, including all inherited members.
| addAllRecords_(const PDBInfo &info, PDB::RecordType type) | PDBFile | [protected] |
| atom_map_ (defined in PDBFile) | PDBFile | [protected] |
| book_keeping_ | PDBFile | [protected] |
| chain_ID_ (defined in PDBFile) | PDBFile | [protected] |
| clear(int state=0) | PDBFile | [virtual] |
| GenericMolFile::clear() | LineBasedFile | [virtual] |
| PropertyManager::clear() | PropertyManager | [virtual] |
| clear_() (defined in PDBFile) | PDBFile | [protected] |
| clearProperty(Property property) | PropertyManager | |
| clearProperty(const string &name) | PropertyManager | |
| close() | File | |
| code_ (defined in PDBFile) | PDBFile | [protected] |
| compare_record_type_format_ (defined in PDBFile) | PDBFile | [protected] |
| copy(String source_name, String destination_name, Size buffer_size=4096) | File | [static] |
| copyTo(const String &destination_name, Size buffer_size=4096) | File | |
| countNamedProperties() const | PropertyManager | |
| countProperties() const | PropertyManager | |
| countRecord(PDB::RecordType record_type, bool from_begin_of_file=true) | PDBFile | |
| countRecordFields() const | PDBFile | |
| countRecords(bool from_begin_of_file=true) | PDBFile | |
| createTemporaryFilename(String &temporary) | File | [static] |
| current_chain_ (defined in PDBFile) | PDBFile | [protected] |
| current_const_atom_ (defined in PDBFile) | PDBFile | [protected] |
| current_const_chain_ (defined in PDBFile) | PDBFile | [protected] |
| current_const_protein_ (defined in PDBFile) | PDBFile | [protected] |
| current_const_residue_ (defined in PDBFile) | PDBFile | [protected] |
| current_model_ (defined in PDBFile) | PDBFile | [protected] |
| current_PDB_atom_ (defined in PDBFile) | PDBFile | [protected] |
| current_protein_ (defined in PDBFile) | PDBFile | [protected] |
| current_record_ (defined in PDBFile) | PDBFile | [protected] |
| current_record_type_ (defined in PDBFile) | PDBFile | [protected] |
| current_residue_ (defined in PDBFile) | PDBFile | [protected] |
| destroy() | PropertyManager | [virtual] |
| disableTransformation(Transformation transformation) (defined in File) | File | [static] |
| dump(std::ostream &s=std::cout, Size depth=0) const | PropertyManager | |
| enableTransformation(Transformation transformation) (defined in File) | File | [static] |
| enableTrimWhitespaces(bool state) | LineBasedFile | |
| extractStructure_(const AtomContainer &ac, PDB::Structure &structure) | PDBFile | [protected, static] |
| File() | File | |
| File(const String &name, OpenMode open_mode=std::ios::in) | File | |
| File(const File &file) | File | |
| fillRecord(const char *line, Size size, PDB::RecordANISOU &record) (defined in PDBFile) | PDBFile | [virtual] |
| fillRecord(const char *line, Size size, PDB::RecordATOM &record) (defined in PDBFile) | PDBFile | [virtual] |
| fillRecord(const char *line, Size size, PDB::RecordAUTHOR &record) (defined in PDBFile) | PDBFile | [virtual] |
| fillRecord(const char *line, Size size, PDB::RecordCAVEAT &record) (defined in PDBFile) | PDBFile | [virtual] |
| fillRecord(const char *line, Size size, PDB::RecordCISPEP &record) (defined in PDBFile) | PDBFile | [virtual] |
| fillRecord(const char *line, Size size, PDB::RecordCOMPND &record) (defined in PDBFile) | PDBFile | [virtual] |
| fillRecord(const char *line, Size size, PDB::RecordCONECT &record) (defined in PDBFile) | PDBFile | [virtual] |
| fillRecord(const char *line, Size size, PDB::RecordCRYST1 &record) (defined in PDBFile) | PDBFile | [virtual] |
| fillRecord(const char *line, Size size, PDB::RecordDBREF &record) (defined in PDBFile) | PDBFile | [virtual] |
| fillRecord(const char *line, Size size, PDB::RecordEND &record) (defined in PDBFile) | PDBFile | [virtual] |
| fillRecord(const char *line, Size size, PDB::RecordENDMDL &record) (defined in PDBFile) | PDBFile | [virtual] |
| fillRecord(const char *line, Size size, PDB::RecordEXPDTA &record) (defined in PDBFile) | PDBFile | [virtual] |
| fillRecord(const char *line, Size size, PDB::RecordFORMUL &record) (defined in PDBFile) | PDBFile | [virtual] |
| fillRecord(const char *line, Size size, PDB::RecordFTNOTE &record) (defined in PDBFile) | PDBFile | [virtual] |
| fillRecord(const char *line, Size size, PDB::RecordHEADER &record) (defined in PDBFile) | PDBFile | [virtual] |
| fillRecord(const char *line, Size size, PDB::RecordHELIX &record) (defined in PDBFile) | PDBFile | [virtual] |
| fillRecord(const char *line, Size size, PDB::RecordHET &record) (defined in PDBFile) | PDBFile | [virtual] |
| fillRecord(const char *line, Size size, PDB::RecordHETATM &record) (defined in PDBFile) | PDBFile | [virtual] |
| fillRecord(const char *line, Size size, PDB::RecordHETNAM &record) (defined in PDBFile) | PDBFile | [virtual] |
| fillRecord(const char *line, Size size, PDB::RecordHETSYN &record) (defined in PDBFile) | PDBFile | [virtual] |
| fillRecord(const char *line, Size size, PDB::RecordHYDBND &record) (defined in PDBFile) | PDBFile | [virtual] |
| fillRecord(const char *line, Size size, PDB::RecordJRNL &record) (defined in PDBFile) | PDBFile | [virtual] |
| fillRecord(const char *line, Size size, PDB::RecordKEYWDS &record) (defined in PDBFile) | PDBFile | [virtual] |
| fillRecord(const char *line, Size size, PDB::RecordLINK &record) (defined in PDBFile) | PDBFile | [virtual] |
| fillRecord(const char *line, Size size, PDB::RecordMASTER &record) (defined in PDBFile) | PDBFile | [virtual] |
| fillRecord(const char *line, Size size, PDB::RecordMODEL &record) (defined in PDBFile) | PDBFile | [virtual] |
| fillRecord(const char *line, Size size, PDB::RecordMODRES &record) (defined in PDBFile) | PDBFile | [virtual] |
| fillRecord(const char *line, Size size, PDB::RecordMTRIX1 &record) (defined in PDBFile) | PDBFile | [virtual] |
| fillRecord(const char *line, Size size, PDB::RecordMTRIX2 &record) (defined in PDBFile) | PDBFile | [virtual] |
| fillRecord(const char *line, Size size, PDB::RecordMTRIX3 &record) (defined in PDBFile) | PDBFile | [virtual] |
| fillRecord(const char *line, Size size, PDB::RecordOBSLTE &record) (defined in PDBFile) | PDBFile | [virtual] |
| fillRecord(const char *line, Size size, PDB::RecordORIGX1 &record) (defined in PDBFile) | PDBFile | [virtual] |
| fillRecord(const char *line, Size size, PDB::RecordORIGX2 &record) (defined in PDBFile) | PDBFile | [virtual] |
| fillRecord(const char *line, Size size, PDB::RecordORIGX3 &record) (defined in PDBFile) | PDBFile | [virtual] |
| fillRecord(const char *line, Size size, PDB::RecordREMARK &record) (defined in PDBFile) | PDBFile | [virtual] |
| fillRecord(const char *line, Size size, PDB::RecordREVDAT &record) (defined in PDBFile) | PDBFile | [virtual] |
| fillRecord(const char *line, Size size, PDB::RecordSCALE1 &record) (defined in PDBFile) | PDBFile | [virtual] |
| fillRecord(const char *line, Size size, PDB::RecordSCALE2 &record) (defined in PDBFile) | PDBFile | [virtual] |
| fillRecord(const char *line, Size size, PDB::RecordSCALE3 &record) (defined in PDBFile) | PDBFile | [virtual] |
| fillRecord(const char *line, Size size, PDB::RecordSEQADV &record) (defined in PDBFile) | PDBFile | [virtual] |
| fillRecord(const char *line, Size size, PDB::RecordSEQRES &record) (defined in PDBFile) | PDBFile | [virtual] |
| fillRecord(const char *line, Size size, PDB::RecordSHEET &record) (defined in PDBFile) | PDBFile | [virtual] |
| fillRecord(const char *line, Size size, PDB::RecordSIGATM &record) (defined in PDBFile) | PDBFile | [virtual] |
| fillRecord(const char *line, Size size, PDB::RecordSIGUIJ &record) (defined in PDBFile) | PDBFile | [virtual] |
| fillRecord(const char *line, Size size, PDB::RecordSITE &record) (defined in PDBFile) | PDBFile | [virtual] |
| fillRecord(const char *line, Size size, PDB::RecordSLTBRG &record) (defined in PDBFile) | PDBFile | [virtual] |
| fillRecord(const char *line, Size size, PDB::RecordSOURCE &record) (defined in PDBFile) | PDBFile | [virtual] |
| fillRecord(const char *line, Size size, PDB::RecordSPRSDE &record) (defined in PDBFile) | PDBFile | [virtual] |
| fillRecord(const char *line, Size size, PDB::RecordSSBOND &record) (defined in PDBFile) | PDBFile | [virtual] |
| fillRecord(const char *line, Size size, PDB::RecordTER &record) (defined in PDBFile) | PDBFile | [virtual] |
| fillRecord(const char *line, Size size, PDB::RecordTITLE &record) (defined in PDBFile) | PDBFile | [virtual] |
| fillRecord(const char *line, Size size, PDB::RecordTURN &record) (defined in PDBFile) | PDBFile | [virtual] |
| fillRecord(const char *line, Size size, PDB::RecordTVECT &record) (defined in PDBFile) | PDBFile | [virtual] |
| GenericMolFile() | GenericMolFile | |
| GenericMolFile(const String &filename, File::OpenMode open_mode=std::ios::in) | GenericMolFile | |
| GenericMolFile(const GenericMolFile &file) | GenericMolFile | |
| get(PropertyManager &property_manager) const | PropertyManager | |
| getAtomBranchDesignator(const PDB::Atom atom_name) | PDBFile | [virtual] |
| getAtomElementSymbol(const PDB::Atom atom_name, PDB::Atom element_symbol) | PDBFile | [virtual] |
| getAtomName(const PDB::Atom atom_name) | PDBFile | [virtual] |
| getAtomRemotenessIndicator(const PDB::Atom atom_name) | PDBFile | [virtual] |
| getBitVector() | PropertyManager | |
| getBitVector() const | PropertyManager | |
| getCurrentModel() const | PDBFile | |
| getField(Index pos=0, const String "es="", const String &delimiters=String::CHARACTER_CLASS__WHITESPACE) const | LineBasedFile | |
| getFileStream() | File | |
| getLine() const | LineBasedFile | |
| getLine() | LineBasedFile | |
| getLineNumber() const | LineBasedFile | |
| getName() const | File | |
| getNamedProperty(Position index) const | PropertyManager | |
| getNamedProperty(Position index) | PropertyManager | |
| getOpenMode() const | File | |
| getOriginalName() const (defined in File) | File | |
| getProperty(const string &name) const | PropertyManager | |
| getRecordNumber() const | PDBFile | |
| getRecordString() | PDBFile | |
| getRecordString() const | PDBFile | |
| getRecordType() const | PDBFile | |
| getSelectedModel() const | PDBFile | |
| getSize() | File | |
| getSize(String name) | File | [static] |
| getTransformationManager() | File | |
| getTransformationManager() const | File | |
| getType(String name, bool trace_link) | File | [static] |
| getType(bool trace_link) const | File | |
| getVersion() const | PDBFile | [virtual] |
| gotoLine(Position line_number) | LineBasedFile | |
| has(const String &text) const | LineBasedFile | |
| hasFormat() | PDBFile | [virtual] |
| hasProperty(Property property) const | PropertyManager | |
| hasProperty(const string &name) const | PropertyManager | |
| helix_list_ (defined in PDBFile) | PDBFile | [protected] |
| ignore_xplor_pseudo_atoms_ | PDBFile | [protected] |
| info | PDBFile | |
| init_() (defined in PDBFile) | PDBFile | [protected] |
| initRead_() | GenericMolFile | [protected, virtual] |
| initWrite_() | GenericMolFile | [protected, virtual] |
| insertion_code_ (defined in PDBFile) | PDBFile | [protected] |
| interpretRecord(const PDB::RecordANISOU &record) | PDBFile | [virtual] |
| interpretRecord(const PDB::RecordATOM &record) | PDBFile | [virtual] |
| interpretRecord(const PDB::RecordAUTHOR &record) | PDBFile | [virtual] |
| interpretRecord(const PDB::RecordCAVEAT &record) | PDBFile | [virtual] |
| interpretRecord(const PDB::RecordCISPEP &record) | PDBFile | [virtual] |
| interpretRecord(const PDB::RecordCOMPND &record) | PDBFile | [virtual] |
| interpretRecord(const PDB::RecordCONECT &record) | PDBFile | [virtual] |
| interpretRecord(const PDB::RecordCRYST1 &record) | PDBFile | [virtual] |
| interpretRecord(const PDB::RecordDBREF &record) | PDBFile | [virtual] |
| interpretRecord(const PDB::RecordEND &record) | PDBFile | [virtual] |
| interpretRecord(const PDB::RecordENDMDL &record) | PDBFile | [virtual] |
| interpretRecord(const PDB::RecordEXPDTA &record) | PDBFile | [virtual] |
| interpretRecord(const PDB::RecordFORMUL &record) | PDBFile | [virtual] |
| interpretRecord(const PDB::RecordFTNOTE &record) | PDBFile | [virtual] |
| interpretRecord(const PDB::RecordHEADER &record) | PDBFile | [virtual] |
| interpretRecord(const PDB::RecordHELIX &record) | PDBFile | [virtual] |
| interpretRecord(const PDB::RecordHET &record) | PDBFile | [virtual] |
| interpretRecord(const PDB::RecordHETATM &record) | PDBFile | [virtual] |
| interpretRecord(const PDB::RecordHETNAM &record) | PDBFile | [virtual] |
| interpretRecord(const PDB::RecordHETSYN &record) | PDBFile | [virtual] |
| interpretRecord(const PDB::RecordHYDBND &record) | PDBFile | [virtual] |
| interpretRecord(const PDB::RecordJRNL &record) | PDBFile | [virtual] |
| interpretRecord(const PDB::RecordKEYWDS &record) | PDBFile | [virtual] |
| interpretRecord(const PDB::RecordLINK &record) | PDBFile | [virtual] |
| interpretRecord(const PDB::RecordMASTER &record) | PDBFile | [virtual] |
| interpretRecord(const PDB::RecordMODEL &record) | PDBFile | [virtual] |
| interpretRecord(const PDB::RecordMODRES &record) | PDBFile | [virtual] |
| interpretRecord(const PDB::RecordMTRIX1 &record) | PDBFile | [virtual] |
| interpretRecord(const PDB::RecordMTRIX2 &record) | PDBFile | [virtual] |
| interpretRecord(const PDB::RecordMTRIX3 &record) | PDBFile | [virtual] |
| interpretRecord(const PDB::RecordOBSLTE &record) | PDBFile | [virtual] |
| interpretRecord(const PDB::RecordORIGX1 &record) | PDBFile | [virtual] |
| interpretRecord(const PDB::RecordORIGX2 &record) | PDBFile | [virtual] |
| interpretRecord(const PDB::RecordORIGX3 &record) | PDBFile | [virtual] |
| interpretRecord(const PDB::RecordREMARK &record) | PDBFile | [virtual] |
| interpretRecord(const PDB::RecordREVDAT &record) | PDBFile | [virtual] |
| interpretRecord(const PDB::RecordSCALE1 &record) | PDBFile | [virtual] |
| interpretRecord(const PDB::RecordSCALE2 &record) | PDBFile | [virtual] |
| interpretRecord(const PDB::RecordSCALE3 &record) | PDBFile | [virtual] |
| interpretRecord(const PDB::RecordSEQADV &record) | PDBFile | [virtual] |
| interpretRecord(const PDB::RecordSEQRES &record) | PDBFile | [virtual] |
| interpretRecord(const PDB::RecordSHEET &record) | PDBFile | [virtual] |
| interpretRecord(const PDB::RecordSIGATM &record) | PDBFile | [virtual] |
| interpretRecord(const PDB::RecordSIGUIJ &record) | PDBFile | [virtual] |
| interpretRecord(const PDB::RecordSITE &record) | PDBFile | [virtual] |
| interpretRecord(const PDB::RecordSLTBRG &record) | PDBFile | [virtual] |
| interpretRecord(const PDB::RecordSOURCE &record) | PDBFile | [virtual] |
| interpretRecord(const PDB::RecordSPRSDE &record) | PDBFile | [virtual] |
| interpretRecord(const PDB::RecordSSBOND &record) | PDBFile | [virtual] |
| interpretRecord(const PDB::RecordTER &record) | PDBFile | [virtual] |
| interpretRecord(const PDB::RecordTITLE &record) | PDBFile | [virtual] |
| interpretRecord(const PDB::RecordTURN &record) | PDBFile | [virtual] |
| interpretRecord(const PDB::RecordTVECT &record) | PDBFile | [virtual] |
| is_open_ (defined in File) | File | [protected] |
| is_temporary_ (defined in File) | File | [protected] |
| isAccessible(String name) | File | [static] |
| isAccessible() const | File | |
| isCanonized() const | File | |
| isClosed() const | File | |
| isExecutable(String name) | File | [static] |
| isExecutable() const | File | |
| isHeteroAtom_(const Atom &atom) | PDBFile | [protected, static] |
| isOpen() const | File | |
| isReadable(String name) | File | [static] |
| isReadable() const | File | |
| isTransformationEnabled(Transformation transformation) (defined in File) | File | [static] |
| isValid() const | File | |
| PropertyManager::isValid() const | PropertyManager | |
| isWritable(String name) | File | [static] |
| isWritable() const | File | |
| line_ | LineBasedFile | [protected] |
| line_buffer_ (defined in PDBFile) | PDBFile | [protected] |
| line_number_ | LineBasedFile | [protected] |
| LineBasedFile() | LineBasedFile | |
| LineBasedFile(const String &filename, File::OpenMode open_mode=std::ios::in, bool trim_whitespaces=false) | LineBasedFile | |
| LineBasedFile(const LineBasedFile &f) | LineBasedFile | |
| MODE_APP | File | [static] |
| MODE_ATE | File | [static] |
| MODE_BINARY | File | [static] |
| MODE_IN | File | [static] |
| MODE_OUT | File | [static] |
| MODE_TRUNC | File | [static] |
| move(const String &source_name, const String &destination_name) | File | [static] |
| moveTo(const String &destination_name) | File | |
| name_ (defined in PDBFile) | PDBFile | [protected] |
| new_helix_secstruc_list_ (defined in PDBFile) | PDBFile | [protected] |
| new_sheet_secstruc_list_ (defined in PDBFile) | PDBFile | [protected] |
| new_turn_secstruc_list_ (defined in PDBFile) | PDBFile | [protected] |
| open(const String &name, File::OpenMode open_mode=std::ios::in) | File | |
| open_mode_ (defined in File) | File | [protected] |
| OpenMode typedef | File | |
| operator BitVector &() | PropertyManager | |
| operator!=(const LineBasedFile &f) | LineBasedFile | |
| File::operator!=(const File &file) const | File | |
| PropertyManager::operator!=(const PropertyManager &pm) const | PropertyManager | |
| operator<<(const Protein &protein) | PDBFile | |
| operator<<(const System &system) | PDBFile | [virtual] |
| operator<<(const Molecule &molecule) | PDBFile | [virtual] |
| operator=(const PDBFile &pdbf) (defined in PDBFile) | PDBFile | [protected] |
| GenericMolFile::operator=(const GenericMolFile &rhs) | GenericMolFile | |
| LineBasedFile::operator=(const LineBasedFile &file) | LineBasedFile | |
| File::operator=(const File &file) | File | |
| PropertyManager::operator=(const PropertyManager &property_manager) | PropertyManager | |
| operator==(const LineBasedFile &f) | LineBasedFile | |
| File::operator==(const File &file) const | File | |
| PropertyManager::operator==(const PropertyManager &pm) const | PropertyManager | |
| operator>>(Protein &protein) | PDBFile | |
| operator>>(Molecule &molecule) | PDBFile | [virtual] |
| operator>>(System &system) | PDBFile | [virtual] |
| options | PDBFile | |
| original_name_ (defined in File) | File | [protected] |
| parse_partial_charges_ | PDBFile | [protected] |
| parseColumnFormat(const char *format, Position index, Size length, void *arg) | LineBasedFile | |
| parseLine(const char *line, Size size, const char *format_string,...) | PDBFile | |
| parseRecordANISOU(const char *line, Size size) (defined in PDBFile) | PDBFile | [virtual] |
| parseRecordATOM(const char *line, Size size) (defined in PDBFile) | PDBFile | [virtual] |
| parseRecordAUTHOR(const char *line, Size size) (defined in PDBFile) | PDBFile | [virtual] |
| parseRecordCAVEAT(const char *line, Size size) (defined in PDBFile) | PDBFile | [virtual] |
| parseRecordCISPEP(const char *line, Size size) (defined in PDBFile) | PDBFile | [virtual] |
| parseRecordCOMPND(const char *line, Size size) (defined in PDBFile) | PDBFile | [virtual] |
| parseRecordCONECT(const char *line, Size size) (defined in PDBFile) | PDBFile | [virtual] |
| parseRecordCRYST1(const char *line, Size size) (defined in PDBFile) | PDBFile | [virtual] |
| parseRecordDBREF(const char *line, Size size) (defined in PDBFile) | PDBFile | [virtual] |
| parseRecordEND(const char *line, Size size) (defined in PDBFile) | PDBFile | [virtual] |
| parseRecordENDMDL(const char *line, Size size) (defined in PDBFile) | PDBFile | [virtual] |
| parseRecordEXPDTA(const char *line, Size size) (defined in PDBFile) | PDBFile | [virtual] |
| parseRecordFORMUL(const char *line, Size size) (defined in PDBFile) | PDBFile | [virtual] |
| parseRecordFTNOTE(const char *line, Size size) (defined in PDBFile) | PDBFile | [virtual] |
| parseRecordHEADER(const char *line, Size size) (defined in PDBFile) | PDBFile | [virtual] |
| parseRecordHELIX(const char *line, Size size) (defined in PDBFile) | PDBFile | [virtual] |
| parseRecordHET(const char *line, Size size) (defined in PDBFile) | PDBFile | [virtual] |
| parseRecordHETATM(const char *line, Size size) (defined in PDBFile) | PDBFile | [virtual] |
| parseRecordHETNAM(const char *line, Size size) (defined in PDBFile) | PDBFile | [virtual] |
| parseRecordHETSYN(const char *line, Size size) (defined in PDBFile) | PDBFile | [virtual] |
| parseRecordHYDBND(const char *line, Size size) (defined in PDBFile) | PDBFile | [virtual] |
| parseRecordJRNL(const char *line, Size size) (defined in PDBFile) | PDBFile | [virtual] |
| parseRecordKEYWDS(const char *line, Size size) (defined in PDBFile) | PDBFile | [virtual] |
| parseRecordLINK(const char *line, Size size) (defined in PDBFile) | PDBFile | [virtual] |
| parseRecordMASTER(const char *line, Size size) (defined in PDBFile) | PDBFile | [virtual] |
| parseRecordMODEL(const char *line, Size size) (defined in PDBFile) | PDBFile | [virtual] |
| parseRecordMODRES(const char *line, Size size) (defined in PDBFile) | PDBFile | [virtual] |
| parseRecordMTRIX1(const char *line, Size size) (defined in PDBFile) | PDBFile | [virtual] |
| parseRecordMTRIX2(const char *line, Size size) (defined in PDBFile) | PDBFile | [virtual] |
| parseRecordMTRIX3(const char *line, Size size) (defined in PDBFile) | PDBFile | [virtual] |
| parseRecordOBSLTE(const char *line, Size size) (defined in PDBFile) | PDBFile | [virtual] |
| parseRecordORIGX1(const char *line, Size size) (defined in PDBFile) | PDBFile | [virtual] |
| parseRecordORIGX2(const char *line, Size size) (defined in PDBFile) | PDBFile | [virtual] |
| parseRecordORIGX3(const char *line, Size size) (defined in PDBFile) | PDBFile | [virtual] |
| parseRecordREMARK(const char *line, Size size) (defined in PDBFile) | PDBFile | [virtual] |
| parseRecordREVDAT(const char *line, Size size) (defined in PDBFile) | PDBFile | [virtual] |
| parseRecordSCALE1(const char *line, Size size) (defined in PDBFile) | PDBFile | [virtual] |
| parseRecordSCALE2(const char *line, Size size) (defined in PDBFile) | PDBFile | [virtual] |
| parseRecordSCALE3(const char *line, Size size) (defined in PDBFile) | PDBFile | [virtual] |
| parseRecordSEQADV(const char *line, Size size) (defined in PDBFile) | PDBFile | [virtual] |
| parseRecordSEQRES(const char *line, Size size) (defined in PDBFile) | PDBFile | [virtual] |
| parseRecordSHEET(const char *line, Size size) (defined in PDBFile) | PDBFile | [virtual] |
| parseRecordSIGATM(const char *line, Size size) (defined in PDBFile) | PDBFile | [virtual] |
| parseRecordSIGUIJ(const char *line, Size size) (defined in PDBFile) | PDBFile | [virtual] |
| parseRecordSITE(const char *line, Size size) (defined in PDBFile) | PDBFile | [virtual] |
| parseRecordSLTBRG(const char *line, Size size) (defined in PDBFile) | PDBFile | [virtual] |
| parseRecordSOURCE(const char *line, Size size) (defined in PDBFile) | PDBFile | [virtual] |
| parseRecordSPRSDE(const char *line, Size size) (defined in PDBFile) | PDBFile | [virtual] |
| parseRecordSSBOND(const char *line, Size size) (defined in PDBFile) | PDBFile | [virtual] |
| parseRecordTER(const char *line, Size size) (defined in PDBFile) | PDBFile | [virtual] |
| parseRecordTITLE(const char *line, Size size) (defined in PDBFile) | PDBFile | [virtual] |
| parseRecordTURN(const char *line, Size size) (defined in PDBFile) | PDBFile | [virtual] |
| parseRecordTVECT(const char *line, Size size) (defined in PDBFile) | PDBFile | [virtual] |
| PDB_atom_map_ (defined in PDBFile) | PDBFile | [protected] |
| PDBAtomMap typedef (defined in PDBFile) | PDBFile | |
| PDBFile() | PDBFile | |
| PDBFile(const String &filename, File::OpenMode open_mode=std::ios::in) | PDBFile | |
| PDBFile(const Options &new_options) | PDBFile | |
| PDBFile(const PDBFile &file) | PDBFile | |
| PDBFile(const File &pdbf) (defined in PDBFile) | PDBFile | [protected] |
| postprocessHelices_() (defined in PDBFile) | PDBFile | [protected] |
| postprocessRandomCoils_() (defined in PDBFile) | PDBFile | [protected] |
| postprocessSheetsTurns_(QuadrupleList §ruct_list, SecStructList &new_secstruct_list) (defined in PDBFile) | PDBFile | [protected] |
| postprocessSSBonds_() (defined in PDBFile) | PDBFile | [protected] |
| PropertyManager() | PropertyManager | |
| PropertyManager(const PropertyManager &property_manager) | PropertyManager | |
| QuadrupleList typedef (defined in PDBFile) | PDBFile | |
| read(Protein &protein) (defined in PDBFile) | PDBFile | |
| read(Molecule &protein) (defined in PDBFile) | PDBFile | |
| read(System &system) | PDBFile | [virtual] |
| GenericMolFile::read() | GenericMolFile | [virtual] |
| PropertyManager::read(PersistenceManager &pm) | PropertyManager | |
| readFirstRecord(bool read_values=true) | PDBFile | |
| readInvalidRecord(const char *line) | PDBFile | [virtual] |
| readLine(char *line, Size size, bool extract_values) | PDBFile | |
| GenericMolFile::readLine() | LineBasedFile | |
| readNextRecord(bool read_values=true) | PDBFile | |
| readRecords() | PDBFile | |
| readUnknownRecord(const char *line) | PDBFile | [virtual] |
| record_fields_ (defined in PDBFile) | PDBFile | [protected] |
| registerTransformation(const String &pattern, const String &exec) (defined in File) | File | [static] |
| remove(String name) | File | [static] |
| remove() | File | |
| rename(String old_path, String new_path) | File | [static] |
| renameTo(const String &new_path) | File | |
| reopen() | File | |
| reopen(File::OpenMode open_mode) | File | |
| residue_map_ (defined in PDBFile) | PDBFile | [protected] |
| residue_name_ (defined in PDBFile) | PDBFile | [protected] |
| residue_sequence_number_ (defined in PDBFile) | PDBFile | [protected] |
| ResidueMap typedef (defined in PDBFile) | PDBFile | |
| ResidueQuadruple typedef (defined in PDBFile) | PDBFile | |
| rewind() | LineBasedFile | |
| search(const String &text, bool return_to_start=false) | LineBasedFile | |
| search(const String &text, const String &stop, bool return_to_start=false) (defined in LineBasedFile) | LineBasedFile | |
| SecStructList typedef (defined in PDBFile) | PDBFile | |
| selectAllModels() | PDBFile | |
| selected_model_ | PDBFile | [protected] |
| selectModel(Index index) | PDBFile | |
| sequence_number_ (defined in PDBFile) | PDBFile | [protected] |
| set(const PropertyManager &property_manager) | PropertyManager | |
| setName(const String &name) | File | |
| setProperty(Property property) | PropertyManager | |
| setProperty(const NamedProperty &property) | PropertyManager | |
| setProperty(const string &name) | PropertyManager | |
| setProperty(const string &name, bool value) | PropertyManager | |
| setProperty(const string &name, int value) | PropertyManager | |
| setProperty(const string &name, unsigned int value) | PropertyManager | |
| setProperty(const string &name, float value) | PropertyManager | |
| setProperty(const string &name, double value) | PropertyManager | |
| setProperty(const string &name, const string &value) | PropertyManager | |
| setProperty(const string &name, const PersistentObject &value) | PropertyManager | |
| sheet_list_ (defined in PDBFile) | PDBFile | [protected] |
| skipCurrentRecord() | PDBFile | |
| skipLines(Size number=1) | LineBasedFile | |
| ssbond_list_ (defined in PDBFile) | PDBFile | [protected] |
| startsWith(const String &text) const | LineBasedFile | |
| store_skipped_records_ | PDBFile | [protected] |
| strict_line_checking_ (defined in PDBFile) | PDBFile | [protected] |
| swap(PropertyManager &property_manager) | PropertyManager | |
| switchString(const std::vector< String > &data) const | LineBasedFile | |
| test(const char *file, int line, bool condition, const String &msg) const | LineBasedFile | |
| toggleProperty(Property property) | PropertyManager | |
| Transformation enum name | File | |
| TRANSFORMATION__EXEC enum value (defined in File) | File | |
| TRANSFORMATION__FILTER enum value (defined in File) | File | |
| TRANSFORMATION__URL enum value (defined in File) | File | |
| TRANSFORMATION_EXEC_PREFIX | File | [static] |
| TRANSFORMATION_FILE_PREFIX | File | [static] |
| TRANSFORMATION_FTP_PREFIX | File | [static] |
| TRANSFORMATION_HTTP_PREFIX | File | [static] |
| transformation_manager_ (defined in File) | File | [protected, static] |
| transformation_methods_ (defined in File) | File | [protected, static] |
| trim_whitespaces_ (defined in LineBasedFile) | LineBasedFile | [protected] |
| trimWhiteSpacesEnabled() const (defined in LineBasedFile) | LineBasedFile | |
| truncate(String path, Size size=0) | File | [static] |
| truncate(Size size=0) | File | |
| turn_list_ (defined in PDBFile) | PDBFile | [protected] |
| Type enum name | File | |
| TYPE__BLOCK_SPECIAL_FILE enum value (defined in File) | File | |
| TYPE__CHAR_SPECIAL_FILE enum value (defined in File) | File | |
| TYPE__DIRECTORY enum value (defined in File) | File | |
| TYPE__FIFO_SPECIAL_FILE enum value (defined in File) | File | |
| TYPE__REGULAR_FILE enum value (defined in File) | File | |
| TYPE__SOCKET enum value (defined in File) | File | |
| TYPE__SYMBOLIC_LINK enum value (defined in File) | File | |
| TYPE__UNKNOWN enum value (defined in File) | File | |
| unregisterTransformation(const String &pattern) (defined in File) | File | [static] |
| updateAdditionalAtomInfo_(const PDB::Structure::AtomEntry &atom, PDB::AdditionalAtomInfo &cr) | PDBFile | [protected, static] |
| verbosity_ | PDBFile | [protected] |
| write(const Protein &protein) (defined in PDBFile) | PDBFile | |
| write(const Molecule &molecule) | PDBFile | [virtual] |
| write(const System &system, const PDBInfo &info=PDBInfo()) (defined in PDBFile) | PDBFile | |
| GenericMolFile::write(const System &system) | GenericMolFile | [virtual] |
| PropertyManager::write(PersistenceManager &pm) const | PropertyManager | |
| write_(const AtomContainer &ac, const PDBInfo &info=PDBInfo()) (defined in PDBFile) | PDBFile | [protected] |
| writeAtom_(const PDB::Structure::AtomEntry &atom, PDB::AdditionalAtomInfo &cr, bool hetatm=false) (defined in PDBFile) | PDBFile | [protected] |
| writeBookKeepingSection_(const PDB::Structure &structure, const PDBInfo &info) (defined in PDBFile) | PDBFile | [protected] |
| writeCONECTRecords_(PDB::Structure::ConectAtomList &cl) (defined in PDBFile) | PDBFile | [protected] |
| writeConnectivityAnnotationSection_(const PDB::Structure &structure, const PDBInfo &info) (defined in PDBFile) | PDBFile | [protected] |
| writeConnectivitySection_(const PDB::Structure &structure, const PDBInfo &info) (defined in PDBFile) | PDBFile | [protected] |
| writeCoordinateSection_(const PDB::Structure &structure, const PDBInfo &info) (defined in PDBFile) | PDBFile | [protected] |
| writeCrystallographicSection_(const PDB::Structure &structure, const PDBInfo &info) (defined in PDBFile) | PDBFile | [protected] |
| writeHELIXSection_(const PDB::Structure &structure) (defined in PDBFile) | PDBFile | [protected] |
| writeHeterogenSection_(const PDB::Structure &structure, const PDBInfo &info) (defined in PDBFile) | PDBFile | [protected] |
| writeHYDBNDSection_(const PDB::Structure &structure) (defined in PDBFile) | PDBFile | [protected] |
| writeMiscellaneousFeaturesSection_(const PDB::Structure &structure, const PDBInfo &info) (defined in PDBFile) | PDBFile | [protected] |
| writePrimaryStructureSection_(const PDB::Structure &structure, const PDBInfo &info) (defined in PDBFile) | PDBFile | [protected] |
| writeRawRecord_(const char *format, const char *tag,...) | PDBFile | [protected] |
| writeRecord_(PDB::RecordType record,...) | PDBFile | [protected] |
| writeRecord_(const PDB::RecordSEQRES &seqres) | PDBFile | [protected] |
| writeRecord_(const PDB::RecordHELIX &helix) | PDBFile | [protected] |
| writeRecord_(const PDB::RecordSHEET &helix) | PDBFile | [protected] |
| writeRecord_(const PDB::RecordTURN &helix) | PDBFile | [protected] |
| writeRecord_(const PDB::RecordSSBOND &helix) | PDBFile | [protected] |
| writeRecord_(const PDB::RecordCONECT &helix) | PDBFile | [protected] |
| writeSecondaryStructureSection_(const PDB::Structure &structure, const PDBInfo &info) (defined in PDBFile) | PDBFile | [protected] |
| writeSEQRESSection_(const std::vector< std::pair< char, String > > &chain_residues) (defined in PDBFile) | PDBFile | [protected] |
| writeSHEETSection_(const PDB::Structure &structure) (defined in PDBFile) | PDBFile | [protected] |
| writeSLTBRGSection_(const PDB::Structure &structure) (defined in PDBFile) | PDBFile | [protected] |
| writeSSBONDSection_(const PDB::Structure &structure) (defined in PDBFile) | PDBFile | [protected] |
| writeTitleSection_(const PDB::Structure &structure, const PDBInfo &info) (defined in PDBFile) | PDBFile | [protected] |
| writeTURNSection_(const PDB::Structure &structure) (defined in PDBFile) | PDBFile | [protected] |
| ~File() | File | [virtual] |
| ~GenericMolFile() | GenericMolFile | [virtual] |
| ~PDBFile() | PDBFile | [virtual] |
| ~PropertyManager() | PropertyManager | [virtual] |