750 if ( (*atoms->atomname[i])[0] != 'H')
752 atoms->atomname[j] = atoms->atomname[i];
753 atoms->atom[j] = atoms->atom[i];
754 copy_rvec(x[i], x[j]);
761 int add_h(t_atoms **pdbaptr, rvec *xptr[],
762 int nah, t_hackblock ah[],
763 int nterpairs, t_hackblock **ntdb, t_hackblock **ctdb,
764 int *rN, int *rC, gmx_bool bAllowMissing,
765 int **nabptr, t_hack ***abptr,
766 gmx_bool bUpdate_pdba, gmx_bool bKeep_old_pdba)
768 int nold, nnew, niter;
770 /* Here we loop to be able to add atoms to added atoms.
771 * We should not check for missing atoms here.
778 nnew = add_h_low(pdbaptr, xptr, nah, ah, nterpairs, ntdb, ctdb, rN, rC, FALSE,
779 nabptr, abptr, bUpdate_pdba, bKeep_old_pdba);
783 gmx_fatal(FARGS, "More than 100 iterations of add_h. Maybe you are trying to replace an added atom (this is not supported)?");
790 /* Call add_h_low once more, now only for the missing atoms check */
791 add_h_low(pdbaptr, xptr, nah, ah, nterpairs, ntdb, ctdb, rN, rC, TRUE,
792 nabptr, abptr, bUpdate_pdba, bKeep_old_pdba);
798 int protonate(t_atoms **atomsptr, rvec **xptr, t_protonate *protdata)
802 gmx_bool bUpdate_pdba, bKeep_old_pdba;
803 int nntdb, nctdb, nt, ct;
807 if (!protdata->bInit)
811 fprintf(debug, "protonate: Initializing protdata\n");
814 /* set forcefield to use: */
815 strcpy(protdata->FF, "oplsaa.ff");
817 /* get the databases: */
818 protdata->nah = read_h_db(protdata->FF, &protdata->ah);
819 open_symtab(&protdata->tab);
820 protdata->atype = read_atype(protdata->FF, &protdata->tab);
821 nntdb = read_ter_db(protdata->FF, 'n', &protdata->ntdb, protdata->atype);
824 gmx_fatal(FARGS, "no N-terminus database");
826 nctdb = read_ter_db(protdata->FF, 'c', &protdata->ctdb, protdata->atype);
829 gmx_fatal(FARGS, "no C-terminus database");
832 /* set terminus types: -NH3+ (different for Proline) and -COO- */
834 snew(protdata->sel_ntdb, NTERPAIRS);
835 snew(protdata->sel_ctdb, NTERPAIRS);
837 if (nntdb >= 4 && nctdb >= 2)
839 /* Yuk, yuk, hardcoded default termini selections !!! */
840 if (strncmp(*atoms->resinfo[atoms->atom[atoms->nr-1].resind].name, "PRO", 3) == 0)
855 protdata->sel_ntdb[0] = &(protdata->ntdb[nt]);
856 protdata->sel_ctdb[0] = &(protdata->ctdb[ct]);
858 /* set terminal residue numbers: */
859 snew(protdata->rN, NTERPAIRS);
860 snew(protdata->rC, NTERPAIRS);
862 protdata->rC[0] = atoms->atom[atoms->nr-1].resind;
864 /* keep unprotonated topology: */
865 protdata->upatoms = atoms;
866 /* we don't have these yet: */
867 protdata->patoms = NULL;
869 bKeep_old_pdba = TRUE;
871 /* clear hackblocks: */
872 protdata->nab = NULL;
875 /* set flag to show we're initialized: */
876 protdata->bInit = TRUE;
882 fprintf(debug, "protonate: using available protdata\n");
884 /* add_h will need the unprotonated topology again: */
885 atoms = protdata->upatoms;
886 bUpdate_pdba = FALSE;
887 bKeep_old_pdba = FALSE;
891 nadd = add_h(&atoms, xptr, protdata->nah, protdata->ah,
892 NTERPAIRS, protdata->sel_ntdb, protdata->sel_ctdb,
893 protdata->rN, protdata->rC, TRUE,
894 &protdata->nab, &protdata->ab, bUpdate_pdba, bKeep_old_pdba);
895 if (!protdata->patoms)
897 /* store protonated topology */
898 protdata->patoms = atoms;
900 *atomsptr = protdata->patoms;
903 fprintf(debug, "natoms: %d -> %d (nadd=%d)\n",
904 protdata->upatoms->nr, protdata->patoms->nr, nadd);