BALL: PDBFile.h Source File

00001 // -*- Mode: C++; tab-width: 2; -*-
00002 // vi: set ts=2:
00003 //
00004 
00005 #ifndef BALL_FORMAT_PDBFILE_H
00006 #define BALL_FORMAT_PDBFILE_H
00007 
00008 #ifndef BALL_CONCEPT_PROPERTY_H
00009 # include <BALL/CONCEPT/property.h>
00010 #endif
00011 
00012 #ifndef BALL_FORMAT_GENERICMOLFILE_H
00013 # include <BALL/FORMAT/genericMolFile.h>
00014 #endif
00015 
00016 #ifndef BALL_DATATYPE_OPTIONS_H
00017 # include <BALL/DATATYPE/options.h>
00018 #endif
00019 
00020 #ifndef BALL_DATATYPE_QUADRUPLE_H
00021 # include <BALL/DATATYPE/quadruple.h>
00022 #endif
00023 
00024 #ifndef BALL_FORMAT_PDBDEFS_H
00025 # include <BALL/FORMAT/PDBdefs.h>
00026 #endif
00027 
00028 #ifndef BALL_FORMAT_PDBINFO_H
00029 # include <BALL/FORMAT/PDBInfo.h>
00030 #endif
00031 
00032 #ifndef BALL_KERNEL_PDBAtom_H
00033 # include <BALL/KERNEL/PDBAtom.h>
00034 #endif
00035 
00036 #ifndef BALL_KERNEL_SYSTEM_H
00037 # include <BALL/KERNEL/system.h>
00038 #endif
00039 
00040 #ifndef BALL_KERNEL_RESIDUE_H
00041 # include <BALL/KERNEL/residue.h>
00042 #endif
00043 
00044 #ifndef BALL_KERNEL_SECONDARYSTRUCTURE_H
00045 # include <BALL/KERNEL/secondaryStructure.h>
00046 #endif
00047 
00048 #if defined(BALL_HAS_UNORDERED_MAP) || defined(BALL_HAS_HASH_MAP)
00049 #ifdef BALL_EXTEND_HASH_IN_STD_NS
00050 namespace std
00051 {
00052 #endif
00053   namespace BALL_MAP_NAMESPACE {
00054     template<>
00055     struct hash<BALL::Quadruple<BALL::String, BALL::PDB::Character, BALL::PDB::Integer, BALL::PDB::AChar> >
00056     {
00057       size_t
00058       operator()(const BALL::Quadruple<BALL::String, BALL::PDB::Character, BALL::PDB::Integer, BALL::PDB::AChar>& f) const
00059       { return (size_t)f.third; }
00060     };
00061   }
00062 #ifdef BALL_EXTEND_HASH_IN_STD_NS
00063 }
00064 #endif
00065 #endif
00066 
00067 namespace BALL
00068 {
00069 
00074   class BALL_EXPORT PDBFile
00075     : public GenericMolFile,
00076       public PropertyManager
00077   {
00078     public:
00079 
00085     struct BALL_EXPORT Option 
00086     {
00093       static const char* VERBOSITY;
00094 
00101       static const char* STRICT_LINE_CHECKING;
00102       
00110       static const char* CHOOSE_MODEL;
00111 
00117       static const char* STORE_SKIPPED_RECORDS;
00118 
00124       static const char* IGNORE_XPLOR_PSEUDO_ATOMS;
00125 
00131       static const char* PARSE_PARTIAL_CHARGES;
00132     };
00133 
00136     struct BALL_EXPORT Default 
00137     {
00142       static const Index VERBOSITY;
00143 
00148       static const bool STRICT_LINE_CHECKING;
00149 
00154       static const Index CHOOSE_MODEL;
00155 
00159       static const bool STORE_SKIPPED_RECORDS;
00160 
00164       static const bool IGNORE_XPLOR_PSEUDO_ATOMS;
00165 
00169       static const bool PARSE_PARTIAL_CHARGES;
00170     };
00171 
00175 
00176     Options options;
00178     PDBInfo info;
00180 
00184 
00185     PDBFile();
00186       
00188     PDBFile(const String& filename, File::OpenMode open_mode = std::ios::in) throw(Exception::FileNotFound);
00189 
00191     PDBFile(const Options& new_options);
00192 
00194     virtual ~PDBFile();
00196 
00200 
00202     virtual void clear(int state);
00203 
00205     virtual void clear();
00206 
00208 
00212 
00214     virtual float getVersion() const;
00215 
00220     void selectModel(Index index);
00221 
00233     void selectAltLocationIndicator(char c);
00234 
00236     Index getSelectedModel() const;
00237 
00239     void selectAllModels();
00240 
00242     Index getCurrentModel() const;
00243 
00245     char* getRecordString();
00246 
00248     const char* getRecordString() const;
00249 
00251     Index getRecordNumber() const;
00252 
00254     PDB::RecordType getRecordType() const;
00255 
00259     virtual const char* getAtomElementSymbol
00260       (const PDB::Atom atom_name,
00261        PDB::Atom element_symbol);
00262 
00264     virtual const char* getAtomName
00265       (const PDB::Atom atom_name);
00266 
00268     virtual char getAtomRemotenessIndicator
00269       (const PDB::Atom atom_name);
00270 
00272     virtual short getAtomBranchDesignator
00273       (const PDB::Atom atom_name);
00274 
00276     Size countRecordFields() const;
00277 
00281     Size countRecord
00282       (PDB::RecordType record_type,
00283        bool from_begin_of_file = true);
00284 
00287     Size countRecords
00288       (bool from_begin_of_file = true);
00290 
00297 
00298     bool parseLine(const char* line, Size size, const char* format_string, ...);
00299 
00301     bool readLine(char* line, Size size, bool extract_values);
00302 
00304     bool readFirstRecord(bool read_values = true);
00305 
00307     bool readNextRecord(bool read_values = true);
00308 
00313     bool readRecords();
00314 
00319     virtual bool readUnknownRecord(const char* line);
00320 
00323     virtual bool readInvalidRecord(const char* line);
00324 
00333     bool skipCurrentRecord();
00334 
00336     virtual bool interpretRecord(const PDB::RecordANISOU& record);
00337     virtual bool fillRecord(const char* line, Size size, PDB::RecordANISOU& record);
00338     virtual bool parseRecordANISOU(const char* line, Size size);
00339 
00341     virtual bool interpretRecord(const PDB::RecordATOM& record);
00342     virtual bool fillRecord(const char* line, Size size, PDB::RecordATOM& record);
00343     virtual bool parseRecordATOM(const char* line, Size size);
00344 
00346     virtual bool interpretRecord(const PDB::RecordAUTHOR& record);
00347     virtual bool fillRecord(const char* line, Size size, PDB::RecordAUTHOR& record);
00348     virtual bool parseRecordAUTHOR(const char* line, Size size);
00349 
00351     virtual bool interpretRecord(const PDB::RecordCAVEAT& record);
00352     virtual bool fillRecord(const char* line, Size size, PDB::RecordCAVEAT& record);
00353     virtual bool parseRecordCAVEAT(const char* line, Size size);
00354 
00356     virtual bool interpretRecord(const PDB::RecordCISPEP& record);
00357     virtual bool fillRecord(const char* line, Size size, PDB::RecordCISPEP& record);
00358     virtual bool parseRecordCISPEP(const char* line, Size size);
00359 
00361     virtual bool interpretRecord(const PDB::RecordCOMPND& record);
00362     virtual bool fillRecord(const char* line, Size size, PDB::RecordCOMPND& record);
00363     virtual bool parseRecordCOMPND(const char* line, Size size);
00364 
00366     virtual bool interpretRecord(const PDB::RecordCONECT& record);
00367     virtual bool fillRecord(const char* line, Size size, PDB::RecordCONECT& record);
00368     virtual bool parseRecordCONECT(const char* line, Size size);
00369 
00373     virtual bool interpretRecord(const PDB::RecordCRYST1& record);
00374     virtual bool fillRecord(const char* line, Size size, PDB::RecordCRYST1& record);
00375     virtual bool parseRecordCRYST1(const char* line, Size size);
00376 
00378     virtual bool interpretRecord(const PDB::RecordDBREF& record);
00379     virtual bool fillRecord(const char* line, Size size, PDB::RecordDBREF& record);
00380     virtual bool parseRecordDBREF(const char* line, Size size);
00381 
00383     virtual bool interpretRecord(const PDB::RecordEND& record);
00384     virtual bool fillRecord(const char* line, Size size, PDB::RecordEND& record);
00385     virtual bool parseRecordEND(const char* line, Size size);
00386 
00388     virtual bool interpretRecord(const PDB::RecordENDMDL& record);
00389     virtual bool fillRecord(const char* line, Size size, PDB::RecordENDMDL& record);
00390     virtual bool parseRecordENDMDL(const char* line, Size size);
00391 
00393     virtual bool interpretRecord(const PDB::RecordEXPDTA& record);
00394     virtual bool fillRecord(const char* line, Size size, PDB::RecordEXPDTA& record);
00395     virtual bool parseRecordEXPDTA(const char* line, Size size);
00396 
00400     virtual bool interpretRecord(const PDB::RecordFORMUL& record);
00401     virtual bool fillRecord(const char* line, Size size, PDB::RecordFORMUL& record);
00402     virtual bool parseRecordFORMUL(const char* line, Size size);
00403 
00405     virtual bool interpretRecord(const PDB::RecordFTNOTE& record);
00406     virtual bool fillRecord(const char* line, Size size, PDB::RecordFTNOTE& record);
00407     virtual bool parseRecordFTNOTE(const char* line, Size size);
00408 
00412     virtual bool interpretRecord(const PDB::RecordHEADER& record);
00413     virtual bool fillRecord(const char* line, Size size, PDB::RecordHEADER& record);
00414     virtual bool parseRecordHEADER(const char* line, Size size);
00415 
00417     virtual bool interpretRecord(const PDB::RecordHELIX& record);
00418     virtual bool fillRecord(const char* line, Size size, PDB::RecordHELIX& record);
00419     virtual bool parseRecordHELIX(const char* line, Size size);
00420 
00422     virtual bool interpretRecord(const PDB::RecordHET& record);
00423     virtual bool fillRecord(const char* line, Size size, PDB::RecordHET& record);
00424     virtual bool parseRecordHET(const char* line, Size size);
00425 
00427     virtual bool interpretRecord(const PDB::RecordHETATM& record);
00428     virtual bool fillRecord(const char* line, Size size, PDB::RecordHETATM& record);
00429     virtual bool parseRecordHETATM(const char* line, Size size);
00430 
00432     virtual bool interpretRecord(const PDB::RecordHETNAM& record);
00433     virtual bool fillRecord(const char* line, Size size, PDB::RecordHETNAM& record);
00434     virtual bool parseRecordHETNAM(const char* line, Size size);
00435 
00437     virtual bool interpretRecord(const PDB::RecordHETSYN& record);
00438     virtual bool fillRecord(const char* line, Size size, PDB::RecordHETSYN& record);
00439     virtual bool parseRecordHETSYN(const char* line, Size size);
00440 
00442     virtual bool interpretRecord(const PDB::RecordHYDBND& record);
00443     virtual bool fillRecord(const char* line, Size size, PDB::RecordHYDBND& record);
00444     virtual bool parseRecordHYDBND(const char* line, Size size);
00445 
00447     virtual bool interpretRecord(const PDB::RecordJRNL& record);
00448     virtual bool fillRecord(const char* line, Size size, PDB::RecordJRNL& record);
00449     virtual bool parseRecordJRNL(const char* line, Size size);
00450 
00452     virtual bool interpretRecord(const PDB::RecordKEYWDS& record);
00453     virtual bool fillRecord(const char* line, Size size, PDB::RecordKEYWDS& record);
00454     virtual bool parseRecordKEYWDS(const char* line, Size size);
00455 
00457     virtual bool interpretRecord(const PDB::RecordLINK& record);
00458     virtual bool fillRecord(const char* line, Size size, PDB::RecordLINK& record);
00459     virtual bool parseRecordLINK(const char* line, Size size);
00460 
00464     virtual bool interpretRecord(const PDB::RecordMASTER& record);
00465     virtual bool fillRecord(const char* line, Size size, PDB::RecordMASTER& record);
00466     virtual bool parseRecordMASTER(const char* line, Size size);
00467 
00469     virtual bool interpretRecord(const PDB::RecordMODEL& record);
00470     virtual bool fillRecord(const char* line, Size size, PDB::RecordMODEL& record);
00471     virtual bool parseRecordMODEL(const char* line, Size size);
00472 
00474     virtual bool interpretRecord(const PDB::RecordMODRES& record);
00475     virtual bool fillRecord(const char* line, Size size, PDB::RecordMODRES& record);
00476     virtual bool parseRecordMODRES(const char* line, Size size);
00477 
00481     virtual bool interpretRecord(const PDB::RecordMTRIX1& record);
00482     virtual bool fillRecord(const char* line, Size size, PDB::RecordMTRIX1& record);
00483     virtual bool parseRecordMTRIX1(const char* line, Size size);
00484 
00488     virtual bool interpretRecord(const PDB::RecordMTRIX2& record);
00489     virtual bool fillRecord(const char* line, Size size, PDB::RecordMTRIX2& record);
00490     virtual bool parseRecordMTRIX2(const char* line, Size size);
00491 
00495     virtual bool interpretRecord(const PDB::RecordMTRIX3& record);
00496     virtual bool fillRecord(const char* line, Size size, PDB::RecordMTRIX3& record);
00497     virtual bool parseRecordMTRIX3(const char* line, Size size);
00498 
00502     virtual bool interpretRecord(const PDB::RecordOBSLTE& record);
00503     virtual bool fillRecord(const char* line, Size size, PDB::RecordOBSLTE& record);
00504     virtual bool parseRecordOBSLTE(const char* line, Size size);
00505 
00509     virtual bool interpretRecord(const PDB::RecordORIGX1& record);
00510     virtual bool fillRecord(const char* line, Size size, PDB::RecordORIGX1& record);
00511     virtual bool parseRecordORIGX1(const char* line, Size size);
00512 
00516     virtual bool interpretRecord(const PDB::RecordORIGX2& record);
00517     virtual bool fillRecord(const char* line, Size size, PDB::RecordORIGX2& record);
00518     virtual bool parseRecordORIGX2(const char* line, Size size);
00519 
00523     virtual bool interpretRecord(const PDB::RecordORIGX3& record);
00524     virtual bool fillRecord(const char* line, Size size, PDB::RecordORIGX3& record);
00525     virtual bool parseRecordORIGX3(const char* line, Size size);
00526 
00528     virtual bool interpretRecord(const PDB::RecordREMARK& record);
00529     virtual bool fillRecord(const char* line, Size size, PDB::RecordREMARK& record);
00530     virtual bool parseRecordREMARK(const char* line, Size size);
00531 
00533     virtual bool interpretRecord(const PDB::RecordREVDAT& record);
00534     virtual bool fillRecord(const char* line, Size size, PDB::RecordREVDAT& record);
00535     virtual bool parseRecordREVDAT(const char* line, Size size);
00536 
00538     virtual bool interpretRecord(const PDB::RecordSCALE1& record);
00539     virtual bool fillRecord(const char* line, Size size, PDB::RecordSCALE1& record);
00540     virtual bool parseRecordSCALE1(const char* line, Size size);
00541 
00543     virtual bool interpretRecord(const PDB::RecordSCALE2& record);
00544     virtual bool fillRecord(const char* line, Size size, PDB::RecordSCALE2& record);
00545     virtual bool parseRecordSCALE2(const char* line, Size size);
00546 
00548     virtual bool interpretRecord(const PDB::RecordSCALE3& record);
00549     virtual bool fillRecord(const char* line, Size size, PDB::RecordSCALE3& record);
00550     virtual bool parseRecordSCALE3(const char* line, Size size);
00551 
00553     virtual bool interpretRecord(const PDB::RecordSEQADV& record);
00554     virtual bool fillRecord(const char* line, Size size, PDB::RecordSEQADV& record);
00555     virtual bool parseRecordSEQADV(const char* line, Size size);
00556 
00558     virtual bool interpretRecord(const PDB::RecordSEQRES& record);
00559     virtual bool fillRecord(const char* line, Size size, PDB::RecordSEQRES& record);
00560     virtual bool parseRecordSEQRES(const char* line, Size size);
00561 
00563     virtual bool interpretRecord(const PDB::RecordSHEET& record);
00564     virtual bool fillRecord(const char* line, Size size, PDB::RecordSHEET& record);
00565     virtual bool parseRecordSHEET(const char* line, Size size);
00566 
00568     virtual bool interpretRecord(const PDB::RecordSIGATM& record);
00569     virtual bool fillRecord(const char* line, Size size, PDB::RecordSIGATM& record);
00570     virtual bool parseRecordSIGATM(const char* line, Size size);
00571 
00575     virtual bool interpretRecord(const PDB::RecordSIGUIJ& record);
00576     virtual bool fillRecord(const char* line, Size size, PDB::RecordSIGUIJ& record);
00577     virtual bool parseRecordSIGUIJ(const char* line, Size size);
00578 
00580     virtual bool interpretRecord(const PDB::RecordSITE& record);
00581     virtual bool fillRecord(const char* line, Size size, PDB::RecordSITE& record);
00582     virtual bool parseRecordSITE(const char* line, Size size);
00583 
00585     virtual bool interpretRecord(const PDB::RecordSLTBRG& record);
00586     virtual bool fillRecord(const char* line, Size size, PDB::RecordSLTBRG& record);
00587     virtual bool parseRecordSLTBRG(const char* line, Size size);
00588 
00592     virtual bool interpretRecord(const PDB::RecordSOURCE& record);
00593     virtual bool fillRecord(const char* line, Size size, PDB::RecordSOURCE& record);
00594     virtual bool parseRecordSOURCE(const char* line, Size size);
00595 
00597     virtual bool interpretRecord(const PDB::RecordSPRSDE& record);
00598     virtual bool fillRecord(const char* line, Size size, PDB::RecordSPRSDE& record);
00599     virtual bool parseRecordSPRSDE(const char* line, Size size);
00600 
00602     virtual bool interpretRecord(const PDB::RecordSSBOND& record);
00603     virtual bool fillRecord(const char* line, Size size, PDB::RecordSSBOND& record);
00604     virtual bool parseRecordSSBOND(const char* line, Size size);
00605 
00607     virtual bool interpretRecord(const PDB::RecordTER& record);
00608     virtual bool fillRecord(const char* line, Size size, PDB::RecordTER& record);
00609     virtual bool parseRecordTER(const char* line, Size size);
00610 
00612     virtual bool interpretRecord(const PDB::RecordTITLE& record);
00613     virtual bool fillRecord(const char* line, Size size, PDB::RecordTITLE& record);
00614     virtual bool parseRecordTITLE(const char* line, Size size);
00615 
00617     virtual bool interpretRecord(const PDB::RecordTURN& record);
00618     virtual bool fillRecord(const char* line, Size size, PDB::RecordTURN& record);
00619     virtual bool parseRecordTURN(const char* line, Size size);
00620 
00624     virtual bool interpretRecord(const PDB::RecordTVECT& record);
00625     virtual bool fillRecord(const char* line, Size size, PDB::RecordTVECT& record);
00626     virtual bool parseRecordTVECT(const char* line, Size size);
00628 
00630     virtual bool hasFormat();
00631 
00632     typedef HashMap<PDB::Integer, PDBAtom*> PDBAtomMap;
00633     typedef Quadruple<String, PDB::Character, PDB::Integer, PDB::AChar> ResidueQuadruple;
00634     typedef HashMap<ResidueQuadruple, Residue*> ResidueMap;
00635     typedef std::list<ResidueQuadruple> QuadrupleList;
00636     typedef std::list<SecondaryStructure*> SecStructList;
00637     
00638 
00641 
00642     PDBFile& operator >> (Protein& protein) throw(Exception::ParseError);
00644     PDBFile& operator >> (Molecule& molecule) throw(Exception::ParseError);
00645     // Read system from the file
00646     PDBFile& operator >> (System& system) throw(Exception::ParseError);
00648     PDBFile& operator << (const Protein& protein) throw(File::CannotWrite);
00649     // Write system to the file
00650     PDBFile& operator << (const System& system) throw(File::CannotWrite);
00651     // Write molecule to the file
00652     PDBFile& operator << (const Molecule& molecule) throw(File::CannotWrite);
00654     bool read(Protein& protein) throw(Exception::ParseError);
00656     bool read(Molecule& protein) throw(Exception::ParseError);
00658     bool read(System& system) throw(Exception::ParseError);
00660     Molecule* read() throw(Exception::ParseError);
00662     bool write(const Protein& protein) throw(File::CannotWrite);
00664     bool write(const Molecule& molecule) throw(File::CannotWrite);
00666     bool write(const System& system) throw(File::CannotWrite);
00668     bool write(const System& system, const PDBInfo& info) throw(File::CannotWrite);
00670 
00671     protected:
00672 
00673     //_
00674     PDBFile(const File& pdbf) throw(Exception::FileNotFound);
00675 
00676     //_
00677     PDBFile& operator = (const PDBFile& pdbf);
00678 
00679     /*_ A helper function for initializing certain data structures. Used by
00680         constructors.
00681     */
00682     void init_() ;
00683 
00684     void postprocessSSBonds_();
00685     void postprocessHelices_();
00686     void postprocessSheetsTurns_(QuadrupleList& sectruct_list, SecStructList& new_secstruct_list);
00687     void postprocessRandomCoils_();
00688 
00689     
00690 
00691     // Method related to the writing of PDB files
00692 
00693     // 
00694     void write_(const AtomContainer& ac, const PDBInfo& info = PDBInfo());
00695 
00701     void writeRecord_(PDB::RecordType record, ...);
00702     void writeCONECTRecords_(PDB::Structure::ConectAtomList& cl);
00703 
00710     void writeRawRecord_(const char* format, const char* tag, ...);
00711     
00713     void addAllRecords_(const PDBInfo& info, PDB::RecordType type);
00714     
00716     void writeRecord_(const PDB::RecordSEQRES& seqres);
00718     void writeRecord_(const PDB::RecordHELIX& helix);
00720     void writeRecord_(const PDB::RecordSHEET& helix);
00722     void writeRecord_(const PDB::RecordTURN& helix);
00724     void writeRecord_(const PDB::RecordSSBOND& helix);
00726     void writeRecord_(const PDB::RecordCONECT& helix);
00728     void writeRecord_(const PDB::RecordCRYST1& cryst1);
00730     void writeRecord_(const PDB::RecordMTRIX1& mtrix1);
00732     void writeRecord_(const PDB::RecordMTRIX2& mtrix2);
00734     void writeRecord_(const PDB::RecordMTRIX3& mtrix3);
00735     
00736     void writeAtom_(const PDB::Structure::AtomEntry& atom, PDB::AdditionalAtomInfo& cr, bool hetatm = false);
00737     
00738     void writeTitleSection_(const PDB::Structure& structure, const PDBInfo& info);
00739     void writePrimaryStructureSection_(const PDB::Structure& structure, const PDBInfo& info);
00740     void writeHeterogenSection_(const PDB::Structure& structure, const PDBInfo& info);
00741     void writeSecondaryStructureSection_(const PDB::Structure& structure, const PDBInfo& info);
00742     void writeConnectivityAnnotationSection_(const PDB::Structure& structure, const PDBInfo& info);
00743     void writeMiscellaneousFeaturesSection_(const PDB::Structure& structure, const PDBInfo& info);
00744     void writeCrystallographicSection_(const PDB::Structure& structure, const PDBInfo& info);
00745     void writeCoordinateSection_(const PDB::Structure& structure, const PDBInfo& info);
00746     void writeConnectivitySection_(const PDB::Structure& structure, const PDBInfo& info);
00747     void writeBookKeepingSection_(const PDB::Structure& structure, const PDBInfo& info);
00748 
00749     void writeSEQRESSection_(const std::vector<std::pair<char, String> >& chain_residues);
00750     void writeHELIXSection_(const PDB::Structure& structure);
00751     void writeSHEETSection_(const PDB::Structure& structure);
00752     void writeTURNSection_(const PDB::Structure& structure);
00753     void writeSSBONDSection_(const PDB::Structure& structure);
00754     void writeHYDBNDSection_(const PDB::Structure& structure);
00755     void writeSLTBRGSection_(const PDB::Structure& structure);
00756     void writeCRYST1Section_(const PDB::Structure& structure);
00757     void writeMTRIXnSection_(const PDB::Structure& structure);
00758 
00762     static void extractStructure_(const AtomContainer& ac, PDB::Structure& structure);
00763     
00767     static bool isHeteroAtom_(const Atom& atom);
00768     
00774     static void updateAdditionalAtomInfo_(const PDB::Structure::AtomEntry& atom, PDB::AdditionalAtomInfo& cr);
00775       
00776 
00777     char line_buffer_[PDB::SIZE_OF_PDB_LINE_BUFFER];
00778 
00779     String residue_name_;
00780     Index residue_sequence_number_;
00781     Index current_model_;
00782     Index current_record_;
00783     Size record_fields_;
00784     PDB::RecordType current_record_type_;
00785     PDB::RecordTypeFormat compare_record_type_format_; 
00786 
00787     PDBAtomMap PDB_atom_map_;
00788     ResidueMap residue_map_;
00789     QuadrupleList ssbond_list_;
00790     QuadrupleList helix_list_;
00791     QuadrupleList sheet_list_;
00792     QuadrupleList turn_list_;
00793 
00794     SecStructList new_helix_secstruc_list_;
00795     SecStructList new_sheet_secstruc_list_;
00796     SecStructList new_turn_secstruc_list_;
00797 
00798     char alternate_location_indicator_;
00799     PDB::AChar insertion_code_;
00800     PDB::Character chain_ID_;
00801     PDB::Integer sequence_number_;
00802     PDB::AChar code_;
00803     Protein* current_protein_;
00804     const Protein* current_const_protein_;
00805     Chain* current_chain_;
00806     const Chain* current_const_chain_;
00807     Residue*  current_residue_;
00808     const Residue* current_const_residue_;
00809     PDBAtom* current_PDB_atom_;
00810     const Atom* current_const_atom_;
00811     String name_;
00812     HashMap<const Atom*, Position> atom_map_;
00813     
00815     PDB::BookKeeping book_keeping_;
00816 
00818     int verbosity_;
00819 
00820     bool strict_line_checking_;
00821 
00823     Index selected_model_;
00824 
00826     bool store_skipped_records_;
00827 
00829     bool ignore_xplor_pseudo_atoms_;
00830     
00832     bool parse_partial_charges_;
00833   };
00834 
00835 
00836 
00837 
00838 
00842   inline
00843   BALL_EXPORT HashIndex Hash(const PDBFile::ResidueQuadruple& quadruple)
00844     
00845   {
00846     return (Index)quadruple.third;
00847   }
00848 
00852   inline
00853   BALL_EXPORT std::ostream& operator << (std::ostream& s, const Quadruple<String,PDB::Character,PDB::Integer,PDB::AChar>& /* q */)
00854   {
00855     return s;
00856   }
00857 
00858 
00859 
00860 # ifndef BALL_NO_INLINE_FUNCTIONS
00861 #   include <BALL/FORMAT/PDBFile.iC>
00862 # endif
00863 
00864 } // namespace BALL
00865 
00866 #endif // BALL_FORMAT_PDBFILE_H