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mmcif_info.hh
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1 //------------------------------------------------------------------------------
2 // This file is part of the OpenStructure project <www.openstructure.org>
3 //
4 // Copyright (C) 2008-2011 by the OpenStructure authors
5 //
6 // This library is free software; you can redistribute it and/or modify it under
7 // the terms of the GNU Lesser General Public License as published by the Free
8 // Software Foundation; either version 3.0 of the License, or (at your option)
9 // any later version.
10 // This library is distributed in the hope that it will be useful, but WITHOUT
11 // ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
12 // FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
13 // details.
14 //
15 // You should have received a copy of the GNU Lesser General Public License
16 // along with this library; if not, write to the Free Software Foundation, Inc.,
17 // 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
18 //------------------------------------------------------------------------------
19 #ifndef OST_MMCIF_INFO_HH
20 #define OST_MMCIF_INFO_HH
21 
22 #include <vector>
23 #include <map>
24 #include <boost/shared_ptr.hpp>
25 #include <ost/seq/sequence_list.hh>
26 #include <ost/geom/geom.hh>
27 #include <ost/string_ref.hh>
28 #include <ost/io/module_config.hh>
29 
30 namespace ost { namespace io {
31 
32 class DLLEXPORT_OST_IO MMCifInfoStructDetails {
33 public:
35  MMCifInfoStructDetails(): entry_id_(""), title_(""), casp_flag_('\0'),
36  descriptor_(""), mass_(0.0), mass_method_(""), model_details_(""),
37  model_type_details_("") {};
38 
42  void SetEntryID(String id) { entry_id_ = id; }
46  String GetEntryID() const { return entry_id_; }
47 
51  void SetCASPFlag(char flag) { casp_flag_ = flag; }
55  char GetCASPFlag() const { return casp_flag_; }
56 
60  void SetDescriptor(String desc) { descriptor_ = desc; }
64  String GetDescriptor() const { return descriptor_; }
65 
69  void SetMass(Real mass) { mass_ = mass; }
73  Real GetMass() const { return mass_; }
74 
78  void SetMassMethod(String method) { mass_method_ = method; }
82  String GetMassMethod() const { return mass_method_; }
83 
87  void SetModelDetails(String desc) { model_details_ = desc; }
91  String GetModelDetails() const { return model_details_; }
92 
96  void SetModelTypeDetails(String desc) { model_type_details_ = desc; }
100  String GetModelTypeDetails() const { return model_type_details_; }
101 
105  void SetTitle(String title) { title_ = title; }
109  String GetTitle() const { return title_; }
110 
111  bool operator==(const MMCifInfoStructDetails& sd) const {
112  if (this->entry_id_ != sd.entry_id_) {
113  return false;
114  }
115  if (this->casp_flag_ != sd.casp_flag_) {
116  return false;
117  }
118  if (this->descriptor_ != sd.descriptor_) {
119  return false;
120  }
121  if (this->mass_ != sd.mass_) {
122  return false;
123  }
124  if (this->mass_method_ != sd.mass_method_) {
125  return false;
126  }
127  if (this->model_details_ != sd.model_details_) {
128  return false;
129  }
130  if (this->model_type_details_ != sd.model_type_details_) {
131  return false;
132  }
133  if (this->title_ != sd.title_) {
134  return false;
135  }
136 
137  return true;
138  }
139 
140  bool operator!=(const MMCifInfoStructDetails& sd) const {
141  return !this->operator == (sd);
142  }
143 
144 private:
145  String entry_id_;
146  String title_;
147  char casp_flag_;
148  String descriptor_;
149  Real mass_;
150  String mass_method_;
151  String model_details_;
152  String model_type_details_;
153 };
154 
155 class DLLEXPORT_OST_IO MMCifInfoTransOp {
156 public:
158  MMCifInfoTransOp(): id_(""), type_("")
159  {
160  translation_ = geom::Vec3();
161  };
162 
166  void SetID(String id) { id_ = id; }
170  String GetID() const { return id_; }
171 
175  void SetType(String type) { type_ = type; }
179  String GetType() const { return type_; }
180 
186  void SetVector(Real x, Real y, Real z)
187  {
188  translation_.SetX(x);
189  translation_.SetY(y);
190  translation_.SetZ(z);
191  }
195  geom::Vec3 GetVector() const { return translation_; }
196 
208  void SetMatrix(Real i00, Real i01, Real i02,
209  Real i10, Real i11, Real i12,
210  Real i20, Real i21, Real i22)
211  {
212  rotation_ = geom::Mat3(i00,i01,i02, i10,i11,i12, i20,i21,i22);
213  }
217  geom::Mat3 GetMatrix() const { return rotation_; }
218 
219  bool operator==(const MMCifInfoTransOp& op) const {
220  if (this->id_ != op.id_) {
221  return false;
222  }
223  if (this->type_ != op.type_) {
224  return false;
225  }
226  if (this->translation_ != op.translation_) {
227  return false;
228  }
229  if (this->rotation_ != op.rotation_) {
230  return false;
231  }
232 
233  return true;
234  }
235 
236  bool operator!=(const MMCifInfoTransOp& op) const {
237  return !this->operator==(op);
238  }
239 
240 private:
241  String id_;
242  String type_;
243  geom::Vec3 translation_;
244  geom::Mat3 rotation_;
245 };
246 typedef boost::shared_ptr<MMCifInfoTransOp> MMCifInfoTransOpPtr;
247 
248 
249 class DLLEXPORT_OST_IO MMCifInfoBioUnit {
250 public:
252  MMCifInfoBioUnit(): id_(""), details_("") {};
253 
257  void Merge(MMCifInfoBioUnit& from);
258 
262  void SetID(String id) { id_ = id; }
266  String GetID() const { return id_; }
267 
271  void SetDetails(String details) { details_ = details; }
275  String GetDetails() const { return details_; }
276 
280  void SetMethodDetails(String method_details) {
281  method_details_ = method_details;
282  }
286  String GetMethodDetails() const { return method_details_; }
287 
291  void AddChain(String chain);
292 
296  void SetChainList(std::vector<String> chains);
297 
301  const std::vector<String>& GetChainList() const { return chains_; }
302 
306  const std::vector<std::pair<int, int> >& GetChainIntervalList()
307  {
308  return tr_chains_;
309  }
310 
314  void AddOperations(std::vector<MMCifInfoTransOpPtr> operations);
315 
319  const std::vector<std::pair<int, int> >& GetOperationsIntervalList()
320  {
321  return tr_operations_;
322  }
323 
327  const std::vector<std::vector<MMCifInfoTransOpPtr> >& GetOperations()
328  {
329  return operations_;
330  }
331 
332  bool operator==(const MMCifInfoBioUnit& bu) const {
333  if (this->id_ != bu.id_) {
334  return false;
335  }
336  if (this->details_ != bu.details_) {
337  return false;
338  }
339  if (this->chains_ != bu.chains_) {
340  return false;
341  }
342  if (this->tr_chains_ != bu.tr_chains_) {
343  return false;
344  }
345  if (this->tr_operations_ != bu.tr_operations_) {
346  return false;
347  }
348  if (this->operations_.size() == bu.operations_.size()) {
349  std::vector<std::vector<MMCifInfoTransOpPtr> >::const_iterator th_ops_it;
350  std::vector<std::vector<MMCifInfoTransOpPtr> >::const_iterator bu_ops_it;
351  std::vector<MMCifInfoTransOpPtr>::const_iterator th_op_it;
352  std::vector<MMCifInfoTransOpPtr>::const_iterator bu_op_it;
353 
354  for (th_ops_it = this->operations_.begin(),
355  bu_ops_it = bu.operations_.begin();
356  th_ops_it != this->operations_.end();
357  ++th_ops_it, ++bu_ops_it) {
358  if (th_ops_it->size() == bu_ops_it->size()) {
359  for (th_op_it = th_ops_it->begin(), bu_op_it = bu_ops_it->begin();
360  th_op_it != th_ops_it->end();
361  ++th_op_it, ++bu_op_it) {
362  if (*th_op_it != *bu_op_it) {
363  return false;
364  }
365  }
366  } else {
367  return false;
368  }
369  }
370  } else {
371  return false;
372  }
373 
374  return true;
375  }
376 
377  bool operator!=(const MMCifInfoBioUnit& bu) const {
378  return !this->operator==(bu);
379  }
380 
381 private:
382  String id_;
383  String details_;
384  String method_details_;
385  std::vector<String> chains_;
386  std::vector<std::pair<int, int> > tr_chains_; //< chains of a transformation
387  std::vector<std::vector<MMCifInfoTransOpPtr> > operations_;
388  std::vector<std::pair<int, int> > tr_operations_; //< ops. of a transformation
389 };
390 
391 class DLLEXPORT_OST_IO MMCifInfoCitation {
392 public:
394  MMCifInfoCitation(): id_(""), where_(UNKNOWN), cas_(""), published_in_(""),
395  volume_(""), page_first_(""), page_last_(""), doi_(""), pubmed_(0),
396  year_(0), title_("") {};
397 
401  void SetID(String id) { id_ = id; }
405  String GetID() const { return id_; }
406 
410  void SetCAS(String id) { cas_ = id; }
414  String GetCAS() const { return cas_; }
415 
419  void SetISBN(String code) { isbn_ = code; }
420 
424  String GetISBN() const { return isbn_; }
425 
429  void SetPublishedIn(String title) { published_in_ = title; }
430 
434  String GetPublishedIn() const { return published_in_; }
435 
439  void SetVolume(String volume) { volume_ = volume; }
440 
444  String GetVolume() const { return volume_; }
445 
449  void SetPageFirst(String first) { page_first_ = first; }
450 
454  String GetPageFirst() const { return page_first_; }
455 
459  void SetPageLast(String last) { page_last_ = last; }
460 
464  String GetPageLast() const { return page_last_; }
465 
469  void SetDOI(String doi) { doi_ = doi; }
470 
471 
475  String GetDOI() const { return doi_; }
476 
480  void SetPubMed(int no) { pubmed_ = no; }
481 
485  int GetPubMed() const { return pubmed_; }
486 
490  void SetYear(int year) { year_ = year; }
491 
492 
496  int GetYear() const { return year_; }
497 
498 
502  void SetTitle(String title) { title_ = title; }
503 
507  String GetTitle() const { return title_; }
508 
512  void SetAuthorList(std::vector<String> list) { authors_ = list; }
513 
517  const std::vector<String>& GetAuthorList() const { return authors_; }
518 
519  bool operator==(const MMCifInfoCitation& cit) const {
520  if (this->year_ != cit.year_) {
521  return false;
522  }
523  if (this->pubmed_ != cit.pubmed_) {
524  return false;
525  }
526  if (this->where_ != cit.where_) {
527  return false;
528  }
529  if (StringRef(this->id_.c_str(), this->id_.length()) !=
530  StringRef(cit.id_.c_str(), cit.id_.length())) {
531  return false;
532  }
533  if (StringRef(this->cas_.c_str(), this->cas_.length()) !=
534  StringRef(cit.cas_.c_str(), cit.cas_.length())) {
535  return false;
536  }
537  if (StringRef(this->isbn_.c_str(), this->isbn_.length()) !=
538  StringRef(cit.isbn_.c_str(), cit.isbn_.length())) {
539  return false;
540  }
541  if (StringRef(this->published_in_.c_str(), this->published_in_.length()) !=
542  StringRef(cit.published_in_.c_str(), cit.published_in_.length())) {
543  return false;
544  }
545  if (StringRef(this->volume_.c_str(), this->volume_.length()) !=
546  StringRef(cit.volume_.c_str(), cit.volume_.length())) {
547  return false;
548  }
549  if (StringRef(this->page_first_.c_str(), this->page_first_.length()) !=
550  StringRef(cit.page_first_.c_str(), cit.page_first_.length())) {
551  return false;
552  }
553  if (StringRef(this->page_last_.c_str(), this->page_last_.length()) !=
554  StringRef(cit.page_last_.c_str(), cit.page_last_.length())) {
555  return false;
556  }
557  if (StringRef(this->doi_.c_str(), this->doi_.length()) !=
558  StringRef(cit.doi_.c_str(), cit.doi_.length())) {
559  return false;
560  }
561  if (StringRef(this->title_.c_str(), this->title_.length()) !=
562  StringRef(cit.title_.c_str(), cit.title_.length())) {
563  return false;
564  }
565  if (this->authors_ != cit.authors_) {
566  return false;
567  }
568 
569  return true;
570  }
571 
572  bool operator!=(const MMCifInfoCitation& cit) const {
573  return !this->operator==(cit);
574  }
575 
576 private:
578  typedef enum {
579  JOURNAL,
580  BOOK,
581  UNKNOWN
582  } MMCifInfoCType;
583 
584  String id_;
585  MMCifInfoCType where_;
586  String cas_;
587  String isbn_;
588  String published_in_;
589  String volume_;
590  String page_first_;
591  String page_last_;
592  String doi_;
593  int pubmed_;
594  int year_;
595  String title_;
596  std::vector<String> authors_;
597 };
598 
601 class DLLEXPORT_OST_IO MMCifInfoObsolete {
602 public:
604  MMCifInfoObsolete(): date_(""), id_(UNKNOWN), pdb_id_(""),
605  replaced_pdb_id_("") {};
606 
610  void SetDate(String date) { date_ = date; }
611 
615  String GetDate() { return date_; }
616 
620  void SetID(StringRef type)
621  {
622  if (type == StringRef("OBSLTE", 6)) {
623  id_ = OBSLTE;
624  }
625  else if (type == StringRef("SPRSDE", 6)) {
626  id_ = SPRSDE;
627  }
628  }
629 
634  {
635  if (id_ == OBSLTE) {
636  return "Obsolete";
637  }
638  if (id_ == SPRSDE) {
639  return "Supersede";
640  }
641  return "Unknown";
642  }
643 
647  void SetPDBID(String id) { pdb_id_ = id; }
648 
652  String GetPDBID() { return pdb_id_; }
653 
657  void SetReplacedPDBID(String id) { replaced_pdb_id_ = id; }
658 
662  String GetReplacedPDBID() { return replaced_pdb_id_; }
663 
664 private:
666  typedef enum {
667  OBSLTE,
668  SPRSDE,
669  UNKNOWN
670  } MMCifObsoleteType;
671 
672  String date_;
673  MMCifObsoleteType id_;
674  String pdb_id_;
675  String replaced_pdb_id_;
676 };
677 
680 class DLLEXPORT_OST_IO MMCifInfoRevisions {
681 public:
683  MMCifInfoRevisions(): date_original_("?"), first_release_(0) {};
684 
688  void SetDateOriginal(String date) { date_original_ = date; }
689 
693  String GetDateOriginal() const { return date_original_; }
694 
700  void AddRevision(int num, String date, String status)
701  {
702  if (num_.size() && (num_.back() >= num)) {
703  std::stringstream ss;
704  ss << "Unique ID of revision has to increase with every revision, "
705  << "last was " << num_.back() << ", trying to add " << num;
706  throw IOException(ss.str());
707  }
708  num_.push_back(num);
709  date_.push_back(date);
710  status_.push_back(status);
711  // set first release date if not already occupied
712  if (first_release_ == 0) {
713  if (status == "full release" || status == "Initial release") {
714  first_release_ = status_.size();
715  }
716  }
717  }
718 
722  size_t GetSize() const { return num_.size(); }
723 
728  String GetDate(size_t i) const { return date_.at(i); }
729 
734  int GetNum(size_t i) const { return num_.at(i); }
735 
740  String GetStatus(size_t i) const { return status_.at(i); }
741 
745  String GetLastDate() const {
746  if (date_.empty()) return "?";
747  else return date_.back();
748  }
749 
753  size_t GetFirstRelease() const
754  {
755  return first_release_;
756  }
757 
758 private:
759  String date_original_;
760  size_t first_release_;
761  std::vector<int> num_;
762  std::vector<String> date_;
763  std::vector<String> status_;
764 };
765 
766 
767 class MMCifInfoStructRef;
768 class MMCifInfoStructRefSeq;
769 class MMCifInfoStructRefSeqDif;
770 
771 
772 typedef boost::shared_ptr<MMCifInfoStructRef> MMCifInfoStructRefPtr;
773 typedef boost::shared_ptr<MMCifInfoStructRefSeq> MMCifInfoStructRefSeqPtr;
774 typedef boost::shared_ptr<MMCifInfoStructRefSeqDif> MMCifInfoStructRefSeqDifPtr;
775 
776 typedef std::vector<MMCifInfoStructRefPtr> MMCifInfoStructRefs;
777 typedef std::vector<MMCifInfoStructRefSeqPtr> MMCifInfoStructRefSeqs;
778 typedef std::vector<MMCifInfoStructRefSeqDifPtr> MMCifInfoStructRefSeqDifs;
779 class DLLEXPORT_OST_IO MMCifInfoStructRef {
780 public:
781  MMCifInfoStructRef(const String& id, const String& ent_id,
782  const String& db_name,
783  const String& db_ident, const String& db_access):
784  id_(id), ent_id_(ent_id), db_name_(db_name), db_ident_(db_ident),
785  db_access_(db_access)
786  { }
787  const String& GetID() const { return id_; }
788  const String& GetDBName() const { return db_name_; }
789  const String& GetDBID() const { return db_ident_; }
790  const String& GetEntityID() const { return ent_id_; }
791  const String& GetDBAccess() const { return db_access_; }
792  MMCifInfoStructRefSeqPtr AddAlignedSeq(const String& align_id,
793  const String& chain_name, int seq_begin,
794  int seq_end, int db_begin, int db_end);
795  MMCifInfoStructRefSeqPtr GetAlignedSeq(const String& align_id) const;
797  {
799  seqs.reserve(seqs_.size());
800  for (std::map<String, MMCifInfoStructRefSeqPtr>::const_iterator
801  i=seqs_.begin(), e=seqs_.end(); i!=e; ++i) {
802  seqs.push_back(i->second);
803  }
804  return seqs;
805  }
806 private:
807  String id_;
808  String ent_id_;
809  String db_name_;
810  String db_ident_;
811  String db_access_;
812  std::map<String, MMCifInfoStructRefSeqPtr> seqs_;
813 };
814 
815 class DLLEXPORT_OST_IO MMCifInfoStructRefSeq {
816 public:
817  MMCifInfoStructRefSeq(const String& align_id, const String& chain_name,
818  int seq_begin, int seq_end,
819  int db_begin, int db_end):
820  id_(align_id), chain_name_(chain_name),
821  seq_begin_(seq_begin), seq_end_(seq_end), db_begin_(db_begin), db_end_(db_end)
822  { }
823 
824  const String& GetID() const { return id_; }
825  const String& GetChainName() const { return chain_name_; }
826  int GetSeqBegin() const { return seq_begin_; }
827  int GetSeqEnd() const { return seq_end_; }
828  int GetDBBegin() const { return db_begin_; }
829  int GetDBEnd() const { return db_end_; }
830  MMCifInfoStructRefSeqDifPtr AddDif(int seq_num, const String& db_rnum,
831  const String& details);
832  const std::vector<MMCifInfoStructRefSeqDifPtr>& GetDifs() const { return difs_; }
833 private:
834  String id_;
835  String chain_name_;
836  int seq_begin_;
837  int seq_end_;
838  int db_begin_;
839  int db_end_;
840  std::vector<MMCifInfoStructRefSeqDifPtr> difs_;
841 };
842 
843 class DLLEXPORT_OST_IO MMCifInfoStructRefSeqDif {
844 public:
845  MMCifInfoStructRefSeqDif(int seq_rnum, const String& db_rnum, const String& details):
846  seq_rnum_(seq_rnum), db_rnum_(db_rnum), details_(details) {}
847  int GetSeqRNum() const { return seq_rnum_;}
848  const String& GetDBRNum() const { return db_rnum_; }
849  const String& GetDetails() const { return details_; }
850 private:
851  int seq_rnum_;
852  String db_rnum_;
853  String details_;
854 };
855 
869 class DLLEXPORT_OST_IO MMCifInfo {
870 public:
872  MMCifInfo(): exptl_method_(""), resolution_(0), r_free_(0), r_work_(0) { }
873 
877  void AddCitation(MMCifInfoCitation citation) // unit test
878  {
879  citations_.push_back(citation);
880  }
881 
886  void AddAuthorsToCitation(StringRef id, std::vector<String> list); //unit test
887 
891  const std::vector<MMCifInfoCitation>& GetCitations() const
892  {
893  return citations_;
894  }
895 
899  void SetMethod(String method) { exptl_method_ = method; }
900 
904  const StringRef GetMethod() const
905  {
906  return StringRef(exptl_method_.c_str(), exptl_method_.length());
907  }
908 
912  void SetResolution(Real res) { resolution_ = res; }
913 
917  Real GetResolution() const { return resolution_; }
918 
922  void SetRFree(Real r_free) { r_free_ = r_free; }
923 
927  Real GetRFree() const { return r_free_; }
928 
932  void SetRWork(Real r_work) { r_work_ = r_work; }
933 
937  Real GetRWork() const { return r_work_; }
938 
943  void AddMMCifPDBChainTr(String cif, String pdb);
944 
949  String GetMMCifPDBChainTr(String cif) const;
950 
955  void AddPDBMMCifChainTr(String pdb, String cif);
956 
961  String GetPDBMMCifChainTr(String pdb) const;
962 
967  void AddMMCifEntityIdTr(String cif, String ent_id);
968 
973  String GetMMCifEntityIdTr(String cif) const;
974 
978  void AddBioUnit(MMCifInfoBioUnit bu);
979 
983  const std::vector<MMCifInfoBioUnit>& GetBioUnits() const
984  {
985  return biounits_;
986  }
987 
991  void AddOperation(MMCifInfoTransOpPtr op) // unit test
992  {
993  transops_.push_back(op);
994  }
995 
999  const std::vector<MMCifInfoTransOpPtr>& GetOperations() const
1000  {
1001  return transops_;
1002  }
1003 
1008  {
1009  struct_details_ = details;
1010  }
1011 
1016  {
1017  return struct_details_;
1018  }
1019 
1024  {
1025  obsolete_ = obsolete;
1026  }
1027 
1032  {
1033  return obsolete_;
1034  }
1035  const MMCifInfoStructRefs& GetStructRefs() const { return struct_refs_; }
1036  void SetStructRefs(const MMCifInfoStructRefs& sr) { struct_refs_=sr; }
1037 
1042  {
1043  // only set once
1044  if (revisions_.GetDateOriginal() == "?") {
1045  revisions_.SetDateOriginal(date);
1046  }
1047  }
1048 
1054  void AddRevision(int num, String date, String status)
1055  {
1056  revisions_.AddRevision(num, date, status);
1057  }
1058 
1063  {
1064  return revisions_;
1065  }
1066 //protected:
1067 
1068 private:
1069  // members
1070  String exptl_method_;
1071  Real resolution_;
1072  Real r_free_;
1073  Real r_work_;
1074  MMCifInfoStructDetails struct_details_;
1075  MMCifInfoObsolete obsolete_;
1076  MMCifInfoRevisions revisions_;
1077  std::vector<MMCifInfoCitation> citations_;
1078  std::vector<MMCifInfoBioUnit> biounits_;
1079  std::vector<MMCifInfoTransOpPtr> transops_;
1080  MMCifInfoStructRefs struct_refs_;
1081  std::map<String, String> cif_2_pdb_chain_id_;
1082  std::map<String, String> pdb_2_cif_chain_id_;
1083  std::map<String, String> cif_2_entity_id_;
1084 };
1085 
1086 
1087 }} // ns
1088 
1089 #endif
void SetID(String id)
Set ID.
Definition: mmcif_info.hh:401
const std::vector< MMCifInfoCitation > & GetCitations() const
Get the list of citations stored in an info object.
Definition: mmcif_info.hh:891
container class for information on obsolete entries
Definition: mmcif_info.hh:601
String GetID()
Get type of entry.
Definition: mmcif_info.hh:633
MMCifInfoObsolete GetObsoleteInfo() const
Get information on an obsolete entries.
Definition: mmcif_info.hh:1031
const StringRef GetMethod() const
Get an experimental method.
Definition: mmcif_info.hh:904
bool operator!=(const MMCifInfoStructDetails &sd) const
Definition: mmcif_info.hh:140
convenient datatype for referencing character data
Definition: string_ref.hh:39
void SetTitle(String title)
Set the title of a publication.
Definition: mmcif_info.hh:502
void SetPubMed(int no)
Set the PubMed accession number.
Definition: mmcif_info.hh:480
void SetAuthorList(std::vector< String > list)
Set the list of authors.
Definition: mmcif_info.hh:512
void SetObsoleteInfo(MMCifInfoObsolete obsolete)
Add a block of information on obsolete entries.
Definition: mmcif_info.hh:1023
boost::shared_ptr< MMCifInfoStructRefSeqDif > MMCifInfoStructRefSeqDifPtr
Definition: mmcif_info.hh:774
const String & GetDBAccess() const
Definition: mmcif_info.hh:791
String GetISBN() const
Get an ISBN code.
Definition: mmcif_info.hh:424
std::vector< MMCifInfoStructRefSeqDifPtr > MMCifInfoStructRefSeqDifs
Definition: mmcif_info.hh:778
const MMCifInfoStructRefs & GetStructRefs() const
Definition: mmcif_info.hh:1035
MMCifInfo()
Create an info object.
Definition: mmcif_info.hh:872
String GetDetails() const
Get details.
Definition: mmcif_info.hh:275
std::vector< MMCifInfoStructRefSeqPtr > MMCifInfoStructRefSeqs
Definition: mmcif_info.hh:777
const MMCifInfoStructDetails GetStructDetails() const
Get the list of details about structures.
Definition: mmcif_info.hh:1015
void SetType(String type)
Set type.
Definition: mmcif_info.hh:175
MMCifInfoStructDetails()
Create a details object.
Definition: mmcif_info.hh:35
void SetModelTypeDetails(String desc)
Set a description for the type of the structure model.
Definition: mmcif_info.hh:96
void SetMethod(String method)
Set an experimental method.
Definition: mmcif_info.hh:899
std::string String
Definition: base.hh:54
void SetPublishedIn(String title)
Set a book title or journal name.
Definition: mmcif_info.hh:429
float Real
Definition: base.hh:44
char GetCASPFlag() const
Get CASP flag.
Definition: mmcif_info.hh:55
void SetMethodDetails(String method_details)
Set method details.
Definition: mmcif_info.hh:280
MMCifInfoStructRef(const String &id, const String &ent_id, const String &db_name, const String &db_ident, const String &db_access)
Definition: mmcif_info.hh:781
void SetDetails(String details)
Set details.
Definition: mmcif_info.hh:271
void SetID(String id)
Set id.
Definition: mmcif_info.hh:166
Real GetResolution() const
Get resolution.
Definition: mmcif_info.hh:917
const std::vector< std::pair< int, int > > & GetOperationsIntervalList()
Get the list of intervals of operations.
Definition: mmcif_info.hh:319
void AddCitation(MMCifInfoCitation citation)
Add an item to the list of citations.
Definition: mmcif_info.hh:877
bool operator!=(const MMCifInfoBioUnit &bu) const
Definition: mmcif_info.hh:377
boost::shared_ptr< MMCifInfoStructRef > MMCifInfoStructRefPtr
Definition: mmcif_info.hh:769
const String & GetDBName() const
Definition: mmcif_info.hh:788
const String & GetDetails() const
Definition: mmcif_info.hh:849
String GetVolume() const
Get a journal volume.
Definition: mmcif_info.hh:444
def Merge
Definition: table.py:3052
bool DLLEXPORT_OST_GEOM operator==(const Line2 &l1, const Line2 &l2)
String GetID() const
Get ID.
Definition: mmcif_info.hh:405
const std::vector< MMCifInfoStructRefSeqDifPtr > & GetDifs() const
Definition: mmcif_info.hh:832
size_t GetSize() const
Get number of revisions stored.
Definition: mmcif_info.hh:722
boost::shared_ptr< MMCifInfoTransOp > MMCifInfoTransOpPtr
Definition: mmcif_info.hh:246
Container class for information on file revisions.
Definition: mmcif_info.hh:680
void SetRWork(Real r_work)
Set R-work value.
Definition: mmcif_info.hh:932
String GetTitle() const
Get the title of a publication.
Definition: mmcif_info.hh:507
String GetLastDate() const
Get date of last revision.
Definition: mmcif_info.hh:745
const String & GetDBID() const
Definition: mmcif_info.hh:789
std::vector< MMCifInfoStructRefPtr > MMCifInfoStructRefs
Definition: mmcif_info.hh:776
void SetTitle(String title)
Set a title for the data block.
Definition: mmcif_info.hh:105
void AddRevision(int num, String date, String status)
Add a revision to history.
Definition: mmcif_info.hh:1054
void SetRevisionsDateOriginal(String date)
Set date_original of revisions.
Definition: mmcif_info.hh:1041
Real GetMass() const
Get molecular weight.
Definition: mmcif_info.hh:73
MMCifInfoBioUnit()
Create a biounit.
Definition: mmcif_info.hh:252
String GetDate()
Get the date string.
Definition: mmcif_info.hh:615
void SetCAS(String id)
Set a CAS identifier.
Definition: mmcif_info.hh:410
const std::vector< String > & GetChainList() const
Get vector of chain names.
Definition: mmcif_info.hh:301
void SetResolution(Real res)
Set resolution.
Definition: mmcif_info.hh:912
void SetReplacedPDBID(String id)
Set id of replaced entry.
Definition: mmcif_info.hh:657
const String & GetID() const
Definition: mmcif_info.hh:787
String GetCAS() const
Get a CAS identifier.
Definition: mmcif_info.hh:414
void AddOperation(MMCifInfoTransOpPtr op)
Add a operation.
Definition: mmcif_info.hh:991
geom::Vec3 GetVector() const
Get the translational vector.
Definition: mmcif_info.hh:195
const std::vector< String > & GetAuthorList() const
Get the list of authors.
Definition: mmcif_info.hh:517
int GetPubMed() const
Get the PubMed accession number.
Definition: mmcif_info.hh:485
bool operator!=(const MMCifInfoCitation &cit) const
Definition: mmcif_info.hh:572
const String & GetDBRNum() const
Definition: mmcif_info.hh:848
const std::vector< MMCifInfoTransOpPtr > & GetOperations() const
Get the list of operations stored in an info object.
Definition: mmcif_info.hh:999
String GetID() const
Get id.
Definition: mmcif_info.hh:170
void SetEntryID(String id)
Set id.
Definition: mmcif_info.hh:42
size_t GetFirstRelease() const
Get the index of the full release revision.
Definition: mmcif_info.hh:753
bool operator==(const MMCifInfoCitation &cit) const
Definition: mmcif_info.hh:519
void SetDateOriginal(String date)
Set date the entry entered PDB.
Definition: mmcif_info.hh:688
void SetCASPFlag(char flag)
Set CASP flag.
Definition: mmcif_info.hh:51
void SetDate(String date)
Set date of replacement.
Definition: mmcif_info.hh:610
MMCifInfoTransOp()
Create an operation.
Definition: mmcif_info.hh:158
Real GetRWork() const
Get R-work value.
Definition: mmcif_info.hh:937
String GetPublishedIn() const
Get a book title or journal name.
Definition: mmcif_info.hh:434
MMCifInfoStructRefSeqDif(int seq_rnum, const String &db_rnum, const String &details)
Definition: mmcif_info.hh:845
bool operator==(const MMCifInfoStructDetails &sd) const
Definition: mmcif_info.hh:111
Three dimensional vector class, using Real precision.
Definition: vec3.hh:42
const std::vector< std::vector< MMCifInfoTransOpPtr > > & GetOperations()
Get the list of operations.
Definition: mmcif_info.hh:327
void SetStructDetails(MMCifInfoStructDetails details)
Add a set of structure details.
Definition: mmcif_info.hh:1007
void SetID(String id)
Set id.
Definition: mmcif_info.hh:262
String GetDate(size_t i) const
Get revision date by index in list.
Definition: mmcif_info.hh:728
void AddRevision(int num, String date, String status)
Add a revision to history.
Definition: mmcif_info.hh:700
void SetMassMethod(String method)
Set the method how the molecular weight was detected.
Definition: mmcif_info.hh:78
#define DLLEXPORT_OST_IO
String GetType() const
Get type.
Definition: mmcif_info.hh:179
void SetStructRefs(const MMCifInfoStructRefs &sr)
Definition: mmcif_info.hh:1036
String GetModelDetails() const
Get the details how the structure was determined.
Definition: mmcif_info.hh:91
void SetMatrix(Real i00, Real i01, Real i02, Real i10, Real i11, Real i12, Real i20, Real i21, Real i22)
Set the rotational matrix.
Definition: mmcif_info.hh:208
void SetRFree(Real r_free)
Set R-free value.
Definition: mmcif_info.hh:922
boost::shared_ptr< MMCifInfoStructRefSeq > MMCifInfoStructRefSeqPtr
Definition: mmcif_info.hh:773
bool operator==(const MMCifInfoBioUnit &bu) const
Definition: mmcif_info.hh:332
void SetPageFirst(String first)
Set the start page for a publication.
Definition: mmcif_info.hh:449
void SetMass(Real mass)
Set mass.
Definition: mmcif_info.hh:69
String GetPageFirst() const
Get the start page of a publication.
Definition: mmcif_info.hh:454
void SetID(StringRef type)
Set type of entry.
Definition: mmcif_info.hh:620
const String & GetEntityID() const
Definition: mmcif_info.hh:790
String GetID() const
Get id.
Definition: mmcif_info.hh:266
String GetMassMethod() const
Get the method how the molecular weight was determined.
Definition: mmcif_info.hh:82
int GetYear() const
Get the year of a publication.
Definition: mmcif_info.hh:496
String GetEntryID() const
Get id.
Definition: mmcif_info.hh:46
const std::vector< std::pair< int, int > > & GetChainIntervalList()
Get the list of intervals of chains.
Definition: mmcif_info.hh:306
const String & GetID() const
Definition: mmcif_info.hh:824
const String & GetChainName() const
Definition: mmcif_info.hh:825
void SetModelDetails(String desc)
Set the description about the production of this structure.
Definition: mmcif_info.hh:87
MMCifInfoStructRefSeq(const String &align_id, const String &chain_name, int seq_begin, int seq_end, int db_begin, int db_end)
Definition: mmcif_info.hh:817
MMCifInfoObsolete()
Create an object of information about an obsolete entry.
Definition: mmcif_info.hh:604
void SetPageLast(String last)
Set the end page for a publication.
Definition: mmcif_info.hh:459
String GetMethodDetails() const
Get method details.
Definition: mmcif_info.hh:286
String GetDateOriginal() const
Get date the entry entered PDB.
Definition: mmcif_info.hh:693
bool operator==(const MMCifInfoTransOp &op) const
Definition: mmcif_info.hh:219
String GetDOI() const
Get the DOI of a document.
Definition: mmcif_info.hh:475
String GetPageLast() const
Get the last page of a publication.
Definition: mmcif_info.hh:464
MMCifInfoRevisions()
Start recording a revision process.
Definition: mmcif_info.hh:683
void SetISBN(String code)
Set an ISBN code.
Definition: mmcif_info.hh:419
Real GetRFree() const
Get R-free value.
Definition: mmcif_info.hh:927
String GetStatus(size_t i) const
Get revision status by index in list.
Definition: mmcif_info.hh:740
void SetDescriptor(String desc)
Set descriptor.
Definition: mmcif_info.hh:60
bool operator!=(const MMCifInfoTransOp &op) const
Definition: mmcif_info.hh:236
MMCifInfoStructRefSeqs GetAlignedSeqs() const
Definition: mmcif_info.hh:796
const std::vector< MMCifInfoBioUnit > & GetBioUnits() const
Get the list of biounits stored in an info object.
Definition: mmcif_info.hh:983
String GetDescriptor() const
Get CASP flag.
Definition: mmcif_info.hh:64
int GetNum(size_t i) const
Get revision num by index in list.
Definition: mmcif_info.hh:734
MMCifInfoRevisions GetRevisions() const
Get history.
Definition: mmcif_info.hh:1062
String GetModelTypeDetails() const
Get the description for the type of the structure model.
Definition: mmcif_info.hh:100
String GetPDBID()
Get id of replacement.
Definition: mmcif_info.hh:652
geom::Mat3 GetMatrix() const
Get the rotational matrix.
Definition: mmcif_info.hh:217
void SetVector(Real x, Real y, Real z)
Set the translational vector.
Definition: mmcif_info.hh:186
MMCifInfoCitation()
Create a citation.
Definition: mmcif_info.hh:394
String GetTitle() const
Get the title of the structure model.
Definition: mmcif_info.hh:109
void SetYear(int year)
Set the year of a publication.
Definition: mmcif_info.hh:490
void SetPDBID(String id)
Set id of replacement.
Definition: mmcif_info.hh:647
void SetVolume(String volume)
Set a journal volume.
Definition: mmcif_info.hh:439
void SetDOI(String doi)
Set the DOI of a document.
Definition: mmcif_info.hh:469
String GetReplacedPDBID()
Get id of replaced entry.
Definition: mmcif_info.hh:662