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45 #include "gromacs/fileio/confio.h"
46 #include "gromacs/math/vec.h"
47 #include "gromacs/utility/futil.h"
56 #include "gromacs/topology/symtab.h"
57 #include "gromacs/utility/fatalerror.h"
58 #include "gromacs/utility/smalloc.h"
60 static void copy_atom(t_atoms *atoms1, int a1, t_atoms *atoms2, int a2)
62 atoms2->atom[a2] = atoms1->atom[a1];
63 snew(atoms2->atomname[a2], 1);
64 *atoms2->atomname[a2] = strdup(*atoms1->atomname[a1]);
67 static atom_id pdbasearch_atom(const char *name, int resind, t_atoms *pdba,
68 const char *searchtype, gmx_bool bAllowMissing)
72 for (i = 0; (i < pdba->nr) && (pdba->atom[i].resind != resind); i++)
77 return search_atom(name, i, pdba,
78 searchtype, bAllowMissing);
81 static void hacksearch_atom(int *ii, int *jj, char *name,
82 int nab[], t_hack *ab[],
83 int resind, t_atoms *pdba)
93 for (i = 0; (i < pdba->nr) && (pdba->atom[i].resind != resind); i++)
97 for (; (i < pdba->nr) && (pdba->atom[i].resind == resind) && (*ii < 0); i++)
99 for (j = 0; (j < nab[i]) && (*ii < 0); j++)
101 if (ab[i][j].nname && strcmp(name, ab[i][j].nname) == 0)
112 void dump_ab(FILE *out, int natom, int nab[], t_hack *ab[], gmx_bool bHeader)
116 #define SS(s) (s) ? (s) : "-"
120 fprintf(out, "ADDBLOCK (t_hack) natom=%d\n"
121 "%4s %2s %-4s %-4s %2s %-4s %-4s %-4s %-4s %1s %s\n",
122 natom, "atom", "nr", "old", "new", "tp", "ai", "aj", "ak", "al", "a", "x");
124 for (i = 0; i < natom; i++)
126 for (j = 0; j < nab[i]; j++)
128 fprintf(out, "%4d %2d %-4s %-4s %2d %-4s %-4s %-4s %-4s %s %g %g %g\n",
129 i+1, ab[i][j].nr, SS(ab[i][j].oname), SS(ab[i][j].nname),
131 SS(ab[i][j].AI), SS(ab[i][j].AJ),
132 SS(ab[i][j].AK), SS(ab[i][j].AL),
133 ab[i][j].atom ? "+" : "",
134 ab[i][j].newx[XX], ab[i][j].newx[YY], ab[i][j].newx[ZZ]);
140 static t_hackblock *get_hackblocks(t_atoms *pdba, int nah, t_hackblock ah[],
142 t_hackblock **ntdb, t_hackblock **ctdb,
146 t_hackblock *hb, *ahptr;
149 snew(hb, pdba->nres);
150 /* first the termini */
151 for (i = 0; i < nterpairs; i++)
155 copy_t_hackblock(ntdb[i], &hb[rN[i]]);
159 merge_t_hackblock(ctdb[i], &hb[rC[i]]);
162 /* then the whole hdb */
163 for (rnr = 0; rnr < pdba->nres; rnr++)
165 ahptr = search_h_db(nah, ah, *pdba->resinfo[rnr].rtp);
168 if (hb[rnr].name == NULL)
170 hb[rnr].name = strdup(ahptr->name);
172 merge_hacks(ahptr, &hb[rnr]);
178 static void expand_hackblocks_one(t_hackblock *hbr, char *atomname,
179 int *nabi, t_hack **abi, gmx_bool bN, gmx_bool bC)
184 /* we'll recursively add atoms to atoms */
185 for (j = 0; j < hbr->nhack; j++)
187 /* first check if we're in the N- or C-terminus, then we should ignore
188 all hacks involving atoms from resp. previous or next residue
189 (i.e. which name begins with '-' (N) or '+' (C) */
191 if (bN) /* N-terminus: ignore '-' */
193 for (k = 0; k < 4 && hbr->hack[j].a[k] && !bIgnore; k++)
195 bIgnore = hbr->hack[j].a[k][0] == '-';
198 if (bC) /* C-terminus: ignore '+' */
200 for (k = 0; k < 4 && hbr->hack[j].a[k] && !bIgnore; k++)
202 bIgnore = hbr->hack[j].a[k][0] == '+';
205 /* must be either hdb entry (tp>0) or add from tdb (oname==NULL)
206 and first control aton (AI) matches this atom or
207 delete/replace from tdb (oname!=NULL) and oname matches this atom */
210 fprintf(debug, " %s", hbr->hack[j].oname ? hbr->hack[j].oname : hbr->hack[j].AI);
214 ( ( ( hbr->hack[j].tp > 0 || hbr->hack[j].oname == NULL ) &&
215 strcmp(atomname, hbr->hack[j].AI) == 0 ) ||
216 ( hbr->hack[j].oname != NULL &&
217 strcmp(atomname, hbr->hack[j].oname) == 0) ) )
219 /* now expand all hacks for this atom */
222 fprintf(debug, " +%dh", hbr->hack[j].nr);
224 srenew(*abi, *nabi + hbr->hack[j].nr);
225 for (k = 0; k < hbr->hack[j].nr; k++)
227 copy_t_hack(&hbr->hack[j], &(*abi)[*nabi + k]);
228 (*abi)[*nabi + k].bXSet = FALSE;
229 /* if we're adding (oname==NULL) and don't have a new name (nname)
230 yet, build it from atomname */
231 if ( (*abi)[*nabi + k].nname == NULL)
233 if ( (*abi)[*nabi + k].oname == NULL)
235 (*abi)[*nabi + k].nname = strdup(atomname);
236 (*abi)[*nabi + k].nname[0] = 'H';
243 fprintf(debug, "Hack '%s' %d, replacing nname '%s' with '%s' (old name '%s')\n",
245 (*abi)[*nabi + k].nname, hbr->hack[j].nname,
246 (*abi)[*nabi + k].oname ? (*abi)[*nabi + k].oname : "");
248 sfree((*abi)[*nabi + k].nname);
249 (*abi)[*nabi + k].nname = strdup(hbr->hack[j].nname);
252 if (hbr->hack[j].tp == 10 && k == 2)
254 /* This is a water virtual site, not a hydrogen */
255 /* Ugly hardcoded name hack */
256 (*abi)[*nabi + k].nname[0] = 'M';
258 else if (hbr->hack[j].tp == 11 && k >= 2)
260 /* This is a water lone pair, not a hydrogen */
261 /* Ugly hardcoded name hack */
262 srenew((*abi)[*nabi + k].nname, 4);
263 (*abi)[*nabi + k].nname[0] = 'L';
264 (*abi)[*nabi + k].nname[1] = 'P';
265 (*abi)[*nabi + k].nname[2] = '1' + k - 2;
266 (*abi)[*nabi + k].nname[3] = '\0';
268 else if (hbr->hack[j].nr > 1)
270 /* adding more than one atom, number them */
271 l = strlen((*abi)[*nabi + k].nname);
272 srenew((*abi)[*nabi + k].nname, l+2);
273 (*abi)[*nabi + k].nname[l] = '1' + k;
274 (*abi)[*nabi + k].nname[l+1] = '\0';
277 (*nabi) += hbr->hack[j].nr;
279 /* add hacks to atoms we've just added */
280 if (hbr->hack[j].tp > 0 || hbr->hack[j].oname == NULL)
282 for (k = 0; k < hbr->hack[j].nr; k++)
284 expand_hackblocks_one(hbr, (*abi)[*nabi-hbr->hack[j].nr+k].nname,
292 static void expand_hackblocks(t_atoms *pdba, t_hackblock hb[],
293 int nab[], t_hack *ab[],
294 int nterpairs, int *rN, int *rC)
299 for (i = 0; i < pdba->nr; i++)
302 for (j = 0; j < nterpairs && !bN; j++)
304 bN = pdba->atom[i].resind == rN[j];
307 for (j = 0; j < nterpairs && !bC; j++)
309 bC = pdba->atom[i].resind == rC[j];
312 /* add hacks to this atom */
313 expand_hackblocks_one(&hb[pdba->atom[i].resind], *pdba->atomname[i],
314 &nab[i], &ab[i], bN, bC);
318 fprintf(debug, "\n");
322 static int check_atoms_present(t_atoms *pdba, int nab[], t_hack *ab[])
324 int i, j, k, d, rnr, nadd;
327 for (i = 0; i < pdba->nr; i++)
329 rnr = pdba->atom[i].resind;
330 for (j = 0; j < nab[i]; j++)
332 if (ab[i][j].oname == NULL)
335 if (ab[i][j].nname == NULL)
337 gmx_incons("ab[i][j].nname not allocated");
339 /* check if the atom is already present */
340 k = pdbasearch_atom(ab[i][j].nname, rnr, pdba, "check", TRUE);
343 /* We found the added atom. */
344 ab[i][j].bAlreadyPresent = TRUE;
347 fprintf(debug, "Atom '%s' in residue '%s' %d is already present\n",
349 *pdba->resinfo[rnr].name, pdba->resinfo[rnr].nr);
354 ab[i][j].bAlreadyPresent = FALSE;
355 /* count how many atoms we'll add */
359 else if (ab[i][j].nname == NULL)
370 static void calc_all_pos(t_atoms *pdba, rvec x[], int nab[], t_hack *ab[],
371 gmx_bool bCheckMissing)
373 int i, j, ii, jj, m, ia, d, rnr, l = 0;
375 rvec xa[4]; /* control atoms for calc_h_pos */
376 rvec xh[MAXH]; /* hydrogen positions from calc_h_pos */
381 for (i = 0; i < pdba->nr; i++)
383 rnr = pdba->atom[i].resind;
384 for (j = 0; j < nab[i]; j += ab[i][j].nr)
386 /* check if we're adding: */
387 if (ab[i][j].oname == NULL && ab[i][j].tp > 0)
390 for (m = 0; (m < ab[i][j].nctl && bFoundAll); m++)
392 ia = pdbasearch_atom(ab[i][j].a[m], rnr, pdba,
393 bCheckMissing ? "atom" : "check",
397 /* not found in original atoms, might still be in t_hack (ab) */
398 hacksearch_atom(&ii, &jj, ab[i][j].a[m], nab, ab, rnr, pdba);
401 copy_rvec(ab[ii][jj].newx, xa[m]);
408 gmx_fatal(FARGS, "Atom %s not found in residue %s %d"
410 " while adding hydrogens",
412 *pdba->resinfo[rnr].name,
413 pdba->resinfo[rnr].nr,
414 *pdba->resinfo[rnr].rtp);
420 copy_rvec(x[ia], xa[m]);
425 for (m = 0; (m < MAXH); m++)
427 for (d = 0; d < DIM; d++)
439 calc_h_pos(ab[i][j].tp, xa, xh, &l);
440 for (m = 0; m < ab[i][j].nr; m++)
442 copy_rvec(xh[m], ab[i][j+m].newx);
443 ab[i][j+m].bXSet = TRUE;
451 static void free_ab(int natoms, int *nab, t_hack **ab)
455 for (i = 0; i < natoms; i++)
457 free_t_hack(nab[i], &ab[i]);
463 static int add_h_low(t_atoms **pdbaptr, rvec *xptr[],
464 int nah, t_hackblock ah[],
465 int nterpairs, t_hackblock **ntdb, t_hackblock **ctdb,
466 int *rN, int *rC, gmx_bool bCheckMissing,
467 int **nabptr, t_hack ***abptr,
468 gmx_bool bUpdate_pdba, gmx_bool bKeep_old_pdba)
470 t_atoms *newpdba = NULL, *pdba = NULL;
472 int i, newi, j, d, natoms, nalreadypresent;
479 /* set flags for adding hydrogens (according to hdb) */
485 /* the first time these will be pointers to NULL, but we will
486 return in them the completed arrays, which we will get back
493 fprintf(debug, "pointer to ab found\n");
503 /* WOW, everything was already figured out */
504 bUpdate_pdba = FALSE;
507 fprintf(debug, "pointer to non-null ab found\n");
512 /* We'll have to do all the hard work */
514 /* first get all the hackblocks for each residue: */
515 hb = get_hackblocks(pdba, nah, ah, nterpairs, ntdb, ctdb, rN, rC);
518 dump_hb(debug, pdba->nres, hb);
521 /* expand the hackblocks to atom level */
524 expand_hackblocks(pdba, hb, nab, ab, nterpairs, rN, rC);
525 free_t_hackblock(pdba->nres, &hb);
530 fprintf(debug, "before calc_all_pos\n");
531 dump_ab(debug, natoms, nab, ab, TRUE);
534 /* Now calc the positions */
535 calc_all_pos(pdba, *xptr, nab, ab, bCheckMissing);
539 fprintf(debug, "after calc_all_pos\n");
540 dump_ab(debug, natoms, nab, ab, TRUE);
545 /* we don't have to add atoms that are already present in pdba,
546 so we will remove them from the ab (t_hack) */
547 nadd = check_atoms_present(pdba, nab, ab);
550 fprintf(debug, "removed add hacks that were already in pdba:\n");
551 dump_ab(debug, natoms, nab, ab, TRUE);
552 fprintf(debug, "will be adding %d atoms\n", nadd);
555 /* Copy old atoms, making space for new ones */
557 init_t_atoms(newpdba, natoms+nadd, FALSE);
558 newpdba->nres = pdba->nres;
559 sfree(newpdba->resinfo);
560 newpdba->resinfo = pdba->resinfo;
568 fprintf(debug, "snew xn for %d old + %d new atoms %d total)\n",
569 natoms, nadd, natoms+nadd);
574 /* There is nothing to do: return now */
577 free_ab(natoms, nab, ab);
583 snew(xn, natoms+nadd);
585 for (i = 0; (i < natoms); i++)
587 /* check if this atom wasn't scheduled for deletion */
588 if (nab[i] == 0 || (ab[i][0].nname != NULL) )
590 if (newi >= natoms+nadd)
592 /*gmx_fatal(FARGS,"Not enough space for adding atoms");*/
594 srenew(xn, natoms+nadd);
597 srenew(newpdba->atom, natoms+nadd);
598 srenew(newpdba->atomname, natoms+nadd);
604 fprintf(debug, "(%3d) %3d %4s %4s%3d %3d",
605 i+1, newi+1, *pdba->atomname[i],
606 *pdba->resinfo[pdba->atom[i].resind].name,
607 pdba->resinfo[pdba->atom[i].resind].nr, nab[i]);
611 copy_atom(pdba, i, newpdba, newi);
613 copy_rvec((*xptr)[i], xn[newi]);
614 /* process the hacks for this atom */
616 for (j = 0; j < nab[i]; j++)
618 if (ab[i][j].oname == NULL) /* add */
621 if (newi >= natoms+nadd)
623 /* gmx_fatal(FARGS,"Not enough space for adding atoms");*/
625 srenew(xn, natoms+nadd);
628 srenew(newpdba->atom, natoms+nadd);
629 srenew(newpdba->atomname, natoms+nadd);
635 newpdba->atom[newi].resind = pdba->atom[i].resind;
639 fprintf(debug, " + %d", newi+1);
642 if (ab[i][j].nname != NULL &&
643 (ab[i][j].oname == NULL ||
644 strcmp(ab[i][j].oname, *newpdba->atomname[newi]) == 0))
647 if (ab[i][j].oname == NULL && ab[i][j].bAlreadyPresent)
649 /* This atom is already present, copy it from the input. */
653 copy_atom(pdba, i+nalreadypresent, newpdba, newi);
655 copy_rvec((*xptr)[i+nalreadypresent], xn[newi]);
663 fprintf(debug, "Replacing %d '%s' with (old name '%s') %s\n",
665 (newpdba->atomname[newi] && *newpdba->atomname[newi]) ? *newpdba->atomname[newi] : "",
666 ab[i][j].oname ? ab[i][j].oname : "",
669 snew(newpdba->atomname[newi], 1);
670 *newpdba->atomname[newi] = strdup(ab[i][j].nname);
671 if (ab[i][j].oname != NULL && ab[i][j].atom) /* replace */
672 { /* newpdba->atom[newi].m = ab[i][j].atom->m; */
673 /* newpdba->atom[newi].q = ab[i][j].atom->q; */
674 /* newpdba->atom[newi].type = ab[i][j].atom->type; */
679 copy_rvec(ab[i][j].newx, xn[newi]);
682 if (bUpdate_pdba && debug)
684 fprintf(debug, " %s %g %g", *newpdba->atomname[newi],
685 newpdba->atom[newi].m, newpdba->atom[newi].q);
690 i += nalreadypresent;
693 fprintf(debug, "\n");
710 free_ab(natoms, nab, ab);
717 for (i = 0; i < natoms; i++)
719 /* Do not free the atomname string itself, it might be in symtab */
720 /* sfree(*(pdba->atomname[i])); */
721 /* sfree(pdba->atomname[i]); */
723 sfree(pdba->atomname);
725 sfree(pdba->pdbinfo);
741 void deprotonate(t_atoms *atoms, rvec *x)
746 for (i = 0; i < atoms->nr; i++)
748 if ( (*atoms->atomname[i])[0] != 'H')
750 atoms->atomname[j] = atoms->atomname[i];
751 atoms->atom[j] = atoms->atom[i];
752 copy_rvec(x[i], x[j]);
759 int add_h(t_atoms **pdbaptr, rvec *xptr[],
760 int nah, t_hackblock ah[],
761 int nterpairs, t_hackblock **ntdb, t_hackblock **ctdb,
762 int *rN, int *rC, gmx_bool bAllowMissing,
763 int **nabptr, t_hack ***abptr,
764 gmx_bool bUpdate_pdba, gmx_bool bKeep_old_pdba)
766 int nold, nnew, niter;
768 /* Here we loop to be able to add atoms to added atoms.
769 * We should not check for missing atoms here.
776 nnew = add_h_low(pdbaptr, xptr, nah, ah, nterpairs, ntdb, ctdb, rN, rC, FALSE,
777 nabptr, abptr, bUpdate_pdba, bKeep_old_pdba);
781 gmx_fatal(FARGS, "More than 100 iterations of add_h. Maybe you are trying to replace an added atom (this is not supported)?");
788 /* Call add_h_low once more, now only for the missing atoms check */
789 add_h_low(pdbaptr, xptr, nah, ah, nterpairs, ntdb, ctdb, rN, rC, TRUE,
790 nabptr, abptr, bUpdate_pdba, bKeep_old_pdba);
796 int protonate(t_atoms **atomsptr, rvec **xptr, t_protonate *protdata)
800 gmx_bool bUpdate_pdba, bKeep_old_pdba;
801 int nntdb, nctdb, nt, ct;
805 if (!protdata->bInit)
809 fprintf(debug, "protonate: Initializing protdata\n");
812 /* set forcefield to use: */
813 strcpy(protdata->FF, "oplsaa.ff");
815 /* get the databases: */
816 protdata->nah = read_h_db(protdata->FF, &protdata->ah);
817 open_symtab(&protdata->tab);
818 protdata->atype = read_atype(protdata->FF, &protdata->tab);
819 nntdb = read_ter_db(protdata->FF, 'n', &protdata->ntdb, protdata->atype);
822 gmx_fatal(FARGS, "no N-terminus database");
824 nctdb = read_ter_db(protdata->FF, 'c', &protdata->ctdb, protdata->atype);
827 gmx_fatal(FARGS, "no C-terminus database");
830 /* set terminus types: -NH3+ (different for Proline) and -COO- */
832 snew(protdata->sel_ntdb, NTERPAIRS);
833 snew(protdata->sel_ctdb, NTERPAIRS);
835 if (nntdb >= 4 && nctdb >= 2)
837 /* Yuk, yuk, hardcoded default termini selections !!! */
838 if (strncmp(*atoms->resinfo[atoms->atom[atoms->nr-1].resind].name, "PRO", 3) == 0)
853 protdata->sel_ntdb[0] = &(protdata->ntdb[nt]);
854 protdata->sel_ctdb[0] = &(protdata->ctdb[ct]);
856 /* set terminal residue numbers: */
857 snew(protdata->rN, NTERPAIRS);
858 snew(protdata->rC, NTERPAIRS);
860 protdata->rC[0] = atoms->atom[atoms->nr-1].resind;
862 /* keep unprotonated topology: */
863 protdata->upatoms = atoms;
864 /* we don't have these yet: */
865 protdata->patoms = NULL;
867 bKeep_old_pdba = TRUE;
869 /* clear hackblocks: */
870 protdata->nab = NULL;
873 /* set flag to show we're initialized: */
874 protdata->bInit = TRUE;
880 fprintf(debug, "protonate: using available protdata\n");
882 /* add_h will need the unprotonated topology again: */
883 atoms = protdata->upatoms;
884 bUpdate_pdba = FALSE;
885 bKeep_old_pdba = FALSE;
889 nadd = add_h(&atoms, xptr, protdata->nah, protdata->ah,
890 NTERPAIRS, protdata->sel_ntdb, protdata->sel_ctdb,
891 protdata->rN, protdata->rC, TRUE,
892 &protdata->nab, &protdata->ab, bUpdate_pdba, bKeep_old_pdba);
893 if (!protdata->patoms)
895 /* store protonated topology */
896 protdata->patoms = atoms;
898 *atomsptr = protdata->patoms;
901 fprintf(debug, "natoms: %d -> %d (nadd=%d)\n",
902 protdata->upatoms->nr, protdata->patoms->nr, nadd);