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43 #include "gromacs/fileio/confio.h"
44 #include "gromacs/math/vec.h"
45 #include "gromacs/utility/futil.h"
54 #include "gromacs/topology/symtab.h"
55 #include "gromacs/utility/fatalerror.h"
56 #include "gromacs/utility/smalloc.h"
58 static void copy_atom(t_atoms *atoms1, int a1, t_atoms *atoms2, int a2)
60 atoms2->atom[a2] = atoms1->atom[a1];
61 snew(atoms2->atomname[a2], 1);
62 *atoms2->atomname[a2] = strdup(*atoms1->atomname[a1]);
65 static atom_id pdbasearch_atom(const char *name, int resind, t_atoms *pdba,
66 const char *searchtype, gmx_bool bAllowMissing)
70 for (i = 0; (i < pdba->nr) && (pdba->atom[i].resind != resind); i++)
75 return search_atom(name, i, pdba,
76 searchtype, bAllowMissing);
79 static void hacksearch_atom(int *ii, int *jj, char *name,
80 int nab[], t_hack *ab[],
81 int resind, t_atoms *pdba)
91 for (i = 0; (i < pdba->nr) && (pdba->atom[i].resind != resind); i++)
95 for (; (i < pdba->nr) && (pdba->atom[i].resind == resind) && (*ii < 0); i++)
97 for (j = 0; (j < nab[i]) && (*ii < 0); j++)
99 if (ab[i][j].nname && strcmp(name, ab[i][j].nname) == 0)
110 void dump_ab(FILE *out, int natom, int nab[], t_hack *ab[], gmx_bool bHeader)
114 #define SS(s) (s) ? (s) : "-"
118 fprintf(out, "ADDBLOCK (t_hack) natom=%d\n"
119 "%4s %2s %-4s %-4s %2s %-4s %-4s %-4s %-4s %1s %s\n",
120 natom, "atom", "nr", "old", "new", "tp", "ai", "aj", "ak", "al", "a", "x");
122 for (i = 0; i < natom; i++)
124 for (j = 0; j < nab[i]; j++)
126 fprintf(out, "%4d %2d %-4s %-4s %2d %-4s %-4s %-4s %-4s %s %g %g %g\n",
127 i+1, ab[i][j].nr, SS(ab[i][j].oname), SS(ab[i][j].nname),
129 SS(ab[i][j].AI), SS(ab[i][j].AJ),
130 SS(ab[i][j].AK), SS(ab[i][j].AL),
131 ab[i][j].atom ? "+" : "",
132 ab[i][j].newx[XX], ab[i][j].newx[YY], ab[i][j].newx[ZZ]);
138 static t_hackblock *get_hackblocks(t_atoms *pdba, int nah, t_hackblock ah[],
140 t_hackblock **ntdb, t_hackblock **ctdb,
144 t_hackblock *hb, *ahptr;
147 snew(hb, pdba->nres);
148 /* first the termini */
149 for (i = 0; i < nterpairs; i++)
153 copy_t_hackblock(ntdb[i], &hb[rN[i]]);
157 merge_t_hackblock(ctdb[i], &hb[rC[i]]);
160 /* then the whole hdb */
161 for (rnr = 0; rnr < pdba->nres; rnr++)
163 ahptr = search_h_db(nah, ah, *pdba->resinfo[rnr].rtp);
166 if (hb[rnr].name == NULL)
168 hb[rnr].name = strdup(ahptr->name);
170 merge_hacks(ahptr, &hb[rnr]);
176 static void expand_hackblocks_one(t_hackblock *hbr, char *atomname,
177 int *nabi, t_hack **abi, gmx_bool bN, gmx_bool bC)
182 /* we'll recursively add atoms to atoms */
183 for (j = 0; j < hbr->nhack; j++)
185 /* first check if we're in the N- or C-terminus, then we should ignore
186 all hacks involving atoms from resp. previous or next residue
187 (i.e. which name begins with '-' (N) or '+' (C) */
189 if (bN) /* N-terminus: ignore '-' */
191 for (k = 0; k < 4 && hbr->hack[j].a[k] && !bIgnore; k++)
193 bIgnore = hbr->hack[j].a[k][0] == '-';
196 if (bC) /* C-terminus: ignore '+' */
198 for (k = 0; k < 4 && hbr->hack[j].a[k] && !bIgnore; k++)
200 bIgnore = hbr->hack[j].a[k][0] == '+';
203 /* must be either hdb entry (tp>0) or add from tdb (oname==NULL)
204 and first control aton (AI) matches this atom or
205 delete/replace from tdb (oname!=NULL) and oname matches this atom */
208 fprintf(debug, " %s", hbr->hack[j].oname ? hbr->hack[j].oname : hbr->hack[j].AI);
212 ( ( ( hbr->hack[j].tp > 0 || hbr->hack[j].oname == NULL ) &&
213 strcmp(atomname, hbr->hack[j].AI) == 0 ) ||
214 ( hbr->hack[j].oname != NULL &&
215 strcmp(atomname, hbr->hack[j].oname) == 0) ) )
217 /* now expand all hacks for this atom */
220 fprintf(debug, " +%dh", hbr->hack[j].nr);
222 srenew(*abi, *nabi + hbr->hack[j].nr);
223 for (k = 0; k < hbr->hack[j].nr; k++)
225 copy_t_hack(&hbr->hack[j], &(*abi)[*nabi + k]);
226 (*abi)[*nabi + k].bXSet = FALSE;
227 /* if we're adding (oname==NULL) and don't have a new name (nname)
228 yet, build it from atomname */
229 if ( (*abi)[*nabi + k].nname == NULL)
231 if ( (*abi)[*nabi + k].oname == NULL)
233 (*abi)[*nabi + k].nname = strdup(atomname);
234 (*abi)[*nabi + k].nname[0] = 'H';
241 fprintf(debug, "Hack '%s' %d, replacing nname '%s' with '%s' (old name '%s')\n",
243 (*abi)[*nabi + k].nname, hbr->hack[j].nname,
244 (*abi)[*nabi + k].oname ? (*abi)[*nabi + k].oname : "");
246 sfree((*abi)[*nabi + k].nname);
247 (*abi)[*nabi + k].nname = strdup(hbr->hack[j].nname);
250 if (hbr->hack[j].tp == 10 && k == 2)
252 /* This is a water virtual site, not a hydrogen */
253 /* Ugly hardcoded name hack */
254 (*abi)[*nabi + k].nname[0] = 'M';
256 else if (hbr->hack[j].tp == 11 && k >= 2)
258 /* This is a water lone pair, not a hydrogen */
259 /* Ugly hardcoded name hack */
260 srenew((*abi)[*nabi + k].nname, 4);
261 (*abi)[*nabi + k].nname[0] = 'L';
262 (*abi)[*nabi + k].nname[1] = 'P';
263 (*abi)[*nabi + k].nname[2] = '1' + k - 2;
264 (*abi)[*nabi + k].nname[3] = '\0';
266 else if (hbr->hack[j].nr > 1)
268 /* adding more than one atom, number them */
269 l = strlen((*abi)[*nabi + k].nname);
270 srenew((*abi)[*nabi + k].nname, l+2);
271 (*abi)[*nabi + k].nname[l] = '1' + k;
272 (*abi)[*nabi + k].nname[l+1] = '\0';
275 (*nabi) += hbr->hack[j].nr;
277 /* add hacks to atoms we've just added */
278 if (hbr->hack[j].tp > 0 || hbr->hack[j].oname == NULL)
280 for (k = 0; k < hbr->hack[j].nr; k++)
282 expand_hackblocks_one(hbr, (*abi)[*nabi-hbr->hack[j].nr+k].nname,
290 static void expand_hackblocks(t_atoms *pdba, t_hackblock hb[],
291 int nab[], t_hack *ab[],
292 int nterpairs, int *rN, int *rC)
297 for (i = 0; i < pdba->nr; i++)
300 for (j = 0; j < nterpairs && !bN; j++)
302 bN = pdba->atom[i].resind == rN[j];
305 for (j = 0; j < nterpairs && !bC; j++)
307 bC = pdba->atom[i].resind == rC[j];
310 /* add hacks to this atom */
311 expand_hackblocks_one(&hb[pdba->atom[i].resind], *pdba->atomname[i],
312 &nab[i], &ab[i], bN, bC);
316 fprintf(debug, "\n");
320 static int check_atoms_present(t_atoms *pdba, int nab[], t_hack *ab[])
322 int i, j, k, d, rnr, nadd;
325 for (i = 0; i < pdba->nr; i++)
327 rnr = pdba->atom[i].resind;
328 for (j = 0; j < nab[i]; j++)
330 if (ab[i][j].oname == NULL)
333 if (ab[i][j].nname == NULL)
335 gmx_incons("ab[i][j].nname not allocated");
337 /* check if the atom is already present */
338 k = pdbasearch_atom(ab[i][j].nname, rnr, pdba, "check", TRUE);
341 /* We found the added atom. */
342 ab[i][j].bAlreadyPresent = TRUE;
345 fprintf(debug, "Atom '%s' in residue '%s' %d is already present\n",
347 *pdba->resinfo[rnr].name, pdba->resinfo[rnr].nr);
352 ab[i][j].bAlreadyPresent = FALSE;
353 /* count how many atoms we'll add */
357 else if (ab[i][j].nname == NULL)
368 static void calc_all_pos(t_atoms *pdba, rvec x[], int nab[], t_hack *ab[],
369 gmx_bool bCheckMissing)
371 int i, j, ii, jj, m, ia, d, rnr, l = 0;
373 rvec xa[4]; /* control atoms for calc_h_pos */
374 rvec xh[MAXH]; /* hydrogen positions from calc_h_pos */
379 for (i = 0; i < pdba->nr; i++)
381 rnr = pdba->atom[i].resind;
382 for (j = 0; j < nab[i]; j += ab[i][j].nr)
384 /* check if we're adding: */
385 if (ab[i][j].oname == NULL && ab[i][j].tp > 0)
388 for (m = 0; (m < ab[i][j].nctl && bFoundAll); m++)
390 ia = pdbasearch_atom(ab[i][j].a[m], rnr, pdba,
391 bCheckMissing ? "atom" : "check",
395 /* not found in original atoms, might still be in t_hack (ab) */
396 hacksearch_atom(&ii, &jj, ab[i][j].a[m], nab, ab, rnr, pdba);
399 copy_rvec(ab[ii][jj].newx, xa[m]);
406 gmx_fatal(FARGS, "Atom %s not found in residue %s %d"
408 " while adding hydrogens",
410 *pdba->resinfo[rnr].name,
411 pdba->resinfo[rnr].nr,
412 *pdba->resinfo[rnr].rtp);
418 copy_rvec(x[ia], xa[m]);
423 for (m = 0; (m < MAXH); m++)
425 for (d = 0; d < DIM; d++)
437 calc_h_pos(ab[i][j].tp, xa, xh, &l);
438 for (m = 0; m < ab[i][j].nr; m++)
440 copy_rvec(xh[m], ab[i][j+m].newx);
441 ab[i][j+m].bXSet = TRUE;
449 static void free_ab(int natoms, int *nab, t_hack **ab)
453 for (i = 0; i < natoms; i++)
455 free_t_hack(nab[i], &ab[i]);
461 static int add_h_low(t_atoms **pdbaptr, rvec *xptr[],
462 int nah, t_hackblock ah[],
463 int nterpairs, t_hackblock **ntdb, t_hackblock **ctdb,
464 int *rN, int *rC, gmx_bool bCheckMissing,
465 int **nabptr, t_hack ***abptr,
466 gmx_bool bUpdate_pdba, gmx_bool bKeep_old_pdba)
468 t_atoms *newpdba = NULL, *pdba = NULL;
470 int i, newi, j, d, natoms, nalreadypresent;
477 /* set flags for adding hydrogens (according to hdb) */
483 /* the first time these will be pointers to NULL, but we will
484 return in them the completed arrays, which we will get back
491 fprintf(debug, "pointer to ab found\n");
501 /* WOW, everything was already figured out */
502 bUpdate_pdba = FALSE;
505 fprintf(debug, "pointer to non-null ab found\n");
510 /* We'll have to do all the hard work */
512 /* first get all the hackblocks for each residue: */
513 hb = get_hackblocks(pdba, nah, ah, nterpairs, ntdb, ctdb, rN, rC);
516 dump_hb(debug, pdba->nres, hb);
519 /* expand the hackblocks to atom level */
522 expand_hackblocks(pdba, hb, nab, ab, nterpairs, rN, rC);
523 free_t_hackblock(pdba->nres, &hb);
528 fprintf(debug, "before calc_all_pos\n");
529 dump_ab(debug, natoms, nab, ab, TRUE);
532 /* Now calc the positions */
533 calc_all_pos(pdba, *xptr, nab, ab, bCheckMissing);
537 fprintf(debug, "after calc_all_pos\n");
538 dump_ab(debug, natoms, nab, ab, TRUE);
543 /* we don't have to add atoms that are already present in pdba,
544 so we will remove them from the ab (t_hack) */
545 nadd = check_atoms_present(pdba, nab, ab);
548 fprintf(debug, "removed add hacks that were already in pdba:\n");
549 dump_ab(debug, natoms, nab, ab, TRUE);
550 fprintf(debug, "will be adding %d atoms\n", nadd);
553 /* Copy old atoms, making space for new ones */
555 init_t_atoms(newpdba, natoms+nadd, FALSE);
556 newpdba->nres = pdba->nres;
557 sfree(newpdba->resinfo);
558 newpdba->resinfo = pdba->resinfo;
566 fprintf(debug, "snew xn for %d old + %d new atoms %d total)\n",
567 natoms, nadd, natoms+nadd);
572 /* There is nothing to do: return now */
575 free_ab(natoms, nab, ab);
581 snew(xn, natoms+nadd);
583 for (i = 0; (i < natoms); i++)
585 /* check if this atom wasn't scheduled for deletion */
586 if (nab[i] == 0 || (ab[i][0].nname != NULL) )
588 if (newi >= natoms+nadd)
590 /*gmx_fatal(FARGS,"Not enough space for adding atoms");*/
592 srenew(xn, natoms+nadd);
595 srenew(newpdba->atom, natoms+nadd);
596 srenew(newpdba->atomname, natoms+nadd);
602 fprintf(debug, "(%3d) %3d %4s %4s%3d %3d",
603 i+1, newi+1, *pdba->atomname[i],
604 *pdba->resinfo[pdba->atom[i].resind].name,
605 pdba->resinfo[pdba->atom[i].resind].nr, nab[i]);
609 copy_atom(pdba, i, newpdba, newi);
611 copy_rvec((*xptr)[i], xn[newi]);
612 /* process the hacks for this atom */
614 for (j = 0; j < nab[i]; j++)
616 if (ab[i][j].oname == NULL) /* add */
619 if (newi >= natoms+nadd)
621 /* gmx_fatal(FARGS,"Not enough space for adding atoms");*/
623 srenew(xn, natoms+nadd);
626 srenew(newpdba->atom, natoms+nadd);
627 srenew(newpdba->atomname, natoms+nadd);
633 newpdba->atom[newi].resind = pdba->atom[i].resind;
637 fprintf(debug, " + %d", newi+1);
640 if (ab[i][j].nname != NULL &&
641 (ab[i][j].oname == NULL ||
642 strcmp(ab[i][j].oname, *newpdba->atomname[newi]) == 0))
645 if (ab[i][j].oname == NULL && ab[i][j].bAlreadyPresent)
647 /* This atom is already present, copy it from the input. */
651 copy_atom(pdba, i+nalreadypresent, newpdba, newi);
653 copy_rvec((*xptr)[i+nalreadypresent], xn[newi]);
661 fprintf(debug, "Replacing %d '%s' with (old name '%s') %s\n",
663 (newpdba->atomname[newi] && *newpdba->atomname[newi]) ? *newpdba->atomname[newi] : "",
664 ab[i][j].oname ? ab[i][j].oname : "",
667 snew(newpdba->atomname[newi], 1);
668 *newpdba->atomname[newi] = strdup(ab[i][j].nname);
669 if (ab[i][j].oname != NULL && ab[i][j].atom) /* replace */
670 { /* newpdba->atom[newi].m = ab[i][j].atom->m; */
671 /* newpdba->atom[newi].q = ab[i][j].atom->q; */
672 /* newpdba->atom[newi].type = ab[i][j].atom->type; */
677 copy_rvec(ab[i][j].newx, xn[newi]);
680 if (bUpdate_pdba && debug)
682 fprintf(debug, " %s %g %g", *newpdba->atomname[newi],
683 newpdba->atom[newi].m, newpdba->atom[newi].q);
688 i += nalreadypresent;
691 fprintf(debug, "\n");
708 free_ab(natoms, nab, ab);
715 for (i = 0; i < natoms; i++)
717 /* Do not free the atomname string itself, it might be in symtab */
718 /* sfree(*(pdba->atomname[i])); */
719 /* sfree(pdba->atomname[i]); */
721 sfree(pdba->atomname);
723 sfree(pdba->pdbinfo);
739 void deprotonate(t_atoms *atoms, rvec *x)
744 for (i = 0; i < atoms->nr; i++)
746 if ( (*atoms->atomname[i])[0] != 'H')
748 atoms->atomname[j] = atoms->atomname[i];
749 atoms->atom[j] = atoms->atom[i];
750 copy_rvec(x[i], x[j]);
757 int add_h(t_atoms **pdbaptr, rvec *xptr[],
758 int nah, t_hackblock ah[],
759 int nterpairs, t_hackblock **ntdb, t_hackblock **ctdb,
760 int *rN, int *rC, gmx_bool bAllowMissing,
761 int **nabptr, t_hack ***abptr,
762 gmx_bool bUpdate_pdba, gmx_bool bKeep_old_pdba)
764 int nold, nnew, niter;
766 /* Here we loop to be able to add atoms to added atoms.
767 * We should not check for missing atoms here.
774 nnew = add_h_low(pdbaptr, xptr, nah, ah, nterpairs, ntdb, ctdb, rN, rC, FALSE,
775 nabptr, abptr, bUpdate_pdba, bKeep_old_pdba);
779 gmx_fatal(FARGS, "More than 100 iterations of add_h. Maybe you are trying to replace an added atom (this is not supported)?");
786 /* Call add_h_low once more, now only for the missing atoms check */
787 add_h_low(pdbaptr, xptr, nah, ah, nterpairs, ntdb, ctdb, rN, rC, TRUE,
788 nabptr, abptr, bUpdate_pdba, bKeep_old_pdba);
794 int protonate(t_atoms **atomsptr, rvec **xptr, t_protonate *protdata)
798 gmx_bool bUpdate_pdba, bKeep_old_pdba;
799 int nntdb, nctdb, nt, ct;
803 if (!protdata->bInit)
807 fprintf(debug, "protonate: Initializing protdata\n");
810 /* set forcefield to use: */
811 strcpy(protdata->FF, "oplsaa.ff");
813 /* get the databases: */
814 protdata->nah = read_h_db(protdata->FF, &protdata->ah);
815 open_symtab(&protdata->tab);
816 protdata->atype = read_atype(protdata->FF, &protdata->tab);
817 nntdb = read_ter_db(protdata->FF, 'n', &protdata->ntdb, protdata->atype);
820 gmx_fatal(FARGS, "no N-terminus database");
822 nctdb = read_ter_db(protdata->FF, 'c', &protdata->ctdb, protdata->atype);
825 gmx_fatal(FARGS, "no C-terminus database");
828 /* set terminus types: -NH3+ (different for Proline) and -COO- */
830 snew(protdata->sel_ntdb, NTERPAIRS);
831 snew(protdata->sel_ctdb, NTERPAIRS);
833 if (nntdb >= 4 && nctdb >= 2)
835 /* Yuk, yuk, hardcoded default termini selections !!! */
836 if (strncmp(*atoms->resinfo[atoms->atom[atoms->nr-1].resind].name, "PRO", 3) == 0)
851 protdata->sel_ntdb[0] = &(protdata->ntdb[nt]);
852 protdata->sel_ctdb[0] = &(protdata->ctdb[ct]);
854 /* set terminal residue numbers: */
855 snew(protdata->rN, NTERPAIRS);
856 snew(protdata->rC, NTERPAIRS);
858 protdata->rC[0] = atoms->atom[atoms->nr-1].resind;
860 /* keep unprotonated topology: */
861 protdata->upatoms = atoms;
862 /* we don't have these yet: */
863 protdata->patoms = NULL;
865 bKeep_old_pdba = TRUE;
867 /* clear hackblocks: */
868 protdata->nab = NULL;
871 /* set flag to show we're initialized: */
872 protdata->bInit = TRUE;
878 fprintf(debug, "protonate: using available protdata\n");
880 /* add_h will need the unprotonated topology again: */
881 atoms = protdata->upatoms;
882 bUpdate_pdba = FALSE;
883 bKeep_old_pdba = FALSE;
887 nadd = add_h(&atoms, xptr, protdata->nah, protdata->ah,
888 NTERPAIRS, protdata->sel_ntdb, protdata->sel_ctdb,
889 protdata->rN, protdata->rC, TRUE,
890 &protdata->nab, &protdata->ab, bUpdate_pdba, bKeep_old_pdba);
891 if (!protdata->patoms)
893 /* store protonated topology */
894 protdata->patoms = atoms;
896 *atomsptr = protdata->patoms;
899 fprintf(debug, "natoms: %d -> %d (nadd=%d)\n",
900 protdata->upatoms->nr, protdata->patoms->nr, nadd);