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48 #include "gromacs/fileio/gmxfio.h"
49 #include "gromacs/math/units.h"
50 #include "gromacs/math/vec.h"
51 #include "gromacs/pbcutil/pbc.h"
52 #include "gromacs/topology/atomprop.h"
53 #include "gromacs/topology/ifunc.h"
54 #include "gromacs/topology/residuetypes.h"
55 #include "gromacs/topology/symtab.h"
56 #include "gromacs/topology/topology.h"
57 #include "gromacs/utility/coolstuff.h"
58 #include "gromacs/utility/cstringutil.h"
59 #include "gromacs/utility/fatalerror.h"
60 #include "gromacs/utility/futil.h"
61 #include "gromacs/utility/smalloc.h"
62 #include "gromacs/utility/snprintf.h"
68 typedef struct gmx_conect_t {
71 gmx_conection_t *conect;
74 static const char *pdbtp[epdbNR] = {
75 "ATOM ", "HETATM", "ANISOU", "CRYST1",
76 "COMPND", "MODEL", "ENDMDL", "TER", "HEADER", "TITLE", "REMARK",
81 #define REMARK_SIM_BOX "REMARK THIS IS A SIMULATION BOX"
83 static void xlate_atomname_pdb2gmx(char *name)
88 length = std::strlen(name);
89 if (length > 3 && std::isdigit(name[0]))
92 for (i = 1; i < length; i++)
96 name[length-1] = temp;
100 static void xlate_atomname_gmx2pdb(char *name)
105 length = std::strlen(name);
106 if (length > 3 && std::isdigit(name[length-1]))
108 temp = name[length-1];
109 for (i = length-1; i > 0; --i)
118 void gmx_write_pdb_box(FILE *out, int ePBC, const matrix box)
120 real alpha, beta, gamma;
124 ePBC = guess_ePBC(box);
127 if (ePBC == epbcNONE)
132 if (norm2(box[YY])*norm2(box[ZZ]) != 0)
134 alpha = RAD2DEG*gmx_angle(box[YY], box[ZZ]);
140 if (norm2(box[XX])*norm2(box[ZZ]) != 0)
142 beta = RAD2DEG*gmx_angle(box[XX], box[ZZ]);
148 if (norm2(box[XX])*norm2(box[YY]) != 0)
150 gamma = RAD2DEG*gmx_angle(box[XX], box[YY]);
156 fprintf(out, "REMARK THIS IS A SIMULATION BOX\n");
157 if (ePBC != epbcSCREW)
159 fprintf(out, "CRYST1%9.3f%9.3f%9.3f%7.2f%7.2f%7.2f %-11s%4d\n",
160 10*norm(box[XX]), 10*norm(box[YY]), 10*norm(box[ZZ]),
161 alpha, beta, gamma, "P 1", 1);
165 /* Double the a-vector length and write the correct space group */
166 fprintf(out, "CRYST1%9.3f%9.3f%9.3f%7.2f%7.2f%7.2f %-11s%4d\n",
167 20*norm(box[XX]), 10*norm(box[YY]), 10*norm(box[ZZ]),
168 alpha, beta, gamma, "P 21 1 1", 1);
173 static void read_cryst1(char *line, int *ePBC, matrix box)
176 char sa[12], sb[12], sc[12], sg[SG_SIZE+1], ident;
177 double fa, fb, fc, alpha, beta, gamma, cosa, cosb, cosg, sing;
178 int syma, symb, symc;
181 sscanf(line, "%*s%s%s%s%lf%lf%lf", sa, sb, sc, &alpha, &beta, &gamma);
184 if (strlen(line) >= 55)
186 strncpy(sg, line+55, SG_SIZE);
192 sscanf(sg, "%c %d %d %d", &ident, &syma, &symb, &symc);
193 if (ident == 'P' && syma == 1 && symb <= 1 && symc <= 1)
195 fc = strtod(sc, nullptr)*0.1;
196 ePBC_file = (fc > 0 ? epbcXYZ : epbcXY);
198 if (ident == 'P' && syma == 21 && symb == 1 && symc == 1)
200 ePBC_file = epbcSCREW;
210 fa = strtod(sa, nullptr)*0.1;
211 fb = strtod(sb, nullptr)*0.1;
212 fc = strtod(sc, nullptr)*0.1;
213 if (ePBC_file == epbcSCREW)
219 if ((alpha != 90.0) || (beta != 90.0) || (gamma != 90.0))
223 cosa = std::cos(alpha*DEG2RAD);
231 cosb = std::cos(beta*DEG2RAD);
239 cosg = std::cos(gamma*DEG2RAD);
240 sing = std::sin(gamma*DEG2RAD);
247 box[YY][XX] = fb*cosg;
248 box[YY][YY] = fb*sing;
249 box[ZZ][XX] = fc*cosb;
250 box[ZZ][YY] = fc*(cosa - cosb*cosg)/sing;
251 box[ZZ][ZZ] = std::sqrt(fc*fc
252 - box[ZZ][XX]*box[ZZ][XX] - box[ZZ][YY]*box[ZZ][YY]);
262 void write_pdbfile_indexed(FILE *out, const char *title,
263 const t_atoms *atoms, const rvec x[],
264 int ePBC, const matrix box, char chainid,
265 int model_nr, int nindex, const int index[],
266 gmx_conect conect, gmx_bool bTerSepChains)
268 gmx_conect_t *gc = (gmx_conect_t *)conect;
269 char resnm[6], nm[6];
272 enum PDB_record type;
273 unsigned char resic, ch;
277 int chainnum, lastchainnum;
278 gmx_residuetype_t*rt;
279 const char *p_restype;
280 const char *p_lastrestype;
282 gmx_residuetype_init(&rt);
284 fprintf(out, "TITLE %s\n", (title && title[0]) ? title : gmx::bromacs().c_str());
285 if (box && ( norm2(box[XX]) || norm2(box[YY]) || norm2(box[ZZ]) ) )
287 gmx_write_pdb_box(out, ePBC, box);
289 if (atoms->havePdbInfo)
291 /* Check whether any occupancies are set, in that case leave it as is,
292 * otherwise set them all to one
295 for (ii = 0; (ii < nindex) && bOccup; ii++)
298 bOccup = bOccup && (atoms->pdbinfo[i].occup == 0.0);
306 fprintf(out, "MODEL %8d\n", model_nr > 0 ? model_nr : 1);
311 for (ii = 0; ii < nindex; ii++)
314 resind = atoms->atom[i].resind;
315 chainnum = atoms->resinfo[resind].chainnum;
316 p_lastrestype = p_restype;
317 gmx_residuetype_get_type(rt, *atoms->resinfo[resind].name, &p_restype);
319 /* Add a TER record if we changed chain, and if either the previous or this chain is protein/DNA/RNA. */
320 if (bTerSepChains && ii > 0 && chainnum != lastchainnum)
322 /* Only add TER if the previous chain contained protein/DNA/RNA. */
323 if (gmx_residuetype_is_protein(rt, p_lastrestype) || gmx_residuetype_is_dna(rt, p_lastrestype) || gmx_residuetype_is_rna(rt, p_lastrestype))
325 fprintf(out, "TER\n");
327 lastchainnum = chainnum;
330 strncpy(resnm, *atoms->resinfo[resind].name, sizeof(resnm)-1);
331 resnm[sizeof(resnm)-1] = 0;
332 strncpy(nm, *atoms->atomname[i], sizeof(nm)-1);
333 nm[sizeof(nm)-1] = 0;
335 /* rename HG12 to 2HG1, etc. */
336 xlate_atomname_gmx2pdb(nm);
337 resnr = atoms->resinfo[resind].nr;
338 resic = atoms->resinfo[resind].ic;
345 ch = atoms->resinfo[resind].chainid;
354 resnr = resnr % 10000;
357 if (atoms->pdbinfo != nullptr)
359 pdbinfo = atoms->pdbinfo[i];
363 gmx_pdbinfo_init_default(&pdbinfo);
365 type = static_cast<enum PDB_record>(pdbinfo.type);
366 altloc = pdbinfo.altloc;
367 if (!isalnum(altloc))
371 occup = bOccup ? 1.0 : pdbinfo.occup;
374 gmx_fprintf_pdb_atomline(out,
383 10*x[i][XX], 10*x[i][YY], 10*x[i][ZZ],
386 atoms->atom[i].elem);
388 if (atoms->pdbinfo && atoms->pdbinfo[i].bAnisotropic)
390 fprintf(out, "ANISOU%5d %-4.4s%4.4s%c%4d%c %7d%7d%7d%7d%7d%7d\n",
391 (i+1)%100000, nm, resnm, ch, resnr,
392 (resic == '\0') ? ' ' : resic,
393 atoms->pdbinfo[i].uij[0], atoms->pdbinfo[i].uij[1],
394 atoms->pdbinfo[i].uij[2], atoms->pdbinfo[i].uij[3],
395 atoms->pdbinfo[i].uij[4], atoms->pdbinfo[i].uij[5]);
399 fprintf(out, "TER\n");
400 fprintf(out, "ENDMDL\n");
404 /* Write conect records */
405 for (i = 0; (i < gc->nconect); i++)
407 fprintf(out, "CONECT%5d%5d\n", gc->conect[i].ai+1, gc->conect[i].aj+1);
411 gmx_residuetype_destroy(rt);
414 void write_pdbfile(FILE *out, const char *title, const t_atoms *atoms, const rvec x[],
415 int ePBC, const matrix box, char chainid, int model_nr, gmx_conect conect, gmx_bool bTerSepChains)
419 snew(index, atoms->nr);
420 for (i = 0; i < atoms->nr; i++)
424 write_pdbfile_indexed(out, title, atoms, x, ePBC, box, chainid, model_nr,
425 atoms->nr, index, conect, bTerSepChains);
429 int line2type(char *line)
434 for (k = 0; (k < 6); k++)
440 for (k = 0; (k < epdbNR); k++)
442 if (std::strncmp(type, pdbtp[k], strlen(pdbtp[k])) == 0)
451 static void read_anisou(char line[], int natom, t_atoms *atoms)
455 char anr[12], anm[12];
459 for (k = 0; (k < 5); k++, j++)
465 for (k = 0; (k < 4); k++, j++)
472 /* Strip off spaces */
475 /* Search backwards for number and name only */
476 atomnr = std::strtol(anr, nullptr, 10);
477 for (i = natom-1; (i >= 0); i--)
479 if ((std::strcmp(anm, *(atoms->atomname[i])) == 0) &&
480 (atomnr == atoms->pdbinfo[i].atomnr))
487 fprintf(stderr, "Skipping ANISOU record (atom %s %d not found)\n",
492 if (sscanf(line+29, "%d%d%d%d%d%d",
493 &atoms->pdbinfo[i].uij[U11], &atoms->pdbinfo[i].uij[U22],
494 &atoms->pdbinfo[i].uij[U33], &atoms->pdbinfo[i].uij[U12],
495 &atoms->pdbinfo[i].uij[U13], &atoms->pdbinfo[i].uij[U23])
498 atoms->pdbinfo[i].bAnisotropic = TRUE;
502 fprintf(stderr, "Invalid ANISOU record for atom %d\n", i);
503 atoms->pdbinfo[i].bAnisotropic = FALSE;
508 void get_pdb_atomnumber(const t_atoms *atoms, gmx_atomprop_t aps)
510 int i, atomnumber, len;
512 char anm[6], anm_copy[6], *ptr;
518 gmx_incons("Trying to deduce atomnumbers when no pdb information is present");
520 for (i = 0; (i < atoms->nr); i++)
522 std::strcpy(anm, atoms->pdbinfo[i].atomnm);
523 std::strcpy(anm_copy, atoms->pdbinfo[i].atomnm);
524 bool atomNumberSet = false;
526 if ((anm[0] != ' ') && ((len <= 2) || !std::isdigit(anm[2])))
529 if (gmx_atomprop_query(aps, epropElement, "???", anm_copy, &eval))
531 atomnumber = std::round(eval);
532 atomNumberSet = true;
537 if (gmx_atomprop_query(aps, epropElement, "???", anm_copy, &eval))
539 atomnumber = std::round(eval);
540 atomNumberSet = true;
547 while ((k < std::strlen(anm)) && (std::isspace(anm[k]) || std::isdigit(anm[k])))
551 anm_copy[0] = anm[k];
553 if (gmx_atomprop_query(aps, epropElement, "???", anm_copy, &eval))
555 atomnumber = std::round(eval);
556 atomNumberSet = true;
561 atoms->atom[i].atomnumber = atomnumber;
562 ptr = gmx_atomprop_element(aps, atomnumber);
565 fprintf(debug, "Atomnumber for atom '%s' is %d\n",
573 std::strncpy(atoms->atom[i].elem, ptr == nullptr ? "" : ptr, 4);
577 static int read_atom(t_symtab *symtab,
578 char line[], int type, int natom,
579 t_atoms *atoms, rvec x[], int chainnum, gmx_bool bChange)
584 char anr[12], anm[12], anm_copy[12], altloc, resnm[12], rnr[12], elem[3];
585 char xc[12], yc[12], zc[12], occup[12], bfac[12];
588 int resnr, atomnumber;
590 if (natom >= atoms->nr)
592 gmx_fatal(FARGS, "\nFound more atoms (%d) in pdb file than expected (%d)",
598 for (k = 0; (k < 5); k++, j++)
605 for (k = 0; (k < 4); k++, j++)
610 std::strcpy(anm_copy, anm);
616 for (k = 0; (k < 4); k++, j++)
626 for (k = 0; (k < 4); k++, j++)
632 resnr = std::strtol(rnr, nullptr, 10);
636 /* X,Y,Z Coordinate */
637 for (k = 0; (k < 8); k++, j++)
642 for (k = 0; (k < 8); k++, j++)
647 for (k = 0; (k < 8); k++, j++)
654 for (k = 0; (k < 6); k++, j++)
661 for (k = 0; (k < 7); k++, j++)
671 for (k = 0; (k < 2); k++, j++)
680 atomn = &(atoms->atom[natom]);
682 atoms->resinfo[atoms->atom[natom-1].resind].nr != resnr ||
683 atoms->resinfo[atoms->atom[natom-1].resind].ic != resic ||
684 (strcmp(*atoms->resinfo[atoms->atom[natom-1].resind].name, resnm) != 0))
692 atomn->resind = atoms->atom[natom-1].resind + 1;
694 atoms->nres = atomn->resind + 1;
695 t_atoms_set_resinfo(atoms, natom, symtab, resnm, resnr, resic, chainnum, chainid);
699 atomn->resind = atoms->atom[natom-1].resind;
703 xlate_atomname_pdb2gmx(anm);
705 atoms->atomname[natom] = put_symtab(symtab, anm);
708 atomn->atomnumber = atomnumber;
709 strncpy(atomn->elem, elem, 4);
711 x[natom][XX] = strtod(xc, nullptr)*0.1;
712 x[natom][YY] = strtod(yc, nullptr)*0.1;
713 x[natom][ZZ] = strtod(zc, nullptr)*0.1;
716 atoms->pdbinfo[natom].type = type;
717 atoms->pdbinfo[natom].atomnr = strtol(anr, nullptr, 10);
718 atoms->pdbinfo[natom].altloc = altloc;
719 strcpy(atoms->pdbinfo[natom].atomnm, anm_copy);
720 atoms->pdbinfo[natom].bfac = strtod(bfac, nullptr);
721 atoms->pdbinfo[natom].occup = strtod(occup, nullptr);
728 gmx_bool is_hydrogen(const char *nm)
732 std::strcpy(buf, nm);
739 else if ((std::isdigit(buf[0])) && (buf[1] == 'H'))
746 gmx_bool is_dummymass(const char *nm)
750 std::strcpy(buf, nm);
753 if ((buf[0] == 'M') && std::isdigit(buf[strlen(buf)-1]))
761 static void gmx_conect_addline(gmx_conect_t *con, char *line)
764 char format[32], form2[32];
766 sprintf(form2, "%%*s");
767 sprintf(format, "%s%%d", form2);
768 if (sscanf(line, format, &ai) == 1)
772 std::strcat(form2, "%*s");
773 sprintf(format, "%s%%d", form2);
774 n = sscanf(line, format, &aj);
777 srenew(con->conect, ++con->nconect);
778 con->conect[con->nconect-1].ai = ai-1;
779 con->conect[con->nconect-1].aj = aj-1;
786 void gmx_conect_dump(FILE *fp, gmx_conect conect)
788 gmx_conect_t *gc = (gmx_conect_t *)conect;
791 for (i = 0; (i < gc->nconect); i++)
793 fprintf(fp, "%6s%5d%5d\n", "CONECT",
794 gc->conect[i].ai+1, gc->conect[i].aj+1);
798 gmx_conect gmx_conect_init()
807 void gmx_conect_done(gmx_conect conect)
809 gmx_conect_t *gc = conect;
814 gmx_bool gmx_conect_exist(gmx_conect conect, int ai, int aj)
816 gmx_conect_t *gc = conect;
822 for (i = 0; (i < gc->nconect); i++)
824 if (((gc->conect[i].ai == ai) &&
825 (gc->conect[i].aj == aj)) ||
826 ((gc->conect[i].aj == ai) &&
827 (gc->conect[i].ai == aj)))
835 void gmx_conect_add(gmx_conect conect, int ai, int aj)
837 gmx_conect_t *gc = (gmx_conect_t *)conect;
842 if (!gmx_conect_exist(conect, ai, aj))
844 srenew(gc->conect, ++gc->nconect);
845 gc->conect[gc->nconect-1].ai = ai;
846 gc->conect[gc->nconect-1].aj = aj;
850 int read_pdbfile(FILE *in, char *title, int *model_nr,
851 t_atoms *atoms, t_symtab *symtab, rvec x[], int *ePBC,
852 matrix box, gmx_bool bChange, gmx_conect conect)
854 gmx_conect_t *gc = conect;
856 gmx_bool bConnWarn = FALSE;
861 gmx_bool bStop = FALSE;
865 /* Only assume pbc when there is a CRYST1 entry */
873 atoms->haveMass = FALSE;
874 atoms->haveCharge = FALSE;
875 atoms->haveType = FALSE;
876 atoms->haveBState = FALSE;
877 atoms->havePdbInfo = (atoms->pdbinfo != nullptr);
883 while (!bStop && (fgets2(line, STRLEN, in) != nullptr))
885 line_type = line2type(line);
891 natom = read_atom(symtab, line, line_type, natom, atoms, x, chainnum, bChange);
895 if (atoms->havePdbInfo)
897 read_anisou(line, natom, atoms);
902 read_cryst1(line, ePBC, box);
907 if (std::strlen(line) > 6)
910 /* skip HEADER or TITLE and spaces */
919 /* truncate after title */
920 d = std::strstr(c, " ");
925 if (std::strlen(c) > 0)
927 std::strcpy(title, c);
933 if ((!std::strstr(line, ": ")) || (std::strstr(line+6, "MOLECULE:")))
935 if (!(c = std::strstr(line+6, "MOLECULE:")) )
939 /* skip 'MOLECULE:' and spaces */
948 /* truncate after title */
952 while ( (d[-1] == ';') && d > c)
962 std::strcat(title, "; ");
963 std::strcat(title, c);
967 std::strcpy(title, c);
981 sscanf(line, "%*s%d", model_nr);
991 gmx_conect_addline(gc, line);
995 fprintf(stderr, "WARNING: all CONECT records are ignored\n");
1008 void get_pdb_coordnum(FILE *in, int *natoms)
1013 while (fgets2(line, STRLEN, in))
1015 if (std::strncmp(line, "ENDMDL", 6) == 0)
1019 if ((std::strncmp(line, "ATOM ", 6) == 0) || (std::strncmp(line, "HETATM", 6) == 0))
1026 void gmx_pdb_read_conf(const char *infile,
1027 t_symtab *symtab, char ***name, t_atoms *atoms,
1028 rvec x[], int *ePBC, matrix box)
1030 FILE *in = gmx_fio_fopen(infile, "r");
1032 read_pdbfile(in, title, nullptr, atoms, symtab, x, ePBC, box, TRUE, nullptr);
1033 *name = put_symtab(symtab, title);
1037 gmx_conect gmx_conect_generate(const t_topology *top)
1042 /* Fill the conect records */
1043 gc = gmx_conect_init();
1045 for (f = 0; (f < F_NRE); f++)
1049 for (i = 0; (i < top->idef.il[f].nr); i += interaction_function[f].nratoms+1)
1051 gmx_conect_add(gc, top->idef.il[f].iatoms[i+1],
1052 top->idef.il[f].iatoms[i+2]);
1060 gmx_fprintf_pdb_atomline(FILE * fp,
1061 enum PDB_record record,
1062 int atom_seq_number,
1063 const char * atom_name,
1064 char alternate_location,
1065 const char * res_name,
1068 char res_insertion_code,
1074 const char * element)
1076 char tmp_atomname[6], tmp_resname[6];
1077 gmx_bool start_name_in_col13;
1080 if (record != epdbATOM && record != epdbHETATM)
1082 gmx_fatal(FARGS, "Can only print PDB atom lines as ATOM or HETATM records");
1085 /* Format atom name */
1086 if (atom_name != nullptr)
1088 /* If the atom name is an element name with two chars, it should start already in column 13.
1089 * Otherwise it should start in column 14, unless the name length is 4 chars.
1091 if ( (element != nullptr) && (std::strlen(element) >= 2) && (gmx_strncasecmp(atom_name, element, 2) == 0) )
1093 start_name_in_col13 = TRUE;
1097 start_name_in_col13 = (std::strlen(atom_name) >= 4);
1099 snprintf(tmp_atomname, sizeof(tmp_atomname), start_name_in_col13 ? "" : " ");
1100 std::strncat(tmp_atomname, atom_name, 4);
1101 tmp_atomname[5] = '\0';
1105 tmp_atomname[0] = '\0';
1108 /* Format residue name */
1109 std::strncpy(tmp_resname, (res_name != nullptr) ? res_name : "", 4);
1110 /* Make sure the string is terminated if strlen was > 4 */
1111 tmp_resname[4] = '\0';
1112 /* String is properly terminated, so now we can use strcat. By adding a
1113 * space we can write it right-justified, and if the original name was
1114 * three characters or less there will be a space added on the right side.
1116 std::strcat(tmp_resname, " ");
1118 /* Truncate integers so they fit */
1119 atom_seq_number = atom_seq_number % 100000;
1120 res_seq_number = res_seq_number % 10000;
1123 "%-6s%5d %-4.4s%c%4.4s%c%4d%c %8.3f%8.3f%8.3f%6.2f%6.2f %2s\n",
1135 (element != nullptr) ? element : "");