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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
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 | protected static
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 | protected static
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 &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 | 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 | protected virtual
initWrite_() | BALL::GenericMolFile | protected virtual
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 | protected static
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 &sectruct_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 | protected static
transformation_methods_ | BALL::File | protected static
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 | protected static
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