BALL::PDBFile Class Reference

#include <BALL/FORMAT/PDBFile.h>

Inheritance diagram for BALL::PDBFile:

Classes
struct	Default
struct	Option
Public Types
typedef HashMap< PDB::Integer, PDBAtom * >	PDBAtomMap
typedef Quadruple< String, PDB::Character, PDB::Integer, PDB::AChar >	ResidueQuadruple
typedef HashMap < ResidueQuadruple, Residue * >	ResidueMap
typedef std::list < ResidueQuadruple >	QuadrupleList
typedef std::list < SecondaryStructure * >	SecStructList
Public Member Functions
virtual bool	hasFormat ()
	Check whether the current file is in PDB format.
Constructurs and destructor.

	PDBFile ()
	Default constructor.
	PDBFile (const String &filename, File::OpenMode open_mode=std::ios::in) throw (Exception::FileNotFound)
	File-like constructor.
	PDBFile (const Options &new_options)
	Construct with options.
virtual	~PDBFile ()
	Destructor.
Assignment.

virtual void	clear (int state)
	Clear the stream state.
virtual void	clear ()
	Clear all members.
Accessors.

virtual float	getVersion () const
	Returns the version number this PDB file reader is able to read.
void	selectModel (Index index)
void	selectAltLocationIndicator (char c)
Index	getSelectedModel () const
	Return the model currently selected.
void	selectAllModels ()
	Selects all models for reading.
Index	getCurrentModel () const
	Returns the number of the model weare currently reading. (?????).
char *	getRecordString ()
	Return a mutable pointer to the line buffer.
const char *	getRecordString () const
	Return a constant pointer to the line buffer.
Index	getRecordNumber () const
	Returns the number of the record we are currently reading.
PDB::RecordType	getRecordType () const
	Returns the type of the record we are currently reading.
virtual const char *	getAtomElementSymbol (const PDB::Atom atom_name, PDB::Atom element_symbol)
virtual const char *	getAtomName (const PDB::Atom atom_name)
	Returns the atom name.
virtual char	getAtomRemotenessIndicator (const PDB::Atom atom_name)
	Extract the PDB remoteness indicator of an atom record.
virtual short	getAtomBranchDesignator (const PDB::Atom atom_name)
	Extract the PDB branch designator of an atom record.
Size	countRecordFields () const
	Returns the number of record fields.
Size	countRecord (PDB::RecordType record_type, bool from_begin_of_file=true)
Size	countRecords (bool from_begin_of_file=true)
Methods for parsing individual records.
These methods are typically required if you want to implement your own PDB parser (derived from PDBFile or PDBFile).
bool	parseLine (const char line, Size size, const char format_string,...)
	Parse a line from a PDBFile. This is a helper function for readLine().
bool	readLine (char *line, Size size, bool extract_values)
	Read and parse a line from a PDB file.
bool	readFirstRecord (bool read_values=true)
	Read the firts record of a file.
bool	readNextRecord (bool read_values=true)
	Read the next record of a PDB file.
bool	readRecords ()
virtual bool	readUnknownRecord (const char *line)
virtual bool	readInvalidRecord (const char *line)
bool	skipCurrentRecord ()
virtual bool	interpretRecord (const PDB::RecordANISOU &record)
	Reads an anisotropic temperature factor record.
virtual bool	fillRecord (const char *line, Size size, PDB::RecordANISOU &record)
virtual bool	parseRecordANISOU (const char *line, Size size)
virtual bool	interpretRecord (const PDB::RecordATOM &record)
	Reads an atom record.
virtual bool	fillRecord (const char *line, Size size, PDB::RecordATOM &record)
virtual bool	parseRecordATOM (const char *line, Size size)
virtual bool	interpretRecord (const PDB::RecordAUTHOR &record)
	Reads an author record.
virtual bool	fillRecord (const char *line, Size size, PDB::RecordAUTHOR &record)
virtual bool	parseRecordAUTHOR (const char *line, Size size)
virtual bool	interpretRecord (const PDB::RecordCAVEAT &record)
	Reads a caveat record.
virtual bool	fillRecord (const char *line, Size size, PDB::RecordCAVEAT &record)
virtual bool	parseRecordCAVEAT (const char *line, Size size)
virtual bool	interpretRecord (const PDB::RecordCISPEP &record)
	Reads a record specifying peptides in cis conformation.
virtual bool	fillRecord (const char *line, Size size, PDB::RecordCISPEP &record)
virtual bool	parseRecordCISPEP (const char *line, Size size)
virtual bool	interpretRecord (const PDB::RecordCOMPND &record)
	Reads the title record containing macroscopic compoubd information.
virtual bool	fillRecord (const char *line, Size size, PDB::RecordCOMPND &record)
virtual bool	parseRecordCOMPND (const char *line, Size size)
virtual bool	interpretRecord (const PDB::RecordCONECT &record)
	Reads a connection record.
virtual bool	fillRecord (const char *line, Size size, PDB::RecordCONECT &record)
virtual bool	parseRecordCONECT (const char *line, Size size)
virtual bool	interpretRecord (const PDB::RecordCRYST1 &record)
virtual bool	fillRecord (const char *line, Size size, PDB::RecordCRYST1 &record)
virtual bool	parseRecordCRYST1 (const char *line, Size size)
virtual bool	interpretRecord (const PDB::RecordDBREF &record)
	Reads a record containing database cross-reference links.
virtual bool	fillRecord (const char *line, Size size, PDB::RecordDBREF &record)
virtual bool	parseRecordDBREF (const char *line, Size size)
virtual bool	interpretRecord (const PDB::RecordEND &record)
	Reads the record defining the end of a PDB file.
virtual bool	fillRecord (const char *line, Size size, PDB::RecordEND &record)
virtual bool	parseRecordEND (const char *line, Size size)
virtual bool	interpretRecord (const PDB::RecordENDMDL &record)
	Reads a model ending record.
virtual bool	fillRecord (const char *line, Size size, PDB::RecordENDMDL &record)
virtual bool	parseRecordENDMDL (const char *line, Size size)
virtual bool	interpretRecord (const PDB::RecordEXPDTA &record)
	Reads a record containing data about the experiment.
virtual bool	fillRecord (const char *line, Size size, PDB::RecordEXPDTA &record)
virtual bool	parseRecordEXPDTA (const char *line, Size size)
virtual bool	interpretRecord (const PDB::RecordFORMUL &record)
virtual bool	fillRecord (const char *line, Size size, PDB::RecordFORMUL &record)
virtual bool	parseRecordFORMUL (const char *line, Size size)
virtual bool	interpretRecord (const PDB::RecordFTNOTE &record)
	Reads a record containing a footnote.
virtual bool	fillRecord (const char *line, Size size, PDB::RecordFTNOTE &record)
virtual bool	parseRecordFTNOTE (const char *line, Size size)
virtual bool	interpretRecord (const PDB::RecordHEADER &record)
virtual bool	fillRecord (const char *line, Size size, PDB::RecordHEADER &record)
virtual bool	parseRecordHEADER (const char *line, Size size)
virtual bool	interpretRecord (const PDB::RecordHELIX &record)
	Reads a helix defining record.
virtual bool	fillRecord (const char *line, Size size, PDB::RecordHELIX &record)
virtual bool	parseRecordHELIX (const char *line, Size size)
virtual bool	interpretRecord (const PDB::RecordHET &record)
	Reads a record defining a non-standard residue.
virtual bool	fillRecord (const char *line, Size size, PDB::RecordHET &record)
virtual bool	parseRecordHET (const char *line, Size size)
virtual bool	interpretRecord (const PDB::RecordHETATM &record)
	Reads atomic coordinates for atoms in non-standard groups.
virtual bool	fillRecord (const char *line, Size size, PDB::RecordHETATM &record)
virtual bool	parseRecordHETATM (const char *line, Size size)
virtual bool	interpretRecord (const PDB::RecordHETNAM &record)
	Reads a record defining the name of a non-standard group.
virtual bool	fillRecord (const char *line, Size size, PDB::RecordHETNAM &record)
virtual bool	parseRecordHETNAM (const char *line, Size size)
virtual bool	interpretRecord (const PDB::RecordHETSYN &record)
	Reads a record defining synonyms of a non-standard group.
virtual bool	fillRecord (const char *line, Size size, PDB::RecordHETSYN &record)
virtual bool	parseRecordHETSYN (const char *line, Size size)
virtual bool	interpretRecord (const PDB::RecordHYDBND &record)
	Reads a record defining a hydrogen bond.
virtual bool	fillRecord (const char *line, Size size, PDB::RecordHYDBND &record)
virtual bool	parseRecordHYDBND (const char *line, Size size)
virtual bool	interpretRecord (const PDB::RecordJRNL &record)
	Reads a record containing a journal reference.
virtual bool	fillRecord (const char *line, Size size, PDB::RecordJRNL &record)
virtual bool	parseRecordJRNL (const char *line, Size size)
virtual bool	interpretRecord (const PDB::RecordKEYWDS &record)
	Reads a record containing keywords for this entry.
virtual bool	fillRecord (const char *line, Size size, PDB::RecordKEYWDS &record)
virtual bool	parseRecordKEYWDS (const char *line, Size size)
virtual bool	interpretRecord (const PDB::RecordLINK &record)
	Reads a record containing supplemental connectivity information.
virtual bool	fillRecord (const char *line, Size size, PDB::RecordLINK &record)
virtual bool	parseRecordLINK (const char *line, Size size)
virtual bool	interpretRecord (const PDB::RecordMASTER &record)
virtual bool	fillRecord (const char *line, Size size, PDB::RecordMASTER &record)
virtual bool	parseRecordMASTER (const char *line, Size size)
virtual bool	interpretRecord (const PDB::RecordMODEL &record)
	Reads a record indicating the beginning of a new model.
virtual bool	fillRecord (const char *line, Size size, PDB::RecordMODEL &record)
virtual bool	parseRecordMODEL (const char *line, Size size)
virtual bool	interpretRecord (const PDB::RecordMODRES &record)
	Reads a record identifying residue modifications.
virtual bool	fillRecord (const char *line, Size size, PDB::RecordMODRES &record)
virtual bool	parseRecordMODRES (const char *line, Size size)
virtual bool	interpretRecord (const PDB::RecordMTRIX1 &record)
virtual bool	fillRecord (const char *line, Size size, PDB::RecordMTRIX1 &record)
virtual bool	parseRecordMTRIX1 (const char *line, Size size)
virtual bool	interpretRecord (const PDB::RecordMTRIX2 &record)
virtual bool	fillRecord (const char *line, Size size, PDB::RecordMTRIX2 &record)
virtual bool	parseRecordMTRIX2 (const char *line, Size size)
virtual bool	interpretRecord (const PDB::RecordMTRIX3 &record)
virtual bool	fillRecord (const char *line, Size size, PDB::RecordMTRIX3 &record)
virtual bool	parseRecordMTRIX3 (const char *line, Size size)
virtual bool	interpretRecord (const PDB::RecordOBSLTE &record)
virtual bool	fillRecord (const char *line, Size size, PDB::RecordOBSLTE &record)
virtual bool	parseRecordOBSLTE (const char *line, Size size)
virtual bool	interpretRecord (const PDB::RecordORIGX1 &record)
virtual bool	fillRecord (const char *line, Size size, PDB::RecordORIGX1 &record)
virtual bool	parseRecordORIGX1 (const char *line, Size size)
virtual bool	interpretRecord (const PDB::RecordORIGX2 &record)
virtual bool	fillRecord (const char *line, Size size, PDB::RecordORIGX2 &record)
virtual bool	parseRecordORIGX2 (const char *line, Size size)
virtual bool	interpretRecord (const PDB::RecordORIGX3 &record)
virtual bool	fillRecord (const char *line, Size size, PDB::RecordORIGX3 &record)
virtual bool	parseRecordORIGX3 (const char *line, Size size)
virtual bool	interpretRecord (const PDB::RecordREMARK &record)
	Reads a record containing remarks.
virtual bool	fillRecord (const char *line, Size size, PDB::RecordREMARK &record)
virtual bool	parseRecordREMARK (const char *line, Size size)
virtual bool	interpretRecord (const PDB::RecordREVDAT &record)
	Reads a record containing a revision history.
virtual bool	fillRecord (const char *line, Size size, PDB::RecordREVDAT &record)
virtual bool	parseRecordREVDAT (const char *line, Size size)
virtual bool	interpretRecord (const PDB::RecordSCALE1 &record)
	Reads a scale transformation record.
virtual bool	fillRecord (const char *line, Size size, PDB::RecordSCALE1 &record)
virtual bool	parseRecordSCALE1 (const char *line, Size size)
virtual bool	interpretRecord (const PDB::RecordSCALE2 &record)
	Reads a scale transformation record.
virtual bool	fillRecord (const char *line, Size size, PDB::RecordSCALE2 &record)
virtual bool	parseRecordSCALE2 (const char *line, Size size)
virtual bool	interpretRecord (const PDB::RecordSCALE3 &record)
	Reads a scale transformation record.
virtual bool	fillRecord (const char *line, Size size, PDB::RecordSCALE3 &record)
virtual bool	parseRecordSCALE3 (const char *line, Size size)
virtual bool	interpretRecord (const PDB::RecordSEQADV &record)
	Sequence information conflicts between atom records and dbref content.
virtual bool	fillRecord (const char *line, Size size, PDB::RecordSEQADV &record)
virtual bool	parseRecordSEQADV (const char *line, Size size)
virtual bool	interpretRecord (const PDB::RecordSEQRES &record)
	Reads a record containing the sequence of residues.
virtual bool	fillRecord (const char *line, Size size, PDB::RecordSEQRES &record)
virtual bool	parseRecordSEQRES (const char *line, Size size)
virtual bool	interpretRecord (const PDB::RecordSHEET &record)
	Reads a record defining a beta-sheet.
virtual bool	fillRecord (const char *line, Size size, PDB::RecordSHEET &record)
virtual bool	parseRecordSHEET (const char *line, Size size)
virtual bool	interpretRecord (const PDB::RecordSIGATM &record)
	Reads a record giving the standard deviation of atomic coordinates.
virtual bool	fillRecord (const char *line, Size size, PDB::RecordSIGATM &record)
virtual bool	parseRecordSIGATM (const char *line, Size size)
virtual bool	interpretRecord (const PDB::RecordSIGUIJ &record)
virtual bool	fillRecord (const char *line, Size size, PDB::RecordSIGUIJ &record)
virtual bool	parseRecordSIGUIJ (const char *line, Size size)
virtual bool	interpretRecord (const PDB::RecordSITE &record)
	Reads a record containing groups comprising a site.
virtual bool	fillRecord (const char *line, Size size, PDB::RecordSITE &record)
virtual bool	parseRecordSITE (const char *line, Size size)
virtual bool	interpretRecord (const PDB::RecordSLTBRG &record)
	Reads a record defining a salt bridge.
virtual bool	fillRecord (const char *line, Size size, PDB::RecordSLTBRG &record)
virtual bool	parseRecordSLTBRG (const char *line, Size size)
virtual bool	interpretRecord (const PDB::RecordSOURCE &record)
virtual bool	fillRecord (const char *line, Size size, PDB::RecordSOURCE &record)
virtual bool	parseRecordSOURCE (const char *line, Size size)
virtual bool	interpretRecord (const PDB::RecordSPRSDE &record)
	List of entries this file supersedes.
virtual bool	fillRecord (const char *line, Size size, PDB::RecordSPRSDE &record)
virtual bool	parseRecordSPRSDE (const char *line, Size size)
virtual bool	interpretRecord (const PDB::RecordSSBOND &record)
	Reads a record specifying a disulfide bond.
virtual bool	fillRecord (const char *line, Size size, PDB::RecordSSBOND &record)
virtual bool	parseRecordSSBOND (const char *line, Size size)
virtual bool	interpretRecord (const PDB::RecordTER &record)
	Reads a record terminating molecule.
virtual bool	fillRecord (const char *line, Size size, PDB::RecordTER &record)
virtual bool	parseRecordTER (const char *line, Size size)
virtual bool	interpretRecord (const PDB::RecordTITLE &record)
	Reads a record specifying the title of the experiment or anaysis.
virtual bool	fillRecord (const char *line, Size size, PDB::RecordTITLE &record)
virtual bool	parseRecordTITLE (const char *line, Size size)
virtual bool	interpretRecord (const PDB::RecordTURN &record)
	Reads a record specifying a turn.
virtual bool	fillRecord (const char *line, Size size, PDB::RecordTURN &record)
virtual bool	parseRecordTURN (const char *line, Size size)
virtual bool	interpretRecord (const PDB::RecordTVECT &record)
virtual bool	fillRecord (const char *line, Size size, PDB::RecordTVECT &record)
virtual bool	parseRecordTVECT (const char *line, Size size)
Reading and writing

PDBFile &	operator>> (Protein &protein) throw (Exception::ParseError)
	Read a protein from the file.
PDBFile &	operator>> (Molecule &molecule) throw (Exception::ParseError)
	Read a molecule from the file.
PDBFile &	operator>> (System &system) throw (Exception::ParseError)
PDBFile &	operator<< (const Protein &protein) throw (File::CannotWrite)
	Write a protein to the file.
PDBFile &	operator<< (const System &system) throw (File::CannotWrite)
PDBFile &	operator<< (const Molecule &molecule) throw (File::CannotWrite)
bool	read (Protein &protein) throw (Exception::ParseError)
bool	read (Molecule &protein) throw (Exception::ParseError)
bool	read (System &system) throw (Exception::ParseError)
Molecule *	read () throw (Exception::ParseError)
bool	write (const Protein &protein) throw (File::CannotWrite)
bool	write (const Molecule &molecule) throw (File::CannotWrite)
bool	write (const System &system) throw (File::CannotWrite)
bool	write (const System &system, const PDBInfo &info) throw (File::CannotWrite)
Public Attributes
Options

Options	options
	The options for parsing the file.
PDBInfo	info
	Summary information on the last file read.
Protected Member Functions
	PDBFile (const File &pdbf) throw (Exception::FileNotFound)
PDBFile &	operator= (const PDBFile &pdbf)
void	init_ ()
void	postprocessSSBonds_ ()
void	postprocessHelices_ ()
void	postprocessSheetsTurns_ (QuadrupleList &sectruct_list, SecStructList &new_secstruct_list)
void	postprocessRandomCoils_ ()
void	write_ (const AtomContainer &ac, const PDBInfo &info=PDBInfo())
void	writeRecord_ (PDB::RecordType record,...)
void	writeCONECTRecords_ (PDB::Structure::ConectAtomList &cl)
void	writeRawRecord_ (const char format, const char tag,...)
void	addAllRecords_ (const PDBInfo &info, PDB::RecordType type)
	Add all records of a specific type in the info object to the current stream.
void	writeRecord_ (const PDB::RecordSEQRES &seqres)
void	writeRecord_ (const PDB::RecordHELIX &helix)
void	writeRecord_ (const PDB::RecordSHEET &helix)
void	writeRecord_ (const PDB::RecordTURN &helix)
void	writeRecord_ (const PDB::RecordSSBOND &helix)
void	writeRecord_ (const PDB::RecordCONECT &helix)
void	writeRecord_ (const PDB::RecordCRYST1 &cryst1)
void	writeRecord_ (const PDB::RecordMTRIX1 &mtrix1)
void	writeRecord_ (const PDB::RecordMTRIX2 &mtrix2)
void	writeRecord_ (const PDB::RecordMTRIX3 &mtrix3)
void	writeAtom_ (const PDB::Structure::AtomEntry &atom, PDB::AdditionalAtomInfo &cr, bool hetatm=false)
void	writeTitleSection_ (const PDB::Structure &structure, const PDBInfo &info)
void	writePrimaryStructureSection_ (const PDB::Structure &structure, const PDBInfo &info)
void	writeHeterogenSection_ (const PDB::Structure &structure, const PDBInfo &info)
void	writeSecondaryStructureSection_ (const PDB::Structure &structure, const PDBInfo &info)
void	writeConnectivityAnnotationSection_ (const PDB::Structure &structure, const PDBInfo &info)
void	writeMiscellaneousFeaturesSection_ (const PDB::Structure &structure, const PDBInfo &info)
void	writeCrystallographicSection_ (const PDB::Structure &structure, const PDBInfo &info)
void	writeCoordinateSection_ (const PDB::Structure &structure, const PDBInfo &info)
void	writeConnectivitySection_ (const PDB::Structure &structure, const PDBInfo &info)
void	writeBookKeepingSection_ (const PDB::Structure &structure, const PDBInfo &info)
void	writeSEQRESSection_ (const std::vector< std::pair< char, String > > &chain_residues)
void	writeHELIXSection_ (const PDB::Structure &structure)
void	writeSHEETSection_ (const PDB::Structure &structure)
void	writeTURNSection_ (const PDB::Structure &structure)
void	writeSSBONDSection_ (const PDB::Structure &structure)
void	writeHYDBNDSection_ (const PDB::Structure &structure)
void	writeSLTBRGSection_ (const PDB::Structure &structure)
void	writeCRYST1Section_ (const PDB::Structure &structure)
void	writeMTRIXnSection_ (const PDB::Structure &structure)
Static Protected Member Functions
static void	extractStructure_ (const AtomContainer &ac, PDB::Structure &structure)
static bool	isHeteroAtom_ (const Atom &atom)
static void	updateAdditionalAtomInfo_ (const PDB::Structure::AtomEntry &atom, PDB::AdditionalAtomInfo &cr)
Protected Attributes
char	line_buffer_ [PDB::SIZE_OF_PDB_LINE_BUFFER]
String	residue_name_
Index	residue_sequence_number_
Index	current_model_
Index	current_record_
Size	record_fields_
PDB::RecordType	current_record_type_
PDB::RecordTypeFormat	compare_record_type_format_
PDBAtomMap	PDB_atom_map_
ResidueMap	residue_map_
QuadrupleList	ssbond_list_
QuadrupleList	helix_list_
QuadrupleList	sheet_list_
QuadrupleList	turn_list_
SecStructList	new_helix_secstruc_list_
SecStructList	new_sheet_secstruc_list_
SecStructList	new_turn_secstruc_list_
char	alternate_location_indicator_
PDB::AChar	insertion_code_
PDB::Character	chain_ID_
PDB::Integer	sequence_number_
PDB::AChar	code_
Protein *	current_protein_
const Protein *	current_const_protein_
Chain *	current_chain_
const Chain *	current_const_chain_
Residue *	current_residue_
const Residue *	current_const_residue_
PDBAtom *	current_PDB_atom_
const Atom *	current_const_atom_
String	name_
HashMap< const Atom *, Position >	atom_map_
PDB::BookKeeping	book_keeping_
	Book keeping struct for the number of records written.
int	verbosity_
	_Verbosity level
bool	strict_line_checking_
Index	selected_model_
	The selected model_.
bool	store_skipped_records_
	Store the skipped records in info?
bool	ignore_xplor_pseudo_atoms_
	Ignore XPLOR pseudo atoms?
bool	parse_partial_charges_
	Read partial charges from cols 76-80?

Detailed Description

PDB file class.

Definition at line 74 of file PDBFile.h.

Member Typedef Documentation

typedef HashMap<PDB::Integer, PDBAtom*> BALL::PDBFile::PDBAtomMap

Definition at line 632 of file PDBFile.h.

typedef std::list<ResidueQuadruple> BALL::PDBFile::QuadrupleList

Definition at line 635 of file PDBFile.h.

typedef HashMap<ResidueQuadruple, Residue*> BALL::PDBFile::ResidueMap

Definition at line 634 of file PDBFile.h.

typedef Quadruple<String, PDB::Character, PDB::Integer, PDB::AChar> BALL::PDBFile::ResidueQuadruple

Definition at line 633 of file PDBFile.h.

typedef std::list<SecondaryStructure*> BALL::PDBFile::SecStructList

Definition at line 636 of file PDBFile.h.

Constructor & Destructor Documentation

BALL::PDBFile::PDBFile ( )

Default constructor.

BALL::PDBFile::PDBFile	(	const String &	filename,
		File::OpenMode	open_mode = `std::ios::in`
	)			throw (Exception::FileNotFound)

File-like constructor.

BALL::PDBFile::PDBFile ( const Options & new_options )

Construct with options.

virtual BALL::PDBFile::~PDBFile ( ) [virtual]

Destructor.

BALL::PDBFile::PDBFile ( const File & pdbf ) throw (Exception::FileNotFound) [protected]

Member Function Documentation

void BALL::PDBFile::addAllRecords_	(	const PDBInfo &	info,
		PDB::RecordType	type
	)			`[protected]`

Add all records of a specific type in the info object to the current stream.

virtual void BALL::PDBFile::clear ( ) [virtual]

Clear all members.

Reimplemented from BALL::PropertyManager.

virtual void BALL::PDBFile::clear ( int state ) [virtual]

Clear the stream state.

Size BALL::PDBFile::countRecord	(	PDB::RecordType	record_type,
		bool	from_begin_of_file = `true`
	)

Returns the number of records of type record_type in the file being read.

Size BALL::PDBFile::countRecordFields ( ) const

Returns the number of record fields.

Size BALL::PDBFile::countRecords ( bool from_begin_of_file = true )

Returns the number of all records in the file.

static void BALL::PDBFile::extractStructure_	(	const AtomContainer &	ac,
		PDB::Structure &	structure
	)			`[static, protected]`

Extract the atom and bond information from an atom container prior to writing a PDB file. This method is called by write_.

virtual bool BALL::PDBFile::fillRecord	(	const char *	line,
		Size	size,
		PDB::RecordTVECT &	record
	)			`[virtual]`

virtual bool BALL::PDBFile::fillRecord	(	const char *	line,
		Size	size,
		PDB::RecordTURN &	record
	)			`[virtual]`

virtual bool BALL::PDBFile::fillRecord	(	const char *	line,
		Size	size,
		PDB::RecordTITLE &	record
	)			`[virtual]`

virtual bool BALL::PDBFile::fillRecord	(	const char *	line,
		Size	size,
		PDB::RecordTER &	record
	)			`[virtual]`

virtual bool BALL::PDBFile::fillRecord	(	const char *	line,
		Size	size,
		PDB::RecordSSBOND &	record
	)			`[virtual]`

virtual bool BALL::PDBFile::fillRecord	(	const char *	line,
		Size	size,
		PDB::RecordSPRSDE &	record
	)			`[virtual]`

virtual bool BALL::PDBFile::fillRecord	(	const char *	line,
		Size	size,
		PDB::RecordSOURCE &	record
	)			`[virtual]`

virtual bool BALL::PDBFile::fillRecord	(	const char *	line,
		Size	size,
		PDB::RecordSLTBRG &	record
	)			`[virtual]`

virtual bool BALL::PDBFile::fillRecord	(	const char *	line,
		Size	size,
		PDB::RecordSITE &	record
	)			`[virtual]`

virtual bool BALL::PDBFile::fillRecord	(	const char *	line,
		Size	size,
		PDB::RecordSIGUIJ &	record
	)			`[virtual]`

virtual bool BALL::PDBFile::fillRecord	(	const char *	line,
		Size	size,
		PDB::RecordSIGATM &	record
	)			`[virtual]`

virtual bool BALL::PDBFile::fillRecord	(	const char *	line,
		Size	size,
		PDB::RecordSHEET &	record
	)			`[virtual]`

virtual bool BALL::PDBFile::fillRecord	(	const char *	line,
		Size	size,
		PDB::RecordSEQRES &	record
	)			`[virtual]`

virtual bool BALL::PDBFile::fillRecord	(	const char *	line,
		Size	size,
		PDB::RecordSEQADV &	record
	)			`[virtual]`

virtual bool BALL::PDBFile::fillRecord	(	const char *	line,
		Size	size,
		PDB::RecordSCALE3 &	record
	)			`[virtual]`

virtual bool BALL::PDBFile::fillRecord	(	const char *	line,
		Size	size,
		PDB::RecordSCALE2 &	record
	)			`[virtual]`

virtual bool BALL::PDBFile::fillRecord	(	const char *	line,
		Size	size,
		PDB::RecordSCALE1 &	record
	)			`[virtual]`

virtual bool BALL::PDBFile::fillRecord	(	const char *	line,
		Size	size,
		PDB::RecordREVDAT &	record
	)			`[virtual]`

virtual bool BALL::PDBFile::fillRecord	(	const char *	line,
		Size	size,
		PDB::RecordREMARK &	record
	)			`[virtual]`

virtual bool BALL::PDBFile::fillRecord	(	const char *	line,
		Size	size,
		PDB::RecordORIGX3 &	record
	)			`[virtual]`

virtual bool BALL::PDBFile::fillRecord	(	const char *	line,
		Size	size,
		PDB::RecordORIGX2 &	record
	)			`[virtual]`

virtual bool BALL::PDBFile::fillRecord	(	const char *	line,
		Size	size,
		PDB::RecordORIGX1 &	record
	)			`[virtual]`

virtual bool BALL::PDBFile::fillRecord	(	const char *	line,
		Size	size,
		PDB::RecordOBSLTE &	record
	)			`[virtual]`

virtual bool BALL::PDBFile::fillRecord	(	const char *	line,
		Size	size,
		PDB::RecordMTRIX3 &	record
	)			`[virtual]`

virtual bool BALL::PDBFile::fillRecord	(	const char *	line,
		Size	size,
		PDB::RecordMTRIX2 &	record
	)			`[virtual]`

virtual bool BALL::PDBFile::fillRecord	(	const char *	line,
		Size	size,
		PDB::RecordMTRIX1 &	record
	)			`[virtual]`

virtual bool BALL::PDBFile::fillRecord	(	const char *	line,
		Size	size,
		PDB::RecordMODRES &	record
	)			`[virtual]`

virtual bool BALL::PDBFile::fillRecord	(	const char *	line,
		Size	size,
		PDB::RecordMODEL &	record
	)			`[virtual]`

virtual bool BALL::PDBFile::fillRecord	(	const char *	line,
		Size	size,
		PDB::RecordMASTER &	record
	)			`[virtual]`

virtual bool BALL::PDBFile::fillRecord	(	const char *	line,
		Size	size,
		PDB::RecordLINK &	record
	)			`[virtual]`

virtual bool BALL::PDBFile::fillRecord	(	const char *	line,
		Size	size,
		PDB::RecordKEYWDS &	record
	)			`[virtual]`

virtual bool BALL::PDBFile::fillRecord	(	const char *	line,
		Size	size,
		PDB::RecordJRNL &	record
	)			`[virtual]`

virtual bool BALL::PDBFile::fillRecord	(	const char *	line,
		Size	size,
		PDB::RecordHYDBND &	record
	)			`[virtual]`

virtual bool BALL::PDBFile::fillRecord	(	const char *	line,
		Size	size,
		PDB::RecordHETSYN &	record
	)			`[virtual]`

virtual bool BALL::PDBFile::fillRecord	(	const char *	line,
		Size	size,
		PDB::RecordHETNAM &	record
	)			`[virtual]`

virtual bool BALL::PDBFile::fillRecord	(	const char *	line,
		Size	size,
		PDB::RecordHETATM &	record
	)			`[virtual]`

virtual bool BALL::PDBFile::fillRecord	(	const char *	line,
		Size	size,
		PDB::RecordHET &	record
	)			`[virtual]`

virtual bool BALL::PDBFile::fillRecord	(	const char *	line,
		Size	size,
		PDB::RecordHELIX &	record
	)			`[virtual]`

virtual bool BALL::PDBFile::fillRecord	(	const char *	line,
		Size	size,
		PDB::RecordHEADER &	record
	)			`[virtual]`

virtual bool BALL::PDBFile::fillRecord	(	const char *	line,
		Size	size,
		PDB::RecordFTNOTE &	record
	)			`[virtual]`

virtual bool BALL::PDBFile::fillRecord	(	const char *	line,
		Size	size,
		PDB::RecordFORMUL &	record
	)			`[virtual]`

virtual bool BALL::PDBFile::fillRecord	(	const char *	line,
		Size	size,
		PDB::RecordEXPDTA &	record
	)			`[virtual]`

virtual bool BALL::PDBFile::fillRecord	(	const char *	line,
		Size	size,
		PDB::RecordENDMDL &	record
	)			`[virtual]`

virtual bool BALL::PDBFile::fillRecord	(	const char *	line,
		Size	size,
		PDB::RecordEND &	record
	)			`[virtual]`

virtual bool BALL::PDBFile::fillRecord	(	const char *	line,
		Size	size,
		PDB::RecordDBREF &	record
	)			`[virtual]`

virtual bool BALL::PDBFile::fillRecord	(	const char *	line,
		Size	size,
		PDB::RecordCRYST1 &	record
	)			`[virtual]`

virtual bool BALL::PDBFile::fillRecord	(	const char *	line,
		Size	size,
		PDB::RecordCONECT &	record
	)			`[virtual]`

virtual bool BALL::PDBFile::fillRecord	(	const char *	line,
		Size	size,
		PDB::RecordCOMPND &	record
	)			`[virtual]`

virtual bool BALL::PDBFile::fillRecord	(	const char *	line,
		Size	size,
		PDB::RecordCISPEP &	record
	)			`[virtual]`

virtual bool BALL::PDBFile::fillRecord	(	const char *	line,
		Size	size,
		PDB::RecordCAVEAT &	record
	)			`[virtual]`

virtual bool BALL::PDBFile::fillRecord	(	const char *	line,
		Size	size,
		PDB::RecordAUTHOR &	record
	)			`[virtual]`

virtual bool BALL::PDBFile::fillRecord	(	const char *	line,
		Size	size,
		PDB::RecordATOM &	record
	)			`[virtual]`

virtual bool BALL::PDBFile::fillRecord	(	const char *	line,
		Size	size,
		PDB::RecordANISOU &	record
	)			`[virtual]`

virtual short BALL::PDBFile::getAtomBranchDesignator ( const PDB::Atom atom_name ) [virtual]

Extract the PDB branch designator of an atom record.

virtual const char* BALL::PDBFile::getAtomElementSymbol	(	const PDB::Atom	atom_name,
		PDB::Atom	element_symbol
	)			`[virtual]`

Returns the element symbol of an atom. If element_symbol is invalid we try to reconstruct the element symbol from the atom name.

virtual const char* BALL::PDBFile::getAtomName ( const PDB::Atom atom_name ) [virtual]

Returns the atom name.

virtual char BALL::PDBFile::getAtomRemotenessIndicator ( const PDB::Atom atom_name ) [virtual]

Extract the PDB remoteness indicator of an atom record.

Index BALL::PDBFile::getCurrentModel ( ) const

Returns the number of the model weare currently reading. (?????).

Index BALL::PDBFile::getRecordNumber ( ) const

Returns the number of the record we are currently reading.

const char* BALL::PDBFile::getRecordString ( ) const

Return a constant pointer to the line buffer.

char* BALL::PDBFile::getRecordString ( )

Return a mutable pointer to the line buffer.

PDB::RecordType BALL::PDBFile::getRecordType ( ) const

Returns the type of the record we are currently reading.

Index BALL::PDBFile::getSelectedModel ( ) const

Return the model currently selected.

virtual float BALL::PDBFile::getVersion ( ) const [virtual]

Returns the version number this PDB file reader is able to read.

virtual bool BALL::PDBFile::hasFormat ( ) [virtual]

Check whether the current file is in PDB format.

void BALL::PDBFile::init_ ( ) [protected]

virtual bool BALL::PDBFile::interpretRecord ( const PDB::RecordTVECT & record ) [virtual]

Reads a record specifying the translation vector for infinite covalently connected structures.

virtual bool BALL::PDBFile::interpretRecord ( const PDB::RecordTURN & record ) [virtual]

Reads a record specifying a turn.

virtual bool BALL::PDBFile::interpretRecord ( const PDB::RecordTITLE & record ) [virtual]

Reads a record specifying the title of the experiment or anaysis.

virtual bool BALL::PDBFile::interpretRecord ( const PDB::RecordTER & record ) [virtual]

Reads a record terminating molecule.

virtual bool BALL::PDBFile::interpretRecord ( const PDB::RecordSSBOND & record ) [virtual]

Reads a record specifying a disulfide bond.

virtual bool BALL::PDBFile::interpretRecord ( const PDB::RecordSPRSDE & record ) [virtual]

List of entries this file supersedes.

virtual bool BALL::PDBFile::interpretRecord ( const PDB::RecordSOURCE & record ) [virtual]

Reads a record specifies the chemical/biological source of each molecule in the entry.

virtual bool BALL::PDBFile::interpretRecord ( const PDB::RecordSLTBRG & record ) [virtual]

Reads a record defining a salt bridge.

virtual bool BALL::PDBFile::interpretRecord ( const PDB::RecordSITE & record ) [virtual]

Reads a record containing groups comprising a site.

virtual bool BALL::PDBFile::interpretRecord ( const PDB::RecordSIGUIJ & record ) [virtual]

Reads a record giving the standard deviation of anisotropic temperature factors.

virtual bool BALL::PDBFile::interpretRecord ( const PDB::RecordSIGATM & record ) [virtual]

Reads a record giving the standard deviation of atomic coordinates.

virtual bool BALL::PDBFile::interpretRecord ( const PDB::RecordSHEET & record ) [virtual]

Reads a record defining a beta-sheet.

virtual bool BALL::PDBFile::interpretRecord ( const PDB::RecordSEQRES & record ) [virtual]

Reads a record containing the sequence of residues.

virtual bool BALL::PDBFile::interpretRecord ( const PDB::RecordSEQADV & record ) [virtual]

Sequence information conflicts between atom records and dbref content.

virtual bool BALL::PDBFile::interpretRecord ( const PDB::RecordSCALE3 & record ) [virtual]

Reads a scale transformation record.

virtual bool BALL::PDBFile::interpretRecord ( const PDB::RecordSCALE2 & record ) [virtual]

Reads a scale transformation record.

virtual bool BALL::PDBFile::interpretRecord ( const PDB::RecordSCALE1 & record ) [virtual]

Reads a scale transformation record.

virtual bool BALL::PDBFile::interpretRecord ( const PDB::RecordREVDAT & record ) [virtual]

Reads a record containing a revision history.

virtual bool BALL::PDBFile::interpretRecord ( const PDB::RecordREMARK & record ) [virtual]

Reads a record containing remarks.

virtual bool BALL::PDBFile::interpretRecord ( const PDB::RecordORIGX3 & record ) [virtual]

Reads a record defining the transformation from the orthogonal coordinates contained in the entry to the submitted coordinates.

virtual bool BALL::PDBFile::interpretRecord ( const PDB::RecordORIGX2 & record ) [virtual]

Reads a record defining the transformation from the orthogonal coordinates contained in the entry to the submitted coordinates.

virtual bool BALL::PDBFile::interpretRecord ( const PDB::RecordORIGX1 & record ) [virtual]

Reads a record defining the transformation from the orthogonal coordinates contained in the entry to the submitted coordinates.

virtual bool BALL::PDBFile::interpretRecord ( const PDB::RecordOBSLTE & record ) [virtual]

Reads a record indicating that this structura has been withdrawnform the database.

virtual bool BALL::PDBFile::interpretRecord ( const PDB::RecordMTRIX3 & record ) [virtual]

Reads a record defining transformations expressing non-crystallographic symmetry.

virtual bool BALL::PDBFile::interpretRecord ( const PDB::RecordMTRIX2 & record ) [virtual]

Reads a record defining transformations expressing non-crystallographic symmetry.

virtual bool BALL::PDBFile::interpretRecord ( const PDB::RecordMTRIX1 & record ) [virtual]

Reads a record defining transformations expressing non-crystallographic symmetry.

virtual bool BALL::PDBFile::interpretRecord ( const PDB::RecordMODRES & record ) [virtual]

Reads a record identifying residue modifications.

virtual bool BALL::PDBFile::interpretRecord ( const PDB::RecordMODEL & record ) [virtual]

Reads a record indicating the beginning of a new model.

virtual bool BALL::PDBFile::interpretRecord ( const PDB::RecordMASTER & record ) [virtual]

Reads the master record containing numerous counts for bookkeeping purposes.

virtual bool BALL::PDBFile::interpretRecord ( const PDB::RecordLINK & record ) [virtual]

Reads a record containing supplemental connectivity information.

virtual bool BALL::PDBFile::interpretRecord ( const PDB::RecordKEYWDS & record ) [virtual]

Reads a record containing keywords for this entry.

virtual bool BALL::PDBFile::interpretRecord ( const PDB::RecordJRNL & record ) [virtual]

Reads a record containing a journal reference.

virtual bool BALL::PDBFile::interpretRecord ( const PDB::RecordHYDBND & record ) [virtual]

Reads a record defining a hydrogen bond.

virtual bool BALL::PDBFile::interpretRecord ( const PDB::RecordHETSYN & record ) [virtual]

Reads a record defining synonyms of a non-standard group.

virtual bool BALL::PDBFile::interpretRecord ( const PDB::RecordHETNAM & record ) [virtual]

Reads a record defining the name of a non-standard group.

virtual bool BALL::PDBFile::interpretRecord ( const PDB::RecordHETATM & record ) [virtual]

Reads atomic coordinates for atoms in non-standard groups.

virtual bool BALL::PDBFile::interpretRecord ( const PDB::RecordHET & record ) [virtual]

Reads a record defining a non-standard residue.

virtual bool BALL::PDBFile::interpretRecord ( const PDB::RecordHELIX & record ) [virtual]

Reads a helix defining record.

virtual bool BALL::PDBFile::interpretRecord ( const PDB::RecordHEADER & record ) [virtual]

Reads the header recors which contains the idCode field, entry classification and deposition date.

virtual bool BALL::PDBFile::interpretRecord ( const PDB::RecordFTNOTE & record ) [virtual]

Reads a record containing a footnote.

virtual bool BALL::PDBFile::interpretRecord ( const PDB::RecordFORMUL & record ) [virtual]

Reads a record containing the chemical formula of a non-standard group.

virtual bool BALL::PDBFile::interpretRecord ( const PDB::RecordEXPDTA & record ) [virtual]

Reads a record containing data about the experiment.

virtual bool BALL::PDBFile::interpretRecord ( const PDB::RecordENDMDL & record ) [virtual]

Reads a model ending record.

virtual bool BALL::PDBFile::interpretRecord ( const PDB::RecordEND & record ) [virtual]

Reads the record defining the end of a PDB file.

virtual bool BALL::PDBFile::interpretRecord ( const PDB::RecordDBREF & record ) [virtual]

Reads a record containing database cross-reference links.

virtual bool BALL::PDBFile::interpretRecord ( const PDB::RecordCRYST1 & record ) [virtual]

Reads the record specifying the unit cell parameters, space group, and Z value for crystographically determined structures.

virtual bool BALL::PDBFile::interpretRecord ( const PDB::RecordCONECT & record ) [virtual]

Reads a connection record.

virtual bool BALL::PDBFile::interpretRecord ( const PDB::RecordCOMPND & record ) [virtual]

Reads the title record containing macroscopic compoubd information.

virtual bool BALL::PDBFile::interpretRecord ( const PDB::RecordCISPEP & record ) [virtual]

Reads a record specifying peptides in cis conformation.

virtual bool BALL::PDBFile::interpretRecord ( const PDB::RecordCAVEAT & record ) [virtual]

Reads a caveat record.

virtual bool BALL::PDBFile::interpretRecord ( const PDB::RecordAUTHOR & record ) [virtual]

Reads an author record.

virtual bool BALL::PDBFile::interpretRecord ( const PDB::RecordATOM & record ) [virtual]

Reads an atom record.

virtual bool BALL::PDBFile::interpretRecord ( const PDB::RecordANISOU & record ) [virtual]

Reads an anisotropic temperature factor record.

static bool BALL::PDBFile::isHeteroAtom_ ( const Atom & atom ) [static, protected]

Determine whether an atom is a hetero atom or part of a standard amino acid or nucleotide. This test is performed by checking for the corresponding properties defined in Residue.

PDBFile& BALL::PDBFile::operator<< ( const Molecule & molecule ) throw (File::CannotWrite) [virtual]

Stream operator for writing a system of molecules. Calls write()

Reimplemented from BALL::GenericMolFile.

PDBFile& BALL::PDBFile::operator<< ( const System & system ) throw (File::CannotWrite) [virtual]

Stream operator for writing a system of molecules. Calls write(const System& system) const .

Reimplemented from BALL::GenericMolFile.

PDBFile& BALL::PDBFile::operator<< ( const Protein & protein ) throw (File::CannotWrite)

Write a protein to the file.

PDBFile& BALL::PDBFile::operator= ( const PDBFile & pdbf ) [protected]

PDBFile& BALL::PDBFile::operator>> ( System & system ) throw (Exception::ParseError) [virtual]

Stream operator for reading a system. Calls read(System&) .

Reimplemented from BALL::GenericMolFile.

PDBFile& BALL::PDBFile::operator>> ( Molecule & molecule ) throw (Exception::ParseError) [virtual]

Read a molecule from the file.

Reimplemented from BALL::GenericMolFile.

PDBFile& BALL::PDBFile::operator>> ( Protein & protein ) throw (Exception::ParseError)

Read a protein from the file.

bool BALL::PDBFile::parseLine	(	const char *	line,
		Size	size,
		const char *	format_string,
			...
	)

Parse a line from a PDBFile. This is a helper function for readLine().

virtual bool BALL::PDBFile::parseRecordANISOU	(	const char *	line,
		Size	size
	)			`[virtual]`

virtual bool BALL::PDBFile::parseRecordATOM	(	const char *	line,
		Size	size
	)			`[virtual]`

virtual bool BALL::PDBFile::parseRecordAUTHOR	(	const char *	line,
		Size	size
	)			`[virtual]`

virtual bool BALL::PDBFile::parseRecordCAVEAT	(	const char *	line,
		Size	size
	)			`[virtual]`

virtual bool BALL::PDBFile::parseRecordCISPEP	(	const char *	line,
		Size	size
	)			`[virtual]`

virtual bool BALL::PDBFile::parseRecordCOMPND	(	const char *	line,
		Size	size
	)			`[virtual]`

virtual bool BALL::PDBFile::parseRecordCONECT	(	const char *	line,
		Size	size
	)			`[virtual]`

virtual bool BALL::PDBFile::parseRecordCRYST1	(	const char *	line,
		Size	size
	)			`[virtual]`

virtual bool BALL::PDBFile::parseRecordDBREF	(	const char *	line,
		Size	size
	)			`[virtual]`

virtual bool BALL::PDBFile::parseRecordEND	(	const char *	line,
		Size	size
	)			`[virtual]`

virtual bool BALL::PDBFile::parseRecordENDMDL	(	const char *	line,
		Size	size
	)			`[virtual]`

virtual bool BALL::PDBFile::parseRecordEXPDTA	(	const char *	line,
		Size	size
	)			`[virtual]`

virtual bool BALL::PDBFile::parseRecordFORMUL	(	const char *	line,
		Size	size
	)			`[virtual]`

virtual bool BALL::PDBFile::parseRecordFTNOTE	(	const char *	line,
		Size	size
	)			`[virtual]`

virtual bool BALL::PDBFile::parseRecordHEADER	(	const char *	line,
		Size	size
	)			`[virtual]`

virtual bool BALL::PDBFile::parseRecordHELIX	(	const char *	line,
		Size	size
	)			`[virtual]`

virtual bool BALL::PDBFile::parseRecordHET	(	const char *	line,
		Size	size
	)			`[virtual]`

virtual bool BALL::PDBFile::parseRecordHETATM	(	const char *	line,
		Size	size
	)			`[virtual]`

virtual bool BALL::PDBFile::parseRecordHETNAM	(	const char *	line,
		Size	size
	)			`[virtual]`

virtual bool BALL::PDBFile::parseRecordHETSYN	(	const char *	line,
		Size	size
	)			`[virtual]`

virtual bool BALL::PDBFile::parseRecordHYDBND	(	const char *	line,
		Size	size
	)			`[virtual]`

virtual bool BALL::PDBFile::parseRecordJRNL	(	const char *	line,
		Size	size
	)			`[virtual]`

virtual bool BALL::PDBFile::parseRecordKEYWDS	(	const char *	line,
		Size	size
	)			`[virtual]`

virtual bool BALL::PDBFile::parseRecordLINK	(	const char *	line,
		Size	size
	)			`[virtual]`

virtual bool BALL::PDBFile::parseRecordMASTER	(	const char *	line,
		Size	size
	)			`[virtual]`

virtual bool BALL::PDBFile::parseRecordMODEL	(	const char *	line,
		Size	size
	)			`[virtual]`

virtual bool BALL::PDBFile::parseRecordMODRES	(	const char *	line,
		Size	size
	)			`[virtual]`

virtual bool BALL::PDBFile::parseRecordMTRIX1	(	const char *	line,
		Size	size
	)			`[virtual]`

virtual bool BALL::PDBFile::parseRecordMTRIX2	(	const char *	line,
		Size	size
	)			`[virtual]`

virtual bool BALL::PDBFile::parseRecordMTRIX3	(	const char *	line,
		Size	size
	)			`[virtual]`

virtual bool BALL::PDBFile::parseRecordOBSLTE	(	const char *	line,
		Size	size
	)			`[virtual]`

virtual bool BALL::PDBFile::parseRecordORIGX1	(	const char *	line,
		Size	size
	)			`[virtual]`

virtual bool BALL::PDBFile::parseRecordORIGX2	(	const char *	line,
		Size	size
	)			`[virtual]`

virtual bool BALL::PDBFile::parseRecordORIGX3	(	const char *	line,
		Size	size
	)			`[virtual]`

virtual bool BALL::PDBFile::parseRecordREMARK	(	const char *	line,
		Size	size
	)			`[virtual]`

virtual bool BALL::PDBFile::parseRecordREVDAT	(	const char *	line,
		Size	size
	)			`[virtual]`

virtual bool BALL::PDBFile::parseRecordSCALE1	(	const char *	line,
		Size	size
	)			`[virtual]`

virtual bool BALL::PDBFile::parseRecordSCALE2	(	const char *	line,
		Size	size
	)			`[virtual]`

virtual bool BALL::PDBFile::parseRecordSCALE3	(	const char *	line,
		Size	size
	)			`[virtual]`

virtual bool BALL::PDBFile::parseRecordSEQADV	(	const char *	line,
		Size	size
	)			`[virtual]`

virtual bool BALL::PDBFile::parseRecordSEQRES	(	const char *	line,
		Size	size
	)			`[virtual]`

virtual bool BALL::PDBFile::parseRecordSHEET	(	const char *	line,
		Size	size
	)			`[virtual]`

virtual bool BALL::PDBFile::parseRecordSIGATM	(	const char *	line,
		Size	size
	)			`[virtual]`

virtual bool BALL::PDBFile::parseRecordSIGUIJ	(	const char *	line,
		Size	size
	)			`[virtual]`

virtual bool BALL::PDBFile::parseRecordSITE	(	const char *	line,
		Size	size
	)			`[virtual]`

virtual bool BALL::PDBFile::parseRecordSLTBRG	(	const char *	line,
		Size	size
	)			`[virtual]`

virtual bool BALL::PDBFile::parseRecordSOURCE	(	const char *	line,
		Size	size
	)			`[virtual]`

virtual bool BALL::PDBFile::parseRecordSPRSDE	(	const char *	line,
		Size	size
	)			`[virtual]`

virtual bool BALL::PDBFile::parseRecordSSBOND	(	const char *	line,
		Size	size
	)			`[virtual]`

virtual bool BALL::PDBFile::parseRecordTER	(	const char *	line,
		Size	size
	)			`[virtual]`

virtual bool BALL::PDBFile::parseRecordTITLE	(	const char *	line,
		Size	size
	)			`[virtual]`

virtual bool BALL::PDBFile::parseRecordTURN	(	const char *	line,
		Size	size
	)			`[virtual]`

virtual bool BALL::PDBFile::parseRecordTVECT	(	const char *	line,
		Size	size
	)			`[virtual]`

void BALL::PDBFile::postprocessHelices_ ( ) [protected]

void BALL::PDBFile::postprocessRandomCoils_ ( ) [protected]

void BALL::PDBFile::postprocessSheetsTurns_	(	QuadrupleList &	sectruct_list,
		SecStructList &	new_secstruct_list
	)			`[protected]`

void BALL::PDBFile::postprocessSSBonds_ ( ) [protected]

Molecule* BALL::PDBFile::read ( ) throw (Exception::ParseError) [virtual]

Read a molecule. This method will load the first (or the next, on subsequent invocation) molecule from the file. If the file format does not support multiple molecules, only the first call to read will be successful. This method will create an instance of molecule and its the user's responsibility to destroy that molecule.

Returns:: a pointer to a molecule, 0 if the file was not open, empty, or at its end

Exceptions:

Exception::ParseError

if the contents of the file could not be parsed

Reimplemented from BALL::GenericMolFile.

bool BALL::PDBFile::read ( System & system ) throw (Exception::ParseError) [virtual]

Read a system. This method will read all molecules contained in the file and add them to the system.

: The default implementation calls read() until false is returned and adds the molecules read to the system.

Returns:: true if anything could be read

Exceptions:

Exception::ParseError

if the file could not be parsed while reading a molecule

Reimplemented from BALL::GenericMolFile.

bool BALL::PDBFile::read ( Molecule & protein ) throw (Exception::ParseError)

bool BALL::PDBFile::read ( Protein & protein ) throw (Exception::ParseError)

bool BALL::PDBFile::readFirstRecord ( bool read_values = true )

Read the firts record of a file.

virtual bool BALL::PDBFile::readInvalidRecord ( const char * line ) [virtual]

Called an invalid record by simply returning true.

bool BALL::PDBFile::readLine	(	char *	line,
		Size	size,
		bool	extract_values
	)

Read and parse a line from a PDB file.

bool BALL::PDBFile::readNextRecord ( bool read_values = true )

Read the next record of a PDB file.

bool BALL::PDBFile::readRecords ( )

Reads all records of a file.

Returns:: true if all records were parsed without error; false otherwise

virtual bool BALL::PDBFile::readUnknownRecord ( const char * line ) [virtual]

Called for unknown PDB records. The default implementation does nothing, it always returns true.

Returns:: true

void BALL::PDBFile::selectAllModels ( )

Selects all models for reading.

void BALL::PDBFile::selectAltLocationIndicator ( char c )

This function allows to select the alternate location indicator That should be parsed if one is specified. Default is 'A'.

If other location indicators exist, but the specified one is missing for an atom nothing will be parsed. Thus this option should be used with caution.

Exceptions:

IllegalArgument

This exception is thrown if an invalid Location indicator (not a letter) was passed.

void BALL::PDBFile::selectModel ( Index index )

Selects one of multiple models for reading. Default behaviour is reading model 1. If a file does not contain a MODEL specifier, all coordinates will be assigned to model 1.

bool BALL::PDBFile::skipCurrentRecord ( )

Skip the current record. If storeSkippedRecords is set to true, the records are added to the skipped records of info. Otherwise, they are just ignored. This method should be called by those readRecord methods that want to skip a particular record (this is the default behavior implemented in PDBFile).

Returns:: true

static void BALL::PDBFile::updateAdditionalAtomInfo_	(	const PDB::Structure::AtomEntry &	atom,
		PDB::AdditionalAtomInfo &	cr
	)			`[static, protected]`

Compute the current name and id of chain and residue. This method guesses more or less correct values for names and IDs or uses decent default values. It does so only of the pointers to the residue and chain in cr differ from the values in atom.

bool BALL::PDBFile::write	(	const System &	system,
		const PDBInfo &	info
	)			throw (File::CannotWrite)

bool BALL::PDBFile::write ( const System & system ) throw (File::CannotWrite) [virtual]

Write the molecules of a system. If the file format does not support multiple molecules in a single file, a warning should be printed and only the first molecule should be stored.

: The default implementation iterates over the system and calls write(const Molecule& molecule) for each molecule.

Reimplemented from BALL::GenericMolFile.

bool BALL::PDBFile::write ( const Molecule & molecule ) throw (File::CannotWrite) [virtual]

Write a molecule. Repeated invocations of this method append molecules to the same file.

: The default implementation does nothing.

Reimplemented from BALL::GenericMolFile.

bool BALL::PDBFile::write ( const Protein & protein ) throw (File::CannotWrite)

void BALL::PDBFile::write_	(	const AtomContainer &	ac,
		const PDBInfo &	info = `PDBInfo()`
	)			`[protected]`

void BALL::PDBFile::writeAtom_	(	const PDB::Structure::AtomEntry &	atom,
		PDB::AdditionalAtomInfo &	cr,
		bool	hetatm = `false`
	)			`[protected]`

void BALL::PDBFile::writeBookKeepingSection_	(	const PDB::Structure &	structure,
		const PDBInfo &	info
	)			`[protected]`

void BALL::PDBFile::writeCONECTRecords_ ( PDB::Structure::ConectAtomList & cl ) [protected]

void BALL::PDBFile::writeConnectivityAnnotationSection_	(	const PDB::Structure &	structure,
		const PDBInfo &	info
	)			`[protected]`

void BALL::PDBFile::writeConnectivitySection_	(	const PDB::Structure &	structure,
		const PDBInfo &	info
	)			`[protected]`

void BALL::PDBFile::writeCoordinateSection_	(	const PDB::Structure &	structure,
		const PDBInfo &	info
	)			`[protected]`

void BALL::PDBFile::writeCRYST1Section_ ( const PDB::Structure & structure ) [protected]

void BALL::PDBFile::writeCrystallographicSection_	(	const PDB::Structure &	structure,
		const PDBInfo &	info
	)			`[protected]`

void BALL::PDBFile::writeHELIXSection_ ( const PDB::Structure & structure ) [protected]

void BALL::PDBFile::writeHeterogenSection_	(	const PDB::Structure &	structure,
		const PDBInfo &	info
	)			`[protected]`

void BALL::PDBFile::writeHYDBNDSection_ ( const PDB::Structure & structure ) [protected]

void BALL::PDBFile::writeMiscellaneousFeaturesSection_	(	const PDB::Structure &	structure,
		const PDBInfo &	info
	)			`[protected]`

void BALL::PDBFile::writeMTRIXnSection_ ( const PDB::Structure & structure ) [protected]

void BALL::PDBFile::writePrimaryStructureSection_	(	const PDB::Structure &	structure,
		const PDBInfo &	info
	)			`[protected]`

void BALL::PDBFile::writeRawRecord_	(	const char *	format,
		const char *	tag,
			...
	)			`[protected]`

Write a record to the stream using a predefined format string. You should not use this method unless you know what you are doing. Use writeRecord_ instead, as this method also updates the record book keeping required for the MASTER record. If you use it, you'll have to update the book keeping structure yourself!

void BALL::PDBFile::writeRecord_ ( const PDB::RecordMTRIX3 & mtrix3 ) [protected]

Write a MTRIX3 record to the current stream

void BALL::PDBFile::writeRecord_ ( const PDB::RecordMTRIX2 & mtrix2 ) [protected]

Write a MTRIX2 record to the current stream

void BALL::PDBFile::writeRecord_ ( const PDB::RecordMTRIX1 & mtrix1 ) [protected]

Write a MTRIX1 record to the current stream

void BALL::PDBFile::writeRecord_ ( const PDB::RecordCRYST1 & cryst1 ) [protected]

Write a CRYST1 record to the current stream

void BALL::PDBFile::writeRecord_ ( const PDB::RecordCONECT & helix ) [protected]

Write a CONECT record to the current stream

void BALL::PDBFile::writeRecord_ ( const PDB::RecordSSBOND & helix ) [protected]

Write a SSBOND record to the current stream

void BALL::PDBFile::writeRecord_ ( const PDB::RecordTURN & helix ) [protected]

Write a TURN record to the current stream

void BALL::PDBFile::writeRecord_ ( const PDB::RecordSHEET & helix ) [protected]

Write a SHEET record to the current stream

void BALL::PDBFile::writeRecord_ ( const PDB::RecordHELIX & helix ) [protected]

Write a HELIX record to the current stream

void BALL::PDBFile::writeRecord_ ( const PDB::RecordSEQRES & seqres ) [protected]

Write a SEQRES record to the current stream

void BALL::PDBFile::writeRecord_	(	PDB::RecordType	record,
			...
	)			`[protected]`

Write a record to the stream using a predefined record type. This method updates the internal book keeping data structure required for writing the MASTER record.