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BALL
1.4.79
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BALL
1.4.79
|
This is the complete list of members for BALL::PDBFile, including all inherited members.
| addAllRecords_(const PDBInfo &info, PDB::RecordType type) | BALL::PDBFile | protected |
| alternate_location_indicator_ | BALL::PDBFile | protected |
| atom_map_ | BALL::PDBFile | protected |
| beginNamedProperty() | BALL::PropertyManager | |
| book_keeping_ | BALL::PDBFile | protected |
| chain_ID_ | BALL::PDBFile | protected |
| clear(int state) | BALL::PDBFile | virtual |
| clear() | BALL::PDBFile | virtual |
| clearProperty(Property property) | BALL::PropertyManager | |
| clearProperty(const std::string &name) | BALL::PropertyManager | |
| close() | BALL::GenericMolFile | virtual |
| code_ | BALL::PDBFile | protected |
| col_buffer_ | BALL::LineBasedFile | protected |
| compare_record_type_format_ | BALL::PDBFile | protected |
| compress_output_ | BALL::GenericMolFile | protected |
| copy(String source_name, String destination_name, Size buffer_size=4096) | BALL::File | static |
| copyTo(const String &destination_name, Size buffer_size=4096) | BALL::File | |
| countNamedProperties() const | BALL::PropertyManager | |
| countProperties() const | BALL::PropertyManager | |
| countRecord(PDB::RecordType record_type, bool from_begin_of_file=true) | BALL::PDBFile | |
| countRecordFields() const | BALL::PDBFile | |
| countRecords(bool from_begin_of_file=true) | BALL::PDBFile | |
| created_temp_filenames_ | BALL::File | protectedstatic |
| createTemporaryFilename(String &temporary, const String &suffix=".TMP") | BALL::File | static |
| current_chain_ | BALL::PDBFile | protected |
| current_const_atom_ | BALL::PDBFile | protected |
| current_const_chain_ | BALL::PDBFile | protected |
| current_const_protein_ | BALL::PDBFile | protected |
| current_const_residue_ | BALL::PDBFile | protected |
| current_model_ | BALL::PDBFile | protected |
| current_PDB_atom_ | BALL::PDBFile | protected |
| current_protein_ | BALL::PDBFile | protected |
| current_record_ | BALL::PDBFile | protected |
| current_record_type_ | BALL::PDBFile | protected |
| current_residue_ | BALL::PDBFile | protected |
| defineInputAsTemporary(bool b=true) | BALL::GenericMolFile | |
| destroy() | BALL::PropertyManager | virtual |
| disableTransformation(Transformation transformation) | BALL::File | static |
| dump(std::ostream &s=std::cout, Size depth=0) const | BALL::PropertyManager | |
| enableOutputCompression(String zipped_filename) | BALL::GenericMolFile | |
| enableTransformation(Transformation transformation) | BALL::File | static |
| enableTrimWhitespaces(bool state) | BALL::LineBasedFile | |
| endNamedProperty() | BALL::PropertyManager | |
| extractStructure_(const AtomContainer &ac, PDB::Structure &structure) | BALL::PDBFile | protectedstatic |
| File() | BALL::File | |
| File(const String &name, OpenMode open_mode=std::ios::in) | BALL::File | |
| fillRecord(const char *line, Size size, PDB::RecordANISOU &record) | BALL::PDBFile | virtual |
| fillRecord(const char *line, Size size, PDB::RecordATOM &record) | BALL::PDBFile | virtual |
| fillRecord(const char *line, Size size, PDB::RecordAUTHOR &record) | BALL::PDBFile | virtual |
| fillRecord(const char *line, Size size, PDB::RecordCAVEAT &record) | BALL::PDBFile | virtual |
| fillRecord(const char *line, Size size, PDB::RecordCISPEP &record) | BALL::PDBFile | virtual |
| fillRecord(const char *line, Size size, PDB::RecordCOMPND &record) | BALL::PDBFile | virtual |
| fillRecord(const char *line, Size size, PDB::RecordCONECT &record) | BALL::PDBFile | virtual |
| fillRecord(const char *line, Size size, PDB::RecordCRYST1 &record) | BALL::PDBFile | virtual |
| fillRecord(const char *line, Size size, PDB::RecordDBREF &record) | BALL::PDBFile | virtual |
| fillRecord(const char *line, Size size, PDB::RecordEND &record) | BALL::PDBFile | virtual |
| fillRecord(const char *line, Size size, PDB::RecordENDMDL &record) | BALL::PDBFile | virtual |
| fillRecord(const char *line, Size size, PDB::RecordEXPDTA &record) | BALL::PDBFile | virtual |
| fillRecord(const char *line, Size size, PDB::RecordFORMUL &record) | BALL::PDBFile | virtual |
| fillRecord(const char *line, Size size, PDB::RecordFTNOTE &record) | BALL::PDBFile | virtual |
| fillRecord(const char *line, Size size, PDB::RecordHEADER &record) | BALL::PDBFile | virtual |
| fillRecord(const char *line, Size size, PDB::RecordHELIX &record) | BALL::PDBFile | virtual |
| fillRecord(const char *line, Size size, PDB::RecordHET &record) | BALL::PDBFile | virtual |
| fillRecord(const char *line, Size size, PDB::RecordHETATM &record) | BALL::PDBFile | virtual |
| fillRecord(const char *line, Size size, PDB::RecordHETNAM &record) | BALL::PDBFile | virtual |
| fillRecord(const char *line, Size size, PDB::RecordHETSYN &record) | BALL::PDBFile | virtual |
| fillRecord(const char *line, Size size, PDB::RecordHYDBND &record) | BALL::PDBFile | virtual |
| fillRecord(const char *line, Size size, PDB::RecordJRNL &record) | BALL::PDBFile | virtual |
| fillRecord(const char *line, Size size, PDB::RecordKEYWDS &record) | BALL::PDBFile | virtual |
| fillRecord(const char *line, Size size, PDB::RecordLINK &record) | BALL::PDBFile | virtual |
| fillRecord(const char *line, Size size, PDB::RecordMASTER &record) | BALL::PDBFile | virtual |
| fillRecord(const char *line, Size size, PDB::RecordMODEL &record) | BALL::PDBFile | virtual |
| fillRecord(const char *line, Size size, PDB::RecordMODRES &record) | BALL::PDBFile | virtual |
| fillRecord(const char *line, Size size, PDB::RecordMTRIX1 &record) | BALL::PDBFile | virtual |
| fillRecord(const char *line, Size size, PDB::RecordMTRIX2 &record) | BALL::PDBFile | virtual |
| fillRecord(const char *line, Size size, PDB::RecordMTRIX3 &record) | BALL::PDBFile | virtual |
| fillRecord(const char *line, Size size, PDB::RecordOBSLTE &record) | BALL::PDBFile | virtual |
| fillRecord(const char *line, Size size, PDB::RecordORIGX1 &record) | BALL::PDBFile | virtual |
| fillRecord(const char *line, Size size, PDB::RecordORIGX2 &record) | BALL::PDBFile | virtual |
| fillRecord(const char *line, Size size, PDB::RecordORIGX3 &record) | BALL::PDBFile | virtual |
| fillRecord(const char *line, Size size, PDB::RecordREMARK &record) | BALL::PDBFile | virtual |
| fillRecord(const char *line, Size size, PDB::RecordREVDAT &record) | BALL::PDBFile | virtual |
| fillRecord(const char *line, Size size, PDB::RecordSCALE1 &record) | BALL::PDBFile | virtual |
| fillRecord(const char *line, Size size, PDB::RecordSCALE2 &record) | BALL::PDBFile | virtual |
| fillRecord(const char *line, Size size, PDB::RecordSCALE3 &record) | BALL::PDBFile | virtual |
| fillRecord(const char *line, Size size, PDB::RecordSEQADV &record) | BALL::PDBFile | virtual |
| fillRecord(const char *line, Size size, PDB::RecordSEQRES &record) | BALL::PDBFile | virtual |
| fillRecord(const char *line, Size size, PDB::RecordSHEET &record) | BALL::PDBFile | virtual |
| fillRecord(const char *line, Size size, PDB::RecordSIGATM &record) | BALL::PDBFile | virtual |
| fillRecord(const char *line, Size size, PDB::RecordSIGUIJ &record) | BALL::PDBFile | virtual |
| fillRecord(const char *line, Size size, PDB::RecordSITE &record) | BALL::PDBFile | virtual |
| fillRecord(const char *line, Size size, PDB::RecordSLTBRG &record) | BALL::PDBFile | virtual |
| fillRecord(const char *line, Size size, PDB::RecordSOURCE &record) | BALL::PDBFile | virtual |
| fillRecord(const char *line, Size size, PDB::RecordSPRSDE &record) | BALL::PDBFile | virtual |
| fillRecord(const char *line, Size size, PDB::RecordSSBOND &record) | BALL::PDBFile | virtual |
| fillRecord(const char *line, Size size, PDB::RecordTER &record) | BALL::PDBFile | virtual |
| fillRecord(const char *line, Size size, PDB::RecordTITLE &record) | BALL::PDBFile | virtual |
| fillRecord(const char *line, Size size, PDB::RecordTURN &record) | BALL::PDBFile | virtual |
| fillRecord(const char *line, Size size, PDB::RecordTVECT &record) | BALL::PDBFile | virtual |
| GenericMolFile() | BALL::GenericMolFile | |
| GenericMolFile(const String &filename, File::OpenMode open_mode=std::ios::in) | BALL::GenericMolFile | |
| get(PropertyManager &property_manager) const | BALL::PropertyManager | |
| getAtomBranchDesignator(const PDB::Atom atom_name) | BALL::PDBFile | virtual |
| getAtomElementSymbol(const PDB::Atom atom_name, PDB::Atom element_symbol) | BALL::PDBFile | virtual |
| getAtomName(const PDB::Atom atom_name) | BALL::PDBFile | virtual |
| getAtomRemotenessIndicator(const PDB::Atom atom_name) | BALL::PDBFile | virtual |
| getBitVector() | BALL::PropertyManager | |
| getBitVector() const | BALL::PropertyManager | |
| getCurrentModel() const | BALL::PDBFile | |
| getField(Index pos=0, const String "es="", const String &delimiters=String::CHARACTER_CLASS__WHITESPACE) const | BALL::LineBasedFile | |
| getFileStream() | BALL::File | |
| getLine() const | BALL::LineBasedFile | |
| getLine() | BALL::LineBasedFile | |
| getLineNumber() const | BALL::LineBasedFile | |
| getName() const | BALL::File | |
| getNamedProperty(Position index) const | BALL::PropertyManager | |
| getNamedProperty(Position index) | BALL::PropertyManager | |
| getOpenMode() const | BALL::File | |
| getOriginalName() const | BALL::File | |
| getProperty(const std::string &name) const | BALL::PropertyManager | |
| getRecordNumber() const | BALL::PDBFile | |
| getRecordString() | BALL::PDBFile | |
| getRecordString() const | BALL::PDBFile | |
| getRecordType() const | BALL::PDBFile | |
| getSelectedModel() const | BALL::PDBFile | |
| getSize() | BALL::File | |
| getSize(String name) | BALL::File | static |
| getTransformationManager() | BALL::File | |
| getTransformationManager() const | BALL::File | |
| getType(String name, bool trace_link) | BALL::File | static |
| getType(bool trace_link) const | BALL::File | |
| getVersion() const | BALL::PDBFile | virtual |
| gmf_is_closed_ | BALL::GenericMolFile | protected |
| gotoLine(Position line_number) | BALL::LineBasedFile | |
| has(const String &text) const | BALL::LineBasedFile | |
| hasFormat() | BALL::PDBFile | virtual |
| hasProperty(Property property) const | BALL::PropertyManager | |
| hasProperty(const std::string &name) const | BALL::PropertyManager | |
| helix_list_ | BALL::PDBFile | protected |
| ignore_xplor_pseudo_atoms_ | BALL::PDBFile | protected |
| info | BALL::PDBFile | |
| init_() | BALL::PDBFile | protected |
| initRead_() | BALL::GenericMolFile | protectedvirtual |
| initWrite_() | BALL::GenericMolFile | protectedvirtual |
| input_is_temporary_ | BALL::GenericMolFile | protected |
| insertion_code_ | BALL::PDBFile | protected |
| interpretRecord(const PDB::RecordANISOU &record) | BALL::PDBFile | virtual |
| interpretRecord(const PDB::RecordATOM &record) | BALL::PDBFile | virtual |
| interpretRecord(const PDB::RecordAUTHOR &record) | BALL::PDBFile | virtual |
| interpretRecord(const PDB::RecordCAVEAT &record) | BALL::PDBFile | virtual |
| interpretRecord(const PDB::RecordCISPEP &record) | BALL::PDBFile | virtual |
| interpretRecord(const PDB::RecordCOMPND &record) | BALL::PDBFile | virtual |
| interpretRecord(const PDB::RecordCONECT &record) | BALL::PDBFile | virtual |
| interpretRecord(const PDB::RecordCRYST1 &record) | BALL::PDBFile | virtual |
| interpretRecord(const PDB::RecordDBREF &record) | BALL::PDBFile | virtual |
| interpretRecord(const PDB::RecordEND &record) | BALL::PDBFile | virtual |
| interpretRecord(const PDB::RecordENDMDL &record) | BALL::PDBFile | virtual |
| interpretRecord(const PDB::RecordEXPDTA &record) | BALL::PDBFile | virtual |
| interpretRecord(const PDB::RecordFORMUL &record) | BALL::PDBFile | virtual |
| interpretRecord(const PDB::RecordFTNOTE &record) | BALL::PDBFile | virtual |
| interpretRecord(const PDB::RecordHEADER &record) | BALL::PDBFile | virtual |
| interpretRecord(const PDB::RecordHELIX &record) | BALL::PDBFile | virtual |
| interpretRecord(const PDB::RecordHET &record) | BALL::PDBFile | virtual |
| interpretRecord(const PDB::RecordHETATM &record) | BALL::PDBFile | virtual |
| interpretRecord(const PDB::RecordHETNAM &record) | BALL::PDBFile | virtual |
| interpretRecord(const PDB::RecordHETSYN &record) | BALL::PDBFile | virtual |
| interpretRecord(const PDB::RecordHYDBND &record) | BALL::PDBFile | virtual |
| interpretRecord(const PDB::RecordJRNL &record) | BALL::PDBFile | virtual |
| interpretRecord(const PDB::RecordKEYWDS &record) | BALL::PDBFile | virtual |
| interpretRecord(const PDB::RecordLINK &record) | BALL::PDBFile | virtual |
| interpretRecord(const PDB::RecordMASTER &record) | BALL::PDBFile | virtual |
| interpretRecord(const PDB::RecordMODEL &record) | BALL::PDBFile | virtual |
| interpretRecord(const PDB::RecordMODRES &record) | BALL::PDBFile | virtual |
| interpretRecord(const PDB::RecordMTRIX1 &record) | BALL::PDBFile | virtual |
| interpretRecord(const PDB::RecordMTRIX2 &record) | BALL::PDBFile | virtual |
| interpretRecord(const PDB::RecordMTRIX3 &record) | BALL::PDBFile | virtual |
| interpretRecord(const PDB::RecordOBSLTE &record) | BALL::PDBFile | virtual |
| interpretRecord(const PDB::RecordORIGX1 &record) | BALL::PDBFile | virtual |
| interpretRecord(const PDB::RecordORIGX2 &record) | BALL::PDBFile | virtual |
| interpretRecord(const PDB::RecordORIGX3 &record) | BALL::PDBFile | virtual |
| interpretRecord(const PDB::RecordREMARK &record) | BALL::PDBFile | virtual |
| interpretRecord(const PDB::RecordREVDAT &record) | BALL::PDBFile | virtual |
| interpretRecord(const PDB::RecordSCALE1 &record) | BALL::PDBFile | virtual |
| interpretRecord(const PDB::RecordSCALE2 &record) | BALL::PDBFile | virtual |
| interpretRecord(const PDB::RecordSCALE3 &record) | BALL::PDBFile | virtual |
| interpretRecord(const PDB::RecordSEQADV &record) | BALL::PDBFile | virtual |
| interpretRecord(const PDB::RecordSEQRES &record) | BALL::PDBFile | virtual |
| interpretRecord(const PDB::RecordSHEET &record) | BALL::PDBFile | virtual |
| interpretRecord(const PDB::RecordSIGATM &record) | BALL::PDBFile | virtual |
| interpretRecord(const PDB::RecordSIGUIJ &record) | BALL::PDBFile | virtual |
| interpretRecord(const PDB::RecordSITE &record) | BALL::PDBFile | virtual |
| interpretRecord(const PDB::RecordSLTBRG &record) | BALL::PDBFile | virtual |
| interpretRecord(const PDB::RecordSOURCE &record) | BALL::PDBFile | virtual |
| interpretRecord(const PDB::RecordSPRSDE &record) | BALL::PDBFile | virtual |
| interpretRecord(const PDB::RecordSSBOND &record) | BALL::PDBFile | virtual |
| interpretRecord(const PDB::RecordTER &record) | BALL::PDBFile | virtual |
| interpretRecord(const PDB::RecordTITLE &record) | BALL::PDBFile | virtual |
| interpretRecord(const PDB::RecordTURN &record) | BALL::PDBFile | virtual |
| interpretRecord(const PDB::RecordTVECT &record) | BALL::PDBFile | virtual |
| is_open_ | BALL::File | protected |
| is_temporary_ | BALL::File | protected |
| isAccessible(String name) | BALL::File | static |
| isAccessible() const | BALL::File | |
| isCanonized() const | BALL::File | |
| isClosed() const | BALL::File | |
| isCompressedFile() | BALL::GenericMolFile | |
| isExecutable(String name) | BALL::File | static |
| isExecutable() const | BALL::File | |
| isHeteroAtom_(const Atom &atom) | BALL::PDBFile | protectedstatic |
| isOpen() const | BALL::File | |
| isReadable(String name) | BALL::File | static |
| isReadable() const | BALL::File | |
| isTransformationEnabled(Transformation transformation) | BALL::File | static |
| BALL::isValid() const | BALL::File | |
| BALL::PropertyManager::isValid() const | BALL::PropertyManager | |
| isWritable(String name) | BALL::File | static |
| isWritable() const | BALL::File | |
| line_ | BALL::LineBasedFile | protected |
| line_buffer_ | BALL::PDBFile | protected |
| line_number_ | BALL::LineBasedFile | protected |
| LineBasedFile() | BALL::LineBasedFile | |
| LineBasedFile(const String &filename, File::OpenMode open_mode=std::ios::in, bool trim_whitespaces=false) | BALL::LineBasedFile | |
| MODE_APP | BALL::File | static |
| MODE_ATE | BALL::File | static |
| MODE_BINARY | BALL::File | static |
| MODE_IN | BALL::File | static |
| MODE_OUT | BALL::File | static |
| MODE_TRUNC | BALL::File | static |
| move(const String &source_name, const String &destination_name) | BALL::File | static |
| moveTo(const String &destination_name) | BALL::File | |
| name_ | BALL::PDBFile | protected |
| new_helix_secstruc_list_ | BALL::PDBFile | protected |
| new_sheet_secstruc_list_ | BALL::PDBFile | protected |
| new_turn_secstruc_list_ | BALL::PDBFile | protected |
| open(const String &name, File::OpenMode open_mode=std::ios::in) | BALL::PDBFile | |
| open_mode_ | BALL::File | protected |
| OpenMode typedef | BALL::File | |
| operator BitVector &() | BALL::PropertyManager | |
| BALL::operator!=(const LineBasedFile &f) | BALL::LineBasedFile | |
| BALL::File::operator!=(const File &file) const | BALL::File | |
| BALL::PropertyManager::operator!=(const PropertyManager &pm) const | BALL::PropertyManager | |
| operator<<(const Protein &protein) | BALL::PDBFile | |
| operator<<(const System &system) | BALL::PDBFile | virtual |
| operator<<(const Molecule &molecule) | BALL::PDBFile | virtual |
| operator=(const PDBFile &pdbf) | BALL::PDBFile | protected |
| BALL::GenericMolFile::operator=(const GenericMolFile &rhs) | BALL::GenericMolFile | |
| BALL::LineBasedFile::operator=(const LineBasedFile &file) | BALL::LineBasedFile | |
| BALL::PropertyManager::operator=(const PropertyManager &property_manager) | BALL::PropertyManager | |
| BALL::operator==(const LineBasedFile &f) | BALL::LineBasedFile | |
| BALL::File::operator==(const File &file) const | BALL::File | |
| BALL::PropertyManager::operator==(const PropertyManager &pm) const | BALL::PropertyManager | |
| operator>>(Protein &protein) | BALL::PDBFile | |
| operator>>(Molecule &molecule) | BALL::PDBFile | virtual |
| operator>>(System &system) | BALL::PDBFile | virtual |
| options | BALL::PDBFile | |
| original_name_ | BALL::File | protected |
| parse_partial_charges_ | BALL::PDBFile | protected |
| parseColumnFormat(const char *format, Position index, Size length, void *arg) | BALL::LineBasedFile | |
| parseLine(const char *line, Size size, const char *format_string,...) | BALL::PDBFile | |
| parseRecordANISOU(const char *line, Size size) | BALL::PDBFile | virtual |
| parseRecordATOM(const char *line, Size size) | BALL::PDBFile | virtual |
| parseRecordAUTHOR(const char *line, Size size) | BALL::PDBFile | virtual |
| parseRecordCAVEAT(const char *line, Size size) | BALL::PDBFile | virtual |
| parseRecordCISPEP(const char *line, Size size) | BALL::PDBFile | virtual |
| parseRecordCOMPND(const char *line, Size size) | BALL::PDBFile | virtual |
| parseRecordCONECT(const char *line, Size size) | BALL::PDBFile | virtual |
| parseRecordCRYST1(const char *line, Size size) | BALL::PDBFile | virtual |
| parseRecordDBREF(const char *line, Size size) | BALL::PDBFile | virtual |
| parseRecordEND(const char *line, Size size) | BALL::PDBFile | virtual |
| parseRecordENDMDL(const char *line, Size size) | BALL::PDBFile | virtual |
| parseRecordEXPDTA(const char *line, Size size) | BALL::PDBFile | virtual |
| parseRecordFORMUL(const char *line, Size size) | BALL::PDBFile | virtual |
| parseRecordFTNOTE(const char *line, Size size) | BALL::PDBFile | virtual |
| parseRecordHEADER(const char *line, Size size) | BALL::PDBFile | virtual |
| parseRecordHELIX(const char *line, Size size) | BALL::PDBFile | virtual |
| parseRecordHET(const char *line, Size size) | BALL::PDBFile | virtual |
| parseRecordHETATM(const char *line, Size size) | BALL::PDBFile | virtual |
| parseRecordHETNAM(const char *line, Size size) | BALL::PDBFile | virtual |
| parseRecordHETSYN(const char *line, Size size) | BALL::PDBFile | virtual |
| parseRecordHYDBND(const char *line, Size size) | BALL::PDBFile | virtual |
| parseRecordJRNL(const char *line, Size size) | BALL::PDBFile | virtual |
| parseRecordKEYWDS(const char *line, Size size) | BALL::PDBFile | virtual |
| parseRecordLINK(const char *line, Size size) | BALL::PDBFile | virtual |
| parseRecordMASTER(const char *line, Size size) | BALL::PDBFile | virtual |
| parseRecordMODEL(const char *line, Size size) | BALL::PDBFile | virtual |
| parseRecordMODRES(const char *line, Size size) | BALL::PDBFile | virtual |
| parseRecordMTRIX1(const char *line, Size size) | BALL::PDBFile | virtual |
| parseRecordMTRIX2(const char *line, Size size) | BALL::PDBFile | virtual |
| parseRecordMTRIX3(const char *line, Size size) | BALL::PDBFile | virtual |
| parseRecordOBSLTE(const char *line, Size size) | BALL::PDBFile | virtual |
| parseRecordORIGX1(const char *line, Size size) | BALL::PDBFile | virtual |
| parseRecordORIGX2(const char *line, Size size) | BALL::PDBFile | virtual |
| parseRecordORIGX3(const char *line, Size size) | BALL::PDBFile | virtual |
| parseRecordREMARK(const char *line, Size size) | BALL::PDBFile | virtual |
| parseRecordREVDAT(const char *line, Size size) | BALL::PDBFile | virtual |
| parseRecordSCALE1(const char *line, Size size) | BALL::PDBFile | virtual |
| parseRecordSCALE2(const char *line, Size size) | BALL::PDBFile | virtual |
| parseRecordSCALE3(const char *line, Size size) | BALL::PDBFile | virtual |
| parseRecordSEQADV(const char *line, Size size) | BALL::PDBFile | virtual |
| parseRecordSEQRES(const char *line, Size size) | BALL::PDBFile | virtual |
| parseRecordSHEET(const char *line, Size size) | BALL::PDBFile | virtual |
| parseRecordSIGATM(const char *line, Size size) | BALL::PDBFile | virtual |
| parseRecordSIGUIJ(const char *line, Size size) | BALL::PDBFile | virtual |
| parseRecordSITE(const char *line, Size size) | BALL::PDBFile | virtual |
| parseRecordSLTBRG(const char *line, Size size) | BALL::PDBFile | virtual |
| parseRecordSOURCE(const char *line, Size size) | BALL::PDBFile | virtual |
| parseRecordSPRSDE(const char *line, Size size) | BALL::PDBFile | virtual |
| parseRecordSSBOND(const char *line, Size size) | BALL::PDBFile | virtual |
| parseRecordTER(const char *line, Size size) | BALL::PDBFile | virtual |
| parseRecordTITLE(const char *line, Size size) | BALL::PDBFile | virtual |
| parseRecordTURN(const char *line, Size size) | BALL::PDBFile | virtual |
| parseRecordTVECT(const char *line, Size size) | BALL::PDBFile | virtual |
| PDB_atom_map_ | BALL::PDBFile | protected |
| PDBAtomMap typedef | BALL::PDBFile | |
| PDBFile() | BALL::PDBFile | |
| PDBFile(const String &filename, File::OpenMode open_mode=std::ios::in) | BALL::PDBFile | |
| PDBFile(const Options &new_options) | BALL::PDBFile | |
| PDBFile(const File &pdbf) | BALL::PDBFile | protected |
| postprocessHelices_() | BALL::PDBFile | protected |
| postprocessRandomCoils_() | BALL::PDBFile | protected |
| postprocessSheetsTurns_(QuadrupleList §ruct_list, SecStructList &new_secstruct_list) | BALL::PDBFile | protected |
| postprocessSSBonds_() | BALL::PDBFile | protected |
| PropertyManager() | BALL::PropertyManager | |
| PropertyManager(const PropertyManager &property_manager) | BALL::PropertyManager | |
| QuadrupleList typedef | BALL::PDBFile | |
| read(Protein &protein) | BALL::PDBFile | |
| read(Molecule &protein) | BALL::PDBFile | |
| read(System &system) | BALL::PDBFile | virtual |
| read() | BALL::PDBFile | virtual |
| BALL::PropertyManager::read(PersistenceManager &pm) | BALL::PropertyManager | |
| read_done_ | BALL::PDBFile | protected |
| readFirstRecord(bool read_values=true) | BALL::PDBFile | |
| readInvalidRecord(const char *line) | BALL::PDBFile | virtual |
| readLine(char *line, Size size, bool extract_values) | BALL::PDBFile | |
| BALL::GenericMolFile::readLine() | BALL::LineBasedFile | |
| readNextRecord(bool read_values=true) | BALL::PDBFile | |
| readRecords() | BALL::PDBFile | |
| readUnknownRecord(const char *line) | BALL::PDBFile | virtual |
| record_fields_ | BALL::PDBFile | protected |
| registerTransformation(const String &pattern, const String &exec) | BALL::File | static |
| remove(String name) | BALL::File | static |
| remove() | BALL::File | |
| rename(String old_path, String new_path) | BALL::File | static |
| renameTo(const String &new_path) | BALL::File | |
| reopen() | BALL::File | |
| reopen(File::OpenMode open_mode) | BALL::File | |
| residue_map_ | BALL::PDBFile | protected |
| residue_name_ | BALL::PDBFile | protected |
| residue_sequence_number_ | BALL::PDBFile | protected |
| ResidueMap typedef | BALL::PDBFile | |
| ResidueQuadruple typedef | BALL::PDBFile | |
| rewind() | BALL::LineBasedFile | |
| search(const String &text, bool return_to_start=false) | BALL::LineBasedFile | |
| search(const String &text, const String &stop, bool return_to_start=false) | BALL::LineBasedFile | |
| SecStructList typedef | BALL::PDBFile | |
| selectAllModels() | BALL::PDBFile | |
| selectAltLocationIndicator(char c) | BALL::PDBFile | |
| selected_model_ | BALL::PDBFile | protected |
| selectModel(Index index) | BALL::PDBFile | |
| sequence_number_ | BALL::PDBFile | protected |
| set(const PropertyManager &property_manager) | BALL::PropertyManager | |
| setName(const String &name) | BALL::File | |
| setProperty(Property property) | BALL::PropertyManager | |
| setProperty(const NamedProperty &property) | BALL::PropertyManager | |
| setProperty(const std::string &name) | BALL::PropertyManager | |
| setProperty(const std::string &name, bool value) | BALL::PropertyManager | |
| setProperty(const std::string &name, int value) | BALL::PropertyManager | |
| setProperty(const std::string &name, unsigned int value) | BALL::PropertyManager | |
| setProperty(const std::string &name, float value) | BALL::PropertyManager | |
| setProperty(const std::string &name, double value) | BALL::PropertyManager | |
| setProperty(const std::string &name, const std::string &value) | BALL::PropertyManager | |
| setProperty(const std::string &name, const PersistentObject &value) | BALL::PropertyManager | |
| sheet_list_ | BALL::PDBFile | protected |
| skipCurrentRecord() | BALL::PDBFile | |
| skipLines(Size number=1) | BALL::LineBasedFile | |
| ssbond_list_ | BALL::PDBFile | protected |
| startsWith(const String &text) const | BALL::LineBasedFile | |
| store_skipped_records_ | BALL::PDBFile | protected |
| strict_line_checking_ | BALL::PDBFile | protected |
| swap(PropertyManager &property_manager) | BALL::PropertyManager | |
| switchString(const std::vector< String > &data) const | BALL::LineBasedFile | |
| test(const char *file, int line, bool condition, const String &msg) const | BALL::LineBasedFile | |
| toggleProperty(Property property) | BALL::PropertyManager | |
| Transformation enum name | BALL::File | |
| TRANSFORMATION__EXEC enum value | BALL::File | |
| TRANSFORMATION__FILTER enum value | BALL::File | |
| TRANSFORMATION__URL enum value | BALL::File | |
| TRANSFORMATION_EXEC_PREFIX | BALL::File | static |
| TRANSFORMATION_FILE_PREFIX | BALL::File | static |
| TRANSFORMATION_FTP_PREFIX | BALL::File | static |
| TRANSFORMATION_HTTP_PREFIX | BALL::File | static |
| transformation_manager_ | BALL::File | protectedstatic |
| transformation_methods_ | BALL::File | protectedstatic |
| trim_whitespaces_ | BALL::LineBasedFile | protected |
| trimWhiteSpacesEnabled() const | BALL::LineBasedFile | |
| truncate(String path, Size size=0) | BALL::File | static |
| truncate(Size size=0) | BALL::File | |
| turn_list_ | BALL::PDBFile | protected |
| Type enum name | BALL::File | |
| TYPE__BLOCK_SPECIAL_FILE enum value | BALL::File | |
| TYPE__CHAR_SPECIAL_FILE enum value | BALL::File | |
| TYPE__DIRECTORY enum value | BALL::File | |
| TYPE__FIFO_SPECIAL_FILE enum value | BALL::File | |
| TYPE__REGULAR_FILE enum value | BALL::File | |
| TYPE__SOCKET enum value | BALL::File | |
| TYPE__SYMBOLIC_LINK enum value | BALL::File | |
| TYPE__UNKNOWN enum value | BALL::File | |
| unregisterTransformation(const String &pattern) | BALL::File | static |
| updateAdditionalAtomInfo_(const PDB::Structure::AtomEntry &atom, PDB::AdditionalAtomInfo &cr) | BALL::PDBFile | protectedstatic |
| verbosity_ | BALL::PDBFile | protected |
| write(const Protein &protein) | BALL::PDBFile | |
| write(const Molecule &molecule) | BALL::PDBFile | virtual |
| write(const System &system) | BALL::PDBFile | virtual |
| write(const System &system, const PDBInfo &info) | BALL::PDBFile | |
| BALL::PropertyManager::write(PersistenceManager &pm) const | BALL::PropertyManager | |
| write_(const AtomContainer &ac, const PDBInfo &info=PDBInfo()) | BALL::PDBFile | protected |
| write_pdbformat_1996_ | BALL::PDBFile | protected |
| writeAtom_(const PDB::Structure::AtomEntry &atom, PDB::AdditionalAtomInfo &cr, bool hetatm=false) | BALL::PDBFile | protected |
| writeBookKeepingSection_(const PDB::Structure &structure, const PDBInfo &info) | BALL::PDBFile | protected |
| writeCONECTRecords_(PDB::Structure::ConectAtomList &cl) | BALL::PDBFile | protected |
| writeConnectivityAnnotationSection_(const PDB::Structure &structure, const PDBInfo &info) | BALL::PDBFile | protected |
| writeConnectivitySection_(const PDB::Structure &structure, const PDBInfo &info) | BALL::PDBFile | protected |
| writeCoordinateSection_(const PDB::Structure &structure, const PDBInfo &info) | BALL::PDBFile | protected |
| writeCRYST1Section_(const PDB::Structure &structure) | BALL::PDBFile | protected |
| writeCrystallographicSection_(const PDB::Structure &structure, const PDBInfo &info) | BALL::PDBFile | protected |
| writeHELIXSection_(const PDB::Structure &structure) | BALL::PDBFile | protected |
| writeHeterogenSection_(const PDB::Structure &structure, const PDBInfo &info) | BALL::PDBFile | protected |
| writeHYDBNDSection_(const PDB::Structure &structure) | BALL::PDBFile | protected |
| writeMiscellaneousFeaturesSection_(const PDB::Structure &structure, const PDBInfo &info) | BALL::PDBFile | protected |
| writeMTRIXnSection_(const PDB::Structure &structure) | BALL::PDBFile | protected |
| writePrimaryStructureSection_(const PDB::Structure &structure, const PDBInfo &info) | BALL::PDBFile | protected |
| writeRawRecord_(const char *format, const char *tag,...) | BALL::PDBFile | protected |
| writeRecord_(PDB::RecordType record,...) | BALL::PDBFile | protected |
| writeRecord_(const PDB::RecordSEQRES &seqres) | BALL::PDBFile | protected |
| writeRecord_(const PDB::RecordHELIX &helix) | BALL::PDBFile | protected |
| writeRecord_(const PDB::RecordSHEET &helix) | BALL::PDBFile | protected |
| writeRecord_(const PDB::RecordTURN &helix) | BALL::PDBFile | protected |
| writeRecord_(const PDB::RecordSSBOND &helix) | BALL::PDBFile | protected |
| writeRecord_(const PDB::RecordCONECT &helix) | BALL::PDBFile | protected |
| writeRecord_(const PDB::RecordCRYST1 &cryst1) | BALL::PDBFile | protected |
| writeRecord_(const PDB::RecordMTRIX1 &mtrix1) | BALL::PDBFile | protected |
| writeRecord_(const PDB::RecordMTRIX2 &mtrix2) | BALL::PDBFile | protected |
| writeRecord_(const PDB::RecordMTRIX3 &mtrix3) | BALL::PDBFile | protected |
| writeSecondaryStructureSection_(const PDB::Structure &structure, const PDBInfo &info) | BALL::PDBFile | protected |
| writeSEQRESSection_(const std::vector< std::pair< char, String > > &chain_residues) | BALL::PDBFile | protected |
| writeSHEETSection_(const PDB::Structure &structure) | BALL::PDBFile | protected |
| writeSLTBRGSection_(const PDB::Structure &structure) | BALL::PDBFile | protected |
| writeSSBONDSection_(const PDB::Structure &structure) | BALL::PDBFile | protected |
| writeTitleSection_(const PDB::Structure &structure, const PDBInfo &info) | BALL::PDBFile | protected |
| writeTURNSection_(const PDB::Structure &structure) | BALL::PDBFile | protected |
| zipped_filename_ | BALL::GenericMolFile | protected |
| ~File() | BALL::File | virtual |
| ~GenericMolFile() | BALL::GenericMolFile | virtual |
| ~PDBFile() | BALL::PDBFile | virtual |
| ~PropertyManager() | BALL::PropertyManager | virtual |
1.8.7