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PDBdefs.h
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1 // -*- Mode: C++; tab-width: 2; -*-
2 // vi: set ts=2:
3 //
4 
5 #ifndef BALL_FORMAT_PDBDEFS_H
6 #define BALL_FORMAT_PDBDEFS_H
7 
8 #ifndef BALL_COMMON_H
9 # include <BALL/common.h>
10 #endif
11 
12 #ifndef BALL_KERNEL_ATOM_H
13 # include <BALL/KERNEL/atom.h>
14 #endif
15 
16 #ifndef BALL_KERNEL_SECONDARYSTRUCTURE_H
17 # include <BALL/KERNEL/secondaryStructure.h>
18 #endif
19 
20 #ifndef BALL_KERNEL_CHAIN_H
21 # include <BALL/KERNEL/chain.h>
22 #endif
23 
24 #ifndef BALL_KERNEL_RESIDUE_H
25 # include <BALL/KERNEL/residue.h>
26 #endif
27 
28 #ifndef BALL_DATATYPES_HASHSET_H
29 # include <BALL/DATATYPE/hashSet.h>
30 #endif
31 
32 #ifndef BALL_MATHS_MATRIX44_H
33 # include <BALL/MATHS/matrix44.h>
34 #endif
35 
36 namespace BALL
37 {
38 
39 
45  namespace PDB
46  {
49  enum
50  {
51  SIZE_OF_PDB_RECORD_LINE = 80,
52  SIZE_OF_PDB_LINE_BUFFER = 256,
53  SIZE_OF_FORMAT_STRING_BUFFER = 256
54  };
55 
58  enum RecordType
59  {
60  RECORD_TYPE__UNKNOWN = 0,
61  RECORD_TYPE__ANISOU,
62  RECORD_TYPE__ATOM,
63  RECORD_TYPE__AUTHOR,
64  RECORD_TYPE__CAVEAT,
65  RECORD_TYPE__CISPEP,
66  RECORD_TYPE__COMPND,
67  RECORD_TYPE__CONECT,
68  RECORD_TYPE__CON06,
69  RECORD_TYPE__CON061,
70  RECORD_TYPE__CON062,
71  RECORD_TYPE__CON063,
72  RECORD_TYPE__CON064,
73  RECORD_TYPE__CRYST1,
74  RECORD_TYPE__DBREF,
75  RECORD_TYPE__END,
76  RECORD_TYPE__ENDMDL,
77  RECORD_TYPE__EXPDTA,
78  RECORD_TYPE__FORMUL,
79  RECORD_TYPE__FTNOTE,
80  RECORD_TYPE__HEADER,
81  RECORD_TYPE__HELIX,
82  RECORD_TYPE__HET,
83  RECORD_TYPE__HETATM,
84  RECORD_TYPE__HETNAM,
85  RECORD_TYPE__HETSYN,
86  RECORD_TYPE__HYDBND,
87  RECORD_TYPE__JRNL,
88  RECORD_TYPE__KEYWDS,
89  RECORD_TYPE__LINK,
90  RECORD_TYPE__MASTER,
91  RECORD_TYPE__MODEL,
92  RECORD_TYPE__MODRES,
93  RECORD_TYPE__MTRIX1,
94  RECORD_TYPE__MTRIX2,
95  RECORD_TYPE__MTRIX3,
96  RECORD_TYPE__OBSLTE,
97  RECORD_TYPE__ORIGX1,
98  RECORD_TYPE__ORIGX2,
99  RECORD_TYPE__ORIGX3,
100  RECORD_TYPE__REMARK,
101  RECORD_TYPE__REVDAT,
102  RECORD_TYPE__SCALE1,
103  RECORD_TYPE__SCALE2,
104  RECORD_TYPE__SCALE3,
105  RECORD_TYPE__SEQADV,
106  RECORD_TYPE__SEQRES,
107  RECORD_TYPE__SHEET,
108  RECORD_TYPE__SIGATM,
109  RECORD_TYPE__SIGUIJ,
110  RECORD_TYPE__SITE,
111  RECORD_TYPE__SLTBRG,
112  RECORD_TYPE__SOURCE,
113  RECORD_TYPE__SPRSDE,
114  RECORD_TYPE__SSBOND,
115  RECORD_TYPE__TER,
116  RECORD_TYPE__TITLE,
117  RECORD_TYPE__TURN,
118  RECORD_TYPE__TVECT,
119 
120  NUMBER_OF_REGISTERED_RECORD_TYPES,
121 
122  ALL_RECORD_TYPES
123  };
124 
127  BALL_EXPORT extern const char* FORMAT_UNKNOWN;
128  BALL_EXPORT extern const char* FORMAT_ANISOU;
129  BALL_EXPORT extern const char* FORMAT_ATOM;
130  BALL_EXPORT extern const char* FORMAT_ATOM_PARTIAL_CRG;
131  BALL_EXPORT extern const char* FORMAT_AUTHOR;
132  BALL_EXPORT extern const char* FORMAT_CAVEAT;
133  BALL_EXPORT extern const char* FORMAT_CISPEP;
134  BALL_EXPORT extern const char* FORMAT_COMPND;
135  BALL_EXPORT extern const char* FORMAT_CONECT;
136  BALL_EXPORT extern const char* FORMAT_CON06;
137  BALL_EXPORT extern const char* FORMAT_CON06_1;
138  BALL_EXPORT extern const char* FORMAT_CON06_2;
139  BALL_EXPORT extern const char* FORMAT_CON06_3;
140  BALL_EXPORT extern const char* FORMAT_CON06_4;
141  BALL_EXPORT extern const char* FORMAT_CRYST1;
142  BALL_EXPORT extern const char* FORMAT_DBREF;
143  BALL_EXPORT extern const char* FORMAT_END;
144  BALL_EXPORT extern const char* FORMAT_ENDMDL;
145  BALL_EXPORT extern const char* FORMAT_EXPDTA;
146  BALL_EXPORT extern const char* FORMAT_FORMUL;
147  BALL_EXPORT extern const char* FORMAT_FTNOTE;
148  BALL_EXPORT extern const char* FORMAT_HEADER;
149  BALL_EXPORT extern const char* FORMAT_HELIX;
150  BALL_EXPORT extern const char* FORMAT_HET;
151  BALL_EXPORT extern const char* FORMAT_HETATM;
152  BALL_EXPORT extern const char* FORMAT_HETNAM;
153  BALL_EXPORT extern const char* FORMAT_HETSYN;
154  BALL_EXPORT extern const char* FORMAT_HYDBND;
155  BALL_EXPORT extern const char* FORMAT_JRNL;
156  BALL_EXPORT extern const char* FORMAT_KEYWDS;
157  BALL_EXPORT extern const char* FORMAT_LINK;
158  BALL_EXPORT extern const char* FORMAT_MASTER;
159  BALL_EXPORT extern const char* FORMAT_MODEL;
160  BALL_EXPORT extern const char* FORMAT_MODRES;
161  BALL_EXPORT extern const char* FORMAT_MTRIX1;
162  BALL_EXPORT extern const char* FORMAT_MTRIX2;
163  BALL_EXPORT extern const char* FORMAT_MTRIX3;
164  BALL_EXPORT extern const char* FORMAT_OBSLTE;
165  BALL_EXPORT extern const char* FORMAT_ORIGX1;
166  BALL_EXPORT extern const char* FORMAT_ORIGX2;
167  BALL_EXPORT extern const char* FORMAT_ORIGX3;
168  BALL_EXPORT extern const char* FORMAT_REMARK;
169  BALL_EXPORT extern const char* FORMAT_REVDAT;
170  BALL_EXPORT extern const char* FORMAT_SCALE1;
171  BALL_EXPORT extern const char* FORMAT_SCALE2;
172  BALL_EXPORT extern const char* FORMAT_SCALE3;
173  BALL_EXPORT extern const char* FORMAT_SEQADV;
174  BALL_EXPORT extern const char* FORMAT_SEQRES;
175  BALL_EXPORT extern const char* FORMAT_SHEET;
176  BALL_EXPORT extern const char* FORMAT_SIGATM;
177  BALL_EXPORT extern const char* FORMAT_SIGUIJ;
178  BALL_EXPORT extern const char* FORMAT_SITE;
179  BALL_EXPORT extern const char* FORMAT_SLTBRG;
180  BALL_EXPORT extern const char* FORMAT_SOURCE;
181  BALL_EXPORT extern const char* FORMAT_SPRSDE;
182  BALL_EXPORT extern const char* FORMAT_SSBOND;
183  BALL_EXPORT extern const char* FORMAT_TER;
184  BALL_EXPORT extern const char* FORMAT_TITLE;
185  BALL_EXPORT extern const char* FORMAT_TURN;
186  BALL_EXPORT extern const char* FORMAT_TVECT;
188 
191  BALL_EXPORT extern const char* RECORD_TAG_ANISOU;
192  BALL_EXPORT extern const char* RECORD_TAG_ATOM;
193  BALL_EXPORT extern const char* RECORD_TAG_AUTHOR;
194  BALL_EXPORT extern const char* RECORD_TAG_CAVEAT;
195  BALL_EXPORT extern const char* RECORD_TAG_CISPEP;
196  BALL_EXPORT extern const char* RECORD_TAG_COMPND;
197  BALL_EXPORT extern const char* RECORD_TAG_CONECT;
198  BALL_EXPORT extern const char* RECORD_TAG_CON06;
199  BALL_EXPORT extern const char* RECORD_TAG_CON061;
200  BALL_EXPORT extern const char* RECORD_TAG_CON062;
201  BALL_EXPORT extern const char* RECORD_TAG_CON063;
202  BALL_EXPORT extern const char* RECORD_TAG_CON064;
203  BALL_EXPORT extern const char* RECORD_TAG_CRYST1;
204  BALL_EXPORT extern const char* RECORD_TAG_DBREF;
205  BALL_EXPORT extern const char* RECORD_TAG_END;
206  BALL_EXPORT extern const char* RECORD_TAG_ENDMDL;
207  BALL_EXPORT extern const char* RECORD_TAG_EXPDTA;
208  BALL_EXPORT extern const char* RECORD_TAG_FORMUL;
209  BALL_EXPORT extern const char* RECORD_TAG_FTNOTE;
210  BALL_EXPORT extern const char* RECORD_TAG_HEADER;
211  BALL_EXPORT extern const char* RECORD_TAG_HELIX;
212  BALL_EXPORT extern const char* RECORD_TAG_HET;
213  BALL_EXPORT extern const char* RECORD_TAG_HETATM;
214  BALL_EXPORT extern const char* RECORD_TAG_HETNAM;
215  BALL_EXPORT extern const char* RECORD_TAG_HETSYN;
216  BALL_EXPORT extern const char* RECORD_TAG_HYDBND;
217  BALL_EXPORT extern const char* RECORD_TAG_JRNL;
218  BALL_EXPORT extern const char* RECORD_TAG_KEYWDS;
219  BALL_EXPORT extern const char* RECORD_TAG_LINK;
220  BALL_EXPORT extern const char* RECORD_TAG_MASTER;
221  BALL_EXPORT extern const char* RECORD_TAG_MODEL;
222  BALL_EXPORT extern const char* RECORD_TAG_MODRES;
223  BALL_EXPORT extern const char* RECORD_TAG_MTRIX1;
224  BALL_EXPORT extern const char* RECORD_TAG_MTRIX2;
225  BALL_EXPORT extern const char* RECORD_TAG_MTRIX3;
226  BALL_EXPORT extern const char* RECORD_TAG_OBSLTE;
227  BALL_EXPORT extern const char* RECORD_TAG_ORIGX1;
228  BALL_EXPORT extern const char* RECORD_TAG_ORIGX2;
229  BALL_EXPORT extern const char* RECORD_TAG_ORIGX3;
230  BALL_EXPORT extern const char* RECORD_TAG_REMARK;
231  BALL_EXPORT extern const char* RECORD_TAG_REVDAT;
232  BALL_EXPORT extern const char* RECORD_TAG_SCALE1;
233  BALL_EXPORT extern const char* RECORD_TAG_SCALE2;
234  BALL_EXPORT extern const char* RECORD_TAG_SCALE3;
235  BALL_EXPORT extern const char* RECORD_TAG_SEQADV;
236  BALL_EXPORT extern const char* RECORD_TAG_SEQRES;
237  BALL_EXPORT extern const char* RECORD_TAG_SHEET;
238  BALL_EXPORT extern const char* RECORD_TAG_SIGATM;
239  BALL_EXPORT extern const char* RECORD_TAG_SIGUIJ;
240  BALL_EXPORT extern const char* RECORD_TAG_SITE;
241  BALL_EXPORT extern const char* RECORD_TAG_SLTBRG;
242  BALL_EXPORT extern const char* RECORD_TAG_SOURCE;
243  BALL_EXPORT extern const char* RECORD_TAG_SPRSDE;
244  BALL_EXPORT extern const char* RECORD_TAG_SSBOND;
245  BALL_EXPORT extern const char* RECORD_TAG_TER;
246  BALL_EXPORT extern const char* RECORD_TAG_TITLE;
247  BALL_EXPORT extern const char* RECORD_TAG_TURN;
248  BALL_EXPORT extern const char* RECORD_TAG_TVECT;
250 
254 
255  typedef char AChar;
257  typedef char Atom[5];
259  typedef char Character;
261  typedef long Continuation;
263  typedef char Date[10];
265  typedef char IDcode[5];
267  typedef long Integer;
269  typedef char PDBList[SIZE_OF_PDB_RECORD_LINE + 1];
271  typedef char LString[SIZE_OF_PDB_RECORD_LINE + 1];
273  typedef char LString2[3];
275  typedef char LString3[4];
277  typedef char LString4[5];
279  typedef char LString5[6];
281  typedef char LString6[7];
283  typedef char LString7[8];
285  typedef char LString8[9];
287  typedef char LString9[10];
289  typedef char LString10[11];
291  typedef char LString11[12];
293  typedef char LString12[13];
295  typedef char LString13[14];
297  typedef char LString21[22];
299  typedef double Real;
301  typedef char RecordName[7];
303  typedef char ResidueName[4];
305  typedef char SList[SIZE_OF_PDB_RECORD_LINE + 1];
307  typedef char Specification[SIZE_OF_PDB_RECORD_LINE + 1];
309  typedef char SpecificationList[SIZE_OF_PDB_RECORD_LINE + 1];
311  typedef char PDBString[SIZE_OF_PDB_RECORD_LINE + 1];
313  typedef char String2[3];
315  typedef char String3[4];
317  typedef char String4[5];
319  typedef char String5[6];
321  typedef char String40[41];
323  typedef long SymmetryOperator;
325 
329 
332  struct BALL_EXPORT RecordTypeFormat
333  {
334  public:
335  RecordType record_type;
336  char string[7];
337  const char* format_string;
338  };
339 
340  struct BALL_EXPORT Residue
341  {
342  ResidueName name;
343  Character chain_ID;
344  Integer sequence_number;
345  AChar insertion_code;
346 
347  Residue() { clear(); }
348  void clear()
349  {
350  name[0] = '\0';
351  chain_ID = ' ';
352  sequence_number = 0;
353  insertion_code = ' ';
354  }
355  void set(const ::BALL::Residue& residue)
356  {
357  strncpy(name, residue.getName().c_str(), 3);
358  sequence_number = residue.getID().toInt();
359  const Chain* chain = residue.getChain();
360  chain_ID = (chain == 0 ? ' ' : chain->getName().c_str()[0]);
361  insertion_code = residue.getInsertionCode();
362  }
363  };
364 
365 
368  struct BALL_EXPORT RecordUNKNOWN
369  {
370  Real max_record_size[SIZE_OF_PDB_RECORD_LINE];
371  };
372 
375  struct BALL_EXPORT RecordANISOU
376  {
377  RecordType record_type;
378  RecordName record_name;
379  Integer serial_number;
380  Atom atom_name;
381  Character alternate_location_indicator;
382  Residue residue;
383  Integer u11;
384  Integer u22;
385  Integer u33;
386  Integer u12;
387  Integer u13;
388  Integer u23;
389  LString4 segment_ID;
390  LString2 element_symbol;
391  LString2 charge;
392  };
393 
396  struct BALL_EXPORT RecordATOM
397  {
398  RecordType record_type;
399  RecordName record_name;
400  Integer serial_number;
401  Atom atom_name;
402  Character alternate_location_indicator;
403  Residue residue;
404  Real orthogonal_vector[3];
405  Real occupancy;
406  Real temperature_factor;
407  LString4 segment_ID;
408  LString2 element_symbol;
409  LString2 charge;
410  LString4 partial_charge; // not standard! Read if option PARSE_PARTIAL_CHARGES is set!
411  };
412 
415  struct BALL_EXPORT RecordAUTHOR
416  {
417  RecordType record_type;
418  RecordName record_name;
419  Continuation continuation;
420  PDBList authors;
421  };
422 
425  struct BALL_EXPORT RecordCAVEAT
426  {
427  RecordType record_type;
428  RecordName record_name;
429  Continuation continuation;
430  IDcode entry_code;
431  PDBString comment;
432  };
433 
436  struct BALL_EXPORT RecordCISPEP
437  {
439  RecordType record_type;
440  RecordName record_name;
441  Integer record_serial_number;
442  Residue residue[2];
443  Integer specific_model_ID;
444  Real angle_measure;
445  };
446 
449  struct BALL_EXPORT RecordCOMPND
450  {
451  RecordType record_type;
452  RecordName record_name;
453  Continuation continuation;
454  SpecificationList component_description;
455  };
456 
459  struct BALL_EXPORT RecordCONECT
460  {
461  RecordType record_type;
462  RecordName record_name;
463  Integer atom_serial_number;
464  Integer bond_atom[4];
465  Integer hbond_atom[4];
466  Integer salt_bridge_atom[2];
467 
468  void clear()
469  {
470  record_type = PDB::RECORD_TYPE__CONECT;
471  record_name[0] = '\0';
472  atom_serial_number = 0;
473  bond_atom[0] = bond_atom[1] = bond_atom[2] = bond_atom[3] = 0;
474  hbond_atom[0] = hbond_atom[1] = hbond_atom[2] = hbond_atom[3] = 0;
475  salt_bridge_atom[0] = salt_bridge_atom[1] = 0;
476  }
477  };
478 
481  struct BALL_EXPORT RecordCON06
482  {
483  RecordType record_type;
484  RecordName record_name;
485  Integer atom_serial_number;
486  Integer bond_atom[4];
487 
488  void clear()
489  {
490  record_type = PDB::RECORD_TYPE__CON06;
491  record_name[0] = '\0';
492  atom_serial_number = 0;
493  bond_atom[0] = bond_atom[1] = bond_atom[2] = bond_atom[3] = 0;
494  }
495  };
496 
497  struct BALL_EXPORT RecordCON061
498  {
499  RecordType record_type;
500  RecordName record_name;
501  Integer atom_serial_number;
502  Integer bond_atom[4];
503 
504  void clear()
505  {
506  record_type = PDB::RECORD_TYPE__CON061;
507  record_name[0] = '\0';
508  atom_serial_number = 0;
509  bond_atom[0] = bond_atom[1] = bond_atom[2] = bond_atom[3] = 0;
510  }
511  };
512 
513  struct BALL_EXPORT RecordCON062
514  {
515  RecordType record_type;
516  RecordName record_name;
517  Integer atom_serial_number;
518  Integer bond_atom[1];
519 
520  void clear()
521  {
522  record_type = PDB::RECORD_TYPE__CON062;
523  record_name[0] = '\0';
524  atom_serial_number = 0;
525  bond_atom[0] = 0;
526  }
527  };
528 
529  struct BALL_EXPORT RecordCON063
530  {
531  RecordType record_type;
532  RecordName record_name;
533  Integer atom_serial_number;
534  Integer bond_atom[2];
535 
536  void clear()
537  {
538  record_type = PDB::RECORD_TYPE__CON063;
539  record_name[0] = '\0';
540  atom_serial_number = 0;
541  bond_atom[0] = bond_atom[1] = 0;
542  }
543  };
544 
545  struct BALL_EXPORT RecordCON064
546  {
547  RecordType record_type;
548  RecordName record_name;
549  Integer atom_serial_number;
550  Integer bond_atom[3];
551 
552  void clear()
553  {
554  record_type = PDB::RECORD_TYPE__CON064;
555  record_name[0] = '\0';
556  atom_serial_number = 0;
557  bond_atom[0] = bond_atom[1] = bond_atom[2] = 0;
558  }
559  };
560 
561 
564  struct BALL_EXPORT RecordCRYST1
565  {
566  RecordType record_type;
567  RecordName record_name;
569  struct UnitCell
570  {
571  Real a;
572  Real b;
573  Real c;
574  Real alpha;
575  Real beta;
576  Real gamma;
577  LString space_group;
578  Integer z_value;
579  } unit_cell;
580  };
581 
584  struct BALL_EXPORT RecordDBREF
585  {
586  RecordType record_type;
587  RecordName record_name;
588  IDcode entry_code;
589  Character chain_ID;
591  struct InitialSequence
592  {
593  Integer number;
594  AChar insertion_code;
595  } initial_sequence;
597  struct EndingSequence
598  {
599  Integer number;
600  AChar insertion_code;
601  } ending_sequence;
602  LString6 sequence_database_name;
603  LString8 sequence_database_accession_code;
604  LString12 sequence_database_ID_code;
606  struct InitialDatabaseSegment
607  {
608  Integer number;
609  AChar insertion_code;
610  } initial_database_segment;
612  struct EndingDatabaseSegment
613  {
614  Integer number;
615  AChar insertion_code;
616  } ending_database_segment;
617  };
618 
620  struct BALL_EXPORT RecordEND
621  {
622  RecordType record_type;
623  RecordName record_name;
624  };
625 
627  struct BALL_EXPORT RecordENDMDL
628  {
629  RecordType record_type;
630  RecordName record_name;
631  };
632 
634  struct BALL_EXPORT RecordEXPDTA
635  {
636  RecordType record_type;
637  RecordName record_name;
638  Continuation continuation;
639  SList technique;
640  };
641 
643  struct BALL_EXPORT RecordFORMUL
644  {
645  RecordType record_type;
646  RecordName record_name;
647  Integer component_number;
648  LString3 het_ID;
649  Integer continuation_number;
650  Character is_water;
651  PDBString chemical_formula;
652  };
653 
655  struct BALL_EXPORT RecordFTNOTE
656  {
657  RecordType record_type;
658  RecordName record_name;
659  Integer number;
660  PDBString text;
661  };
662 
664  struct BALL_EXPORT RecordHEADER
665  {
666  RecordType record_type;
667  RecordName record_name;
668  String40 classification;
669  Date deposition_date;
670  IDcode ID_code;
671  };
672 
674  struct BALL_EXPORT RecordHELIX
675  {
676  RecordType record_type;
677  RecordName record_name;
678  Integer serial_number;
679  LString3 helix_ID;
680  Residue initial_residue;
681  Residue terminal_residue;
682  Integer helix_class;
683  PDBString comment;
684  Integer length;
685 
686  RecordHELIX() { clear(); }
687  void clear()
688  {
689  record_type = RECORD_TYPE__HELIX;
690  strncpy(record_name, RECORD_TAG_HELIX, 6);
691  serial_number = 0;
692  helix_ID[0] = '\0';
693  initial_residue.clear();
694  terminal_residue.clear();
695  helix_class = 0;
696  comment[0] = '\0';
697  length = 0;
698  }
699  };
700 
702  struct BALL_EXPORT RecordHET
703  {
704  RecordType record_type;
705  RecordName record_name;
706  Residue residue;
707  Integer number_of_HETATM_records;
708  PDBString text;
709  };
710 
712  struct BALL_EXPORT RecordHETATM
713  {
714  RecordType record_type;
715  RecordName record_name;
716  Integer serial_number;
717  Atom atom_name;
718  Character alternate_location_indicator;
719  Residue residue;
720  Real orthogonal_vector[3];
721  Real occupancy;
722  Real temperature_factor;
723  LString4 segment_ID;
724  LString2 element_symbol;
725  LString2 charge;
726  };
727 
729  struct BALL_EXPORT RecordHETNAM
730  {
731  RecordType record_type;
732  RecordName record_name;
733  Continuation continuation;
734  LString3 het_ID;
735  PDBString chemical_name;
736  };
737 
739  struct BALL_EXPORT RecordHETSYN
740  {
741  RecordType record_type;
742  RecordName record_name;
743  Continuation continuation;
744  LString3 het_ID;
745  SList het_synonyms;
746  };
747 
749  struct BALL_EXPORT RecordHYDBND
750  {
751  RecordType record_type;
752  RecordName record_name;
754  struct BALL_EXPORT HydrogenPartnerAtom
755  {
756  Atom atom_name;
757  Character alternate_location_indicator;
758  Residue residue;
759  };
760 
761  HydrogenPartnerAtom hydrogen_partner_atom[2];
763  struct BALL_EXPORT HydrogenAtom
764  {
765  Atom atom_name;
766  Character alternate_location_indicator;
767  Residue residue;
768  };
769  HydrogenAtom hydrogen_atom;
770  SymmetryOperator first_non_hydrogen_atom;
771  SymmetryOperator second_non_hydrogen_atom;
772  };
773 
775  struct BALL_EXPORT RecordJRNL
776  {
777  RecordType record_type;
778  RecordName record_name;
779  LString text;
780  };
782  struct BALL_EXPORT RecordKEYWDS
783  {
784  RecordType record_type;
785  RecordName record_name;
786  Continuation continuation;
787  PDBList keywords;
788  };
790  struct BALL_EXPORT RecordLINK
791  {
792  RecordType record_type;
793  RecordName record_name;
795  struct BALL_EXPORT LinkPartner
796  {
797  Atom atom_name;
798  Character alternate_location_indicator;
799  Residue residue;
800  };
801  LinkPartner link_partner[2];
802  SymmetryOperator first_atom;
803  SymmetryOperator second_atom;
804  };
806  struct BALL_EXPORT RecordMASTER
807  {
808  RecordType record_type;
809  RecordName record_name;
810  Integer number_of_REMARK_records;
811  Integer zero;
812  Integer number_of_HET_records;
813  Integer number_of_HELIX_records;
814  Integer number_of_SHEET_records;
815  Integer number_of_TURN_records;
816  Integer number_of_SITE_records;
817  Integer number_of_ORIGX_SCALE_MTRIX_records;
818  Integer number_of_ATOM_HETATM_records;
819  Integer number_of_TER_records;
820  Integer number_of_CONECT_records;
821  Integer number_of_SEQRES_records;
822 
823  RecordMASTER() { clear(); }
824  void clear()
825  {
826  record_type = RECORD_TYPE__MASTER;
827  strcpy(record_name, RECORD_TAG_MASTER);
828  zero = number_of_HET_records = number_of_HELIX_records
829  = number_of_SHEET_records = number_of_TURN_records
830  = number_of_SITE_records = number_of_ORIGX_SCALE_MTRIX_records
831  = number_of_ATOM_HETATM_records = number_of_TER_records
832  = number_of_CONECT_records = number_of_SEQRES_records = 0;
833  }
834  };
836  struct BALL_EXPORT RecordMODEL
837  {
838  RecordType record_type;
839  RecordName record_name;
840  Integer model_serial_number;
841  };
843  struct BALL_EXPORT RecordMODRES
844  {
845  RecordType record_type;
846  RecordName record_name;
847  IDcode entry_code;
848  Residue residue;
849  ResidueName standard_residue_name;
850  PDBString comment;
851  };
853  struct BALL_EXPORT RecordMTRIX1
854  {
855  RecordType record_type;
856  RecordName record_name;
857  Integer serial_number;
858  Real transformation_matrix[4];
859  Integer is_given;
860  };
862  struct BALL_EXPORT RecordMTRIX2
863  {
864  RecordType record_type;
865  RecordName record_name;
866  Integer serial_number;
867  Real transformation_matrix[4];
868  Integer is_given;
869  };
871  struct BALL_EXPORT RecordMTRIX3
872  {
873  RecordType record_type;
874  RecordName record_name;
875  Integer serial_number;
876  Real transformation_matrix[4];
877  Integer is_given;
878  };
880  struct BALL_EXPORT RecordOBSLTE
881  {
882  RecordType record_type;
883  RecordName record_name;
884  Continuation continuation;
885  Date entry_replaced_date;
886  IDcode entry_code;
887  IDcode replacing_entry_code[8];
888  };
890  struct BALL_EXPORT RecordORIGX1
891  {
892  RecordType record_type;
893  RecordName record_name;
894  Real transformation_matrix[4];
895  };
897  struct BALL_EXPORT RecordORIGX2
898  {
899  RecordType record_type;
900  RecordName record_name;
901  Real transformation_matrix[4];
902  };
904  struct BALL_EXPORT RecordORIGX3
905  {
906  RecordType record_type;
907  RecordName record_name;
908  Real transformation_matrix[4];
909  };
911  struct BALL_EXPORT RecordREMARK
912  {
913  RecordType record_type;
914  RecordName record_name;
915  Integer remark_number;
916  LString text;
917  };
919  struct BALL_EXPORT RecordREVDAT
920  {
921  RecordType record_type;
922  RecordName record_name;
923  Integer modification_number;
924  Continuation continuation;
925  Date modification_date;
926  String5 modification_ID;
927  Integer modification_type;
928  LString6 name_of_modified_record[4];
929  };
930 
932  struct BALL_EXPORT RecordSCALE1
933  {
934  RecordType record_type;
935  RecordName record_name;
936  Real transformation_matrix[4];
937  };
938 
940  struct BALL_EXPORT RecordSCALE2
941  {
942  RecordType record_type;
943  RecordName record_name;
944  Real transformation_matrix[4];
945  };
946 
948  struct BALL_EXPORT RecordSCALE3
949  {
950  RecordType record_type;
951  RecordName record_name;
952  Real transformation_matrix[4];
953  };
954 
956  struct BALL_EXPORT RecordSEQADV
957  {
958  RecordType record_type;
959  RecordName record_name;
960  IDcode id_code;
961  Residue residue;
962  LString4 database;
963  LString9 db_id_code;
964  LString3 db_res;
965  Integer db_seq;
966  LString21 comment;
967  };
968 
970  struct BALL_EXPORT RecordSEQRES
971  {
972  RecordType record_type;
973  RecordName record_name;
974  Integer serial_number;
975  Character chain_ID;
976  Integer number_of_residues_in_chain;
977  ResidueName residue_name[13];
978 
979  RecordSEQRES()
980  {
981  clear();
982  }
983 
984  void clear()
985  {
986  record_type = RECORD_TYPE__SEQRES;
987  strncpy(record_name, RECORD_TAG_SEQRES, 6);
988  serial_number = 0;
989  chain_ID = ' ';
990  number_of_residues_in_chain = 0L;
991  residue_name[0][0] = '\0';
992  residue_name[1][0] = '\0';
993  residue_name[2][0] = '\0';
994  residue_name[3][0] = '\0';
995  residue_name[4][0] = '\0';
996  residue_name[5][0] = '\0';
997  residue_name[6][0] = '\0';
998  residue_name[7][0] = '\0';
999  residue_name[8][0] = '\0';
1000  residue_name[9][0] = '\0';
1001  residue_name[10][0] = '\0';
1002  residue_name[11][0] = '\0';
1003  residue_name[12][0] = '\0';
1004  }
1005  };
1006 
1008  struct BALL_EXPORT RecordSHEET
1009  {
1010  RecordType record_type;
1011  RecordName record_name;
1012  Integer strand_number;
1013  LString3 sheet_ID;
1014  Integer number_of_strands;
1015  Residue initial_residue;
1016  Residue terminal_residue;
1017  Integer sense_of_strand;
1018  Atom atom_name_in_current_strand;
1019  Residue residue_in_current_strand;
1020  Atom atom_name_in_previous_strand;
1021  Residue residue_in_previous_strand;
1022 
1023  RecordSHEET() { clear(); }
1024  void clear()
1025  {
1026  record_type = RECORD_TYPE__SHEET;
1027  strncpy(record_name, RECORD_TAG_SHEET, 6);
1028  strand_number = 0;
1029  sheet_ID[0] = '\0';;
1030  number_of_strands = 0;
1031  initial_residue.clear();
1032  terminal_residue.clear();
1033  sense_of_strand = 0;
1034  atom_name_in_current_strand[0] = '\0';
1035  residue_in_current_strand.clear();
1036  atom_name_in_previous_strand[0] = '\0';
1037  residue_in_previous_strand.clear();
1038  }
1039  };
1040 
1042  struct BALL_EXPORT RecordSIGATM
1043  {
1044  RecordType record_type;
1045  RecordName record_name;
1046  Integer serial_number;
1047  Atom atom_name;
1048  Character alternate_location_indicator;
1049  Residue residue;
1050  Real standard_vector_deviation[3];
1051  Real standard_occupancy_deviation;
1052  Real standard_temperature_deviation;
1053  LString4 segment_ID;
1054  LString2 element_symbol;
1055  LString2 charge;
1056  };
1057 
1059  struct BALL_EXPORT RecordSIGUIJ
1060  {
1061  RecordType record_type;
1062  RecordName record_name;
1063  Integer serial_number;
1064  Atom atom_name;
1065  Character alternate_location_indicator;
1066  Residue residue;
1067  Integer sig11;
1068  Integer sig22;
1069  Integer sig33;
1070  Integer sig12;
1071  Integer sig13;
1072  Integer sig23;
1073  LString4 segment_ID;
1074  LString2 element_symbol;
1075  LString2 charge;
1076  };
1077 
1079  struct BALL_EXPORT RecordSITE
1080  {
1081  RecordType record_type;
1082  RecordName record_name;
1083  Integer sequence_number;
1084  LString3 name;
1085  Integer number_of_residues;
1086  Residue residue[4];
1087  };
1088 
1090  struct BALL_EXPORT RecordSLTBRG
1091  {
1092  RecordType record_type;
1093  RecordName record_name;
1095  struct BALL_EXPORT PartnerAtom
1096  {
1097  Atom atom_name;
1098  Character alternate_location_indicator;
1099  Residue residue;
1100  };
1101 
1102  PartnerAtom partner_atom[2];
1103  SymmetryOperator first_atom;
1104  SymmetryOperator second_atom;
1105  };
1106 
1108  struct BALL_EXPORT RecordSOURCE
1109  {
1110  RecordType record_type;
1111  RecordName record_name;
1112  Continuation continuation;
1113  SpecificationList sources;
1114  };
1115 
1117  struct BALL_EXPORT RecordSPRSDE
1118  {
1119  RecordType record_type;
1120  RecordName record_name;
1121  Continuation continuation;
1122  Date date;
1123  IDcode id_code;
1124  IDcode old_codes[8];
1125  };
1126 
1128  struct BALL_EXPORT RecordSSBOND
1129  {
1130  RecordType record_type;
1131  RecordName record_name;
1132  Integer serial_number;
1133  Residue partner_residue[2];
1134  SymmetryOperator symmetry_operator[2];
1135 
1136  RecordSSBOND() { clear(); }
1137  void clear()
1138  {
1139  record_type = RECORD_TYPE__SSBOND;
1140  strncpy(record_name, RECORD_TAG_SSBOND, 6);
1141  serial_number = 0;
1142  partner_residue[0].clear();
1143  partner_residue[1].clear();
1144  symmetry_operator[0] = 0;
1145  symmetry_operator[1] = 0;
1146  }
1147  };
1148 
1151  struct BALL_EXPORT RecordTER
1152  {
1153  RecordType record_type;
1154  RecordName record_name;
1155  Integer serial_number;
1156  Residue residue;
1157  };
1158 
1161  struct BALL_EXPORT RecordTITLE
1162  {
1163  RecordType record_type;
1164  RecordName record_name;
1165  Continuation continuation;
1166  PDBString title;
1167  };
1168 
1171  struct BALL_EXPORT RecordTURN
1172  {
1173  RecordType record_type;
1174  RecordName record_name;
1175  Integer sequence_number;
1176  LString3 turn_ID;
1177  Residue initial_residue;
1178  Residue terminal_residue;
1179  PDBString comment;
1180 
1181  RecordTURN() { clear(); }
1182  void clear()
1183  {
1184  record_type = RECORD_TYPE__TURN;
1185  strncpy(record_name, RECORD_TAG_TURN, 6);
1186  sequence_number = 0;
1187  turn_ID[0] = '\0';;
1188  initial_residue.clear();
1189  terminal_residue.clear();
1190  comment[0] = '\0';
1191  }
1192  };
1193 
1196  struct BALL_EXPORT RecordTVECT
1197  {
1198  RecordType record_type;
1199  RecordName record_name;
1200  Integer serial_number;
1201  Real translation_vector[3];
1202  PDBString comment;
1203  };
1205 
1209  struct BALL_EXPORT BookKeeping
1210  {
1211  Size remark_records;
1212  Size het_records;
1213  Size helix_records;
1214  Size sheet_records;
1215  Size turn_records;
1216  Size site_records;
1217  Size coordinate_transformation_records;
1218  Size atomic_coordinate_records;
1219  Size ter_records;
1220  Size conect_records;
1221  Size seqres_records;
1222 
1223  BookKeeping()
1224  {
1225  clear();
1226  }
1227 
1228  void clear()
1229  {
1230  remark_records = 0;
1231  het_records = 0;
1232  helix_records = 0;
1233  sheet_records = 0;
1234  turn_records = 0;
1235  site_records = 0;
1236  coordinate_transformation_records = 0;
1237  atomic_coordinate_records = 0;
1238  ter_records = 0;
1239  conect_records = 0;
1240  seqres_records = 0;
1241  }
1242  };
1243 
1244 
1245  struct BALL_EXPORT Structure
1246  {
1247  struct BALL_EXPORT AtomEntry
1248  {
1249  const BALL::Atom* atom;
1250  const BALL::Residue* residue;
1251  const BALL::SecondaryStructure* sec_struct;
1252  const BALL::Chain* chain;
1253  AtomEntry(const BALL::Atom& a)
1254  {
1255  atom = &a;
1256  residue = a.getResidue();
1257  sec_struct = a.getSecondaryStructure();
1258  chain = a.getChain();
1259  }
1260  };
1261 
1262 
1263  struct BALL_EXPORT ConectAtomList
1264  {
1265  Position serial_number;
1266  std::list<Position> bonds;
1267  std::list<Position> hbonds;
1268  std::list<Position> saltbridges;
1269  };
1270 
1271  struct BALL_EXPORT UnitCellInfo
1272  {
1273  Real a;
1274  Real b;
1275  Real c;
1276  Real alpha;
1277  Real beta;
1278  Real gamma;
1279  LString space_group;
1280  Integer z_value;
1281 
1282  UnitCellInfo()
1283  : a(0),
1284  b(0),
1285  c(0),
1286  alpha(0),
1287  beta(0),
1288  gamma(0),
1289  z_value(-1)
1290  {
1291  strcpy(space_group, "");
1292  }
1293  } unitcell_info;
1294 
1295  struct BALL_EXPORT NCSMatrix
1296  {
1297  Real matrix[12];
1298  Integer isgiven;
1299  NCSMatrix(const BALL::Matrix4x4& m, bool is_given)
1300  {
1301  matrix[0] = m(0,0); matrix[1] = m(0,1); matrix[2] = m(0,2); matrix[3] = m(0,3);
1302  matrix[4] = m(1,0); matrix[5] = m(1,1); matrix[6] = m(1,2); matrix[7] = m(1,3);
1303  matrix[8] = m(2,0); matrix[9] = m(2,1); matrix[10] = m(2,2); matrix[11] = m(2,3);
1304  isgiven = is_given;
1305  }
1306  };
1307 
1308  std::vector<NCSMatrix> ncs_matrices;
1309  std::vector<AtomEntry> atoms;
1310 
1311  HashSet<const ::BALL::Atom*> conect_atoms;
1312  std::vector<const Bond*> hydrogen_bonds;
1313  std::vector<const Bond*> saltbridges;
1314  std::vector<const Bond*> ssbonds;
1315 
1316  std::vector<std::pair<AChar, String> > chain_residue_names;
1317  std::vector<const SecondaryStructure*> sec_structs;
1318 
1319  void clear()
1320  {
1321  atoms.clear();
1322  conect_atoms.clear();
1323  hydrogen_bonds.clear();
1324  saltbridges.clear();
1325  ssbonds.clear();
1326  }
1327 
1328  };
1329 
1333  struct BALL_EXPORT AdditionalAtomInfo
1334  {
1335  const Chain* current_chain;
1336  const ::BALL::Residue* current_residue;
1337  Integer residue_id;
1338  AChar residue_insertion_code;
1339  AChar chain_id;
1340  LString3 residue_name;
1341  LString4 pdb_id;
1342  Position number; // number of the ATOM/HETATM/TER record
1343 
1344  AdditionalAtomInfo()
1345  : current_chain(0x0),
1346  current_residue(0x0),
1347  residue_id(1),
1348  residue_insertion_code(' '),
1349  chain_id(' '),
1350  number(1)
1351  {
1352  strncpy(residue_name, "UNK", 4);
1353  strncpy(pdb_id, " ", 5);
1354  }
1355  };
1356 
1359  BALL_EXPORT extern const RecordTypeFormat RECORD_TYPE_FORMAT [];
1360 
1361  } // namespace PDB
1362 
1363 } // namespace BALL
1364 
1365 #endif // BALL_FORMAT_PDBDEFS_H
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