BALL::PDBFile Member List

This is the complete list of members for BALL::PDBFile, including all inherited members.

addAllRecords_(const PDBInfo &info, PDB::RecordType type)	BALL::PDBFile	[protected]
atom_map_ (defined in BALL::PDBFile)	BALL::PDBFile	[protected]
book_keeping_	BALL::PDBFile	[protected]
chain_ID_ (defined in BALL::PDBFile)	BALL::PDBFile	[protected]
clear(int state)	BALL::PDBFile	[virtual]
clear()	BALL::PDBFile	[virtual]
clearProperty(Property property)	BALL::PropertyManager
clearProperty(const string &name)	BALL::PropertyManager
close()	BALL::File
code_ (defined in BALL::PDBFile)	BALL::PDBFile	[protected]
compare_record_type_format_ (defined in BALL::PDBFile)	BALL::PDBFile	[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
createTemporaryFilename(String &temporary)	BALL::File	[static]
current_chain_ (defined in BALL::PDBFile)	BALL::PDBFile	[protected]
current_const_atom_ (defined in BALL::PDBFile)	BALL::PDBFile	[protected]
current_const_chain_ (defined in BALL::PDBFile)	BALL::PDBFile	[protected]
current_const_protein_ (defined in BALL::PDBFile)	BALL::PDBFile	[protected]
current_const_residue_ (defined in BALL::PDBFile)	BALL::PDBFile	[protected]
current_model_ (defined in BALL::PDBFile)	BALL::PDBFile	[protected]
current_PDB_atom_ (defined in BALL::PDBFile)	BALL::PDBFile	[protected]
current_protein_ (defined in BALL::PDBFile)	BALL::PDBFile	[protected]
current_record_ (defined in BALL::PDBFile)	BALL::PDBFile	[protected]
current_record_type_ (defined in BALL::PDBFile)	BALL::PDBFile	[protected]
current_residue_ (defined in BALL::PDBFile)	BALL::PDBFile	[protected]
destroy()	BALL::PropertyManager	[virtual]
disableTransformation(Transformation transformation) (defined in BALL::File)	BALL::File	[static]
dump(std::ostream &s=std::cout, Size depth=0) const	BALL::PropertyManager
enableTransformation(Transformation transformation) (defined in BALL::File)	BALL::File	[static]
enableTrimWhitespaces(bool state)	BALL::LineBasedFile
extractStructure_(const AtomContainer &ac, PDB::Structure &structure)	BALL::PDBFile	[protected, static]
File()	BALL::File
File(const String &name, OpenMode open_mode=std::ios::in)	BALL::File
File(const File &file)	BALL::File
fillRecord(const char *line, Size size, PDB::RecordANISOU &record) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
fillRecord(const char *line, Size size, PDB::RecordATOM &record) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
fillRecord(const char *line, Size size, PDB::RecordAUTHOR &record) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
fillRecord(const char *line, Size size, PDB::RecordCAVEAT &record) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
fillRecord(const char *line, Size size, PDB::RecordCISPEP &record) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
fillRecord(const char *line, Size size, PDB::RecordCOMPND &record) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
fillRecord(const char *line, Size size, PDB::RecordCONECT &record) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
fillRecord(const char *line, Size size, PDB::RecordCRYST1 &record) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
fillRecord(const char *line, Size size, PDB::RecordDBREF &record) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
fillRecord(const char *line, Size size, PDB::RecordEND &record) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
fillRecord(const char *line, Size size, PDB::RecordENDMDL &record) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
fillRecord(const char *line, Size size, PDB::RecordEXPDTA &record) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
fillRecord(const char *line, Size size, PDB::RecordFORMUL &record) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
fillRecord(const char *line, Size size, PDB::RecordFTNOTE &record) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
fillRecord(const char *line, Size size, PDB::RecordHEADER &record) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
fillRecord(const char *line, Size size, PDB::RecordHELIX &record) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
fillRecord(const char *line, Size size, PDB::RecordHET &record) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
fillRecord(const char *line, Size size, PDB::RecordHETATM &record) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
fillRecord(const char *line, Size size, PDB::RecordHETNAM &record) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
fillRecord(const char *line, Size size, PDB::RecordHETSYN &record) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
fillRecord(const char *line, Size size, PDB::RecordHYDBND &record) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
fillRecord(const char *line, Size size, PDB::RecordJRNL &record) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
fillRecord(const char *line, Size size, PDB::RecordKEYWDS &record) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
fillRecord(const char *line, Size size, PDB::RecordLINK &record) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
fillRecord(const char *line, Size size, PDB::RecordMASTER &record) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
fillRecord(const char *line, Size size, PDB::RecordMODEL &record) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
fillRecord(const char *line, Size size, PDB::RecordMODRES &record) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
fillRecord(const char *line, Size size, PDB::RecordMTRIX1 &record) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
fillRecord(const char *line, Size size, PDB::RecordMTRIX2 &record) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
fillRecord(const char *line, Size size, PDB::RecordMTRIX3 &record) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
fillRecord(const char *line, Size size, PDB::RecordOBSLTE &record) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
fillRecord(const char *line, Size size, PDB::RecordORIGX1 &record) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
fillRecord(const char *line, Size size, PDB::RecordORIGX2 &record) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
fillRecord(const char *line, Size size, PDB::RecordORIGX3 &record) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
fillRecord(const char *line, Size size, PDB::RecordREMARK &record) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
fillRecord(const char *line, Size size, PDB::RecordREVDAT &record) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
fillRecord(const char *line, Size size, PDB::RecordSCALE1 &record) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
fillRecord(const char *line, Size size, PDB::RecordSCALE2 &record) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
fillRecord(const char *line, Size size, PDB::RecordSCALE3 &record) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
fillRecord(const char *line, Size size, PDB::RecordSEQADV &record) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
fillRecord(const char *line, Size size, PDB::RecordSEQRES &record) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
fillRecord(const char *line, Size size, PDB::RecordSHEET &record) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
fillRecord(const char *line, Size size, PDB::RecordSIGATM &record) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
fillRecord(const char *line, Size size, PDB::RecordSIGUIJ &record) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
fillRecord(const char *line, Size size, PDB::RecordSITE &record) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
fillRecord(const char *line, Size size, PDB::RecordSLTBRG &record) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
fillRecord(const char *line, Size size, PDB::RecordSOURCE &record) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
fillRecord(const char *line, Size size, PDB::RecordSPRSDE &record) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
fillRecord(const char *line, Size size, PDB::RecordSSBOND &record) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
fillRecord(const char *line, Size size, PDB::RecordTER &record) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
fillRecord(const char *line, Size size, PDB::RecordTITLE &record) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
fillRecord(const char *line, Size size, PDB::RecordTURN &record) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
fillRecord(const char *line, Size size, PDB::RecordTVECT &record) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
GenericMolFile()	BALL::GenericMolFile
GenericMolFile(const String &filename, File::OpenMode open_mode=std::ios::in)	BALL::GenericMolFile
GenericMolFile(const GenericMolFile &file)	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 &quotes="", 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 (defined in BALL::File)	BALL::File
getProperty(const 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]
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 string &name) const	BALL::PropertyManager
helix_list_ (defined in BALL::PDBFile)	BALL::PDBFile	[protected]
ignore_xplor_pseudo_atoms_	BALL::PDBFile	[protected]
info	BALL::PDBFile
init_() (defined in BALL::PDBFile)	BALL::PDBFile	[protected]
initRead_()	BALL::GenericMolFile	[protected, virtual]
initWrite_()	BALL::GenericMolFile	[protected, virtual]
insertion_code_ (defined in BALL::PDBFile)	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_ (defined in BALL::File)	BALL::File	[protected]
is_temporary_ (defined in BALL::File)	BALL::File	[protected]
isAccessible(String name)	BALL::File	[static]
isAccessible() const	BALL::File
isCanonized() const	BALL::File
isClosed() const	BALL::File
isExecutable(String name)	BALL::File	[static]
isExecutable() const	BALL::File
isHeteroAtom_(const Atom &atom)	BALL::PDBFile	[protected, static]
isOpen() const	BALL::File
isReadable(String name)	BALL::File	[static]
isReadable() const	BALL::File
isTransformationEnabled(Transformation transformation) (defined in BALL::File)	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_ (defined in BALL::PDBFile)	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
LineBasedFile(const LineBasedFile &f)	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_ (defined in BALL::PDBFile)	BALL::PDBFile	[protected]
new_helix_secstruc_list_ (defined in BALL::PDBFile)	BALL::PDBFile	[protected]
new_sheet_secstruc_list_ (defined in BALL::PDBFile)	BALL::PDBFile	[protected]
new_turn_secstruc_list_ (defined in BALL::PDBFile)	BALL::PDBFile	[protected]
open(const String &name, File::OpenMode open_mode=std::ios::in)	BALL::File
open_mode_ (defined in BALL::File)	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) (defined in BALL::PDBFile)	BALL::PDBFile	[protected]
BALL::GenericMolFile::operator=(const GenericMolFile &rhs)	BALL::GenericMolFile
BALL::LineBasedFile::operator=(const LineBasedFile &file)	BALL::LineBasedFile
BALL::File::operator=(const File &file)	BALL::File
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_ (defined in BALL::File)	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) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
parseRecordATOM(const char *line, Size size) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
parseRecordAUTHOR(const char *line, Size size) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
parseRecordCAVEAT(const char *line, Size size) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
parseRecordCISPEP(const char *line, Size size) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
parseRecordCOMPND(const char *line, Size size) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
parseRecordCONECT(const char *line, Size size) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
parseRecordCRYST1(const char *line, Size size) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
parseRecordDBREF(const char *line, Size size) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
parseRecordEND(const char *line, Size size) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
parseRecordENDMDL(const char *line, Size size) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
parseRecordEXPDTA(const char *line, Size size) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
parseRecordFORMUL(const char *line, Size size) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
parseRecordFTNOTE(const char *line, Size size) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
parseRecordHEADER(const char *line, Size size) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
parseRecordHELIX(const char *line, Size size) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
parseRecordHET(const char *line, Size size) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
parseRecordHETATM(const char *line, Size size) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
parseRecordHETNAM(const char *line, Size size) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
parseRecordHETSYN(const char *line, Size size) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
parseRecordHYDBND(const char *line, Size size) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
parseRecordJRNL(const char *line, Size size) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
parseRecordKEYWDS(const char *line, Size size) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
parseRecordLINK(const char *line, Size size) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
parseRecordMASTER(const char *line, Size size) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
parseRecordMODEL(const char *line, Size size) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
parseRecordMODRES(const char *line, Size size) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
parseRecordMTRIX1(const char *line, Size size) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
parseRecordMTRIX2(const char *line, Size size) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
parseRecordMTRIX3(const char *line, Size size) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
parseRecordOBSLTE(const char *line, Size size) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
parseRecordORIGX1(const char *line, Size size) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
parseRecordORIGX2(const char *line, Size size) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
parseRecordORIGX3(const char *line, Size size) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
parseRecordREMARK(const char *line, Size size) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
parseRecordREVDAT(const char *line, Size size) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
parseRecordSCALE1(const char *line, Size size) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
parseRecordSCALE2(const char *line, Size size) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
parseRecordSCALE3(const char *line, Size size) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
parseRecordSEQADV(const char *line, Size size) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
parseRecordSEQRES(const char *line, Size size) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
parseRecordSHEET(const char *line, Size size) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
parseRecordSIGATM(const char *line, Size size) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
parseRecordSIGUIJ(const char *line, Size size) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
parseRecordSITE(const char *line, Size size) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
parseRecordSLTBRG(const char *line, Size size) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
parseRecordSOURCE(const char *line, Size size) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
parseRecordSPRSDE(const char *line, Size size) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
parseRecordSSBOND(const char *line, Size size) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
parseRecordTER(const char *line, Size size) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
parseRecordTITLE(const char *line, Size size) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
parseRecordTURN(const char *line, Size size) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
parseRecordTVECT(const char *line, Size size) (defined in BALL::PDBFile)	BALL::PDBFile	[virtual]
PDB_atom_map_ (defined in BALL::PDBFile)	BALL::PDBFile	[protected]
PDBAtomMap typedef (defined in BALL::PDBFile)	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 PDBFile &file)	BALL::PDBFile
PDBFile(const File &pdbf) (defined in BALL::PDBFile)	BALL::PDBFile	[protected]
postprocessHelices_() (defined in BALL::PDBFile)	BALL::PDBFile	[protected]
postprocessRandomCoils_() (defined in BALL::PDBFile)	BALL::PDBFile	[protected]
postprocessSheetsTurns_(QuadrupleList &sectruct_list, SecStructList &new_secstruct_list) (defined in BALL::PDBFile)	BALL::PDBFile	[protected]
postprocessSSBonds_() (defined in BALL::PDBFile)	BALL::PDBFile	[protected]
PropertyManager()	BALL::PropertyManager
PropertyManager(const PropertyManager &property_manager)	BALL::PropertyManager
QuadrupleList typedef (defined in BALL::PDBFile)	BALL::PDBFile
read(Protein &protein) (defined in BALL::PDBFile)	BALL::PDBFile
read(Molecule &protein) (defined in BALL::PDBFile)	BALL::PDBFile
read(System &system)	BALL::PDBFile	[virtual]
read()	BALL::PDBFile	[virtual]
BALL::PropertyManager::read(PersistenceManager &pm)	BALL::PropertyManager
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_ (defined in BALL::PDBFile)	BALL::PDBFile	[protected]
registerTransformation(const String &pattern, const String &exec) (defined in BALL::File)	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_ (defined in BALL::PDBFile)	BALL::PDBFile	[protected]
residue_name_ (defined in BALL::PDBFile)	BALL::PDBFile	[protected]
residue_sequence_number_ (defined in BALL::PDBFile)	BALL::PDBFile	[protected]
ResidueMap typedef (defined in BALL::PDBFile)	BALL::PDBFile
ResidueQuadruple typedef (defined in BALL::PDBFile)	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) (defined in BALL::LineBasedFile)	BALL::LineBasedFile
SecStructList typedef (defined in BALL::PDBFile)	BALL::PDBFile
selectAllModels()	BALL::PDBFile
selected_model_	BALL::PDBFile	[protected]
selectModel(Index index)	BALL::PDBFile
sequence_number_ (defined in BALL::PDBFile)	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 string &name)	BALL::PropertyManager
setProperty(const string &name, bool value)	BALL::PropertyManager
setProperty(const string &name, int value)	BALL::PropertyManager
setProperty(const string &name, unsigned int value)	BALL::PropertyManager
setProperty(const string &name, float value)	BALL::PropertyManager
setProperty(const string &name, double value)	BALL::PropertyManager
setProperty(const string &name, const string &value)	BALL::PropertyManager
setProperty(const string &name, const PersistentObject &value)	BALL::PropertyManager
sheet_list_ (defined in BALL::PDBFile)	BALL::PDBFile	[protected]
skipCurrentRecord()	BALL::PDBFile
skipLines(Size number=1)	BALL::LineBasedFile
ssbond_list_ (defined in BALL::PDBFile)	BALL::PDBFile	[protected]
startsWith(const String &text) const	BALL::LineBasedFile
store_skipped_records_	BALL::PDBFile	[protected]
strict_line_checking_ (defined in BALL::PDBFile)	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 (defined in BALL::File)	BALL::File
TRANSFORMATION__FILTER enum value (defined in BALL::File)	BALL::File
TRANSFORMATION__URL enum value (defined in BALL::File)	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_ (defined in BALL::File)	BALL::File	[protected, static]
transformation_methods_ (defined in BALL::File)	BALL::File	[protected, static]
trim_whitespaces_ (defined in BALL::LineBasedFile)	BALL::LineBasedFile	[protected]
trimWhiteSpacesEnabled() const (defined in BALL::LineBasedFile)	BALL::LineBasedFile
truncate(String path, Size size=0)	BALL::File	[static]
truncate(Size size=0)	BALL::File
turn_list_ (defined in BALL::PDBFile)	BALL::PDBFile	[protected]
Type enum name	BALL::File
TYPE__BLOCK_SPECIAL_FILE enum value (defined in BALL::File)	BALL::File
TYPE__CHAR_SPECIAL_FILE enum value (defined in BALL::File)	BALL::File
TYPE__DIRECTORY enum value (defined in BALL::File)	BALL::File
TYPE__FIFO_SPECIAL_FILE enum value (defined in BALL::File)	BALL::File
TYPE__REGULAR_FILE enum value (defined in BALL::File)	BALL::File
TYPE__SOCKET enum value (defined in BALL::File)	BALL::File
TYPE__SYMBOLIC_LINK enum value (defined in BALL::File)	BALL::File
TYPE__UNKNOWN enum value (defined in BALL::File)	BALL::File
unregisterTransformation(const String &pattern) (defined in BALL::File)	BALL::File	[static]
updateAdditionalAtomInfo_(const PDB::Structure::AtomEntry &atom, PDB::AdditionalAtomInfo &cr)	BALL::PDBFile	[protected, static]
verbosity_	BALL::PDBFile	[protected]
write(const Protein &protein) (defined in BALL::PDBFile)	BALL::PDBFile
write(const Molecule &molecule)	BALL::PDBFile	[virtual]
write(const System &system)	BALL::PDBFile	[virtual]
write(const System &system, const PDBInfo &info) (defined in BALL::PDBFile)	BALL::PDBFile
BALL::PropertyManager::write(PersistenceManager &pm) const	BALL::PropertyManager
write_(const AtomContainer &ac, const PDBInfo &info=PDBInfo()) (defined in BALL::PDBFile)	BALL::PDBFile	[protected]
writeAtom_(const PDB::Structure::AtomEntry &atom, PDB::AdditionalAtomInfo &cr, bool hetatm=false) (defined in BALL::PDBFile)	BALL::PDBFile	[protected]
writeBookKeepingSection_(const PDB::Structure &structure, const PDBInfo &info) (defined in BALL::PDBFile)	BALL::PDBFile	[protected]
writeCONECTRecords_(PDB::Structure::ConectAtomList &cl) (defined in BALL::PDBFile)	BALL::PDBFile	[protected]
writeConnectivityAnnotationSection_(const PDB::Structure &structure, const PDBInfo &info) (defined in BALL::PDBFile)	BALL::PDBFile	[protected]
writeConnectivitySection_(const PDB::Structure &structure, const PDBInfo &info) (defined in BALL::PDBFile)	BALL::PDBFile	[protected]
writeCoordinateSection_(const PDB::Structure &structure, const PDBInfo &info) (defined in BALL::PDBFile)	BALL::PDBFile	[protected]
writeCrystallographicSection_(const PDB::Structure &structure, const PDBInfo &info) (defined in BALL::PDBFile)	BALL::PDBFile	[protected]
writeHELIXSection_(const PDB::Structure &structure) (defined in BALL::PDBFile)	BALL::PDBFile	[protected]
writeHeterogenSection_(const PDB::Structure &structure, const PDBInfo &info) (defined in BALL::PDBFile)	BALL::PDBFile	[protected]
writeHYDBNDSection_(const PDB::Structure &structure) (defined in BALL::PDBFile)	BALL::PDBFile	[protected]
writeMiscellaneousFeaturesSection_(const PDB::Structure &structure, const PDBInfo &info) (defined in BALL::PDBFile)	BALL::PDBFile	[protected]
writePrimaryStructureSection_(const PDB::Structure &structure, const PDBInfo &info) (defined in BALL::PDBFile)	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]
writeSecondaryStructureSection_(const PDB::Structure &structure, const PDBInfo &info) (defined in BALL::PDBFile)	BALL::PDBFile	[protected]
writeSEQRESSection_(const std::vector< std::pair< char, String > > &chain_residues) (defined in BALL::PDBFile)	BALL::PDBFile	[protected]
writeSHEETSection_(const PDB::Structure &structure) (defined in BALL::PDBFile)	BALL::PDBFile	[protected]
writeSLTBRGSection_(const PDB::Structure &structure) (defined in BALL::PDBFile)	BALL::PDBFile	[protected]
writeSSBONDSection_(const PDB::Structure &structure) (defined in BALL::PDBFile)	BALL::PDBFile	[protected]
writeTitleSection_(const PDB::Structure &structure, const PDBInfo &info) (defined in BALL::PDBFile)	BALL::PDBFile	[protected]
writeTURNSection_(const PDB::Structure &structure) (defined in BALL::PDBFile)	BALL::PDBFile	[protected]
~File()	BALL::File	[virtual]
~GenericMolFile()	BALL::GenericMolFile	[virtual]
~PDBFile()	BALL::PDBFile	[virtual]
~PropertyManager()	BALL::PropertyManager	[virtual]