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40 #include "gromacs/fileio/pdbio.h"
50 #include "gromacs/fileio/gmxfio.h"
51 #include "gromacs/math/units.h"
52 #include "gromacs/math/vec.h"
53 #include "gromacs/pbcutil/pbc.h"
54 #include "gromacs/topology/atomprop.h"
55 #include "gromacs/topology/ifunc.h"
56 #include "gromacs/topology/residuetypes.h"
57 #include "gromacs/topology/symtab.h"
58 #include "gromacs/topology/topology.h"
59 #include "gromacs/utility/coolstuff.h"
60 #include "gromacs/utility/cstringutil.h"
61 #include "gromacs/utility/enumerationhelpers.h"
62 #include "gromacs/utility/fatalerror.h"
63 #include "gromacs/utility/futil.h"
64 #include "gromacs/utility/smalloc.h"
65 #include "gromacs/utility/snprintf.h"
72 typedef struct gmx_conect_t
76 gmx_conection_t* conect;
79 const char* enumValueToString(PdbRecordType enumValue)
81 static constexpr gmx::EnumerationArray<PdbRecordType, const char*> pdbRecordTypeName = {
82 "ATOM ", "HETATM", "ANISOU", "CRYST1", "COMPND", "MODEL",
83 "ENDMDL", "TER", "HEADER", "TITLE", "REMARK", "CONECT"
85 return pdbRecordTypeName[enumValue];
88 #define REMARK_SIM_BOX "REMARK THIS IS A SIMULATION BOX"
90 void gmx_write_pdb_box(FILE* out, PbcType pbcType, const matrix box)
92 real alpha, beta, gamma;
94 if (pbcType == PbcType::Unset)
96 pbcType = guessPbcType(box);
99 if (pbcType == PbcType::No)
104 if (norm2(box[YY]) * norm2(box[ZZ]) != 0)
106 alpha = RAD2DEG * gmx_angle(box[YY], box[ZZ]);
112 if (norm2(box[XX]) * norm2(box[ZZ]) != 0)
114 beta = RAD2DEG * gmx_angle(box[XX], box[ZZ]);
120 if (norm2(box[XX]) * norm2(box[YY]) != 0)
122 gamma = RAD2DEG * gmx_angle(box[XX], box[YY]);
128 fprintf(out, "REMARK THIS IS A SIMULATION BOX\n");
129 if (pbcType != PbcType::Screw)
132 "CRYST1%9.3f%9.3f%9.3f%7.2f%7.2f%7.2f %-11s%4d\n",
144 /* Double the a-vector length and write the correct space group */
146 "CRYST1%9.3f%9.3f%9.3f%7.2f%7.2f%7.2f %-11s%4d\n",
158 static void read_cryst1(char* line, PbcType* pbcType, matrix box)
161 char sa[12], sb[12], sc[12], sg[SG_SIZE + 1], ident;
162 double fa, fb, fc, alpha, beta, gamma, cosa, cosb, cosg, sing;
163 int syma, symb, symc;
166 sscanf(line, "%*s%s%s%s%lf%lf%lf", sa, sb, sc, &alpha, &beta, &gamma);
168 pbcTypeFile = PbcType::Unset;
169 if (strlen(line) >= 55)
171 strncpy(sg, line + 55, SG_SIZE);
177 sscanf(sg, "%c %d %d %d", &ident, &syma, &symb, &symc);
178 if (ident == 'P' && syma == 1 && symb <= 1 && symc <= 1)
180 fc = strtod(sc, nullptr) * 0.1;
181 pbcTypeFile = (fc > 0 ? PbcType::Xyz : PbcType::XY);
183 if (ident == 'P' && syma == 21 && symb == 1 && symc == 1)
185 pbcTypeFile = PbcType::Screw;
190 *pbcType = pbcTypeFile;
195 fa = strtod(sa, nullptr) * 0.1;
196 fb = strtod(sb, nullptr) * 0.1;
197 fc = strtod(sc, nullptr) * 0.1;
198 if (pbcTypeFile == PbcType::Screw)
204 if ((alpha != 90.0) || (beta != 90.0) || (gamma != 90.0))
208 cosa = std::cos(alpha * DEG2RAD);
216 cosb = std::cos(beta * DEG2RAD);
224 cosg = std::cos(gamma * DEG2RAD);
225 sing = std::sin(gamma * DEG2RAD);
232 box[YY][XX] = fb * cosg;
233 box[YY][YY] = fb * sing;
234 box[ZZ][XX] = fc * cosb;
235 box[ZZ][YY] = fc * (cosa - cosb * cosg) / sing;
236 box[ZZ][ZZ] = std::sqrt(fc * fc - box[ZZ][XX] * box[ZZ][XX] - box[ZZ][YY] * box[ZZ][YY]);
246 static int gmx_fprintf_pqr_atomline(FILE* fp,
247 PdbRecordType record,
249 const char* atom_name,
250 const char* res_name,
259 GMX_RELEASE_ASSERT(record == PdbRecordType::Atom || record == PdbRecordType::Hetatm,
260 "Can only print PQR atom lines as ATOM or HETATM records");
262 /* Check atom name */
263 GMX_RELEASE_ASSERT(atom_name != nullptr, "Need atom information to print pqr");
265 /* Check residue name */
266 GMX_RELEASE_ASSERT(res_name != nullptr, "Need residue information to print pqr");
268 /* Truncate integers so they fit */
269 atom_seq_number = atom_seq_number % 100000;
270 res_seq_number = res_seq_number % 10000;
273 "%-6s%5d %-4.4s%4.4s%c%4d %8.3f %8.3f %8.3f %6.2f %6.2f\n",
274 enumValueToString(record),
289 void write_pdbfile_indexed(FILE* out,
291 const t_atoms* atoms,
302 gmx_conect_t* gc = static_cast<gmx_conect_t*>(conect);
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, pbcType, 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 int resnr = atoms->resinfo[resind].nr;
342 unsigned char resic = atoms->resinfo[resind].ic;
350 ch = atoms->resinfo[resind].chainid;
359 resnr = resnr % 10000;
362 if (atoms->pdbinfo != nullptr)
364 pdbinfo = atoms->pdbinfo[i];
368 gmx_pdbinfo_init_default(&pdbinfo);
371 altloc = pdbinfo.altloc;
372 if (!isalnum(altloc))
376 occup = bOccup ? 1.0 : pdbinfo.occup;
380 gmx_fprintf_pdb_atomline(out,
394 atoms->atom[i].elem);
396 if (atoms->pdbinfo && atoms->pdbinfo[i].bAnisotropic)
399 "ANISOU%5d %-4.4s%4.4s%c%4d%c %7d%7d%7d%7d%7d%7d\n",
405 (resic == '\0') ? ' ' : resic,
406 atoms->pdbinfo[i].uij[0],
407 atoms->pdbinfo[i].uij[1],
408 atoms->pdbinfo[i].uij[2],
409 atoms->pdbinfo[i].uij[3],
410 atoms->pdbinfo[i].uij[4],
411 atoms->pdbinfo[i].uij[5]);
416 gmx_fprintf_pqr_atomline(out,
431 fprintf(out, "TER\n");
432 fprintf(out, "ENDMDL\n");
436 /* Write conect records */
437 for (int i = 0; (i < gc->nconect); i++)
439 fprintf(out, "CONECT%5d%5d\n", gc->conect[i].ai + 1, gc->conect[i].aj + 1);
444 void write_pdbfile(FILE* out,
446 const t_atoms* atoms,
456 snew(index, atoms->nr);
457 for (i = 0; i < atoms->nr; i++)
461 write_pdbfile_indexed(
462 out, title, atoms, x, pbcType, box, chainid, model_nr, atoms->nr, index, conect, false);
466 static PdbRecordType line2type(const char* line)
471 for (k = 0; (k < 6); k++)
477 using PdbRecordArray = gmx::EnumerationArray<PdbRecordType, bool>;
478 auto entry = std::find_if(
479 PdbRecordArray::keys().begin(), PdbRecordArray::keys().end(), [type](const auto& key) {
480 return std::strncmp(type, enumValueToString(key), strlen(enumValueToString(key))) == 0;
482 return (entry != PdbRecordArray::keys().end()) ? *entry : PdbRecordType::Count;
485 static void read_anisou(char line[], int natom, t_atoms* atoms)
489 char anr[12], anm[12];
493 for (k = 0; (k < 5); k++, j++)
499 for (k = 0; (k < 4); k++, j++)
506 /* Strip off spaces */
509 /* Search backwards for number and name only */
510 atomnr = std::strtol(anr, nullptr, 10);
511 for (i = natom - 1; (i >= 0); i--)
513 if ((std::strcmp(anm, *(atoms->atomname[i])) == 0) && (atomnr == atoms->pdbinfo[i].atomnr))
520 fprintf(stderr, "Skipping ANISOU record (atom %s %d not found)\n", anm, atomnr);
524 if (sscanf(line + 29,
526 &atoms->pdbinfo[i].uij[U11],
527 &atoms->pdbinfo[i].uij[U22],
528 &atoms->pdbinfo[i].uij[U33],
529 &atoms->pdbinfo[i].uij[U12],
530 &atoms->pdbinfo[i].uij[U13],
531 &atoms->pdbinfo[i].uij[U23])
534 atoms->pdbinfo[i].bAnisotropic = TRUE;
538 fprintf(stderr, "Invalid ANISOU record for atom %d\n", i);
539 atoms->pdbinfo[i].bAnisotropic = FALSE;
544 void get_pdb_atomnumber(const t_atoms* atoms, AtomProperties* aps)
546 int i, atomnumber, len;
548 char anm[6], anm_copy[6];
554 gmx_incons("Trying to deduce atomnumbers when no pdb information is present");
556 for (i = 0; (i < atoms->nr); i++)
558 std::strcpy(anm, atoms->pdbinfo[i].atomnm);
559 std::strcpy(anm_copy, atoms->pdbinfo[i].atomnm);
560 bool atomNumberSet = false;
562 if ((anm[0] != ' ') && ((len <= 2) || !std::isdigit(anm[2])))
565 if (aps->setAtomProperty(epropElement, "???", anm_copy, &eval))
567 atomnumber = gmx::roundToInt(eval);
568 atomNumberSet = true;
573 if (aps->setAtomProperty(epropElement, "???", anm_copy, &eval))
575 atomnumber = gmx::roundToInt(eval);
576 atomNumberSet = true;
583 while ((k < std::strlen(anm)) && (std::isspace(anm[k]) || std::isdigit(anm[k])))
587 anm_copy[0] = anm[k];
589 if (aps->setAtomProperty(epropElement, "???", anm_copy, &eval))
591 atomnumber = gmx::roundToInt(eval);
592 atomNumberSet = true;
598 atoms->atom[i].atomnumber = atomnumber;
599 buf = aps->elementFromAtomNumber(atomnumber);
602 fprintf(debug, "Atomnumber for atom '%s' is %d\n", anm, atomnumber);
606 std::strncpy(atoms->atom[i].elem, buf.c_str(), 4);
611 read_atom(t_symtab* symtab, const char line[], PdbRecordType type, int natom, t_atoms* atoms, rvec x[], int chainnum)
616 char anr[12], anm[12], anm_copy[12], altloc, resnm[12], rnr[12], elem[3];
617 char xc[12], yc[12], zc[12], occup[12], bfac[12];
620 int resnr, atomnumber;
622 if (natom >= atoms->nr)
624 gmx_fatal(FARGS, "\nFound more atoms (%d) in pdb file than expected (%d)", natom + 1, atoms->nr);
629 for (k = 0; (k < 5); k++, j++)
636 for (k = 0; (k < 4); k++, j++)
641 std::strcpy(anm_copy, anm);
647 for (k = 0; (k < 4); k++, j++)
657 for (k = 0; (k < 4); k++, j++)
663 resnr = std::strtol(rnr, nullptr, 10);
667 /* X,Y,Z Coordinate */
668 for (k = 0; (k < 8); k++, j++)
673 for (k = 0; (k < 8); k++, j++)
678 for (k = 0; (k < 8); k++, j++)
685 for (k = 0; (k < 6); k++, j++)
692 for (k = 0; (k < 7); k++, j++)
702 for (k = 0; (k < 2); k++, j++)
711 atomn = &(atoms->atom[natom]);
712 if ((natom == 0) || atoms->resinfo[atoms->atom[natom - 1].resind].nr != resnr
713 || atoms->resinfo[atoms->atom[natom - 1].resind].ic != resic
714 || (strcmp(*atoms->resinfo[atoms->atom[natom - 1].resind].name, resnm) != 0))
722 atomn->resind = atoms->atom[natom - 1].resind + 1;
724 atoms->nres = atomn->resind + 1;
725 t_atoms_set_resinfo(atoms, natom, symtab, resnm, resnr, resic, chainnum, chainid);
729 atomn->resind = atoms->atom[natom - 1].resind;
731 atoms->atomname[natom] = put_symtab(symtab, anm);
734 atomn->atomnumber = atomnumber;
735 strncpy(atomn->elem, elem, 4);
737 x[natom][XX] = strtod(xc, nullptr) * 0.1;
738 x[natom][YY] = strtod(yc, nullptr) * 0.1;
739 x[natom][ZZ] = strtod(zc, nullptr) * 0.1;
742 atoms->pdbinfo[natom].type = type;
743 atoms->pdbinfo[natom].atomnr = strtol(anr, nullptr, 10);
744 atoms->pdbinfo[natom].altloc = altloc;
745 strcpy(atoms->pdbinfo[natom].atomnm, anm_copy);
746 atoms->pdbinfo[natom].bfac = strtod(bfac, nullptr);
747 atoms->pdbinfo[natom].occup = strtod(occup, nullptr);
754 gmx_bool is_hydrogen(const char* nm)
758 std::strcpy(buf, nm);
761 return ((buf[0] == 'H') || ((std::isdigit(buf[0]) != 0) && (buf[1] == 'H')));
764 gmx_bool is_dummymass(const char* nm)
768 std::strcpy(buf, nm);
771 return (buf[0] == 'M') && (std::isdigit(buf[strlen(buf) - 1]) != 0);
774 static void gmx_conect_addline(gmx_conect_t* con, char* line)
778 std::string form2 = "%*s";
779 std::string format = form2 + "%d";
780 if (sscanf(line, format.c_str(), &ai) == 1)
785 format = form2 + "%d";
786 n = sscanf(line, format.c_str(), &aj);
789 gmx_conect_add(con, ai - 1, aj - 1); /* to prevent duplicated records */
795 void gmx_conect_dump(FILE* fp, gmx_conect conect)
797 gmx_conect_t* gc = static_cast<gmx_conect_t*>(conect);
800 for (i = 0; (i < gc->nconect); i++)
802 fprintf(fp, "%6s%5d%5d\n", "CONECT", gc->conect[i].ai + 1, gc->conect[i].aj + 1);
806 gmx_conect gmx_conect_init()
815 void gmx_conect_done(gmx_conect conect)
817 gmx_conect_t* gc = conect;
822 gmx_bool gmx_conect_exist(gmx_conect conect, int ai, int aj)
824 gmx_conect_t* gc = conect;
830 for (i = 0; (i < gc->nconect); i++)
832 if (((gc->conect[i].ai == ai) && (gc->conect[i].aj == aj))
833 || ((gc->conect[i].aj == ai) && (gc->conect[i].ai == aj)))
841 void gmx_conect_add(gmx_conect conect, int ai, int aj)
843 gmx_conect_t* gc = static_cast<gmx_conect_t*>(conect);
848 if (!gmx_conect_exist(conect, ai, aj))
850 srenew(gc->conect, ++gc->nconect);
851 gc->conect[gc->nconect - 1].ai = ai;
852 gc->conect[gc->nconect - 1].aj = aj;
856 int read_pdbfile(FILE* in,
866 gmx_conect_t* gc = conect;
868 gmx_bool bConnWarn = FALSE;
869 char line[STRLEN + 1];
872 gmx_bool bStop = FALSE;
876 /* Only assume pbc when there is a CRYST1 entry */
877 *pbcType = PbcType::No;
884 atoms->haveMass = FALSE;
885 atoms->haveCharge = FALSE;
886 atoms->haveType = FALSE;
887 atoms->haveBState = FALSE;
888 atoms->havePdbInfo = (atoms->pdbinfo != nullptr);
894 while (!bStop && (fgets2(line, STRLEN, in) != nullptr))
896 PdbRecordType line_type = line2type(line);
900 case PdbRecordType::Atom:
901 case PdbRecordType::Hetatm:
902 natom = read_atom(symtab, line, line_type, natom, atoms, x, chainnum);
905 case PdbRecordType::Anisou:
906 if (atoms->havePdbInfo)
908 read_anisou(line, natom, atoms);
912 case PdbRecordType::Cryst1: read_cryst1(line, pbcType, box); break;
914 case PdbRecordType::Title:
915 case PdbRecordType::Header:
916 if (std::strlen(line) > 6)
919 /* skip HEADER or TITLE and spaces */
928 /* truncate after title */
929 d = std::strstr(c, " ");
934 if (std::strlen(c) > 0)
936 std::strcpy(title, c);
941 case PdbRecordType::Compound:
942 if ((!std::strstr(line, ": ")) || (std::strstr(line + 6, "MOLECULE:")))
944 if (!(c = std::strstr(line + 6, "MOLECULE:")))
948 /* skip 'MOLECULE:' and spaces */
957 /* truncate after title */
961 while ((d[-1] == ';') && d > c)
971 std::strcat(title, "; ");
972 std::strcat(title, c);
976 std::strcpy(title, c);
983 case PdbRecordType::Ter: chainnum++; break;
985 case PdbRecordType::Model:
988 sscanf(line, "%*s%d", model_nr);
992 case PdbRecordType::EndModel: bStop = TRUE; break;
993 case PdbRecordType::Conect:
996 gmx_conect_addline(gc, line);
1000 fprintf(stderr, "WARNING: all CONECT records are ignored\n");
1012 void get_pdb_coordnum(FILE* in, int* natoms)
1017 while (fgets2(line, STRLEN, in))
1019 if (std::strncmp(line, "ENDMDL", 6) == 0)
1023 if ((std::strncmp(line, "ATOM ", 6) == 0) || (std::strncmp(line, "HETATM", 6) == 0))
1030 void gmx_pdb_read_conf(const char* infile, t_symtab* symtab, char** name, t_atoms* atoms, rvec x[], PbcType* pbcType, matrix box)
1032 FILE* in = gmx_fio_fopen(infile, "r");
1034 read_pdbfile(in, title, nullptr, atoms, symtab, x, pbcType, box, nullptr);
1035 if (name != nullptr)
1037 *name = gmx_strdup(title);
1042 gmx_conect gmx_conect_generate(const t_topology* top)
1047 /* Fill the conect records */
1048 gc = gmx_conect_init();
1050 for (f = 0; (f < F_NRE); f++)
1054 for (i = 0; (i < top->idef.il[f].nr); i += interaction_function[f].nratoms + 1)
1056 gmx_conect_add(gc, top->idef.il[f].iatoms[i + 1], top->idef.il[f].iatoms[i + 2]);
1063 int gmx_fprintf_pdb_atomline(FILE* fp,
1064 PdbRecordType record,
1065 int atom_seq_number,
1066 const char* atom_name,
1067 char alternate_location,
1068 const char* res_name,
1071 char res_insertion_code,
1077 const char* element)
1079 char tmp_atomname[6], tmp_resname[6];
1080 gmx_bool start_name_in_col13;
1083 if (record != PdbRecordType::Atom && record != PdbRecordType::Hetatm)
1085 gmx_fatal(FARGS, "Can only print PDB atom lines as ATOM or HETATM records");
1088 /* Format atom name */
1089 if (atom_name != nullptr)
1091 /* If the atom name is an element name with two chars, it should start already in column 13.
1092 * Otherwise it should start in column 14, unless the name length is 4 chars.
1094 if ((element != nullptr) && (std::strlen(element) >= 2)
1095 && (gmx_strncasecmp(atom_name, element, 2) == 0))
1097 start_name_in_col13 = TRUE;
1101 start_name_in_col13 = (std::strlen(atom_name) >= 4);
1103 snprintf(tmp_atomname, sizeof(tmp_atomname), start_name_in_col13 ? "" : " ");
1104 std::strncat(tmp_atomname, atom_name, 4);
1105 tmp_atomname[5] = '\0';
1109 tmp_atomname[0] = '\0';
1112 /* Format residue name */
1113 std::strncpy(tmp_resname, (res_name != nullptr) ? res_name : "", 4);
1114 /* Make sure the string is terminated if strlen was > 4 */
1115 tmp_resname[4] = '\0';
1116 /* String is properly terminated, so now we can use strcat. By adding a
1117 * space we can write it right-justified, and if the original name was
1118 * three characters or less there will be a space added on the right side.
1120 std::strcat(tmp_resname, " ");
1122 /* Truncate integers so they fit */
1123 atom_seq_number = atom_seq_number % 100000;
1124 res_seq_number = res_seq_number % 10000;
1127 "%-6s%5d %-4.4s%c%4.4s%c%4d%c %8.3f%8.3f%8.3f%6.2f%6.2f %2s\n",
1128 enumValueToString(record),
1141 (element != nullptr) ? element : "");