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PDBFile.h
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// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//
#ifndef BALL_FORMAT_PDBFILE_H
#define BALL_FORMAT_PDBFILE_H
#ifndef BALL_CONCEPT_PROPERTY_H
# include <BALL/CONCEPT/property.h>
#endif
#ifndef BALL_FORMAT_GENERICMOLFILE_H
# include <BALL/FORMAT/genericMolFile.h>
#endif
#ifndef BALL_DATATYPE_OPTIONS_H
# include <BALL/DATATYPE/options.h>
#endif
#ifndef BALL_DATATYPE_QUADRUPLE_H
# include <BALL/DATATYPE/quadruple.h>
#endif
#ifndef BALL_FORMAT_PDBDEFS_H
# include <BALL/FORMAT/PDBdefs.h>
#endif
#ifndef BALL_FORMAT_PDBINFO_H
# include <BALL/FORMAT/PDBInfo.h>
#endif
#ifndef BALL_KERNEL_PDBAtom_H
# include <BALL/KERNEL/PDBAtom.h>
#endif
#ifndef BALL_KERNEL_SYSTEM_H
# include <BALL/KERNEL/system.h>
#endif
#ifndef BALL_KERNEL_RESIDUE_H
# include <BALL/KERNEL/residue.h>
#endif
#ifndef BALL_KERNEL_SECONDARYSTRUCTURE_H
# include <BALL/KERNEL/secondaryStructure.h>
#endif
namespace BALL
{
class BALL_EXPORT PDBFile
: public GenericMolFile,
public PropertyManager
{
public:
struct BALL_EXPORT Option
{
static const char* VERBOSITY;
static const char* STRICT_LINE_CHECKING;
static const char* CHOOSE_MODEL;
static const char* STORE_SKIPPED_RECORDS;
static const char* IGNORE_XPLOR_PSEUDO_ATOMS;
static const char* PARSE_PARTIAL_CHARGES;
static const char* WRITE_PDBFORMAT_1996;
};
struct BALL_EXPORT Default
{
static const Index VERBOSITY;
static const bool STRICT_LINE_CHECKING;
static const Index CHOOSE_MODEL;
static const bool STORE_SKIPPED_RECORDS;
static const bool IGNORE_XPLOR_PSEUDO_ATOMS;
static const bool PARSE_PARTIAL_CHARGES;
static const bool WRITE_PDBFORMAT_1996;
};
Options options;
PDBInfo info;
PDBFile();
PDBFile(const String& filename, File::OpenMode open_mode = std::ios::in);
PDBFile(const Options& new_options);
virtual ~PDBFile();
virtual void clear(int state);
virtual void clear();
virtual float getVersion() const;
void open(const String& name, File::OpenMode open_mode=std::ios::in);
void selectModel(Index index);
void selectAltLocationIndicator(char c);
Index getSelectedModel() const;
void selectAllModels();
Index getCurrentModel() const;
char* getRecordString();
const char* getRecordString() const;
Index getRecordNumber() const;
PDB::RecordType getRecordType() const;
virtual const char* getAtomElementSymbol
(const PDB::Atom atom_name,
PDB::Atom element_symbol);
virtual const char* getAtomName
(const PDB::Atom atom_name);
virtual char getAtomRemotenessIndicator
(const PDB::Atom atom_name);
virtual short getAtomBranchDesignator
(const PDB::Atom atom_name);
Size countRecordFields() const;
Size countRecord
(PDB::RecordType record_type,
bool from_begin_of_file = true);
Size countRecords
(bool from_begin_of_file = true);
bool parseLine(const char* line, Size size, const char* format_string, ...);
bool readLine(char* line, Size size, bool extract_values);
bool readFirstRecord(bool read_values = true);
bool readNextRecord(bool read_values = true);
bool readRecords();
virtual bool readUnknownRecord(const char* line);
virtual bool readInvalidRecord(const char* line);
bool skipCurrentRecord();
virtual bool interpretRecord(const PDB::RecordANISOU& record);
virtual bool fillRecord(const char* line, Size size, PDB::RecordANISOU& record);
virtual bool parseRecordANISOU(const char* line, Size size);
virtual bool interpretRecord(const PDB::RecordATOM& record);
virtual bool fillRecord(const char* line, Size size, PDB::RecordATOM& record);
virtual bool parseRecordATOM(const char* line, Size size);
virtual bool interpretRecord(const PDB::RecordAUTHOR& record);
virtual bool fillRecord(const char* line, Size size, PDB::RecordAUTHOR& record);
virtual bool parseRecordAUTHOR(const char* line, Size size);
virtual bool interpretRecord(const PDB::RecordCAVEAT& record);
virtual bool fillRecord(const char* line, Size size, PDB::RecordCAVEAT& record);
virtual bool parseRecordCAVEAT(const char* line, Size size);
virtual bool interpretRecord(const PDB::RecordCISPEP& record);
virtual bool fillRecord(const char* line, Size size, PDB::RecordCISPEP& record);
virtual bool parseRecordCISPEP(const char* line, Size size);
virtual bool interpretRecord(const PDB::RecordCOMPND& record);
virtual bool fillRecord(const char* line, Size size, PDB::RecordCOMPND& record);
virtual bool parseRecordCOMPND(const char* line, Size size);
virtual bool interpretRecord(const PDB::RecordCONECT& record);
virtual bool fillRecord(const char* line, Size size, PDB::RecordCONECT& record);
virtual bool parseRecordCONECT(const char* line, Size size);
virtual bool interpretRecord(const PDB::RecordCRYST1& record);
virtual bool fillRecord(const char* line, Size size, PDB::RecordCRYST1& record);
virtual bool parseRecordCRYST1(const char* line, Size size);
virtual bool interpretRecord(const PDB::RecordDBREF& record);
virtual bool fillRecord(const char* line, Size size, PDB::RecordDBREF& record);
virtual bool parseRecordDBREF(const char* line, Size size);
virtual bool interpretRecord(const PDB::RecordEND& record);
virtual bool fillRecord(const char* line, Size size, PDB::RecordEND& record);
virtual bool parseRecordEND(const char* line, Size size);
virtual bool interpretRecord(const PDB::RecordENDMDL& record);
virtual bool fillRecord(const char* line, Size size, PDB::RecordENDMDL& record);
virtual bool parseRecordENDMDL(const char* line, Size size);
virtual bool interpretRecord(const PDB::RecordEXPDTA& record);
virtual bool fillRecord(const char* line, Size size, PDB::RecordEXPDTA& record);
virtual bool parseRecordEXPDTA(const char* line, Size size);
virtual bool interpretRecord(const PDB::RecordFORMUL& record);
virtual bool fillRecord(const char* line, Size size, PDB::RecordFORMUL& record);
virtual bool parseRecordFORMUL(const char* line, Size size);
virtual bool interpretRecord(const PDB::RecordFTNOTE& record);
virtual bool fillRecord(const char* line, Size size, PDB::RecordFTNOTE& record);
virtual bool parseRecordFTNOTE(const char* line, Size size);
virtual bool interpretRecord(const PDB::RecordHEADER& record);
virtual bool fillRecord(const char* line, Size size, PDB::RecordHEADER& record);
virtual bool parseRecordHEADER(const char* line, Size size);
virtual bool interpretRecord(const PDB::RecordHELIX& record);
virtual bool fillRecord(const char* line, Size size, PDB::RecordHELIX& record);
virtual bool parseRecordHELIX(const char* line, Size size);
virtual bool interpretRecord(const PDB::RecordHET& record);
virtual bool fillRecord(const char* line, Size size, PDB::RecordHET& record);
virtual bool parseRecordHET(const char* line, Size size);
virtual bool interpretRecord(const PDB::RecordHETATM& record);
virtual bool fillRecord(const char* line, Size size, PDB::RecordHETATM& record);
virtual bool parseRecordHETATM(const char* line, Size size);
virtual bool interpretRecord(const PDB::RecordHETNAM& record);
virtual bool fillRecord(const char* line, Size size, PDB::RecordHETNAM& record);
virtual bool parseRecordHETNAM(const char* line, Size size);
virtual bool interpretRecord(const PDB::RecordHETSYN& record);
virtual bool fillRecord(const char* line, Size size, PDB::RecordHETSYN& record);
virtual bool parseRecordHETSYN(const char* line, Size size);
virtual bool interpretRecord(const PDB::RecordHYDBND& record);
virtual bool fillRecord(const char* line, Size size, PDB::RecordHYDBND& record);
virtual bool parseRecordHYDBND(const char* line, Size size);
virtual bool interpretRecord(const PDB::RecordJRNL& record);
virtual bool fillRecord(const char* line, Size size, PDB::RecordJRNL& record);
virtual bool parseRecordJRNL(const char* line, Size size);
virtual bool interpretRecord(const PDB::RecordKEYWDS& record);
virtual bool fillRecord(const char* line, Size size, PDB::RecordKEYWDS& record);
virtual bool parseRecordKEYWDS(const char* line, Size size);
virtual bool interpretRecord(const PDB::RecordLINK& record);
virtual bool fillRecord(const char* line, Size size, PDB::RecordLINK& record);
virtual bool parseRecordLINK(const char* line, Size size);
virtual bool interpretRecord(const PDB::RecordMASTER& record);
virtual bool fillRecord(const char* line, Size size, PDB::RecordMASTER& record);
virtual bool parseRecordMASTER(const char* line, Size size);
virtual bool interpretRecord(const PDB::RecordMODEL& record);
virtual bool fillRecord(const char* line, Size size, PDB::RecordMODEL& record);
virtual bool parseRecordMODEL(const char* line, Size size);
virtual bool interpretRecord(const PDB::RecordMODRES& record);
virtual bool fillRecord(const char* line, Size size, PDB::RecordMODRES& record);
virtual bool parseRecordMODRES(const char* line, Size size);
virtual bool interpretRecord(const PDB::RecordMTRIX1& record);
virtual bool fillRecord(const char* line, Size size, PDB::RecordMTRIX1& record);
virtual bool parseRecordMTRIX1(const char* line, Size size);
virtual bool interpretRecord(const PDB::RecordMTRIX2& record);
virtual bool fillRecord(const char* line, Size size, PDB::RecordMTRIX2& record);
virtual bool parseRecordMTRIX2(const char* line, Size size);
virtual bool interpretRecord(const PDB::RecordMTRIX3& record);
virtual bool fillRecord(const char* line, Size size, PDB::RecordMTRIX3& record);
virtual bool parseRecordMTRIX3(const char* line, Size size);
virtual bool interpretRecord(const PDB::RecordOBSLTE& record);
virtual bool fillRecord(const char* line, Size size, PDB::RecordOBSLTE& record);
virtual bool parseRecordOBSLTE(const char* line, Size size);
virtual bool interpretRecord(const PDB::RecordORIGX1& record);
virtual bool fillRecord(const char* line, Size size, PDB::RecordORIGX1& record);
virtual bool parseRecordORIGX1(const char* line, Size size);
virtual bool interpretRecord(const PDB::RecordORIGX2& record);
virtual bool fillRecord(const char* line, Size size, PDB::RecordORIGX2& record);
virtual bool parseRecordORIGX2(const char* line, Size size);
virtual bool interpretRecord(const PDB::RecordORIGX3& record);
virtual bool fillRecord(const char* line, Size size, PDB::RecordORIGX3& record);
virtual bool parseRecordORIGX3(const char* line, Size size);
virtual bool interpretRecord(const PDB::RecordREMARK& record);
virtual bool fillRecord(const char* line, Size size, PDB::RecordREMARK& record);
virtual bool parseRecordREMARK(const char* line, Size size);
virtual bool interpretRecord(const PDB::RecordREVDAT& record);
virtual bool fillRecord(const char* line, Size size, PDB::RecordREVDAT& record);
virtual bool parseRecordREVDAT(const char* line, Size size);
virtual bool interpretRecord(const PDB::RecordSCALE1& record);
virtual bool fillRecord(const char* line, Size size, PDB::RecordSCALE1& record);
virtual bool parseRecordSCALE1(const char* line, Size size);
virtual bool interpretRecord(const PDB::RecordSCALE2& record);
virtual bool fillRecord(const char* line, Size size, PDB::RecordSCALE2& record);
virtual bool parseRecordSCALE2(const char* line, Size size);
virtual bool interpretRecord(const PDB::RecordSCALE3& record);
virtual bool fillRecord(const char* line, Size size, PDB::RecordSCALE3& record);
virtual bool parseRecordSCALE3(const char* line, Size size);
virtual bool interpretRecord(const PDB::RecordSEQADV& record);
virtual bool fillRecord(const char* line, Size size, PDB::RecordSEQADV& record);
virtual bool parseRecordSEQADV(const char* line, Size size);
virtual bool interpretRecord(const PDB::RecordSEQRES& record);
virtual bool fillRecord(const char* line, Size size, PDB::RecordSEQRES& record);
virtual bool parseRecordSEQRES(const char* line, Size size);
virtual bool interpretRecord(const PDB::RecordSHEET& record);
virtual bool fillRecord(const char* line, Size size, PDB::RecordSHEET& record);
virtual bool parseRecordSHEET(const char* line, Size size);
virtual bool interpretRecord(const PDB::RecordSIGATM& record);
virtual bool fillRecord(const char* line, Size size, PDB::RecordSIGATM& record);
virtual bool parseRecordSIGATM(const char* line, Size size);
virtual bool interpretRecord(const PDB::RecordSIGUIJ& record);
virtual bool fillRecord(const char* line, Size size, PDB::RecordSIGUIJ& record);
virtual bool parseRecordSIGUIJ(const char* line, Size size);
virtual bool interpretRecord(const PDB::RecordSITE& record);
virtual bool fillRecord(const char* line, Size size, PDB::RecordSITE& record);
virtual bool parseRecordSITE(const char* line, Size size);
virtual bool interpretRecord(const PDB::RecordSLTBRG& record);
virtual bool fillRecord(const char* line, Size size, PDB::RecordSLTBRG& record);
virtual bool parseRecordSLTBRG(const char* line, Size size);
virtual bool interpretRecord(const PDB::RecordSOURCE& record);
virtual bool fillRecord(const char* line, Size size, PDB::RecordSOURCE& record);
virtual bool parseRecordSOURCE(const char* line, Size size);
virtual bool interpretRecord(const PDB::RecordSPRSDE& record);
virtual bool fillRecord(const char* line, Size size, PDB::RecordSPRSDE& record);
virtual bool parseRecordSPRSDE(const char* line, Size size);
virtual bool interpretRecord(const PDB::RecordSSBOND& record);
virtual bool fillRecord(const char* line, Size size, PDB::RecordSSBOND& record);
virtual bool parseRecordSSBOND(const char* line, Size size);
virtual bool interpretRecord(const PDB::RecordTER& record);
virtual bool fillRecord(const char* line, Size size, PDB::RecordTER& record);
virtual bool parseRecordTER(const char* line, Size size);
virtual bool interpretRecord(const PDB::RecordTITLE& record);
virtual bool fillRecord(const char* line, Size size, PDB::RecordTITLE& record);
virtual bool parseRecordTITLE(const char* line, Size size);
virtual bool interpretRecord(const PDB::RecordTURN& record);
virtual bool fillRecord(const char* line, Size size, PDB::RecordTURN& record);
virtual bool parseRecordTURN(const char* line, Size size);
virtual bool interpretRecord(const PDB::RecordTVECT& record);
virtual bool fillRecord(const char* line, Size size, PDB::RecordTVECT& record);
virtual bool parseRecordTVECT(const char* line, Size size);
virtual bool hasFormat();
typedef HashMap<PDB::Integer, PDBAtom*> PDBAtomMap;
typedef Quadruple<String, PDB::Character, PDB::Integer, PDB::AChar> ResidueQuadruple;
typedef HashMap<ResidueQuadruple, Residue*> ResidueMap;
typedef std::list<ResidueQuadruple> QuadrupleList;
typedef std::list<SecondaryStructure*> SecStructList;
PDBFile& operator >> (Protein& protein);
PDBFile& operator >> (Molecule& molecule);
PDBFile& operator >> (System& system);
PDBFile& operator << (const Protein& protein);
PDBFile& operator << (const System& system);
PDBFile& operator << (const Molecule& molecule);
bool read(Protein& protein);
bool read(Molecule& protein);
bool read(System& system);
Molecule* read();
bool write(const Protein& protein);
bool write(const Molecule& molecule);
bool write(const System& system);
bool write(const System& system, const PDBInfo& info);
protected:
//_
PDBFile(const File& pdbf);
//_
PDBFile& operator = (const PDBFile& pdbf);
/*_ A helper function for initializing certain data structures. Used by
constructors.
*/
void init_() ;
void postprocessSSBonds_();
void postprocessHelices_();
void postprocessSheetsTurns_(QuadrupleList& sectruct_list, SecStructList& new_secstruct_list);
void postprocessRandomCoils_();
// Method related to the writing of PDB files
//
void write_(const AtomContainer& ac, const PDBInfo& info = PDBInfo());
void writeRecord_(PDB::RecordType record, ...);
void writeCONECTRecords_(PDB::Structure::ConectAtomList& cl);
void writeRawRecord_(const char* format, const char* tag, ...);
void addAllRecords_(const PDBInfo& info, PDB::RecordType type);
void writeRecord_(const PDB::RecordSEQRES& seqres);
void writeRecord_(const PDB::RecordHELIX& helix);
void writeRecord_(const PDB::RecordSHEET& helix);
void writeRecord_(const PDB::RecordTURN& helix);
void writeRecord_(const PDB::RecordSSBOND& helix);
void writeRecord_(const PDB::RecordCONECT& helix);
void writeRecord_(const PDB::RecordCRYST1& cryst1);
void writeRecord_(const PDB::RecordMTRIX1& mtrix1);
void writeRecord_(const PDB::RecordMTRIX2& mtrix2);
void writeRecord_(const PDB::RecordMTRIX3& mtrix3);
void writeAtom_(const PDB::Structure::AtomEntry& atom, PDB::AdditionalAtomInfo& cr, bool hetatm = false);
void writeTitleSection_(const PDB::Structure& structure, const PDBInfo& info);
void writePrimaryStructureSection_(const PDB::Structure& structure, const PDBInfo& info);
void writeHeterogenSection_(const PDB::Structure& structure, const PDBInfo& info);
void writeSecondaryStructureSection_(const PDB::Structure& structure, const PDBInfo& info);
void writeConnectivityAnnotationSection_(const PDB::Structure& structure, const PDBInfo& info);
void writeMiscellaneousFeaturesSection_(const PDB::Structure& structure, const PDBInfo& info);
void writeCrystallographicSection_(const PDB::Structure& structure, const PDBInfo& info);
void writeCoordinateSection_(const PDB::Structure& structure, const PDBInfo& info);
void writeConnectivitySection_(const PDB::Structure& structure, const PDBInfo& info);
void writeBookKeepingSection_(const PDB::Structure& structure, const PDBInfo& info);
void writeSEQRESSection_(const std::vector<std::pair<char, String> >& chain_residues);
void writeHELIXSection_(const PDB::Structure& structure);
void writeSHEETSection_(const PDB::Structure& structure);
void writeTURNSection_(const PDB::Structure& structure);
void writeSSBONDSection_(const PDB::Structure& structure);
void writeHYDBNDSection_(const PDB::Structure& structure);
void writeSLTBRGSection_(const PDB::Structure& structure);
void writeCRYST1Section_(const PDB::Structure& structure);
void writeMTRIXnSection_(const PDB::Structure& structure);
static void extractStructure_(const AtomContainer& ac, PDB::Structure& structure);
static bool isHeteroAtom_(const Atom& atom);
static void updateAdditionalAtomInfo_(const PDB::Structure::AtomEntry& atom, PDB::AdditionalAtomInfo& cr);
char line_buffer_[PDB::SIZE_OF_PDB_LINE_BUFFER];
String residue_name_;
Index residue_sequence_number_;
Index current_model_;
Index current_record_;
Size record_fields_;
PDB::RecordType current_record_type_;
PDB::RecordTypeFormat compare_record_type_format_;
PDBAtomMap PDB_atom_map_;
ResidueMap residue_map_;
QuadrupleList ssbond_list_;
QuadrupleList helix_list_;
QuadrupleList sheet_list_;
QuadrupleList turn_list_;
SecStructList new_helix_secstruc_list_;
SecStructList new_sheet_secstruc_list_;
SecStructList new_turn_secstruc_list_;
char alternate_location_indicator_;
PDB::AChar insertion_code_;
PDB::Character chain_ID_;
PDB::Integer sequence_number_;
PDB::AChar code_;
Protein* current_protein_;
const Protein* current_const_protein_;
Chain* current_chain_;
const Chain* current_const_chain_;
Residue* current_residue_;
const Residue* current_const_residue_;
PDBAtom* current_PDB_atom_;
const Atom* current_const_atom_;
String name_;
HashMap<const Atom*, Position> atom_map_;
PDB::BookKeeping book_keeping_;
int verbosity_;
bool strict_line_checking_;
Index selected_model_;
bool store_skipped_records_;
bool ignore_xplor_pseudo_atoms_;
bool parse_partial_charges_;
bool write_pdbformat_1996_;
bool read_done_;
};
inline
BALL_EXPORT HashIndex Hash(const PDBFile::ResidueQuadruple& quadruple)
{
return (Index)quadruple.third;
}
inline
BALL_EXPORT std::ostream& operator << (std::ostream& s, const Quadruple<String,PDB::Character,PDB::Integer,PDB::AChar>& /* q */)
{
return s;
}
# ifndef BALL_NO_INLINE_FUNCTIONS
# include <BALL/FORMAT/PDBFile.iC>
# endif
} // namespace BALL
#endif // BALL_FORMAT_PDBFILE_H
BALL_EXPORT
#define BALL_EXPORT
Definition COMMON/global.h:50
system.h
PDBAtom.h
PDBInfo.h
PDBdefs.h
BALL::AtomContainer
Definition atomContainer.h:32
BALL::Atom
Definition atom.h:90
BALL::Chain
Definition chain.h:32
BALL::File
Definition file.h:136
BALL::File::OpenMode
std::ios::openmode OpenMode
Definition file.h:165
BALL::GenericMolFile::GenericMolFile
GenericMolFile()
BALL::HashMap
HashMap class based on the STL map (containing serveral convenience functions).
Definition hashMap.h:74
BALL::Molecule
Definition molecule.h:31
BALL::Options
Definition options.h:48
BALL::PDBAtom
Definition PDBAtom.h:40
BALL::PDBFile::parseRecordMTRIX2
virtual bool parseRecordMTRIX2(const char *line, Size size)
BALL::PDBFile::fillRecord
virtual bool fillRecord(const char *line, Size size, PDB::RecordFTNOTE &record)
BALL::PDBFile::strict_line_checking_
bool strict_line_checking_
Definition PDBFile.h:880
BALL::PDBFile::interpretRecord
virtual bool interpretRecord(const PDB::RecordSLTBRG &record)
Reads a record defining a salt bridge.
BALL::PDBFile::postprocessSheetsTurns_
void postprocessSheetsTurns_(QuadrupleList &sectruct_list, SecStructList &new_secstruct_list)
BALL::PDBFile::fillRecord
virtual bool fillRecord(const char *line, Size size, PDB::RecordOBSLTE &record)
BALL::PDBFile::parseRecordSCALE3
virtual bool parseRecordSCALE3(const char *line, Size size)
BALL::PDBFile::readRecords
bool readRecords()
BALL::PDBFile::writeTitleSection_
void writeTitleSection_(const PDB::Structure &structure, const PDBInfo &info)
BALL::PDBFile::read_done_
bool read_done_
Definition PDBFile.h:899
BALL::PDBFile::interpretRecord
virtual bool interpretRecord(const PDB::RecordANISOU &record)
Reads an anisotropic temperature factor record.
BALL::PDBFile::fillRecord
virtual bool fillRecord(const char *line, Size size, PDB::RecordSPRSDE &record)
BALL::PDBFile::parseRecordDBREF
virtual bool parseRecordDBREF(const char *line, Size size)
BALL::PDBFile::interpretRecord
virtual bool interpretRecord(const PDB::RecordKEYWDS &record)
Reads a record containing keywords for this entry.
BALL::PDBFile::insertion_code_
PDB::AChar insertion_code_
Definition PDBFile.h:859
BALL::PDBFile::getAtomName
virtual const char * getAtomName(const PDB::Atom atom_name)
Returns the atom name.
BALL::PDBFile::interpretRecord
virtual bool interpretRecord(const PDB::RecordORIGX1 &record)
BALL::PDBFile::fillRecord
virtual bool fillRecord(const char *line, Size size, PDB::RecordKEYWDS &record)
BALL::PDBFile::residue_name_
String residue_name_
Definition PDBFile.h:839
BALL::PDBFile::interpretRecord
virtual bool interpretRecord(const PDB::RecordTITLE &record)
Reads a record specifying the title of the experiment or anaysis.
BALL::PDBFile::fillRecord
virtual bool fillRecord(const char *line, Size size, PDB::RecordSITE &record)
BALL::PDBFile::writeRecord_
void writeRecord_(const PDB::RecordHELIX &helix)
BALL::PDBFile::interpretRecord
virtual bool interpretRecord(const PDB::RecordMODEL &record)
Reads a record indicating the beginning of a new model.
BALL::PDBFile::interpretRecord
virtual bool interpretRecord(const PDB::RecordSOURCE &record)
BALL::PDBFile::parseRecordSOURCE
virtual bool parseRecordSOURCE(const char *line, Size size)
BALL::PDBFile::code_
PDB::AChar code_
Definition PDBFile.h:862
BALL::PDBFile::parseRecordFTNOTE
virtual bool parseRecordFTNOTE(const char *line, Size size)
BALL::PDBFile::updateAdditionalAtomInfo_
static void updateAdditionalAtomInfo_(const PDB::Structure::AtomEntry &atom, PDB::AdditionalAtomInfo &cr)
BALL::PDBFile::interpretRecord
virtual bool interpretRecord(const PDB::RecordMTRIX3 &record)
BALL::PDBFile::countRecord
Size countRecord(PDB::RecordType record_type, bool from_begin_of_file=true)
BALL::PDBFile::interpretRecord
virtual bool interpretRecord(const PDB::RecordEXPDTA &record)
Reads a record containing data about the experiment.
BALL::PDBFile::parseRecordMASTER
virtual bool parseRecordMASTER(const char *line, Size size)
BALL::PDBFile::sheet_list_
QuadrupleList sheet_list_
Definition PDBFile.h:851
BALL::PDBFile::writeTURNSection_
void writeTURNSection_(const PDB::Structure &structure)
BALL::PDBFile::fillRecord
virtual bool fillRecord(const char *line, Size size, PDB::RecordHETNAM &record)
BALL::PDBFile::current_record_type_
PDB::RecordType current_record_type_
Definition PDBFile.h:844
BALL::PDBFile::ssbond_list_
QuadrupleList ssbond_list_
Definition PDBFile.h:849
BALL::PDBFile::SecStructList
std::list< SecondaryStructure * > SecStructList
Definition PDBFile.h:638
BALL::PDBFile::writeHYDBNDSection_
void writeHYDBNDSection_(const PDB::Structure &structure)
BALL::PDBFile::parseRecordKEYWDS
virtual bool parseRecordKEYWDS(const char *line, Size size)
BALL::PDBFile::fillRecord
virtual bool fillRecord(const char *line, Size size, PDB::RecordHET &record)
BALL::PDBFile::compare_record_type_format_
PDB::RecordTypeFormat compare_record_type_format_
Definition PDBFile.h:845
BALL::PDBFile::~PDBFile
virtual ~PDBFile()
BALL::PDBFile::writeBookKeepingSection_
void writeBookKeepingSection_(const PDB::Structure &structure, const PDBInfo &info)
BALL::PDBFile::writeHELIXSection_
void writeHELIXSection_(const PDB::Structure &structure)
BALL::PDBFile::parse_partial_charges_
bool parse_partial_charges_
Read partial charges from cols 76-80?
Definition PDBFile.h:892
BALL::PDBFile::fillRecord
virtual bool fillRecord(const char *line, Size size, PDB::RecordSHEET &record)
BALL::PDBFile::current_const_atom_
const Atom * current_const_atom_
Definition PDBFile.h:870
BALL::PDBFile::write
bool write(const System &system, const PDBInfo &info)
BALL::PDBFile::fillRecord
virtual bool fillRecord(const char *line, Size size, PDB::RecordHYDBND &record)
BALL::PDBFile::fillRecord
virtual bool fillRecord(const char *line, Size size, PDB::RecordANISOU &record)
BALL::PDBFile::writeSSBONDSection_
void writeSSBONDSection_(const PDB::Structure &structure)
BALL::PDBFile::PDBAtomMap
HashMap< PDB::Integer, PDBAtom * > PDBAtomMap
Definition PDBFile.h:634
BALL::PDBFile::fillRecord
virtual bool fillRecord(const char *line, Size size, PDB::RecordSIGATM &record)
BALL::PDBFile::interpretRecord
virtual bool interpretRecord(const PDB::RecordMASTER &record)
BALL::PDBFile::fillRecord
virtual bool fillRecord(const char *line, Size size, PDB::RecordJRNL &record)
BALL::PDBFile::PDBFile
PDBFile(const String &filename, File::OpenMode open_mode=std::ios::in)
BALL::PDBFile::interpretRecord
virtual bool interpretRecord(const PDB::RecordLINK &record)
Reads a record containing supplemental connectivity information.
BALL::PDBFile::fillRecord
virtual bool fillRecord(const char *line, Size size, PDB::RecordSSBOND &record)
BALL::PDBFile::interpretRecord
virtual bool interpretRecord(const PDB::RecordCISPEP &record)
Reads a record specifying peptides in cis conformation.
BALL::PDBFile::writeMTRIXnSection_
void writeMTRIXnSection_(const PDB::Structure &structure)
BALL::PDBFile::sequence_number_
PDB::Integer sequence_number_
Definition PDBFile.h:861
BALL::PDBFile::writePrimaryStructureSection_
void writePrimaryStructureSection_(const PDB::Structure &structure, const PDBInfo &info)
BALL::PDBFile::writeCONECTRecords_
void writeCONECTRecords_(PDB::Structure::ConectAtomList &cl)
BALL::PDBFile::isHeteroAtom_
static bool isHeteroAtom_(const Atom &atom)
BALL::PDBFile::fillRecord
virtual bool fillRecord(const char *line, Size size, PDB::RecordSEQADV &record)
BALL::PDBFile::fillRecord
virtual bool fillRecord(const char *line, Size size, PDB::RecordCAVEAT &record)
BALL::PDBFile::getVersion
virtual float getVersion() const
Returns the version number this PDB file reader is able to read.
BALL::PDBFile::postprocessSSBonds_
void postprocessSSBonds_()
BALL::PDBFile::parseRecordTURN
virtual bool parseRecordTURN(const char *line, Size size)
BALL::PDBFile::parseRecordCOMPND
virtual bool parseRecordCOMPND(const char *line, Size size)
BALL::PDBFile::fillRecord
virtual bool fillRecord(const char *line, Size size, PDB::RecordMASTER &record)
BALL::PDBFile::parseRecordMTRIX1
virtual bool parseRecordMTRIX1(const char *line, Size size)
BALL::PDBFile::fillRecord
virtual bool fillRecord(const char *line, Size size, PDB::RecordMODRES &record)
BALL::PDBFile::fillRecord
virtual bool fillRecord(const char *line, Size size, PDB::RecordORIGX3 &record)
BALL::PDBFile::getSelectedModel
Index getSelectedModel() const
Return the model currently selected.
BALL::PDBFile::parseRecordCONECT
virtual bool parseRecordCONECT(const char *line, Size size)
BALL::PDBFile::interpretRecord
virtual bool interpretRecord(const PDB::RecordHEADER &record)
BALL::PDBFile::selected_model_
Index selected_model_
The selected model_.
Definition PDBFile.h:883
BALL::PDBFile::residue_sequence_number_
Index residue_sequence_number_
Definition PDBFile.h:840
BALL::PDBFile::interpretRecord
virtual bool interpretRecord(const PDB::RecordCAVEAT &record)
Reads a caveat record.
BALL::PDBFile::countRecords
Size countRecords(bool from_begin_of_file=true)
BALL::PDBFile::current_const_protein_
const Protein * current_const_protein_
Definition PDBFile.h:864
BALL::PDBFile::fillRecord
virtual bool fillRecord(const char *line, Size size, PDB::RecordSCALE3 &record)
BALL::PDBFile::ResidueMap
HashMap< ResidueQuadruple, Residue * > ResidueMap
Definition PDBFile.h:636
BALL::PDBFile::interpretRecord
virtual bool interpretRecord(const PDB::RecordREMARK &record)
Reads a record containing remarks.
BALL::PDBFile::parseRecordHEADER
virtual bool parseRecordHEADER(const char *line, Size size)
BALL::PDBFile::turn_list_
QuadrupleList turn_list_
Definition PDBFile.h:852
BALL::PDBFile::fillRecord
virtual bool fillRecord(const char *line, Size size, PDB::RecordTER &record)
BALL::PDBFile::name_
String name_
Definition PDBFile.h:871
BALL::PDBFile::info
PDBInfo info
Summary information on the last file read.
Definition PDBFile.h:172
BALL::PDBFile::line_buffer_
char line_buffer_[PDB::SIZE_OF_PDB_LINE_BUFFER]
Definition PDBFile.h:837
BALL::PDBFile::writeRecord_
void writeRecord_(const PDB::RecordSEQRES &seqres)
BALL::PDBFile::interpretRecord
virtual bool interpretRecord(const PDB::RecordJRNL &record)
Reads a record containing a journal reference.
BALL::PDBFile::interpretRecord
virtual bool interpretRecord(const PDB::RecordTER &record)
Reads a record terminating molecule.
BALL::PDBFile::current_const_chain_
const Chain * current_const_chain_
Definition PDBFile.h:866
BALL::PDBFile::parseRecordMODRES
virtual bool parseRecordMODRES(const char *line, Size size)
BALL::PDBFile::getRecordNumber
Index getRecordNumber() const
Returns the number of the record we are currently reading.
BALL::PDBFile::parseRecordSPRSDE
virtual bool parseRecordSPRSDE(const char *line, Size size)
BALL::PDBFile::interpretRecord
virtual bool interpretRecord(const PDB::RecordDBREF &record)
Reads a record containing database cross-reference links.
BALL::PDBFile::verbosity_
int verbosity_
_Verbosity level
Definition PDBFile.h:878
BALL::PDBFile::fillRecord
virtual bool fillRecord(const char *line, Size size, PDB::RecordMTRIX3 &record)
BALL::PDBFile::PDBFile
PDBFile(const File &pdbf)
BALL::PDBFile::interpretRecord
virtual bool interpretRecord(const PDB::RecordHYDBND &record)
Reads a record defining a hydrogen bond.
BALL::PDBFile::writeHeterogenSection_
void writeHeterogenSection_(const PDB::Structure &structure, const PDBInfo &info)
BALL::PDBFile::writeRecord_
void writeRecord_(const PDB::RecordCRYST1 &cryst1)
BALL::PDBFile::parseLine
bool parseLine(const char *line, Size size, const char *format_string,...)
Parse a line from a PDBFile. This is a helper function for readLine().
BALL::PDBFile::readFirstRecord
bool readFirstRecord(bool read_values=true)
Read the firts record of a file.
BALL::PDBFile::fillRecord
virtual bool fillRecord(const char *line, Size size, PDB::RecordCISPEP &record)
BALL::PDBFile::parseRecordSEQRES
virtual bool parseRecordSEQRES(const char *line, Size size)
BALL::PDBFile::init_
void init_()
BALL::PDBFile::hasFormat
virtual bool hasFormat()
Check whether the current file is in PDB format.
BALL::PDBFile::parseRecordORIGX3
virtual bool parseRecordORIGX3(const char *line, Size size)
BALL::PDBFile::store_skipped_records_
bool store_skipped_records_
Store the skipped records in info?
Definition PDBFile.h:886
BALL::PDBFile::fillRecord
virtual bool fillRecord(const char *line, Size size, PDB::RecordMTRIX2 &record)
BALL::PDBFile::parseRecordTVECT
virtual bool parseRecordTVECT(const char *line, Size size)
BALL::PDBFile::write
bool write(const Molecule &molecule)
BALL::PDBFile::interpretRecord
virtual bool interpretRecord(const PDB::RecordMODRES &record)
Reads a record identifying residue modifications.
BALL::PDBFile::readUnknownRecord
virtual bool readUnknownRecord(const char *line)
BALL::PDBFile::write
bool write(const System &system)
BALL::PDBFile::current_protein_
Protein * current_protein_
Definition PDBFile.h:863
BALL::PDBFile::parseRecordSITE
virtual bool parseRecordSITE(const char *line, Size size)
BALL::PDBFile::interpretRecord
virtual bool interpretRecord(const PDB::RecordTVECT &record)
BALL::PDBFile::parseRecordENDMDL
virtual bool parseRecordENDMDL(const char *line, Size size)
BALL::PDBFile::current_const_residue_
const Residue * current_const_residue_
Definition PDBFile.h:868
BALL::PDBFile::interpretRecord
virtual bool interpretRecord(const PDB::RecordSCALE3 &record)
Reads a scale transformation record.
BALL::PDBFile::ignore_xplor_pseudo_atoms_
bool ignore_xplor_pseudo_atoms_
Ignore XPLOR pseudo atoms?
Definition PDBFile.h:889
BALL::PDBFile::fillRecord
virtual bool fillRecord(const char *line, Size size, PDB::RecordREMARK &record)
BALL::PDBFile::interpretRecord
virtual bool interpretRecord(const PDB::RecordFORMUL &record)
BALL::PDBFile::parseRecordSCALE1
virtual bool parseRecordSCALE1(const char *line, Size size)
BALL::PDBFile::interpretRecord
virtual bool interpretRecord(const PDB::RecordSHEET &record)
Reads a record defining a beta-sheet.
BALL::PDBFile::parseRecordHETSYN
virtual bool parseRecordHETSYN(const char *line, Size size)
BALL::PDBFile::interpretRecord
virtual bool interpretRecord(const PDB::RecordHELIX &record)
Reads a helix defining record.
BALL::PDBFile::writeSHEETSection_
void writeSHEETSection_(const PDB::Structure &structure)
BALL::PDBFile::readLine
bool readLine(char *line, Size size, bool extract_values)
Read and parse a line from a PDB file.
BALL::PDBFile::parseRecordORIGX1
virtual bool parseRecordORIGX1(const char *line, Size size)
BALL::PDBFile::getAtomRemotenessIndicator
virtual char getAtomRemotenessIndicator(const PDB::Atom atom_name)
Extract the PDB remoteness indicator of an atom record.
BALL::PDBFile::parseRecordEND
virtual bool parseRecordEND(const char *line, Size size)
BALL::PDBFile::chain_ID_
PDB::Character chain_ID_
Definition PDBFile.h:860
BALL::PDBFile::fillRecord
virtual bool fillRecord(const char *line, Size size, PDB::RecordEXPDTA &record)
BALL::PDBFile::extractStructure_
static void extractStructure_(const AtomContainer &ac, PDB::Structure &structure)
BALL::PDBFile::open
void open(const String &name, File::OpenMode open_mode=std::ios::in)
BALL::PDBFile::parseRecordREVDAT
virtual bool parseRecordREVDAT(const char *line, Size size)
BALL::PDBFile::getRecordType
PDB::RecordType getRecordType() const
Returns the type of the record we are currently reading.
BALL::PDBFile::parseRecordHETATM
virtual bool parseRecordHETATM(const char *line, Size size)
BALL::PDBFile::interpretRecord
virtual bool interpretRecord(const PDB::RecordHET &record)
Reads a record defining a non-standard residue.
BALL::PDBFile::writeSEQRESSection_
void writeSEQRESSection_(const std::vector< std::pair< char, String > > &chain_residues)
BALL::PDBFile::parseRecordOBSLTE
virtual bool parseRecordOBSLTE(const char *line, Size size)
BALL::PDBFile::interpretRecord
virtual bool interpretRecord(const PDB::RecordSCALE1 &record)
Reads a scale transformation record.
BALL::PDBFile::parseRecordATOM
virtual bool parseRecordATOM(const char *line, Size size)
BALL::PDBFile::residue_map_
ResidueMap residue_map_
Definition PDBFile.h:848
BALL::PDBFile::fillRecord
virtual bool fillRecord(const char *line, Size size, PDB::RecordDBREF &record)
BALL::PDBFile::atom_map_
HashMap< const Atom *, Position > atom_map_
Definition PDBFile.h:872
BALL::PDBFile::current_record_
Index current_record_
Definition PDBFile.h:842
BALL::PDBFile::interpretRecord
virtual bool interpretRecord(const PDB::RecordSEQADV &record)
Sequence information conflicts between atom records and dbref content.
BALL::PDBFile::countRecordFields
Size countRecordFields() const
Returns the number of record fields.
BALL::PDBFile::fillRecord
virtual bool fillRecord(const char *line, Size size, PDB::RecordORIGX1 &record)
BALL::PDBFile::parseRecordTITLE
virtual bool parseRecordTITLE(const char *line, Size size)
BALL::PDBFile::interpretRecord
virtual bool interpretRecord(const PDB::RecordTURN &record)
Reads a record specifying a turn.
BALL::PDBFile::current_chain_
Chain * current_chain_
Definition PDBFile.h:865
BALL::PDBFile::parseRecordHET
virtual bool parseRecordHET(const char *line, Size size)
BALL::PDBFile::parseRecordANISOU
virtual bool parseRecordANISOU(const char *line, Size size)
BALL::PDBFile::parseRecordFORMUL
virtual bool parseRecordFORMUL(const char *line, Size size)
BALL::PDBFile::interpretRecord
virtual bool interpretRecord(const PDB::RecordMTRIX1 &record)
BALL::PDBFile::fillRecord
virtual bool fillRecord(const char *line, Size size, PDB::RecordHETATM &record)
BALL::PDBFile::write
bool write(const Protein &protein)
BALL::PDBFile::writeRecord_
void writeRecord_(const PDB::RecordSHEET &helix)
BALL::PDBFile::interpretRecord
virtual bool interpretRecord(const PDB::RecordCONECT &record)
Reads a connection record.
BALL::PDBFile::fillRecord
virtual bool fillRecord(const char *line, Size size, PDB::RecordCOMPND &record)
BALL::PDBFile::book_keeping_
PDB::BookKeeping book_keeping_
Book keeping struct for the number of records written.
Definition PDBFile.h:875
BALL::PDBFile::PDB_atom_map_
PDBAtomMap PDB_atom_map_
Definition PDBFile.h:847
BALL::PDBFile::writeRecord_
void writeRecord_(const PDB::RecordSSBOND &helix)
BALL::PDBFile::fillRecord
virtual bool fillRecord(const char *line, Size size, PDB::RecordHETSYN &record)
BALL::PDBFile::parseRecordCISPEP
virtual bool parseRecordCISPEP(const char *line, Size size)
BALL::PDBFile::addAllRecords_
void addAllRecords_(const PDBInfo &info, PDB::RecordType type)
Add all records of a specific type in the info object to the current stream.
BALL::PDBFile::interpretRecord
virtual bool interpretRecord(const PDB::RecordMTRIX2 &record)
BALL::PDBFile::interpretRecord
virtual bool interpretRecord(const PDB::RecordORIGX3 &record)
BALL::PDBFile::parseRecordSHEET
virtual bool parseRecordSHEET(const char *line, Size size)
BALL::PDBFile::write_pdbformat_1996_
bool write_pdbformat_1996_
write in the 1996-format?
Definition PDBFile.h:895
BALL::PDBFile::new_turn_secstruc_list_
SecStructList new_turn_secstruc_list_
Definition PDBFile.h:856
BALL::PDBFile::writeCrystallographicSection_
void writeCrystallographicSection_(const PDB::Structure &structure, const PDBInfo &info)
BALL::PDBFile::interpretRecord
virtual bool interpretRecord(const PDB::RecordATOM &record)
Reads an atom record.
BALL::PDBFile::read
bool read(System &system)
BALL::PDBFile::writeSecondaryStructureSection_
void writeSecondaryStructureSection_(const PDB::Structure &structure, const PDBInfo &info)
BALL::PDBFile::parseRecordCAVEAT
virtual bool parseRecordCAVEAT(const char *line, Size size)
BALL::PDBFile::fillRecord
virtual bool fillRecord(const char *line, Size size, PDB::RecordLINK &record)
BALL::PDBFile::new_helix_secstruc_list_
SecStructList new_helix_secstruc_list_
Definition PDBFile.h:854
BALL::PDBFile::interpretRecord
virtual bool interpretRecord(const PDB::RecordHETSYN &record)
Reads a record defining synonyms of a non-standard group.
BALL::PDBFile::fillRecord
virtual bool fillRecord(const char *line, Size size, PDB::RecordAUTHOR &record)
BALL::PDBFile::current_residue_
Residue * current_residue_
Definition PDBFile.h:867
BALL::PDBFile::parseRecordEXPDTA
virtual bool parseRecordEXPDTA(const char *line, Size size)
BALL::PDBFile::readNextRecord
bool readNextRecord(bool read_values=true)
Read the next record of a PDB file.
BALL::PDBFile::fillRecord
virtual bool fillRecord(const char *line, Size size, PDB::RecordSIGUIJ &record)
BALL::PDBFile::parseRecordJRNL
virtual bool parseRecordJRNL(const char *line, Size size)
BALL::PDBFile::parseRecordSCALE2
virtual bool parseRecordSCALE2(const char *line, Size size)
BALL::PDBFile::read
Molecule * read()
BALL::PDBFile::ResidueQuadruple
Quadruple< String, PDB::Character, PDB::Integer, PDB::AChar > ResidueQuadruple
Definition PDBFile.h:635
BALL::PDBFile::writeCRYST1Section_
void writeCRYST1Section_(const PDB::Structure &structure)
BALL::PDBFile::writeRecord_
void writeRecord_(const PDB::RecordTURN &helix)
BALL::PDBFile::parseRecordAUTHOR
virtual bool parseRecordAUTHOR(const char *line, Size size)
BALL::PDBFile::fillRecord
virtual bool fillRecord(const char *line, Size size, PDB::RecordSOURCE &record)
BALL::PDBFile::writeConnectivityAnnotationSection_
void writeConnectivityAnnotationSection_(const PDB::Structure &structure, const PDBInfo &info)
BALL::PDBFile::getRecordString
const char * getRecordString() const
Return a constant pointer to the line buffer.
BALL::PDBFile::parseRecordHELIX
virtual bool parseRecordHELIX(const char *line, Size size)
BALL::PDBFile::writeConnectivitySection_
void writeConnectivitySection_(const PDB::Structure &structure, const PDBInfo &info)
BALL::PDBFile::parseRecordSSBOND
virtual bool parseRecordSSBOND(const char *line, Size size)
BALL::PDBFile::interpretRecord
virtual bool interpretRecord(const PDB::RecordEND &record)
Reads the record defining the end of a PDB file.
BALL::PDBFile::interpretRecord
virtual bool interpretRecord(const PDB::RecordCRYST1 &record)
BALL::PDBFile::postprocessRandomCoils_
void postprocessRandomCoils_()
BALL::PDBFile::selectModel
void selectModel(Index index)
BALL::PDBFile::interpretRecord
virtual bool interpretRecord(const PDB::RecordFTNOTE &record)
Reads a record containing a footnote.
BALL::PDBFile::writeRecord_
void writeRecord_(const PDB::RecordMTRIX3 &mtrix3)
BALL::PDBFile::fillRecord
virtual bool fillRecord(const char *line, Size size, PDB::RecordTVECT &record)
BALL::PDBFile::fillRecord
virtual bool fillRecord(const char *line, Size size, PDB::RecordFORMUL &record)
BALL::PDBFile::interpretRecord
virtual bool interpretRecord(const PDB::RecordSCALE2 &record)
Reads a scale transformation record.
BALL::PDBFile::parseRecordHYDBND
virtual bool parseRecordHYDBND(const char *line, Size size)
BALL::PDBFile::fillRecord
virtual bool fillRecord(const char *line, Size size, PDB::RecordMTRIX1 &record)
BALL::PDBFile::fillRecord
virtual bool fillRecord(const char *line, Size size, PDB::RecordSLTBRG &record)
BALL::PDBFile::alternate_location_indicator_
char alternate_location_indicator_
Definition PDBFile.h:858
BALL::PDBFile::PDBFile
PDBFile()
BALL::PDBFile::parseRecordMTRIX3
virtual bool parseRecordMTRIX3(const char *line, Size size)
BALL::PDBFile::interpretRecord
virtual bool interpretRecord(const PDB::RecordSIGUIJ &record)
BALL::PDBFile::parseRecordSEQADV
virtual bool parseRecordSEQADV(const char *line, Size size)
BALL::PDBFile::getAtomBranchDesignator
virtual short getAtomBranchDesignator(const PDB::Atom atom_name)
Extract the PDB branch designator of an atom record.
BALL::PDBFile::parseRecordCRYST1
virtual bool parseRecordCRYST1(const char *line, Size size)
BALL::PDBFile::fillRecord
virtual bool fillRecord(const char *line, Size size, PDB::RecordENDMDL &record)
BALL::PDBFile::fillRecord
virtual bool fillRecord(const char *line, Size size, PDB::RecordHEADER &record)
BALL::PDBFile::parseRecordSLTBRG
virtual bool parseRecordSLTBRG(const char *line, Size size)
BALL::PDBFile::parseRecordLINK
virtual bool parseRecordLINK(const char *line, Size size)
BALL::PDBFile::current_PDB_atom_
PDBAtom * current_PDB_atom_
Definition PDBFile.h:869
BALL::PDBFile::read
bool read(Protein &protein)
BALL::PDBFile::interpretRecord
virtual bool interpretRecord(const PDB::RecordHETATM &record)
Reads atomic coordinates for atoms in non-standard groups.
BALL::PDBFile::interpretRecord
virtual bool interpretRecord(const PDB::RecordENDMDL &record)
Reads a model ending record.
BALL::PDBFile::fillRecord
virtual bool fillRecord(const char *line, Size size, PDB::RecordATOM &record)
BALL::PDBFile::parseRecordMODEL
virtual bool parseRecordMODEL(const char *line, Size size)
BALL::PDBFile::interpretRecord
virtual bool interpretRecord(const PDB::RecordOBSLTE &record)
BALL::PDBFile::interpretRecord
virtual bool interpretRecord(const PDB::RecordSIGATM &record)
Reads a record giving the standard deviation of atomic coordinates.
BALL::PDBFile::fillRecord
virtual bool fillRecord(const char *line, Size size, PDB::RecordHELIX &record)
BALL::PDBFile::fillRecord
virtual bool fillRecord(const char *line, Size size, PDB::RecordCONECT &record)
BALL::PDBFile::interpretRecord
virtual bool interpretRecord(const PDB::RecordSSBOND &record)
Reads a record specifying a disulfide bond.
BALL::PDBFile::selectAllModels
void selectAllModels()
Selects all models for reading.
BALL::PDBFile::readInvalidRecord
virtual bool readInvalidRecord(const char *line)
BALL::PDBFile::interpretRecord
virtual bool interpretRecord(const PDB::RecordREVDAT &record)
Reads a record containing a revision history.
BALL::PDBFile::clear
virtual void clear(int state)
Clear the stream state.
BALL::PDBFile::interpretRecord
virtual bool interpretRecord(const PDB::RecordHETNAM &record)
Reads a record defining the name of a non-standard group.
BALL::PDBFile::postprocessHelices_
void postprocessHelices_()
BALL::PDBFile::record_fields_
Size record_fields_
Definition PDBFile.h:843
BALL::PDBFile::getCurrentModel
Index getCurrentModel() const
Returns the number of the model weare currently reading. (?????).
BALL::PDBFile::interpretRecord
virtual bool interpretRecord(const PDB::RecordAUTHOR &record)
Reads an author record.
BALL::PDBFile::PDBFile
PDBFile(const Options &new_options)
BALL::PDBFile::parseRecordSIGATM
virtual bool parseRecordSIGATM(const char *line, Size size)
BALL::PDBFile::new_sheet_secstruc_list_
SecStructList new_sheet_secstruc_list_
Definition PDBFile.h:855
BALL::PDBFile::writeRecord_
void writeRecord_(const PDB::RecordCONECT &helix)
BALL::PDBFile::writeMiscellaneousFeaturesSection_
void writeMiscellaneousFeaturesSection_(const PDB::Structure &structure, const PDBInfo &info)
BALL::PDBFile::parseRecordORIGX2
virtual bool parseRecordORIGX2(const char *line, Size size)
BALL::PDBFile::QuadrupleList
std::list< ResidueQuadruple > QuadrupleList
Definition PDBFile.h:637
BALL::PDBFile::interpretRecord
virtual bool interpretRecord(const PDB::RecordORIGX2 &record)
BALL::PDBFile::clear
virtual void clear()
Clear all members.
BALL::PDBFile::writeRecord_
void writeRecord_(const PDB::RecordMTRIX2 &mtrix2)
BALL::PDBFile::fillRecord
virtual bool fillRecord(const char *line, Size size, PDB::RecordEND &record)
BALL::PDBFile::helix_list_
QuadrupleList helix_list_
Definition PDBFile.h:850
BALL::PDBFile::interpretRecord
virtual bool interpretRecord(const PDB::RecordCOMPND &record)
Reads the title record containing macroscopic compoubd information.
BALL::PDBFile::skipCurrentRecord
bool skipCurrentRecord()
BALL::PDBFile::fillRecord
virtual bool fillRecord(const char *line, Size size, PDB::RecordSCALE1 &record)
BALL::PDBFile::write_
void write_(const AtomContainer &ac, const PDBInfo &info=PDBInfo())
BALL::PDBFile::getAtomElementSymbol
virtual const char * getAtomElementSymbol(const PDB::Atom atom_name, PDB::Atom element_symbol)
BALL::PDBFile::current_model_
Index current_model_
Definition PDBFile.h:841
BALL::PDBFile::parseRecordSIGUIJ
virtual bool parseRecordSIGUIJ(const char *line, Size size)
BALL::PDBFile::selectAltLocationIndicator
void selectAltLocationIndicator(char c)
BALL::PDBFile::fillRecord
virtual bool fillRecord(const char *line, Size size, PDB::RecordREVDAT &record)
BALL::PDBFile::fillRecord
virtual bool fillRecord(const char *line, Size size, PDB::RecordCRYST1 &record)
BALL::PDBFile::parseRecordREMARK
virtual bool parseRecordREMARK(const char *line, Size size)
BALL::PDBFile::read
bool read(Molecule &protein)
BALL::PDBFile::fillRecord
virtual bool fillRecord(const char *line, Size size, PDB::RecordSEQRES &record)
BALL::PDBFile::writeRecord_
void writeRecord_(PDB::RecordType record,...)
BALL::PDBFile::parseRecordTER
virtual bool parseRecordTER(const char *line, Size size)
BALL::PDBFile::options
Options options
The options for parsing the file.
Definition PDBFile.h:170
BALL::PDBFile::writeAtom_
void writeAtom_(const PDB::Structure::AtomEntry &atom, PDB::AdditionalAtomInfo &cr, bool hetatm=false)
BALL::PDBFile::getRecordString
char * getRecordString()
Return a mutable pointer to the line buffer.
BALL::PDBFile::interpretRecord
virtual bool interpretRecord(const PDB::RecordSEQRES &record)
Reads a record containing the sequence of residues.
BALL::PDBFile::fillRecord
virtual bool fillRecord(const char *line, Size size, PDB::RecordSCALE2 &record)
BALL::PDBFile::parseRecordHETNAM
virtual bool parseRecordHETNAM(const char *line, Size size)
BALL::PDBFile::writeRecord_
void writeRecord_(const PDB::RecordMTRIX1 &mtrix1)
BALL::PDBFile::writeRawRecord_
void writeRawRecord_(const char *format, const char *tag,...)
BALL::PDBFile::writeCoordinateSection_
void writeCoordinateSection_(const PDB::Structure &structure, const PDBInfo &info)
BALL::PDBFile::fillRecord
virtual bool fillRecord(const char *line, Size size, PDB::RecordTITLE &record)
BALL::PDBFile::fillRecord
virtual bool fillRecord(const char *line, Size size, PDB::RecordMODEL &record)
BALL::PDBFile::interpretRecord
virtual bool interpretRecord(const PDB::RecordSPRSDE &record)
List of entries this file supersedes.
BALL::PDBFile::writeSLTBRGSection_
void writeSLTBRGSection_(const PDB::Structure &structure)
BALL::PDBFile::fillRecord
virtual bool fillRecord(const char *line, Size size, PDB::RecordORIGX2 &record)
BALL::PDBFile::fillRecord
virtual bool fillRecord(const char *line, Size size, PDB::RecordTURN &record)
BALL::PDBFile::interpretRecord
virtual bool interpretRecord(const PDB::RecordSITE &record)
Reads a record containing groups comprising a site.
BALL::PDBInfo
Definition PDBInfo.h:33
BALL::PropertyManager::PropertyManager
BALL_INLINE PropertyManager()
Default constructor.
BALL::Protein
Definition protein.h:30
BALL::Quadruple
Definition quadruple.h:23
BALL::Quadruple::third
T3 third
Definition quadruple.h:132
BALL::Residue
Definition residue.h:38
BALL::String
Definition string.h:57
BALL::System
Definition KERNEL/system.h:40
genericMolFile.h
BALL::operator<<
BALL_EXPORT std::ostream & operator<<(std::ostream &os, const Exception::GeneralException &e)
BALL::PDB::SIZE_OF_PDB_LINE_BUFFER
@ SIZE_OF_PDB_LINE_BUFFER
Definition PDBdefs.h:52
BALL::PDB::Atom
char Atom[5]
Definition PDBdefs.h:257
BALL::PDB::RecordType
RecordType
Definition PDBdefs.h:59
BALL::PDB::Character
char Character
Definition PDBdefs.h:259
BALL::PDB::AChar
char AChar
Definition PDBdefs.h:255
BALL::PDB::Integer
long Integer
Definition PDBdefs.h:267
BALL
Definition constants.h:13
BALL::HashIndex
BALL_SIZE_TYPE HashIndex
Definition COMMON/global.h:131
BALL::Size
BALL_SIZE_TYPE Size
Definition COMMON/global.h:114
BALL::Hash
HashIndex Hash(const T &key)
Definition hash.h:47
BALL::Index
BALL_INDEX_TYPE Index
Definition COMMON/global.h:105
options.h
property.h
quadruple.h
residue.h
secondaryStructure.h
BALL::PDBFile::Default
Definition PDBFile.h:124
BALL::PDBFile::Default::WRITE_PDBFORMAT_1996
static const bool WRITE_PDBFORMAT_1996
Definition PDBFile.h:162
BALL::PDBFile::Default::VERBOSITY
static const Index VERBOSITY
Definition PDBFile.h:129
BALL::PDBFile::Default::STORE_SKIPPED_RECORDS
static const bool STORE_SKIPPED_RECORDS
Definition PDBFile.h:146
BALL::PDBFile::Default::STRICT_LINE_CHECKING
static const bool STRICT_LINE_CHECKING
Definition PDBFile.h:135
BALL::PDBFile::Default::CHOOSE_MODEL
static const Index CHOOSE_MODEL
Definition PDBFile.h:141
BALL::PDBFile::Default::PARSE_PARTIAL_CHARGES
static const bool PARSE_PARTIAL_CHARGES
Definition PDBFile.h:156
BALL::PDBFile::Default::IGNORE_XPLOR_PSEUDO_ATOMS
static const bool IGNORE_XPLOR_PSEUDO_ATOMS
Definition PDBFile.h:151
BALL::PDBFile::Option
Definition PDBFile.h:67
BALL::PDBFile::Option::STORE_SKIPPED_RECORDS
static const char * STORE_SKIPPED_RECORDS
Definition PDBFile.h:98
BALL::PDBFile::Option::CHOOSE_MODEL
static const char * CHOOSE_MODEL
Definition PDBFile.h:91
BALL::PDBFile::Option::VERBOSITY
static const char * VERBOSITY
Definition PDBFile.h:74
BALL::PDBFile::Option::IGNORE_XPLOR_PSEUDO_ATOMS
static const char * IGNORE_XPLOR_PSEUDO_ATOMS
Definition PDBFile.h:105
BALL::PDBFile::Option::PARSE_PARTIAL_CHARGES
static const char * PARSE_PARTIAL_CHARGES
Definition PDBFile.h:112
BALL::PDBFile::Option::STRICT_LINE_CHECKING
static const char * STRICT_LINE_CHECKING
Definition PDBFile.h:82
BALL::PDBFile::Option::WRITE_PDBFORMAT_1996
static const char * WRITE_PDBFORMAT_1996
Definition PDBFile.h:118
BALL::PDB::AdditionalAtomInfo
Definition PDBdefs.h:1334
BALL::PDB::BookKeeping
Definition PDBdefs.h:1210
BALL::PDB::RecordANISOU
Definition PDBdefs.h:376
BALL::PDB::RecordATOM
Definition PDBdefs.h:397
BALL::PDB::RecordAUTHOR
Definition PDBdefs.h:416
BALL::PDB::RecordCAVEAT
Definition PDBdefs.h:426
BALL::PDB::RecordCISPEP
Definition PDBdefs.h:437
BALL::PDB::RecordCOMPND
Definition PDBdefs.h:450
BALL::PDB::RecordCONECT
Definition PDBdefs.h:460
BALL::PDB::RecordCRYST1
Definition PDBdefs.h:565
BALL::PDB::RecordDBREF
Definition PDBdefs.h:585
BALL::PDB::RecordENDMDL
Definition PDBdefs.h:628
BALL::PDB::RecordEND
Definition PDBdefs.h:621
BALL::PDB::RecordEXPDTA
Definition PDBdefs.h:635
BALL::PDB::RecordFORMUL
Definition PDBdefs.h:644
BALL::PDB::RecordFTNOTE
Definition PDBdefs.h:656
BALL::PDB::RecordHEADER
Definition PDBdefs.h:665
BALL::PDB::RecordHELIX
Definition PDBdefs.h:675
BALL::PDB::RecordHETATM
Definition PDBdefs.h:713
BALL::PDB::RecordHETNAM
Definition PDBdefs.h:730
BALL::PDB::RecordHETSYN
Definition PDBdefs.h:740
BALL::PDB::RecordHET
Definition PDBdefs.h:703
BALL::PDB::RecordHYDBND
Definition PDBdefs.h:750
BALL::PDB::RecordJRNL
Definition PDBdefs.h:776
BALL::PDB::RecordKEYWDS
Definition PDBdefs.h:783
BALL::PDB::RecordLINK
Definition PDBdefs.h:791
BALL::PDB::RecordMASTER
Definition PDBdefs.h:807
BALL::PDB::RecordMODEL
Definition PDBdefs.h:837
BALL::PDB::RecordMODRES
Definition PDBdefs.h:844
BALL::PDB::RecordMTRIX1
Definition PDBdefs.h:854
BALL::PDB::RecordMTRIX2
Definition PDBdefs.h:863
BALL::PDB::RecordMTRIX3
Definition PDBdefs.h:872
BALL::PDB::RecordOBSLTE
Definition PDBdefs.h:881
BALL::PDB::RecordORIGX1
Definition PDBdefs.h:891
BALL::PDB::RecordORIGX2
Definition PDBdefs.h:898
BALL::PDB::RecordORIGX3
Definition PDBdefs.h:905
BALL::PDB::RecordREMARK
Definition PDBdefs.h:912
BALL::PDB::RecordREVDAT
Definition PDBdefs.h:920
BALL::PDB::RecordSCALE1
Definition PDBdefs.h:933
BALL::PDB::RecordSCALE2
Definition PDBdefs.h:941
BALL::PDB::RecordSCALE3
Definition PDBdefs.h:949
BALL::PDB::RecordSEQADV
Definition PDBdefs.h:957
BALL::PDB::RecordSEQRES
Definition PDBdefs.h:971
BALL::PDB::RecordSHEET
Definition PDBdefs.h:1009
BALL::PDB::RecordSIGATM
Definition PDBdefs.h:1043
BALL::PDB::RecordSIGUIJ
Definition PDBdefs.h:1060
BALL::PDB::RecordSITE
Definition PDBdefs.h:1080
BALL::PDB::RecordSLTBRG
Definition PDBdefs.h:1091
BALL::PDB::RecordSOURCE
Definition PDBdefs.h:1109
BALL::PDB::RecordSPRSDE
Definition PDBdefs.h:1118
BALL::PDB::RecordSSBOND
Definition PDBdefs.h:1129
BALL::PDB::RecordTER
Definition PDBdefs.h:1152
BALL::PDB::RecordTITLE
Definition PDBdefs.h:1162
BALL::PDB::RecordTURN
Definition PDBdefs.h:1172
BALL::PDB::RecordTVECT
Definition PDBdefs.h:1197
BALL::PDB::RecordTypeFormat
Definition PDBdefs.h:333
BALL::PDB::Structure::AtomEntry
Definition PDBdefs.h:1248
BALL::PDB::Structure::ConectAtomList
Definition PDBdefs.h:1264
BALL::PDB::Structure
Definition PDBdefs.h:1246