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49 #include "gromacs/fileio/gmxfio.h"
50 #include "gromacs/math/units.h"
51 #include "gromacs/math/vec.h"
52 #include "gromacs/pbcutil/pbc.h"
53 #include "gromacs/topology/atomprop.h"
54 #include "gromacs/topology/ifunc.h"
55 #include "gromacs/topology/residuetypes.h"
56 #include "gromacs/topology/symtab.h"
57 #include "gromacs/topology/topology.h"
58 #include "gromacs/utility/coolstuff.h"
59 #include "gromacs/utility/cstringutil.h"
60 #include "gromacs/utility/fatalerror.h"
61 #include "gromacs/utility/futil.h"
62 #include "gromacs/utility/smalloc.h"
63 #include "gromacs/utility/snprintf.h"
70 typedef struct gmx_conect_t
74 gmx_conection_t* conect;
77 static const char* pdbtp[epdbNR] = { "ATOM ", "HETATM", "ANISOU", "CRYST1", "COMPND", "MODEL",
78 "ENDMDL", "TER", "HEADER", "TITLE", "REMARK", "CONECT" };
80 #define REMARK_SIM_BOX "REMARK THIS IS A SIMULATION BOX"
82 static void xlate_atomname_pdb2gmx(char* name)
87 length = std::strlen(name);
88 if (length > 3 && std::isdigit(name[0]))
91 for (i = 1; i < length; i++)
93 name[i - 1] = name[i];
95 name[length - 1] = temp;
99 // Deliberately taking a copy of name to return it later
100 static std::string xlate_atomname_gmx2pdb(std::string name)
102 size_t length = name.size();
103 if (length > 3 && std::isdigit(name[length - 1]))
105 char temp = name[length - 1];
106 for (size_t i = length - 1; i > 0; --i)
108 name[i] = name[i - 1];
116 void gmx_write_pdb_box(FILE* out, int ePBC, const matrix box)
118 real alpha, beta, gamma;
122 ePBC = guess_ePBC(box);
125 if (ePBC == epbcNONE)
130 if (norm2(box[YY]) * norm2(box[ZZ]) != 0)
132 alpha = RAD2DEG * gmx_angle(box[YY], box[ZZ]);
138 if (norm2(box[XX]) * norm2(box[ZZ]) != 0)
140 beta = RAD2DEG * gmx_angle(box[XX], box[ZZ]);
146 if (norm2(box[XX]) * norm2(box[YY]) != 0)
148 gamma = RAD2DEG * gmx_angle(box[XX], box[YY]);
154 fprintf(out, "REMARK THIS IS A SIMULATION BOX\n");
155 if (ePBC != epbcSCREW)
157 fprintf(out, "CRYST1%9.3f%9.3f%9.3f%7.2f%7.2f%7.2f %-11s%4d\n", 10 * norm(box[XX]),
158 10 * norm(box[YY]), 10 * norm(box[ZZ]), alpha, beta, gamma, "P 1", 1);
162 /* Double the a-vector length and write the correct space group */
163 fprintf(out, "CRYST1%9.3f%9.3f%9.3f%7.2f%7.2f%7.2f %-11s%4d\n", 20 * norm(box[XX]),
164 10 * norm(box[YY]), 10 * norm(box[ZZ]), alpha, beta, gamma, "P 21 1 1", 1);
168 static void read_cryst1(char* line, int* ePBC, matrix box)
171 char sa[12], sb[12], sc[12], sg[SG_SIZE + 1], ident;
172 double fa, fb, fc, alpha, beta, gamma, cosa, cosb, cosg, sing;
173 int syma, symb, symc;
176 sscanf(line, "%*s%s%s%s%lf%lf%lf", sa, sb, sc, &alpha, &beta, &gamma);
179 if (strlen(line) >= 55)
181 strncpy(sg, line + 55, SG_SIZE);
187 sscanf(sg, "%c %d %d %d", &ident, &syma, &symb, &symc);
188 if (ident == 'P' && syma == 1 && symb <= 1 && symc <= 1)
190 fc = strtod(sc, nullptr) * 0.1;
191 ePBC_file = (fc > 0 ? epbcXYZ : epbcXY);
193 if (ident == 'P' && syma == 21 && symb == 1 && symc == 1)
195 ePBC_file = epbcSCREW;
205 fa = strtod(sa, nullptr) * 0.1;
206 fb = strtod(sb, nullptr) * 0.1;
207 fc = strtod(sc, nullptr) * 0.1;
208 if (ePBC_file == epbcSCREW)
214 if ((alpha != 90.0) || (beta != 90.0) || (gamma != 90.0))
218 cosa = std::cos(alpha * DEG2RAD);
226 cosb = std::cos(beta * DEG2RAD);
234 cosg = std::cos(gamma * DEG2RAD);
235 sing = std::sin(gamma * DEG2RAD);
242 box[YY][XX] = fb * cosg;
243 box[YY][YY] = fb * sing;
244 box[ZZ][XX] = fc * cosb;
245 box[ZZ][YY] = fc * (cosa - cosb * cosg) / sing;
246 box[ZZ][ZZ] = std::sqrt(fc * fc - box[ZZ][XX] * box[ZZ][XX] - box[ZZ][YY] * box[ZZ][YY]);
256 static int gmx_fprintf_pqr_atomline(FILE* fp,
257 enum PDB_record record,
259 const char* atom_name,
260 const char* res_name,
269 GMX_RELEASE_ASSERT(record == epdbATOM || record == epdbHETATM,
270 "Can only print PQR atom lines as ATOM or HETATM records");
272 /* Check atom name */
273 GMX_RELEASE_ASSERT(atom_name != nullptr, "Need atom information to print pqr");
275 /* Check residue name */
276 GMX_RELEASE_ASSERT(res_name != nullptr, "Need residue information to print pqr");
278 /* Truncate integers so they fit */
279 atom_seq_number = atom_seq_number % 100000;
280 res_seq_number = res_seq_number % 10000;
282 int n = fprintf(fp, "%-6s%5d %-4.4s%4.4s%c%4d %8.3f %8.3f %8.3f %6.2f %6.2f\n", pdbtp[record],
283 atom_seq_number, atom_name, res_name, chain_id, res_seq_number, x, y, z,
284 occupancy, b_factor);
289 void write_pdbfile_indexed(FILE* out,
291 const t_atoms* atoms,
302 gmx_conect_t* gc = static_cast<gmx_conect_t*>(conect);
303 enum PDB_record type;
309 fprintf(out, "TITLE %s\n", (title && title[0]) ? title : gmx::bromacs().c_str());
310 if (box && ((norm2(box[XX]) != 0.0F) || (norm2(box[YY]) != 0.0F) || (norm2(box[ZZ]) != 0.0F)))
312 gmx_write_pdb_box(out, ePBC, box);
314 if (atoms->havePdbInfo)
316 /* Check whether any occupancies are set, in that case leave it as is,
317 * otherwise set them all to one
320 for (int ii = 0; (ii < nindex) && bOccup; ii++)
323 bOccup = bOccup && (atoms->pdbinfo[i].occup == 0.0);
331 fprintf(out, "MODEL %8d\n", model_nr > 0 ? model_nr : 1);
334 for (int ii = 0; ii < nindex; ii++)
337 int resind = atoms->atom[i].resind;
338 std::string resnm = *atoms->resinfo[resind].name;
339 std::string nm = *atoms->atomname[i];
341 /* rename HG12 to 2HG1, etc. */
342 nm = xlate_atomname_gmx2pdb(nm);
343 int resnr = atoms->resinfo[resind].nr;
344 unsigned char resic = atoms->resinfo[resind].ic;
352 ch = atoms->resinfo[resind].chainid;
361 resnr = resnr % 10000;
364 if (atoms->pdbinfo != nullptr)
366 pdbinfo = atoms->pdbinfo[i];
370 gmx_pdbinfo_init_default(&pdbinfo);
372 type = static_cast<enum PDB_record>(pdbinfo.type);
373 altloc = pdbinfo.altloc;
374 if (!isalnum(altloc))
378 occup = bOccup ? 1.0 : pdbinfo.occup;
382 gmx_fprintf_pdb_atomline(out, type, i + 1, nm.c_str(), altloc, resnm.c_str(), ch, resnr,
383 resic, 10 * x[i][XX], 10 * x[i][YY], 10 * x[i][ZZ], occup,
384 bfac, atoms->atom[i].elem);
386 if (atoms->pdbinfo && atoms->pdbinfo[i].bAnisotropic)
388 fprintf(out, "ANISOU%5d %-4.4s%4.4s%c%4d%c %7d%7d%7d%7d%7d%7d\n", (i + 1) % 100000,
389 nm.c_str(), resnm.c_str(), ch, resnr, (resic == '\0') ? ' ' : resic,
390 atoms->pdbinfo[i].uij[0], atoms->pdbinfo[i].uij[1], atoms->pdbinfo[i].uij[2],
391 atoms->pdbinfo[i].uij[3], atoms->pdbinfo[i].uij[4], atoms->pdbinfo[i].uij[5]);
396 gmx_fprintf_pqr_atomline(out, type, i + 1, nm.c_str(), resnm.c_str(), ch, resnr,
397 10 * x[i][XX], 10 * x[i][YY], 10 * x[i][ZZ], occup, bfac);
401 fprintf(out, "TER\n");
402 fprintf(out, "ENDMDL\n");
406 /* Write conect records */
407 for (int i = 0; (i < gc->nconect); i++)
409 fprintf(out, "CONECT%5d%5d\n", gc->conect[i].ai + 1, gc->conect[i].aj + 1);
414 void write_pdbfile(FILE* out,
416 const t_atoms* atoms,
426 snew(index, atoms->nr);
427 for (i = 0; i < atoms->nr; i++)
431 write_pdbfile_indexed(out, title, atoms, x, ePBC, box, chainid, model_nr, atoms->nr, index,
436 static int line2type(const char* line)
441 for (k = 0; (k < 6); k++)
447 for (k = 0; (k < epdbNR); k++)
449 if (std::strncmp(type, pdbtp[k], strlen(pdbtp[k])) == 0)
458 static void read_anisou(char line[], int natom, t_atoms* atoms)
462 char anr[12], anm[12];
466 for (k = 0; (k < 5); k++, j++)
472 for (k = 0; (k < 4); k++, j++)
479 /* Strip off spaces */
482 /* Search backwards for number and name only */
483 atomnr = std::strtol(anr, nullptr, 10);
484 for (i = natom - 1; (i >= 0); i--)
486 if ((std::strcmp(anm, *(atoms->atomname[i])) == 0) && (atomnr == atoms->pdbinfo[i].atomnr))
493 fprintf(stderr, "Skipping ANISOU record (atom %s %d not found)\n", anm, atomnr);
497 if (sscanf(line + 29, "%d%d%d%d%d%d", &atoms->pdbinfo[i].uij[U11], &atoms->pdbinfo[i].uij[U22],
498 &atoms->pdbinfo[i].uij[U33], &atoms->pdbinfo[i].uij[U12],
499 &atoms->pdbinfo[i].uij[U13], &atoms->pdbinfo[i].uij[U23])
502 atoms->pdbinfo[i].bAnisotropic = TRUE;
506 fprintf(stderr, "Invalid ANISOU record for atom %d\n", i);
507 atoms->pdbinfo[i].bAnisotropic = FALSE;
512 void get_pdb_atomnumber(const t_atoms* atoms, AtomProperties* aps)
514 int i, atomnumber, len;
516 char anm[6], anm_copy[6];
522 gmx_incons("Trying to deduce atomnumbers when no pdb information is present");
524 for (i = 0; (i < atoms->nr); i++)
526 std::strcpy(anm, atoms->pdbinfo[i].atomnm);
527 std::strcpy(anm_copy, atoms->pdbinfo[i].atomnm);
528 bool atomNumberSet = false;
530 if ((anm[0] != ' ') && ((len <= 2) || !std::isdigit(anm[2])))
533 if (aps->setAtomProperty(epropElement, "???", anm_copy, &eval))
535 atomnumber = gmx::roundToInt(eval);
536 atomNumberSet = true;
541 if (aps->setAtomProperty(epropElement, "???", anm_copy, &eval))
543 atomnumber = gmx::roundToInt(eval);
544 atomNumberSet = true;
551 while ((k < std::strlen(anm)) && (std::isspace(anm[k]) || std::isdigit(anm[k])))
555 anm_copy[0] = anm[k];
557 if (aps->setAtomProperty(epropElement, "???", anm_copy, &eval))
559 atomnumber = gmx::roundToInt(eval);
560 atomNumberSet = true;
566 atoms->atom[i].atomnumber = atomnumber;
567 buf = aps->elementFromAtomNumber(atomnumber);
570 fprintf(debug, "Atomnumber for atom '%s' is %d\n", anm, atomnumber);
574 std::strncpy(atoms->atom[i].elem, buf.c_str(), 4);
579 read_atom(t_symtab* symtab, const char line[], int type, int natom, 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)", natom + 1, atoms->nr);
597 for (k = 0; (k < 5); k++, j++)
604 for (k = 0; (k < 4); k++, j++)
609 std::strcpy(anm_copy, anm);
615 for (k = 0; (k < 4); k++, j++)
625 for (k = 0; (k < 4); k++, j++)
631 resnr = std::strtol(rnr, nullptr, 10);
635 /* X,Y,Z Coordinate */
636 for (k = 0; (k < 8); k++, j++)
641 for (k = 0; (k < 8); k++, j++)
646 for (k = 0; (k < 8); k++, j++)
653 for (k = 0; (k < 6); k++, j++)
660 for (k = 0; (k < 7); k++, j++)
670 for (k = 0; (k < 2); k++, j++)
679 atomn = &(atoms->atom[natom]);
680 if ((natom == 0) || atoms->resinfo[atoms->atom[natom - 1].resind].nr != resnr
681 || atoms->resinfo[atoms->atom[natom - 1].resind].ic != resic
682 || (strcmp(*atoms->resinfo[atoms->atom[natom - 1].resind].name, resnm) != 0))
690 atomn->resind = atoms->atom[natom - 1].resind + 1;
692 atoms->nres = atomn->resind + 1;
693 t_atoms_set_resinfo(atoms, natom, symtab, resnm, resnr, resic, chainnum, chainid);
697 atomn->resind = atoms->atom[natom - 1].resind;
701 xlate_atomname_pdb2gmx(anm);
703 atoms->atomname[natom] = put_symtab(symtab, anm);
706 atomn->atomnumber = atomnumber;
707 strncpy(atomn->elem, elem, 4);
709 x[natom][XX] = strtod(xc, nullptr) * 0.1;
710 x[natom][YY] = strtod(yc, nullptr) * 0.1;
711 x[natom][ZZ] = strtod(zc, nullptr) * 0.1;
714 atoms->pdbinfo[natom].type = type;
715 atoms->pdbinfo[natom].atomnr = strtol(anr, nullptr, 10);
716 atoms->pdbinfo[natom].altloc = altloc;
717 strcpy(atoms->pdbinfo[natom].atomnm, anm_copy);
718 atoms->pdbinfo[natom].bfac = strtod(bfac, nullptr);
719 atoms->pdbinfo[natom].occup = strtod(occup, nullptr);
726 gmx_bool is_hydrogen(const char* nm)
730 std::strcpy(buf, nm);
737 else if ((std::isdigit(buf[0])) && (buf[1] == 'H'))
744 gmx_bool is_dummymass(const char* nm)
748 std::strcpy(buf, nm);
751 return (buf[0] == 'M') && (std::isdigit(buf[strlen(buf) - 1]) != 0);
754 static void gmx_conect_addline(gmx_conect_t* con, char* line)
758 std::string form2 = "%*s";
759 std::string format = form2 + "%d";
760 if (sscanf(line, format.c_str(), &ai) == 1)
765 format = form2 + "%d";
766 n = sscanf(line, format.c_str(), &aj);
769 gmx_conect_add(con, ai - 1, aj - 1); /* to prevent duplicated records */
775 void gmx_conect_dump(FILE* fp, gmx_conect conect)
777 gmx_conect_t* gc = static_cast<gmx_conect_t*>(conect);
780 for (i = 0; (i < gc->nconect); i++)
782 fprintf(fp, "%6s%5d%5d\n", "CONECT", gc->conect[i].ai + 1, gc->conect[i].aj + 1);
786 gmx_conect gmx_conect_init()
795 void gmx_conect_done(gmx_conect conect)
797 gmx_conect_t* gc = conect;
802 gmx_bool gmx_conect_exist(gmx_conect conect, int ai, int aj)
804 gmx_conect_t* gc = conect;
810 for (i = 0; (i < gc->nconect); i++)
812 if (((gc->conect[i].ai == ai) && (gc->conect[i].aj == aj))
813 || ((gc->conect[i].aj == ai) && (gc->conect[i].ai == aj)))
821 void gmx_conect_add(gmx_conect conect, int ai, int aj)
823 gmx_conect_t* gc = static_cast<gmx_conect_t*>(conect);
828 if (!gmx_conect_exist(conect, ai, aj))
830 srenew(gc->conect, ++gc->nconect);
831 gc->conect[gc->nconect - 1].ai = ai;
832 gc->conect[gc->nconect - 1].aj = aj;
836 int read_pdbfile(FILE* in,
847 gmx_conect_t* gc = conect;
849 gmx_bool bConnWarn = FALSE;
850 char line[STRLEN + 1];
854 gmx_bool bStop = FALSE;
858 /* Only assume pbc when there is a CRYST1 entry */
866 atoms->haveMass = FALSE;
867 atoms->haveCharge = FALSE;
868 atoms->haveType = FALSE;
869 atoms->haveBState = FALSE;
870 atoms->havePdbInfo = (atoms->pdbinfo != nullptr);
876 while (!bStop && (fgets2(line, STRLEN, in) != nullptr))
878 line_type = line2type(line);
884 natom = read_atom(symtab, line, line_type, natom, atoms, x, chainnum, bChange);
888 if (atoms->havePdbInfo)
890 read_anisou(line, natom, atoms);
894 case epdbCRYST1: read_cryst1(line, ePBC, box); break;
898 if (std::strlen(line) > 6)
901 /* skip HEADER or TITLE and spaces */
910 /* truncate after title */
911 d = std::strstr(c, " ");
916 if (std::strlen(c) > 0)
918 std::strcpy(title, c);
924 if ((!std::strstr(line, ": ")) || (std::strstr(line + 6, "MOLECULE:")))
926 if (!(c = std::strstr(line + 6, "MOLECULE:")))
930 /* skip 'MOLECULE:' and spaces */
939 /* truncate after title */
943 while ((d[-1] == ';') && d > c)
953 std::strcat(title, "; ");
954 std::strcat(title, c);
958 std::strcpy(title, c);
965 case epdbTER: chainnum++; break;
970 sscanf(line, "%*s%d", model_nr);
974 case epdbENDMDL: bStop = TRUE; break;
978 gmx_conect_addline(gc, line);
982 fprintf(stderr, "WARNING: all CONECT records are ignored\n");
994 void get_pdb_coordnum(FILE* in, int* natoms)
999 while (fgets2(line, STRLEN, in))
1001 if (std::strncmp(line, "ENDMDL", 6) == 0)
1005 if ((std::strncmp(line, "ATOM ", 6) == 0) || (std::strncmp(line, "HETATM", 6) == 0))
1012 void gmx_pdb_read_conf(const char* infile, t_symtab* symtab, char** name, t_atoms* atoms, rvec x[], int* ePBC, matrix box)
1014 FILE* in = gmx_fio_fopen(infile, "r");
1016 read_pdbfile(in, title, nullptr, atoms, symtab, x, ePBC, box, TRUE, nullptr);
1017 if (name != nullptr)
1019 *name = gmx_strdup(title);
1024 gmx_conect gmx_conect_generate(const t_topology* top)
1029 /* Fill the conect records */
1030 gc = gmx_conect_init();
1032 for (f = 0; (f < F_NRE); f++)
1036 for (i = 0; (i < top->idef.il[f].nr); i += interaction_function[f].nratoms + 1)
1038 gmx_conect_add(gc, top->idef.il[f].iatoms[i + 1], top->idef.il[f].iatoms[i + 2]);
1045 int gmx_fprintf_pdb_atomline(FILE* fp,
1046 enum PDB_record record,
1047 int atom_seq_number,
1048 const char* atom_name,
1049 char alternate_location,
1050 const char* res_name,
1053 char res_insertion_code,
1059 const char* element)
1061 char tmp_atomname[6], tmp_resname[6];
1062 gmx_bool start_name_in_col13;
1065 if (record != epdbATOM && record != epdbHETATM)
1067 gmx_fatal(FARGS, "Can only print PDB atom lines as ATOM or HETATM records");
1070 /* Format atom name */
1071 if (atom_name != nullptr)
1073 /* If the atom name is an element name with two chars, it should start already in column 13.
1074 * Otherwise it should start in column 14, unless the name length is 4 chars.
1076 if ((element != nullptr) && (std::strlen(element) >= 2)
1077 && (gmx_strncasecmp(atom_name, element, 2) == 0))
1079 start_name_in_col13 = TRUE;
1083 start_name_in_col13 = (std::strlen(atom_name) >= 4);
1085 snprintf(tmp_atomname, sizeof(tmp_atomname), start_name_in_col13 ? "" : " ");
1086 std::strncat(tmp_atomname, atom_name, 4);
1087 tmp_atomname[5] = '\0';
1091 tmp_atomname[0] = '\0';
1094 /* Format residue name */
1095 std::strncpy(tmp_resname, (res_name != nullptr) ? res_name : "", 4);
1096 /* Make sure the string is terminated if strlen was > 4 */
1097 tmp_resname[4] = '\0';
1098 /* String is properly terminated, so now we can use strcat. By adding a
1099 * space we can write it right-justified, and if the original name was
1100 * three characters or less there will be a space added on the right side.
1102 std::strcat(tmp_resname, " ");
1104 /* Truncate integers so they fit */
1105 atom_seq_number = atom_seq_number % 100000;
1106 res_seq_number = res_seq_number % 10000;
1108 n = fprintf(fp, "%-6s%5d %-4.4s%c%4.4s%c%4d%c %8.3f%8.3f%8.3f%6.2f%6.2f %2s\n",
1109 pdbtp[record], atom_seq_number, tmp_atomname, alternate_location, tmp_resname,
1110 chain_id, res_seq_number, res_insertion_code, x, y, z, occupancy, b_factor,
1111 (element != nullptr) ? element : "");